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Liu Z, Wang N, Su Y, Long Q, Peng Y, Shangguan L, Zhang F, Cao S, Wang X, Ge M, Xue H, Ma Z, Liu W, Xu X, Li C, Cao X, Ahmad B, Su X, Liu Y, Huang G, Du M, Liu Z, Gan Y, Sun L, Fan X, Zhang C, Zhong H, Leng X, Ren Y, Dong T, Pei D, Wu X, Jin Z, Wang Y, Liu C, Chen J, Gaut B, Huang S, Fang J, Xiao H, Zhou Y. Grapevine pangenome facilitates trait genetics and genomic breeding. Nat Genet 2024; 56:2804-2814. [PMID: 39496880 PMCID: PMC11631756 DOI: 10.1038/s41588-024-01967-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/01/2024] [Indexed: 11/06/2024]
Abstract
Grapevine breeding is hindered by a limited understanding of the genetic basis of complex agronomic traits. This study constructs a graph-based pangenome reference (Grapepan v.1.0) from 18 newly generated phased telomere-to-telomere assemblies and 11 published assemblies. Using Grapepan v.1.0, we build a variation map with 9,105,787 short variations and 236,449 structural variations (SVs) from the resequencing data of 466 grapevine cultivars. Integrating SVs into a genome-wide association study, we map 148 quantitative trait loci for 29 agronomic traits (50.7% newly identified), with 12 traits significantly contributed by SVs. The estimated heritability improves by 22.78% on average when including SVs. We discovered quantitative trait locus regions under divergent artificial selection in metabolism and berry development between wine and table grapes, respectively. Moreover, significant genetic correlations were detected among the 29 traits. Under a polygenic model, we conducted genomic predictions for each trait. In general, our study facilitates the breeding of superior cultivars via the genomic selection of multiple traits.
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Affiliation(s)
- Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Nan Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ying Su
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qiming Long
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lingfei Shangguan
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Fan Zhang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xu Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Mengqing Ge
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Hui Xue
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhiyao Ma
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wenwen Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaodong Xu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chaochao Li
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xuejing Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bilal Ahmad
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiangnian Su
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuting Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guizhou Huang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Mengrui Du
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhenya Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yu Gan
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lei Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiucai Fan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Chuan Zhang
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Haixia Zhong
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xiangpeng Leng
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Yanhua Ren
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Tianyu Dong
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Dan Pei
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xinyu Wu
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Zhongxin Jin
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yiwen Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chonghuai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Jinfeng Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Brandon Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Sanwen Huang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China.
- College of Horticulture, Qingdao Agricultural University, Qingdao, China.
| | - Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
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Peng Y, Mao K, Zhang Z, Ping J, Jin M, Liu X, Wu C, Zhao C, Wang P, Duan X, Yu S, Li Z, Liu J, Li H, Yesaya A, Chen L, Wang H, Wilson K, Xiao Y. Landscape of structural variants reveals insights for local adaptations in the Asian corn borer. Cell Rep 2024; 43:114928. [PMID: 39504240 DOI: 10.1016/j.celrep.2024.114928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 09/20/2024] [Accepted: 10/15/2024] [Indexed: 11/08/2024] Open
Abstract
Capturing the genetic diversity of different wild populations is crucial for unraveling the mechanisms of adaptation and establishing links between genome evolution and local adaptation. The Asian corn borer (ACB) moth has undergone natural selection during its adaptative evolution. However, structural variants (SVs), which play significant roles in these adaptation processes, have not been previously identified. Here, we constructed a multi-assembly graph pan-genome to highlight the importance of SVs in local adaptation. Our analysis revealed that the graph pan-genome contained 176.60 Mb (∼37.33%) of unique sequences. Subsequently, we performed an analysis of expression quantitative trait loci (QTLs) to explore the impact of SVs on gene expression regulation. Notably, through QTL mapping analysis, we identified the FTZ-F1 gene as a potential candidate gene associated with the traits of larval development rate. In sum, we explored the impact of SVs on the local adaptation of pests, therefore facilitating accelerated pest management strategies.
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Affiliation(s)
- Yan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kaikai Mao
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Zhuting Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junfen Ping
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Minghui Jin
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xinye Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chao Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chongjun Zhao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Peng Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xueqing Duan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Songmiao Yu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhimin Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jimin Liu
- Plant Protection Research Institute, Guangxi Academy of Agricultural Science/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, China
| | - Hongran Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Alexander Yesaya
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lin Chen
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Hongru Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kenneth Wilson
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Yutao Xiao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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3
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Kasule F, Diack O, Mbaye M, Kakeeto R, Econopouly BF. Genomic resources, opportunities, and prospects for accelerated improvement of millets. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:273. [PMID: 39565376 PMCID: PMC11579216 DOI: 10.1007/s00122-024-04777-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 10/28/2024] [Indexed: 11/21/2024]
Abstract
KEY MESSAGE Genomic resources, alongside the tools and expertise required to leverage them, are essential for the effective improvement of globally significant millet crop species. Millets are essential for global food security and nutrition, particularly in sub-Saharan Africa and South Asia. They are crucial in promoting nutrition, climate resilience, economic development, and cultural heritage. Despite their critical role, millets have historically received less investment in developing genomic resources than major cereals like wheat, maize, and rice. However, recent advancements in genomics, particularly next-generation sequencing technologies, offer unprecedented opportunities for rapid improvement in millet crops. This review paper provides an overview of the status of genomic resources in millets and in harnessing the recent opportunities in artificial intelligence to address challenges in millet crop improvement to boost productivity, nutrition, and end quality. It emphasizes the significance of genomics in tackling global food security issues and underscores the necessity for innovative breeding strategies to translate genomics and AI into effective breeding strategies for millets.
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Affiliation(s)
- Faizo Kasule
- Interdepartmental Genetics and Genomics (IGG), Iowa State University, Ames, IA, 50011, USA
| | - Oumar Diack
- Centre National de Recherches Agronomiques de Bambey (CNRA), Institut Sénégalais de Recherches Agricoles (ISRA), BP 53, Bambey, Sénégal
| | - Modou Mbaye
- Centre d'Etude Régional Pour L'Amélioration de L'Adaptation À La Sécheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, BP 3320, Thiès, Sénégal
| | - Ronald Kakeeto
- National Agricultural Research Organization (NARO), National Semi-Arid Resources Research Institute (NaSARRI), P.O. Box 56, Soroti, Uganda
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4
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Kaur H, Shannon LM, Samac DA. A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study. BMC Genomics 2024; 25:1022. [PMID: 39482604 PMCID: PMC11526573 DOI: 10.1186/s12864-024-10931-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 10/21/2024] [Indexed: 11/03/2024] Open
Abstract
BACKGROUND The concept of pangenomics and the importance of structural variants is gaining recognition within the plant genomics community. Due to advancements in sequencing and computational technology, it has become feasible to sequence the entire genome of numerous individuals of a single species at a reasonable cost. Pangenomes have been constructed for many major diploid crops, including rice, maize, soybean, sorghum, pearl millet, peas, sunflower, grapes, and mustards. However, pangenomes for polyploid species are relatively scarce and are available in only few crops including wheat, cotton, rapeseed, and potatoes. MAIN BODY In this review, we explore the various methods used in crop pangenome development, discussing the challenges and implications of these techniques based on insights from published pangenome studies. We offer a systematic guide and discuss the tools available for constructing a pangenome and conducting downstream analyses. Alfalfa, a highly heterozygous, cross pollinated and autotetraploid forage crop species, is used as an example to discuss the concerns and challenges offered by polyploid crop species. We conducted a comparative analysis using linear and graph-based methods by constructing an alfalfa graph pangenome using three publicly available genome assemblies. To illustrate the intricacies captured by pangenome graphs for a complex crop genome, we used five different gene sequences and aligned them against the three graph-based pangenomes. The comparison of the three graph pangenome methods reveals notable variations in the genomic variation captured by each pipeline. CONCLUSION Pangenome resources are proving invaluable by offering insights into core and dispensable genes, novel gene discovery, and genome-wide patterns of variation. Developing user-friendly online portals for linear pangenome visualization has made these resources accessible to the broader scientific and breeding community. However, challenges remain with graph-based pangenomes including compatibility with other tools, extraction of sequence for regions of interest, and visualization of genetic variation captured in pangenome graphs. These issues necessitate further refinement of tools and pipelines to effectively address the complexities of polyploid, highly heterozygous, and cross-pollinated species.
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Affiliation(s)
- Harpreet Kaur
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA.
| | - Laura M Shannon
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA
| | - Deborah A Samac
- USDA-ARS, Plant Science Research Unit, St. Paul, MN, 55108, USA
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Skiadas P, Riera Vidal S, Dommisse J, Mendel MN, Elberse J, Van den Ackerveken G, de Jonge R, Seidl MF. Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew. PLoS Genet 2024; 20:e1011452. [PMID: 39453979 PMCID: PMC11540230 DOI: 10.1371/journal.pgen.1011452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 11/06/2024] [Accepted: 10/07/2024] [Indexed: 10/27/2024] Open
Abstract
Plant pathogens adapt at speeds that challenge contemporary disease management strategies like the deployment of disease resistance genes. The strong evolutionary pressure to adapt, shapes pathogens' genomes, and comparative genomics has been instrumental in characterizing this process. With the aim to capture genomic variation at high resolution and study the processes contributing to adaptation, we here leverage an innovative, multi-genome method to construct and annotate the first pangenome graph of an oomycete plant pathogen. We expand on this approach by analysing the graph and creating synteny based single-copy orthogroups for all genes. We generated telomere-to-telomere genome assemblies of six genetically diverse isolates of the oomycete pathogen Peronospora effusa, the economically most important disease in cultivated spinach worldwide. The pangenome graph demonstrates that P. effusa genomes are highly conserved, both in chromosomal structure and gene content, and revealed the continued activity of transposable elements which are directly responsible for 80% of the observed variation between the isolates. While most genes are generally conserved, virulence related genes are highly variable between the isolates. Most of the variation is found in large gene clusters resulting from extensive copy-number expansion. Pangenome graph-based discovery can thus be effectively used to capture genomic variation at exceptional resolution, thereby providing a framework to study the biology and evolution of plant pathogens.
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Affiliation(s)
- Petros Skiadas
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
- Translational Plant Biology, Utrecht University, Utrecht, The Netherlands
| | - Sofía Riera Vidal
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Joris Dommisse
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Melanie N. Mendel
- Translational Plant Biology, Utrecht University, Utrecht, The Netherlands
- Plant-Microbe Interactions, Utrecht University, Utrecht, The Netherlands
| | - Joyce Elberse
- Translational Plant Biology, Utrecht University, Utrecht, The Netherlands
| | | | - Ronnie de Jonge
- Plant-Microbe Interactions, Utrecht University, Utrecht, The Netherlands
- AI Technology for Life, Department of Information and Computing Sciences, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Michael F. Seidl
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
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Liu JN, Yan L, Chai Z, Liang Q, Dong Y, Wang C, Li X, Li C, Mu Y, Gong A, Yang J, Li J, Yang KQ, Wu D, Fang H. Pan-genome analyses of 11 Fraxinus species provide insights into salt adaptation in ash trees. PLANT COMMUNICATIONS 2024:101137. [PMID: 39308021 DOI: 10.1016/j.xplc.2024.101137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 08/01/2024] [Accepted: 09/19/2024] [Indexed: 11/10/2024]
Abstract
Ash trees (Fraxinus) exhibit rich genetic diversity and wide adaptation to various ecological environments, and several species are highly salt tolerant. Dissecting the genomic basis of salt adaptation in Fraxinus is vital for its resistance breeding. Here, we present 11 high-quality chromosome-level genome assemblies for Fraxinus species, which reveal two unequal subgenome compositions and two recent whole-genome triplication events in their evolutionary history. A Fraxinus pan-genome was constructed on the basis of structural variations and revealed that presence-absence variations (PAVs) of transmembrane transport genes have likely contributed to salt adaptation in Fraxinus. Through whole-genome resequencing of an F1 population from an interspecies cross of F. velutina 'Lula 3' (salt tolerant) with F. pennsylvanica 'Lula 5' (salt sensitive), we mapped salt-tolerance PAV-based quantitative trait loci (QTLs) and pinpointed two PAV-QTLs and candidate genes associated with Fraxinus salt tolerance. Mechanistically, FvbHLH85 enhances salt tolerance by mediating reactive oxygen species and Na+/K+ homeostasis, whereas FvSWEET5 enhances salt tolerance by mediating osmotic homeostasis. Collectively, these findings provide valuable genomic resources for Fraxinus salt-resistance breeding and the research community.
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Affiliation(s)
- Jian Ning Liu
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Liping Yan
- Shandong Provincial Academy of Forestry, Jinan 250014, China
| | - Zejia Chai
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Qiang Liang
- College of Forestry, Shandong Agricultural University, Taian 271018, China; State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian 271018, China; Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian 271018, China
| | - Yuhui Dong
- College of Forestry, Shandong Agricultural University, Taian 271018, China; State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian 271018, China; Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian 271018, China
| | - Changxi Wang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Xichen Li
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Chunyu Li
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Yutian Mu
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Andi Gong
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Jinfeng Yang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Jiaxiao Li
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Ke Qiang Yang
- College of Forestry, Shandong Agricultural University, Taian 271018, China; State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian 271018, China; Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian 271018, China.
| | - Dejun Wu
- Shandong Provincial Academy of Forestry, Jinan 250014, China.
| | - Hongcheng Fang
- College of Forestry, Shandong Agricultural University, Taian 271018, China; State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian 271018, China; Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian 271018, China.
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7
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Ou S, Scheben A, Collins T, Qiu Y, Seetharam AS, Menard CC, Manchanda N, Gent JI, Schatz MC, Anderson SN, Hufford MB, Hirsch CN. Differences in activity and stability drive transposable element variation in tropical and temperate maize. Genome Res 2024; 34:1140-1153. [PMID: 39251347 PMCID: PMC11444183 DOI: 10.1101/gr.278131.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/12/2024] [Indexed: 09/11/2024]
Abstract
Much of the profound interspecific variation in genome content has been attributed to transposable elements (TEs). To explore the extent of TE variation within species, we developed an optimized open-source algorithm, panEDTA, to de novo annotate TEs in a pangenome context. We then generated a unified TE annotation for a maize pangenome derived from 26 reference-quality genomes, which reveals an excess of 35.1 Mb of TE sequences per genome in tropical maize relative to temperate maize. A small number (n = 216) of TE families, mainly LTR retrotransposons, drive these differences. Evidence from the methylome, transcriptome, LTR age distribution, and LTR insertional polymorphisms reveals that 64.7% of the variability is contributed by LTR families that are young, less methylated, and more expressed in tropical maize, whereas 18.5% is driven by LTR families with removal or loss in temperate maize. Additionally, we find enrichment for Young LTR families adjacent to nucleotide-binding and leucine-rich repeat (NLR) clusters of varying copy number across lines, suggesting TE activity may be associated with disease resistance in maize.
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Affiliation(s)
- Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Tyler Collins
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Yinjie Qiu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108, USA
| | - Arun S Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Claire C Menard
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108, USA
| | - Nancy Manchanda
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Sarah N Anderson
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA;
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108, USA;
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8
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Mangal V, Verma LK, Singh SK, Saxena K, Roy A, Karn A, Rohit R, Kashyap S, Bhatt A, Sood S. Triumphs of genomic-assisted breeding in crop improvement. Heliyon 2024; 10:e35513. [PMID: 39170454 PMCID: PMC11336775 DOI: 10.1016/j.heliyon.2024.e35513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 07/23/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024] Open
Abstract
Conventional breeding approaches have played a significant role in meeting the food demand remarkably well until now. However, the increasing population, yield plateaus in certain crops, and limited recombination necessitate using genomic resources for genomics-assisted crop improvement programs. As a result of advancements in the next-generation sequence technology, GABs have developed dramatically to characterize allelic variants and facilitate their rapid and efficient incorporation in crop improvement programs. Genomics-assisted breeding (GAB) has played an important role in harnessing the potential of modern genomic tools, exploiting allelic variation from genetic resources and developing cultivars over the past decade. The availability of pangenomes for major crops has been a significant development, albeit with varying degrees of completeness. Even though adopting these technologies is essentially determined on economic grounds and cost-effective assays, which create a wealth of information that can be successfully used to exploit the latent potential of crops. GAB has been instrumental in harnessing the potential of modern genomic resources and exploiting allelic variation for genetic enhancement and cultivar development. GAB strategies will be indispensable for designing future crops and are expected to play a crucial role in breeding climate-smart crop cultivars with higher nutritional value.
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Affiliation(s)
- Vikas Mangal
- ICAR-Central Potato Research Institute (CPRI), Shimla, Himachal Pradesh, 171001, India
| | | | - Sandeep Kumar Singh
- Department of Genetics and Plant Breeding, Faculty of Agricultural Sciences, Siksha ‘O’ Anusandhan University, Bhubaneswar, Odisha, 751030, India
| | - Kanak Saxena
- Department of Genetics and Plant Breeding, Rabindranath Tagore University, Raisen, Madhya Pradesh, India
| | - Anirban Roy
- Division of Genetics and Plant Breeding, Ramakrishna Mission Vivekananda Educational and Research Institute (RKMVERI), Narendrapur, Kolkata, 700103, India
| | - Anandi Karn
- Plant Breeding & Graduate Program, IFAS - University of Florida, Gainesville, USA
| | - Rohit Rohit
- Department of Genetics and Plant Breeding, GBPUA&T, Pantnagar, Uttarakhand, 263145, India
| | - Shruti Kashyap
- Department of Genetics and Plant Breeding, GBPUA&T, Pantnagar, Uttarakhand, 263145, India
| | - Ashish Bhatt
- Department of Genetics and Plant Breeding, GBPUA&T, Pantnagar, Uttarakhand, 263145, India
| | - Salej Sood
- ICAR-Central Potato Research Institute (CPRI), Shimla, Himachal Pradesh, 171001, India
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9
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Schreiber M, Jayakodi M, Stein N, Mascher M. Plant pangenomes for crop improvement, biodiversity and evolution. Nat Rev Genet 2024; 25:563-577. [PMID: 38378816 PMCID: PMC7616794 DOI: 10.1038/s41576-024-00691-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2023] [Indexed: 02/22/2024]
Abstract
Plant genome sequences catalogue genes and the genetic elements that regulate their expression. Such inventories further research aims as diverse as mapping the molecular basis of trait diversity in domesticated plants or inquiries into the origin of evolutionary innovations in flowering plants millions of years ago. The transformative technological progress of DNA sequencing in the past two decades has enabled researchers to sequence ever more genomes with greater ease. Pangenomes - complete sequences of multiple individuals of a species or higher taxonomic unit - have now entered the geneticists' toolkit. The genomes of crop plants and their wild relatives are being studied with translational applications in breeding in mind. But pangenomes are applicable also in ecological and evolutionary studies, as they help classify and monitor biodiversity across the tree of life, deepen our understanding of how plant species diverged and show how plants adapt to changing environments or new selection pressures exerted by human beings.
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Affiliation(s)
- Mona Schreiber
- Department of Biology, University of Marburg, Marburg, Germany
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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10
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Taylor DJ, Eizenga JM, Li Q, Das A, Jenike KM, Kenny EE, Miga KH, Monlong J, McCoy RC, Paten B, Schatz MC. Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References. Annu Rev Genomics Hum Genet 2024; 25:77-104. [PMID: 38663087 PMCID: PMC11451085 DOI: 10.1146/annurev-genom-021623-081639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
The Human Genome Project was an enormous accomplishment, providing a foundation for countless explorations into the genetics and genomics of the human species. Yet for many years, the human genome reference sequence remained incomplete and lacked representation of human genetic diversity. Recently, two major advances have emerged to address these shortcomings: complete gap-free human genome sequences, such as the one developed by the Telomere-to-Telomere Consortium, and high-quality pangenomes, such as the one developed by the Human Pangenome Reference Consortium. Facilitated by advances in long-read DNA sequencing and genome assembly algorithms, complete human genome sequences resolve regions that have been historically difficult to sequence, including centromeres, telomeres, and segmental duplications. In parallel, pangenomes capture the extensive genetic diversity across populations worldwide. Together, these advances usher in a new era of genomics research, enhancing the accuracy of genomic analysis, paving the path for precision medicine, and contributing to deeper insights into human biology.
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Affiliation(s)
- Dylan J Taylor
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA; , ,
| | - Jordan M Eizenga
- Genomics Institute, University of California, Santa Cruz, California, USA; , ,
| | - Qiuhui Li
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA; ,
| | - Arun Das
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA; ,
| | - Katharine M Jenike
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA;
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA;
| | - Karen H Miga
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
- Genomics Institute, University of California, Santa Cruz, California, USA; , ,
| | - Jean Monlong
- Institut de Recherche en Santé Digestive, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France;
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA; , ,
| | - Benedict Paten
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
- Genomics Institute, University of California, Santa Cruz, California, USA; , ,
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA; ,
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA; , ,
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11
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Cui Y, Lin Y, Wei H, Pan Y, He H, Qian H, Yang L, Cao X, Zhang Z, Zeng X, Wang T, He W, Liu X, Shi C, Yuan Q, Yu X, Chen L, Wang F, Zhu Y, Qian Q, Shang L. Identification of salt tolerance-associated presence-absence variations in the OsMADS56 gene through the integration of DEGs dataset and eQTL analysis. THE NEW PHYTOLOGIST 2024; 243:833-838. [PMID: 38840572 DOI: 10.1111/nph.19887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 05/19/2024] [Indexed: 06/07/2024]
Affiliation(s)
- Yuchao Cui
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, 350003, China
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Yarong Lin
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, 350003, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Hua Wei
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yuehan Pan
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Huiying He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Hongge Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Longbo Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xinglan Cao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Zhipeng Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xiaosi Zeng
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Tianyi Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Wenchuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xiangpei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Chuanlin Shi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Qiaoling Yuan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xiaoman Yu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Liang Chen
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Feng Wang
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, 350003, China
| | - Yiwang Zhu
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, 350003, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Yazhouwan National Laboratory, No. 8 Huanjin Road, Yazhou District, Sanya City, Hainan Province, 572024, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310000, Zhejiang, China
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Yazhouwan National Laboratory, No. 8 Huanjin Road, Yazhou District, Sanya City, Hainan Province, 572024, China
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12
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Tuttle HK, Del Rio AH, Bamberg JB, Shannon LM. Potato soup: analysis of cultivated potato gene bank populations reveals high diversity and little structure. FRONTIERS IN PLANT SCIENCE 2024; 15:1429279. [PMID: 39091313 PMCID: PMC11291250 DOI: 10.3389/fpls.2024.1429279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/27/2024] [Indexed: 08/04/2024]
Abstract
Cultivated potatoes are incredibly diverse, ranging from diploid to pentaploid and encompass four different species. They are adapted to disparate environments and conditions and carry unique alleles for resistance to pests and pathogens. Describing how diversity is partitioned within and among these populations is essential to understanding the potato genome and effectively utilizing landraces in breeding. This task is complicated by the difficulty of making comparisons across cytotypes and extensive admixture within section petota. We genotyped 730 accessions from the US Potato genebank including wild diploids and cultivated diploids and tetraploids using Genotype-by-sequencing. This data set allowed us to interrogate population structure and diversity as well as generate core subsets which will support breeders in efficiently screening genebank material for biotic and abiotic stress resistance alleles. We found that even controlling for ploidy, tetraploid material exhibited higher observed and expected heterozygosity than diploid accessions. In particular group chilotanum material was the most heterozygous and the only taxa not to exhibit any inbreeding. This may in part be because group chilotanum has a history of introgression not just from wild species, but landraces as well. All group chilotanum, exhibits introgression from group andigenum except clones from Southern South America near its origin, where the two groups are not highly differentiated. Moving north, we do not observe evidence for the same level of admixture back into group andigenum. This suggests that extensive history of admixture is a particular characteristic of chilotanum.
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Affiliation(s)
- Heather K. Tuttle
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, United States
| | - Alfonso H. Del Rio
- U.S. Department of Agriculture (USDA)/Agricultural Research Service, Potato Genebank, Sturgeon Bay, WI, United States
| | - John B. Bamberg
- U.S. Department of Agriculture (USDA)/Agricultural Research Service, Potato Genebank, Sturgeon Bay, WI, United States
| | - Laura M. Shannon
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, United States
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13
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Phillips AR. Variant calling in polyploids for population and quantitative genetics. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11607. [PMID: 39184203 PMCID: PMC11342233 DOI: 10.1002/aps3.11607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/03/2024] [Accepted: 04/10/2024] [Indexed: 08/27/2024]
Abstract
Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid species. Compared to popular reduced-representation sequencing approaches, the genome-wide coverage and greater marker density provided by WGS data can greatly improve our understanding of polyploid species and polyploid biology. However, biological features that make polyploid species interesting also pose challenges in read mapping, variant identification, and genotype estimation. Accounting for characteristics in variant calling like allelic dosage uncertainty, homology between subgenomes, and variance in chromosome inheritance mode can reduce errors. Here, I discuss the challenges of variant calling in polyploid WGS data and discuss where potential solutions can be integrated into a standard variant calling pipeline.
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Affiliation(s)
- Alyssa R. Phillips
- Department of Evolution and EcologyUniversity of California, DavisDavis95616CaliforniaUSA
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14
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Xie X, Deng X, Chen L, Yuan J, Chen H, Wei C, Liu X, Wuertz S, Qiu G. Integrated genomics provides insights into the evolution of the polyphosphate accumulation trait of Ca. Accumulibacter. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 20:100353. [PMID: 39221073 PMCID: PMC11361876 DOI: 10.1016/j.ese.2023.100353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 11/18/2023] [Accepted: 11/23/2023] [Indexed: 09/04/2024]
Abstract
Candidatus Accumulibacter, a prominent polyphosphate-accumulating organism (PAO) in wastewater treatment, plays a crucial role in enhanced biological phosphorus removal (EBPR). The genetic underpinnings of its polyphosphate accumulation capabilities, however, remain largely unknown. Here, we conducted a comprehensive genomic analysis of Ca. Accumulibacter-PAOs and their relatives within the Rhodocyclaceae family, identifying 124 core genes acquired via horizontal gene transfer (HGT) at its least common ancestor. Metatranscriptomic analysis of an enrichment culture of Ca. Accumulibacter revealed active transcription of 44 of these genes during an EBPR cycle, notably including the polyphosphate kinase 2 (PPK2) gene instead of the commonly recognized polyphosphate kinase 1 (PPK1) gene. Intriguingly, the phosphate regulon (Pho) genes showed minimal transcriptions, pointing to a distinctive fact of Pho dysregulation, where PhoU, the phosphate signaling complex protein, was not regulating the high-affinity phosphate transport (Pst) system, resulting in continuous phosphate uptake. To prevent phosphate toxicity, Ca. Accumulibacter utilized the laterally acquired PPK2 to condense phosphate into polyphosphate, resulting in the polyphosphate-accumulating feature. This study provides novel insights into the evolutionary emergence of the polyphosphate-accumulating trait in Ca. Accumulibacter, offering potential advancements in understanding the PAO phenotype in the EBPR process.
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Affiliation(s)
- Xiaojing Xie
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Xuhan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Liping Chen
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Jing Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Hang Chen
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou, 510006, China
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou, 510006, China
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15
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Poretsky E, Cagirici HB, Andorf CM, Sen TZ. Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits. G3 (BETHESDA, MD.) 2024; 14:jkae059. [PMID: 38492232 PMCID: PMC11075552 DOI: 10.1093/g3journal/jkae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 10/20/2023] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
The recent assembly and annotation of the 26 maize nested association mapping population founder inbreds have enabled large-scale pan-genomic comparative studies. These studies have expanded our understanding of agronomically important traits by integrating pan-transcriptomic data with trait-specific gene candidates from previous association mapping results. In contrast to the availability of pan-transcriptomic data, obtaining reliable protein-protein interaction (PPI) data has remained a challenge due to its high cost and complexity. We generated predicted PPI networks for each of the 26 genomes using the established STRING database. The individual genome-interactomes were then integrated to generate core- and pan-interactomes. We deployed the PPI clustering algorithm ClusterONE to identify numerous PPI clusters that were functionally annotated using gene ontology (GO) functional enrichment, demonstrating a diverse range of enriched GO terms across different clusters. Additional cluster annotations were generated by integrating gene coexpression data and gene description annotations, providing additional useful information. We show that the functionally annotated PPI clusters establish a useful framework for protein function prediction and prioritization of candidate genes of interest. Our study not only provides a comprehensive resource of predicted PPI networks for 26 maize genomes but also offers annotated interactome clusters for predicting protein functions and prioritizing gene candidates. The source code for the Python implementation of the analysis workflow and a standalone web application for accessing the analysis results are available at https://github.com/eporetsky/PanPPI.
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Affiliation(s)
- Elly Poretsky
- Crop Improvement and Genetics Research Unit, U.S. Department of Agriculture, Agricultural Research Service, 800 Buchanan St., Albany, CA 94710, USA
| | - Halise Busra Cagirici
- Crop Improvement and Genetics Research Unit, U.S. Department of Agriculture, Agricultural Research Service, 800 Buchanan St., Albany, CA 94710, USA
| | - Carson M Andorf
- Corn Insects and Crop Genetics Research, U.S. Department of Agriculture, Agricultural Research Service, Ames, IA 50011, USA
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - Taner Z Sen
- Crop Improvement and Genetics Research Unit, U.S. Department of Agriculture, Agricultural Research Service, 800 Buchanan St., Albany, CA 94710, USA
- Department of Bioengineering, University of California, 306 Stanley Hall, Berkeley, CA 94720, USA
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16
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Cannon EK, Portwood JL, Hayford RK, Haley OC, Gardiner JM, Andorf CM, Woodhouse MR. Enhanced pan-genomic resources at the maize genetics and genomics database. Genetics 2024; 227:iyae036. [PMID: 38577974 DOI: 10.1093/genetics/iyae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/13/2024] [Indexed: 04/06/2024] Open
Abstract
Pan-genomes, encompassing the entirety of genetic sequences found in a collection of genomes within a clade, are more useful than single reference genomes for studying species diversity. This is especially true for a species like Zea mays, which has a particularly diverse and complex genome. Presenting pan-genome data, analyses, and visualization is challenging, especially for a diverse species, but more so when pan-genomic data is linked to extensive gene model and gene data, including classical gene information, markers, insertions, expression and proteomic data, and protein structures as is the case at MaizeGDB. Here, we describe MaizeGDB's expansion to include the genic subset of the Zea pan-genome in a pan-gene data center featuring the maize genomes hosted at MaizeGDB, and the outgroup teosinte Zea genomes from the Pan-Andropoganeae project. The new data center offers a variety of browsing and visualization tools, including sequence alignment visualization, gene trees and other tools, to explore pan-genes in Zea that were calculated by the pipeline Pandagma. Combined, these data will help maize researchers study the complexity and diversity of Zea, and to use the comparative functions to validate pan-gene relationships for a selected gene model.
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Affiliation(s)
- Ethalinda K Cannon
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - John L Portwood
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Rita K Hayford
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Olivia C Haley
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Jack M Gardiner
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Carson M Andorf
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
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17
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Lian Q, Huettel B, Walkemeier B, Mayjonade B, Lopez-Roques C, Gil L, Roux F, Schneeberger K, Mercier R. A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range. Nat Genet 2024; 56:982-991. [PMID: 38605175 PMCID: PMC11096106 DOI: 10.1038/s41588-024-01715-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 03/11/2024] [Indexed: 04/13/2024]
Abstract
Although originally primarily a system for functional biology, Arabidopsis thaliana has, owing to its broad geographical distribution and adaptation to diverse environments, developed into a powerful model in population genomics. Here we present chromosome-level genome assemblies of 69 accessions from a global species range. We found that genomic colinearity is very conserved, even among geographically and genetically distant accessions. Along chromosome arms, megabase-scale rearrangements are rare and typically present only in a single accession. This indicates that the karyotype is quasi-fixed and that rearrangements in chromosome arms are counter-selected. Centromeric regions display higher structural dynamics, and divergences in core centromeres account for most of the genome size variations. Pan-genome analyses uncovered 32,986 distinct gene families, 60% being present in all accessions and 40% appearing to be dispensable, including 18% private to a single accession, indicating unexplored genic diversity. These 69 new Arabidopsis thaliana genome assemblies will empower future genetic research.
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Affiliation(s)
- Qichao Lian
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bruno Huettel
- Max Planck-Genome-centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Birgit Walkemeier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Baptiste Mayjonade
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | | | - Lisa Gil
- INRAE, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Fabrice Roux
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany.
- Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Düsseldorf, Germany.
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Düsseldorf, Germany.
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18
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Yang X, Yu S, Yan S, Wang H, Fang W, Chen Y, Ma X, Han L. Progress in Rice Breeding Based on Genomic Research. Genes (Basel) 2024; 15:564. [PMID: 38790193 PMCID: PMC11121554 DOI: 10.3390/genes15050564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
The role of rice genomics in breeding progress is becoming increasingly important. Deeper research into the rice genome will contribute to the identification and utilization of outstanding functional genes, enriching the diversity and genetic basis of breeding materials and meeting the diverse demands for various improvements. Here, we review the significant contributions of rice genomics research to breeding progress over the last 25 years, discussing the profound impact of genomics on rice genome sequencing, functional gene exploration, and novel breeding methods, and we provide valuable insights for future research and breeding practices.
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Affiliation(s)
- Xingye Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Shicong Yu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China;
| | - Shen Yan
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Hao Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Wei Fang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Yanqing Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Xiaoding Ma
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Longzhi Han
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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19
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Li J, Zhao Y, Wu Z, Wang X. Editorial: Crop improvement by omics and bioinformatics. FRONTIERS IN PLANT SCIENCE 2024; 15:1391334. [PMID: 38633453 PMCID: PMC11022161 DOI: 10.3389/fpls.2024.1391334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024]
Affiliation(s)
- Jun Li
- Hainan Institute of Zhejiang University, Sanya, Hainan, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Zhichao Wu
- National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Xueqiang Wang
- Hainan Institute of Zhejiang University, Sanya, Hainan, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
- Yazhouwan National Laboratory, Sanya, Hainan, China
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20
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Aguirre NC, Villalba PV, García MN, Filippi CV, Rivas JG, Martínez MC, Acuña CV, López AJ, López JA, Pathauer P, Palazzini D, Harrand L, Oberschelp J, Marcó MA, Cisneros EF, Carreras R, Martins Alves AM, Rodrigues JC, Hopp HE, Grattapaglia D, Cappa EP, Paniego NB, Marcucci Poltri SN. Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden). Front Genet 2024; 15:1361418. [PMID: 38606359 PMCID: PMC11008695 DOI: 10.3389/fgene.2024.1361418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/19/2024] [Indexed: 04/13/2024] Open
Abstract
Eucalyptus dunnii is one of the most important Eucalyptus species for short-fiber pulp production in regions where other species of the genus are affected by poor soil and climatic conditions. In this context, E. dunnii holds promise as a resource to address and adapt to the challenges of climate change. Despite its rapid growth and favorable wood properties for solid wood products, the advancement of its improvement remains in its early stages. In this work, we evaluated the performance of two single nucleotide polymorphism, (SNP), genotyping methods for population genetics analysis and Genomic Selection in E. dunnii. Double digest restriction-site associated DNA sequencing (ddRADseq) was compared with the EUChip60K array in 308 individuals from a provenance-progeny trial. The compared SNP set included 8,011 and 19,008 informative SNPs distributed along the 11 chromosomes, respectively. Although the two datasets differed in the percentage of missing data, genome coverage, minor allele frequency and estimated genetic diversity parameters, they revealed a similar genetic structure, showing two subpopulations with little differentiation between them, and low linkage disequilibrium. GS analyses were performed for eleven traits using Genomic Best Linear Unbiased Prediction (GBLUP) and a conventional pedigree-based model (ABLUP). Regardless of the SNP dataset, the predictive ability (PA) of GBLUP was better than that of ABLUP for six traits (Cellulose content, Total and Ethanolic extractives, Total and Klason lignin content and Syringyl and Guaiacyl lignin monomer ratio). When contrasting the SNP datasets used to estimate PAs, the GBLUP-EUChip60K model gave higher and significant PA values for six traits, meanwhile, the values estimated using ddRADseq gave higher values for three other traits. The PAs correlated positively with narrow sense heritabilities, with the highest correlations shown by the ABLUP and GBLUP-EUChip60K. The two genotyping methods, ddRADseq and EUChip60K, are generally comparable for population genetics and genomic prediction, demonstrating the utility of the former when subjected to rigorous SNP filtering. The results of this study provide a basis for future whole-genome studies using ddRADseq in non-model forest species for which SNP arrays have not yet been developed.
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Affiliation(s)
| | | | - Martín Nahuel García
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Carla Valeria Filippi
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
- Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Juan Gabriel Rivas
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - María Carolina Martínez
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Cintia Vanesa Acuña
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Augusto J. López
- Estación Experimental Agropecuaria de Bella Vista, Instituto Nacional de Tecnología Agropecuaria, Bella Vista, Argentina
| | - Juan Adolfo López
- Estación Experimental Agropecuaria de Bella Vista, Instituto Nacional de Tecnología Agropecuaria, Bella Vista, Argentina
| | - Pablo Pathauer
- Instituto de Recursos Biológicos, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
| | - Dino Palazzini
- Instituto de Recursos Biológicos, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
| | - Leonel Harrand
- Estación Experimental Agropecuaria de Concordia, Instituto Nacional de Tecnología Agropecuaria, Concordia, Argentina
| | - Javier Oberschelp
- Estación Experimental Agropecuaria de Concordia, Instituto Nacional de Tecnología Agropecuaria, Concordia, Argentina
| | - Martín Alberto Marcó
- Estación Experimental Agropecuaria de Concordia, Instituto Nacional de Tecnología Agropecuaria, Concordia, Argentina
| | - Esteban Felipe Cisneros
- Facultad de Ciencias Forestales, Universidad Nacional de Santiago del Estero (UNSE), Santiago del Estero, Argentina
| | - Rocío Carreras
- Facultad de Ciencias Forestales, Universidad Nacional de Santiago del Estero (UNSE), Santiago del Estero, Argentina
| | - Ana Maria Martins Alves
- Centro de Estudos Florestais e Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, Portugal
| | - José Carlos Rodrigues
- Centro de Estudos Florestais e Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, Portugal
| | - H. Esteban Hopp
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Dario Grattapaglia
- Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Recursos Genéticos e Biotecnologia, Brasilia, Brazil
| | - Eduardo Pablo Cappa
- Instituto de Recursos Biológicos, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Norma Beatriz Paniego
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
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21
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Gepts P. Biocultural diversity and crop improvement. Emerg Top Life Sci 2023; 7:151-196. [PMID: 38084755 PMCID: PMC10754339 DOI: 10.1042/etls20230067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023]
Abstract
Biocultural diversity is the ever-evolving and irreplaceable sum total of all living organisms inhabiting the Earth. It plays a significant role in sustainable productivity and ecosystem services that benefit humanity and is closely allied with human cultural diversity. Despite its essentiality, biodiversity is seriously threatened by the insatiable and inequitable human exploitation of the Earth's resources. One of the benefits of biodiversity is its utilization in crop improvement, including cropping improvement (agronomic cultivation practices) and genetic improvement (plant breeding). Crop improvement has tended to decrease agricultural biodiversity since the origins of agriculture, but awareness of this situation can reverse this negative trend. Cropping improvement can strive to use more diverse cultivars and a broader complement of crops on farms and in landscapes. It can also focus on underutilized crops, including legumes. Genetic improvement can access a broader range of biodiversity sources and, with the assistance of modern breeding tools like genomics, can facilitate the introduction of additional characteristics that improve yield, mitigate environmental stresses, and restore, at least partially, lost crop biodiversity. The current legal framework covering biodiversity includes national intellectual property and international treaty instruments, which have tended to limit access and innovation to biodiversity. A global system of access and benefit sharing, encompassing digital sequence information, would benefit humanity but remains an elusive goal. The Kunming-Montréal Global Biodiversity Framework sets forth an ambitious set of targets and goals to be accomplished by 2030 and 2050, respectively, to protect and restore biocultural diversity, including agrobiodiversity.
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Affiliation(s)
- Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA 95616-8780, U.S.A
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22
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Liu Q, Ye L, Li M, Wang Z, Xiong G, Ye Y, Tu T, Schwarzacher T, Heslop-Harrison JSP. Genome-wide expansion and reorganization during grass evolution: from 30 Mb chromosomes in rice and Brachypodium to 550 Mb in Avena. BMC PLANT BIOLOGY 2023; 23:627. [PMID: 38062402 PMCID: PMC10704644 DOI: 10.1186/s12870-023-04644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND The BOP (Bambusoideae, Oryzoideae, and Pooideae) clade of the Poaceae has a common ancestor, with similarities to the genomes of rice, Oryza sativa (2n = 24; genome size 389 Mb) and Brachypodium, Brachypodium distachyon (2n = 10; 271 Mb). We exploit chromosome-scale genome assemblies to show the nature of genomic expansion, structural variation, and chromosomal rearrangements from rice and Brachypodium, to diploids in the tribe Aveneae (e.g., Avena longiglumis, 2n = 2x = 14; 3,961 Mb assembled to 3,850 Mb in chromosomes). RESULTS Most of the Avena chromosome arms show relatively uniform expansion over the 10-fold to 15-fold genome-size increase. Apart from non-coding sequence diversification and accumulation around the centromeres, blocks of genes are not interspersed with blocks of repeats, even in subterminal regions. As in the tribe Triticeae, blocks of conserved synteny are seen between the analyzed species with chromosome fusion, fission, and nesting (insertion) events showing deep evolutionary conservation of chromosome structure during genomic expansion. Unexpectedly, the terminal gene-rich chromosomal segments (representing about 50 Mb) show translocations between chromosomes during speciation, with homogenization of genome-specific repetitive elements within the tribe Aveneae. Newly-formed intergenomic translocations of similar extent are found in the hexaploid A. sativa. CONCLUSIONS The study provides insight into evolutionary mechanisms and speciation in the BOP clade, which is valuable for measurement of biodiversity, development of a clade-wide pangenome, and exploitation of genomic diversity through breeding programs in Poaceae.
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Affiliation(s)
- Qing Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
- Center for Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Lyuhan Ye
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingzhi Li
- Bio&Data Biotechnologies Co. Ltd, Guangzhou, 510663, China
| | - Ziwei Wang
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China
| | - Gui Xiong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yushi Ye
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Tieyao Tu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Center for Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, LE1 7RH, UK
| | - John Seymour Pat Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, LE1 7RH, UK.
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23
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Kirov I. Toward Transgene-Free Transposon-Mediated Biological Mutagenesis for Plant Breeding. Int J Mol Sci 2023; 24:17054. [PMID: 38069377 PMCID: PMC10706983 DOI: 10.3390/ijms242317054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Genetic diversity is a key factor for plant breeding. The birth of novel genic and genomic variants is also crucial for plant adaptation in nature. Therefore, the genomes of almost all living organisms possess natural mutagenic mechanisms. Transposable elements (TEs) are a major mutagenic force driving genetic diversity in wild plants and modern crops. The relatively rare TE transposition activity during the thousand-year crop domestication process has led to the phenotypic diversity of many cultivated species. The utilization of TE mutagenesis by artificial and transient acceleration of their activity in a controlled mode is an attractive foundation for a novel type of mutagenesis called TE-mediated biological mutagenesis. Here, I focus on TEs as mutagenic sources for plant breeding and discuss existing and emerging transgene-free approaches for TE activation in plants. Furthermore, I also review the non-randomness of TE insertions in a plant genome and the molecular and epigenetic factors involved in shaping TE insertion preferences. Additionally, I discuss the molecular mechanisms that prevent TE transpositions in germline plant cells (e.g., meiocytes, pollen, egg and embryo cells, and shoot apical meristem), thereby reducing the chances of TE insertion inheritance. Knowledge of these mechanisms can expand the TE activation toolbox using novel gene targeting approaches. Finally, the challenges and future perspectives of plant populations with induced novel TE insertions (iTE plant collections) are discussed.
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Affiliation(s)
- Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
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24
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Busoms S, Fischer S, Yant L. Chasing the mechanisms of ecologically adaptive salinity tolerance. PLANT COMMUNICATIONS 2023; 4:100571. [PMID: 36883005 PMCID: PMC10721451 DOI: 10.1016/j.xplc.2023.100571] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/12/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Plants adapted to challenging environments offer fascinating models of evolutionary change. Importantly, they also give information to meet our pressing need to develop resilient, low-input crops. With mounting environmental fluctuation-including temperature, rainfall, and soil salinity and degradation-this is more urgent than ever. Happily, solutions are hiding in plain sight: the adaptive mechanisms from natural adapted populations, once understood, can then be leveraged. Much recent insight has come from the study of salinity, a widespread factor limiting productivity, with estimates of 20% of all cultivated lands affected. This is an expanding problem, given increasing climate volatility, rising sea levels, and poor irrigation practices. We therefore highlight recent benchmark studies of ecologically adaptive salt tolerance in plants, assessing macro- and microevolutionary mechanisms, and the recently recognized role of ploidy and the microbiome on salinity adaptation. We synthesize insight specifically on naturally evolved adaptive salt-tolerance mechanisms, as these works move substantially beyond traditional mutant or knockout studies, to show how evolution can nimbly "tweak" plant physiology to optimize function. We then point to future directions to advance this field that intersect evolutionary biology, abiotic-stress tolerance, breeding, and molecular plant physiology.
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Affiliation(s)
- Silvia Busoms
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Bellaterra, Barcelona E-08193, Spain
| | - Sina Fischer
- Future Food Beacon of Excellence, University of Nottingham, Nottingham NG7 2RD, UK; School of Biosciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Levi Yant
- Future Food Beacon of Excellence, University of Nottingham, Nottingham NG7 2RD, UK; School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK.
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25
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Zhang X, Chen Y, Wang L, Yuan Y, Fang M, Shi L, Lu R, Comes HP, Ma Y, Chen Y, Huang G, Zhou Y, Zheng Z, Qiu Y. Pangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization. HORTICULTURE RESEARCH 2023; 10:uhad203. [PMID: 38046854 PMCID: PMC10689057 DOI: 10.1093/hr/uhad203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/01/2023] [Indexed: 12/05/2023]
Abstract
Water caltrop (Trapa spp., Lythraceae) is a traditional but currently underutilized non-cereal crop. Here, we generated chromosome-level genome assemblies for the two diploid progenitors of allotetraploid Trapa. natans (4x, AABB), i.e., diploid T. natans (2x, AA) and Trapa incisa (2x, BB). In conjunction with four published (sub)genomes of Trapa, we used gene-based and graph-based pangenomic approaches and a pangenomic transposable element (TE) library to develop Trapa genomic resources. The pangenome displayed substantial gene-content variation with dispensable and private gene clusters occupying a large proportion (51.95%) of the total cluster sets in the six (sub)genomes. Genotyping of presence-absence variation (PAVs) identified 40 453 PAVs associated with 2570 genes specific to A- or B-lineages, of which 1428 were differentially expressed, and were enriched in organ development process, organic substance metabolic process and response to stimulus. Comparative genome analyses showed that the allotetraploid T. natans underwent asymmetric subgenome divergence, with the B-subgenome being more dominant than the A-subgenome. Multiple factors, including PAVs, asymmetrical amplification of TEs, homeologous exchanges (HEs), and homeolog expression divergence, together affected genome evolution after polyploidization. Overall, this study sheds lights on the genome architecture and evolution of Trapa, and facilitates its functional genomic studies and breeding program.
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Affiliation(s)
- Xinyi Zhang
- Systematic and Evolutionary Botany and Biodiversity Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Yang Chen
- Systematic and Evolutionary Botany and Biodiversity Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Lingyun Wang
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, 321000, Zhejiang, China
| | - Ye Yuan
- Jiaxing Academy of Agricultural Sciences, Jiaxing, 314016, Zhejiang, China
| | - Mingya Fang
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, 321000, Zhejiang, China
| | - Lin Shi
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, 321000, Zhejiang, China
| | - Ruisen Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, Jiangsu, China
| | - Hans Peter Comes
- Department of Environment & Biodiversity, Salzburg University, Salzburg, 5020, Austria
| | - Yazhen Ma
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Yuanyuan Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Guizhou Huang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture; Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, Guangdong, China
| | - Yongfeng Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture; Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, Guangdong, China
| | - Zhaisheng Zheng
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, 321000, Zhejiang, China
| | - Yingxiong Qiu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
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Xu XD, Zhao RP, Xiao L, Lu L, Gao M, Luo YH, Zhou ZW, Ye SY, Qian YQ, Fan BL, Shang X, Shi P, Zeng W, Cao S, Wu Z, Yan H, Chen LL, Song JM. Telomere-to-telomere assembly of cassava genome reveals the evolution of cassava and divergence of allelic expression. HORTICULTURE RESEARCH 2023; 10:uhad200. [PMID: 38023477 PMCID: PMC10673656 DOI: 10.1093/hr/uhad200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/28/2023] [Indexed: 12/01/2023]
Abstract
Cassava is a crucial crop that makes a significant contribution to ensuring human food security. However, high-quality telomere-to-telomere cassava genomes have not been available up to now, which has restricted the progress of haploid molecular breeding for cassava. In this study, we constructed two nearly complete haploid resolved genomes and an integrated, telomere-to-telomere gap-free reference genome of an excellent cassava variety, 'Xinxuan 048', thereby providing a new high-quality genomic resource. Furthermore, the evolutionary history of several species within the Euphorbiaceae family was revealed. Through comparative analysis of haploid genomes, it was found that two haploid genomes had extensive differences in linear structure, transcriptome features, and epigenetic characteristics. Genes located within the highly divergent regions and differentially expressed alleles are enriched in the functions of auxin response and the starch synthesis pathway. The high heterozygosity of cassava 'Xinxuan 048' leads to rapid trait segregation in the first selfed generation. This study provides a theoretical basis and genomic resource for molecular breeding of cassava haploids.
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Affiliation(s)
- Xin-Dong Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Ru-Peng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Liang Xiao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Liuying Lu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Min Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yu-Hong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zu-Wen Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Si-Ying Ye
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yong-Qing Qian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Bing-Liang Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Xiaohong Shang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Pingli Shi
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Wendan Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Sheng Cao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Zhengdan Wu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Huabing Yan
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jia-Ming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
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27
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Della Coletta R, Fernandes SB, Monnahan PJ, Mikel MA, Bohn MO, Lipka AE, Hirsch CN. Importance of genetic architecture in marker selection decisions for genomic prediction. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:220. [PMID: 37819415 DOI: 10.1007/s00122-023-04469-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
KEY MESSAGE We demonstrate potential for improved multi-environment genomic prediction accuracy using structural variant markers. However, the degree of observed improvement is highly dependent on the genetic architecture of the trait. Breeders commonly use genetic markers to predict the performance of untested individuals as a way to improve the efficiency of breeding programs. These genomic prediction models have almost exclusively used single nucleotide polymorphisms (SNPs) as their source of genetic information, even though other types of markers exist, such as structural variants (SVs). Given that SVs are associated with environmental adaptation and not all of them are in linkage disequilibrium to SNPs, SVs have the potential to bring additional information to multi-environment prediction models that are not captured by SNPs alone. Here, we evaluated different marker types (SNPs and/or SVs) on prediction accuracy across a range of genetic architectures for simulated traits across multiple environments. Our results show that SVs can improve prediction accuracy, but it is highly dependent on the genetic architecture of the trait and the relative gain in accuracy is minimal. When SVs are the only causative variant type, 70% of the time SV predictors outperform SNP predictors. However, the improvement in accuracy in these instances is only 1.5% on average. Further simulations with predictors in varying degrees of LD with causative variants of different types (e.g., SNPs, SVs, SNPs and SVs) showed that prediction accuracy increased as linkage disequilibrium between causative variants and predictors increased regardless of the marker type. This study demonstrates that knowing the genetic architecture of a trait in deciding what markers to use in large-scale genomic prediction modeling in a breeding program is more important than what types of markers to use.
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Affiliation(s)
- Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Samuel B Fernandes
- Department of Crop, Soil and Environmental Sciences at University of Arkansas, Fayetteville, AR, 72701, USA
| | - Patrick J Monnahan
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Mark A Mikel
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Martin O Bohn
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
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28
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Lyu X, Xia Y, Wang C, Zhang K, Deng G, Shen Q, Gao W, Zhang M, Liao N, Ling J, Bo Y, Hu Z, Yang J, Zhang M. Pan-genome analysis sheds light on structural variation-based dissection of agronomic traits in melon crops. PLANT PHYSIOLOGY 2023; 193:1330-1348. [PMID: 37477947 DOI: 10.1093/plphys/kiad405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/21/2023] [Indexed: 07/22/2023]
Abstract
Sweetness and appearance of fresh fruits are key palatable and preference attributes for consumers and are often controlled by multiple genes. However, fine-mapping the key loci or genes of interest by single genome-based genetic analysis is challenging. Herein, we present the chromosome-level genome assembly of 1 landrace melon accession (Cucumis melo ssp. agrestis) with wild morphologic features and thus construct a melon pan-genome atlas via integrating sequenced melon genome datasets. Our comparative genomic analysis reveals a total of 3.4 million genetic variations, of which the presence/absence variations (PAVs) are mainly involved in regulating the function of genes for sucrose metabolism during melon domestication and improvement. We further resolved several loci that are accountable for sucrose contents, flesh color, rind stripe, and suture using a structural variation (SV)-based genome-wide association study. Furthermore, via bulked segregation analysis (BSA)-seq and map-based cloning, we uncovered that a single gene, (CmPIRL6), determines the edible or inedible characteristics of melon fruit exocarp. These findings provide important melon pan-genome information and provide a powerful toolkit for future pan-genome-informed cultivar breeding of melon.
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Affiliation(s)
- Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yuelin Xia
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chenhao Wang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Kejia Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Guancong Deng
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qinghui Shen
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Wei Gao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou District, Sanya 572025, China
| | - Mengyi Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou District, Sanya 572025, China
| | - Nanqiao Liao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jian Ling
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Yongming Bo
- Key Laboratory of Vegetable Breeding, Ningbo Weimeng Seed Co., Ltd, Ningbo 315100, China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
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29
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Naithani S, Deng CH, Sahu SK, Jaiswal P. Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes. Biomolecules 2023; 13:1403. [PMID: 37759803 PMCID: PMC10527062 DOI: 10.3390/biom13091403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution and build clade-specific pan-genomes of several crops. The pan-genomes of crops constructed from various cultivars, accessions, landraces, and wild ancestral species represent a compendium of genes and structural variations and allow researchers to search for the novel genes and alleles that were inadvertently lost in domesticated crops during the historical process of crop domestication or in the process of extensive plant breeding. Fortunately, many valuable genes and alleles associated with desirable traits like disease resistance, abiotic stress tolerance, plant architecture, and nutrition qualities exist in landraces, ancestral species, and crop wild relatives. The novel genes from the wild ancestors and landraces can be introduced back to high-yielding varieties of modern crops by implementing classical plant breeding, genomic selection, and transgenic/gene editing approaches. Thus, pan-genomic represents a great leap in plant research and offers new avenues for targeted breeding to mitigate the impact of global climate change. Here, we summarize the tools used for pan-genome assembly and annotations, web-portals hosting plant pan-genomes, etc. Furthermore, we highlight a few discoveries made in crops using the pan-genomic approach and future potential of this emerging field of study.
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Affiliation(s)
- Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
| | - Cecilia H. Deng
- Molecular & Digital Breeing Group, New Cultivar Innovation, The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand;
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China;
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
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30
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Escudero-Martinez C, Bulgarelli D. Engineering the Crop Microbiota Through Host Genetics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:257-277. [PMID: 37196364 DOI: 10.1146/annurev-phyto-021621-121447] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The microbiota populating the plant-soil continuum defines an untapped resource for sustainable crop production. The host plant is a driver for the taxonomic composition and function of these microbial communities. In this review, we illustrate how the host genetic determinants of the microbiota have been shaped by plant domestication and crop diversification. We discuss how the heritable component of microbiota recruitment may represent, at least partially, a selection for microbial functions underpinning the growth, development, and health of their host plants and how the magnitude of this heritability is influenced by the environment. We illustrate how host-microbiota interactions can be treated as an external quantitative trait and review recent studies associating crop genetics with microbiota-based quantitative traits. We also explore the results of reductionist approaches, including synthetic microbial communities, to establish causal relationships between microbiota and plant phenotypes. Lastly, we propose strategies to integrate microbiota manipulation into crop selection programs. Although a detailed understanding of when and how heritability for microbiota composition can be deployed for breeding purposes is still lacking, we argue that advances in crop genomics are likely to accelerate wider applications of plant-microbiota interactions in agriculture.
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Affiliation(s)
| | - Davide Bulgarelli
- Plant Sciences, School of Life Sciences, University of Dundee, Dundee, United Kingdom; ,
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31
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Chen Y, Guo Y, Xie X, Wang Z, Miao L, Yang Z, Jiao Y, Xie C, Liu J, Hu Z, Xin M, Yao Y, Ni Z, Sun Q, Peng H, Guo W. Pangenome-based trajectories of intracellular gene transfers in Poaceae unveil high cumulation in Triticeae. PLANT PHYSIOLOGY 2023; 193:578-594. [PMID: 37249052 PMCID: PMC10469385 DOI: 10.1093/plphys/kiad319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/04/2023] [Indexed: 05/31/2023]
Abstract
Intracellular gene transfers (IGTs) between the nucleus and organelles, including plastids and mitochondria, constantly reshape the nuclear genome during evolution. Despite the substantial contribution of IGTs to genome variation, the dynamic trajectories of IGTs at the pangenomic level remain elusive. Here, we developed an approach, IGTminer, that maps the evolutionary trajectories of IGTs using collinearity and gene reannotation across multiple genome assemblies. We applied IGTminer to create a nuclear organellar gene (NOG) map across 67 genomes covering 15 Poaceae species, including important crops. The resulting NOGs were verified by experiments and sequencing data sets. Our analysis revealed that most NOGs were recently transferred and lineage specific and that Triticeae species tended to have more NOGs than other Poaceae species. Wheat (Triticum aestivum) had a higher retention rate of NOGs than maize (Zea mays) and rice (Oryza sativa), and the retained NOGs were likely involved in photosynthesis and translation pathways. Large numbers of NOG clusters were aggregated in hexaploid wheat during 2 rounds of polyploidization, contributing to the genetic diversity among modern wheat accessions. We implemented an interactive web server to facilitate the exploration of NOGs in Poaceae. In summary, this study provides resources and insights into the roles of IGTs in shaping interspecies and intraspecies genome variation and driving plant genome evolution.
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Affiliation(s)
- Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yiwen Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiaoming Xie
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhengzhao Yang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaojie Xie
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jie Liu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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32
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Jin X, Du H, Zhu C, Wan H, Liu F, Ruan J, Mower JP, Zhu A. Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry. NATURE PLANTS 2023; 9:1252-1266. [PMID: 37537397 DOI: 10.1038/s41477-023-01473-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 07/03/2023] [Indexed: 08/05/2023]
Abstract
Strawberry is an emerging model for studying polyploid genome evolution and rapid domestication of fruit crops. Here we report haplotype-resolved genomes of two wild octoploids (Fragaria chiloensis and Fragaria virginiana), the progenitor species of cultivated strawberry. Substantial variation is identified between species and between haplotypes. We redefine the four subgenomes and track the genetic contributions of diploid species by additional sequencing of the diploid F. nipponica genome. We provide multiple lines of evidence that F. vesca and F. iinumae, rather than other described extant species, are the closest living relatives of these wild and cultivated octoploids. In response to coexistence with quadruplicate gene copies, the octoploid strawberries have experienced subgenome dominance, homoeologous exchanges and coordinated expression of homoeologous genes. However, some homoeologues have substantially altered expression bias after speciation and during domestication. These findings enhance our understanding of the origin, genome evolution and domestication of strawberries.
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Affiliation(s)
- Xin Jin
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haiyuan Du
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chumeng Zhu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong Wan
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jiwei Ruan
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, USA.
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA.
| | - Andan Zhu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
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33
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Sinha D, Maurya AK, Abdi G, Majeed M, Agarwal R, Mukherjee R, Ganguly S, Aziz R, Bhatia M, Majgaonkar A, Seal S, Das M, Banerjee S, Chowdhury S, Adeyemi SB, Chen JT. Integrated Genomic Selection for Accelerating Breeding Programs of Climate-Smart Cereals. Genes (Basel) 2023; 14:1484. [PMID: 37510388 PMCID: PMC10380062 DOI: 10.3390/genes14071484] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Rapidly rising population and climate changes are two critical issues that require immediate action to achieve sustainable development goals. The rising population is posing increased demand for food, thereby pushing for an acceleration in agricultural production. Furthermore, increased anthropogenic activities have resulted in environmental pollution such as water pollution and soil degradation as well as alterations in the composition and concentration of environmental gases. These changes are affecting not only biodiversity loss but also affecting the physio-biochemical processes of crop plants, resulting in a stress-induced decline in crop yield. To overcome such problems and ensure the supply of food material, consistent efforts are being made to develop strategies and techniques to increase crop yield and to enhance tolerance toward climate-induced stress. Plant breeding evolved after domestication and initially remained dependent on phenotype-based selection for crop improvement. But it has grown through cytological and biochemical methods, and the newer contemporary methods are based on DNA-marker-based strategies that help in the selection of agronomically useful traits. These are now supported by high-end molecular biology tools like PCR, high-throughput genotyping and phenotyping, data from crop morpho-physiology, statistical tools, bioinformatics, and machine learning. After establishing its worth in animal breeding, genomic selection (GS), an improved variant of marker-assisted selection (MAS), has made its way into crop-breeding programs as a powerful selection tool. To develop novel breeding programs as well as innovative marker-based models for genetic evaluation, GS makes use of molecular genetic markers. GS can amend complex traits like yield as well as shorten the breeding period, making it advantageous over pedigree breeding and marker-assisted selection (MAS). It reduces the time and resources that are required for plant breeding while allowing for an increased genetic gain of complex attributes. It has been taken to new heights by integrating innovative and advanced technologies such as speed breeding, machine learning, and environmental/weather data to further harness the GS potential, an approach known as integrated genomic selection (IGS). This review highlights the IGS strategies, procedures, integrated approaches, and associated emerging issues, with a special emphasis on cereal crops. In this domain, efforts have been taken to highlight the potential of this cutting-edge innovation to develop climate-smart crops that can endure abiotic stresses with the motive of keeping production and quality at par with the global food demand.
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Affiliation(s)
- Dwaipayan Sinha
- Department of Botany, Government General Degree College, Mohanpur 721436, India
| | - Arun Kumar Maurya
- Department of Botany, Multanimal Modi College, Modinagar, Ghaziabad 201204, India
| | - Gholamreza Abdi
- Department of Biotechnology, Persian Gulf Research Institute, Persian Gulf University, Bushehr 75169, Iran
| | - Muhammad Majeed
- Department of Botany, University of Gujrat, Punjab 50700, Pakistan
| | - Rachna Agarwal
- Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Rashmi Mukherjee
- Research Center for Natural and Applied Sciences, Department of Botany (UG & PG), Raja Narendralal Khan Women's College, Gope Palace, Midnapur 721102, India
| | - Sharmistha Ganguly
- Department of Dravyaguna, Institute of Post Graduate Ayurvedic Education and Research, Kolkata 700009, India
| | - Robina Aziz
- Department of Botany, Government, College Women University, Sialkot 51310, Pakistan
| | - Manika Bhatia
- TERI School of Advanced Studies, New Delhi 110070, India
| | - Aqsa Majgaonkar
- Department of Botany, St. Xavier's College (Autonomous), Mumbai 400001, India
| | - Sanchita Seal
- Department of Botany, Polba Mahavidyalaya, Polba 712148, India
| | - Moumita Das
- V. Sivaram Research Foundation, Bangalore 560040, India
| | - Swastika Banerjee
- Department of Botany, Kairali College of +3 Science, Champua, Keonjhar 758041, India
| | - Shahana Chowdhury
- Department of Biotechnology, Faculty of Engineering Sciences, German University Bangladesh, TNT Road, Telipara, Chandona Chowrasta, Gazipur 1702, Bangladesh
| | - Sherif Babatunde Adeyemi
- Ethnobotany/Phytomedicine Laboratory, Department of Plant Biology, Faculty of Life Sciences, University of Ilorin, Ilorin P.M.B 1515, Nigeria
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan
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Huff M, Hulse-Kemp AM, Scheffler BE, Youngblood RC, Simpson SA, Babiker E, Staton M. Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa. BMC Genomics 2023; 24:409. [PMID: 37474911 PMCID: PMC10357881 DOI: 10.1186/s12864-023-09514-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/13/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Muscadine grape (Vitis rotundifolia) is resistant to many of the pathogens that negatively impact the production of common grape (V. vinifera), including the bacterial pathogen Xylella fastidiosa subsp. fastidiosa (Xfsf), which causes Pierce's Disease (PD). Previous studies in common grape have indicated Xfsf delays host immune response with a complex O-chain antigen produced by the wzy gene. Muscadine cultivars range from tolerant to completely resistant to Xfsf, but the mechanism is unknown. RESULTS We assembled and annotated a new, long-read genome assembly for 'Carlos', a cultivar of muscadine that exhibits tolerance, to build upon the existing genetic resources available for muscadine. We used these resources to construct an initial pan-genome for three cultivars of muscadine and one cultivar of common grape. This pan-genome contains a total of 34,970 synteny-constrained entries containing genes of similar structure. Comparison of resistance gene content between the 'Carlos' and common grape genomes indicates an expansion of resistance (R) genes in 'Carlos.' We further identified genes involved in Xfsf response by transcriptome sequencing 'Carlos' plants inoculated with Xfsf. We observed 234 differentially expressed genes with functions related to lipid catabolism, oxidation-reduction signaling, and abscisic acid (ABA) signaling as well as seven R genes. Leveraging public data from previous experiments of common grape inoculated with Xfsf, we determined that most differentially expressed genes in the muscadine response were not found in common grape, and three of the R genes identified as differentially expressed in muscadine do not have an ortholog in the common grape genome. CONCLUSIONS Our results support the utility of a pan-genome approach to identify candidate genes for traits of interest, particularly disease resistance to Xfsf, within and between muscadine and common grape.
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Affiliation(s)
- Matthew Huff
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Amanda M Hulse-Kemp
- Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC, 27606, USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27606, USA
| | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS, 38776, USA
| | - Ramey C Youngblood
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, 39762, USA
| | - Sheron A Simpson
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS, 38776, USA
| | - Ebrahiem Babiker
- USDA-ARS Thad Cochran Southern Horticultural Laboratory, Poplarville, MS, 39470, USA.
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA.
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35
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Karikari B, Lemay MA, Belzile F. k-mer-Based Genome-Wide Association Studies in Plants: Advances, Challenges, and Perspectives. Genes (Basel) 2023; 14:1439. [PMID: 37510343 PMCID: PMC10379394 DOI: 10.3390/genes14071439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Genome-wide association studies (GWAS) have allowed the discovery of marker-trait associations in crops over recent decades. However, their power is hampered by a number of limitations, with the key one among them being an overreliance on single-nucleotide polymorphisms (SNPs) as molecular markers. Indeed, SNPs represent only one type of genetic variation and are usually derived from alignment to a single genome assembly that may be poorly representative of the population under study. To overcome this, k-mer-based GWAS approaches have recently been developed. k-mer-based GWAS provide a universal way to assess variation due to SNPs, insertions/deletions, and structural variations without having to specifically detect and genotype these variants. In addition, k-mer-based analyses can be used in species that lack a reference genome. However, the use of k-mers for GWAS presents challenges such as data size and complexity, lack of standard tools, and potential detection of false associations. Nevertheless, efforts are being made to overcome these challenges and a general analysis workflow has started to emerge. We identify the priorities for k-mer-based GWAS in years to come, notably in the development of user-friendly programs for their analysis and approaches for linking significant k-mers to sequence variation.
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Affiliation(s)
- Benjamin Karikari
- Département de Phytologie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale P.O. Box TL 1882, Ghana
| | - Marc-André Lemay
- Département de Phytologie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
| | - François Belzile
- Département de Phytologie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
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36
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Dwivedi SL, Chapman MA, Abberton MT, Akpojotor UL, Ortiz R. Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses. Front Genet 2023; 14:1193780. [PMID: 37396035 PMCID: PMC10311922 DOI: 10.3389/fgene.2023.1193780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/07/2023] [Indexed: 07/04/2023] Open
Abstract
Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or several desirable domestication traits thereby reducing their agronomic value, requiring further genetic enhancement for developing productive, nutritionally dense, and climate resilient cultivars. This review article considers 13 underutilized pulses and focuses on their germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential for breeding and transgenic manipulation, and the genetics of agronomic and stress tolerance traits. Recent progress has shown the potential for crop improvement and food security, for example, the genetic basis of stem determinacy and fragrance in moth bean and rice bean, multiple abiotic stress tolerant traits in horse gram and tepary bean, bruchid resistance in lima bean, low neurotoxin in grass pea, and photoperiod induced flowering and anthocyanin accumulation in adzuki bean have been investigated. Advances in introgression breeding to develop elite genetic stocks of grass pea with low β-ODAP (neurotoxin compound), resistance to Mungbean yellow mosaic India virus in black gram using rice bean, and abiotic stress adaptation in common bean, using genes from tepary bean have been carried out. This highlights their potential in wider breeding programs to introduce such traits in locally adapted cultivars. The potential of de-domestication or feralization in the evolution of new variants in these crops are also highlighted.
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Affiliation(s)
| | - Mark A. Chapman
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | | | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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37
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He Q, Tang S, Zhi H, Chen J, Zhang J, Liang H, Alam O, Li H, Zhang H, Xing L, Li X, Zhang W, Wang H, Shi J, Du H, Wu H, Wang L, Yang P, Xing L, Yan H, Song Z, Liu J, Wang H, Tian X, Qiao Z, Feng G, Guo R, Zhu W, Ren Y, Hao H, Li M, Zhang A, Guo E, Yan F, Li Q, Liu Y, Tian B, Zhao X, Jia R, Feng B, Zhang J, Wei J, Lai J, Jia G, Purugganan M, Diao X. A graph-based genome and pan-genome variation of the model plant Setaria. Nat Genet 2023:10.1038/s41588-023-01423-w. [PMID: 37291196 DOI: 10.1038/s41588-023-01423-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 05/08/2023] [Indexed: 06/10/2023]
Abstract
Setaria italica (foxtail millet), a founder crop of East Asian agriculture, is a model plant for C4 photosynthesis and developing approaches to adaptive breeding across multiple climates. Here we established the Setaria pan-genome by assembling 110 representative genomes from a worldwide collection. The pan-genome is composed of 73,528 gene families, of which 23.8%, 42.9%, 29.4% and 3.9% are core, soft core, dispensable and private genes, respectively; 202,884 nonredundant structural variants were also detected. The characterization of pan-genomic variants suggests their importance during foxtail millet domestication and improvement, as exemplified by the identification of the yield gene SiGW3, where a 366-bp presence/absence promoter variant accompanies gene expression variation. We developed a graph-based genome and performed large-scale genetic studies for 68 traits across 13 environments, identifying potential genes for millet improvement at different geographic sites. These can be used in marker-assisted breeding, genomic selection and genome editing to accelerate crop improvement under different climatic conditions.
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Affiliation(s)
- Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinfeng Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jun Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongkai Liang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ornob Alam
- Center for Genomics and Systems Biology, New York University, New York City, NY, USA
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hui Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Northwest A & F University, Yangling, China
| | - Lihe Xing
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xukai Li
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Wei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hailong Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junpeng Shi
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Huilong Du
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Hongpo Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liwei Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lu Xing
- Anyang Academy of Agriculture Sciences, Anyang, China
| | - Hongshan Yan
- Anyang Academy of Agriculture Sciences, Anyang, China
| | | | - Jinrong Liu
- Anyang Academy of Agriculture Sciences, Anyang, China
| | - Haigang Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Xiang Tian
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Zhijun Qiao
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Guojun Feng
- Research Institute of Cereal Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Ruifeng Guo
- Institute of High Latitude Crops, Shanxi Agricultural University, Datong, China
| | - Wenjuan Zhu
- Institute of High Latitude Crops, Shanxi Agricultural University, Datong, China
| | - Yuemei Ren
- Institute of High Latitude Crops, Shanxi Agricultural University, Datong, China
| | - Hongbo Hao
- Institute of Dry-Land Farming, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Mingzhe Li
- Institute of Dry-Land Farming, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Aiying Zhang
- Millet Research Institute, Shanxi Agricultural University, Changzhi, China
| | - Erhu Guo
- Millet Research Institute, Shanxi Agricultural University, Changzhi, China
| | - Feng Yan
- Qiqihar Sub-Academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Qingquan Li
- Qiqihar Sub-Academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Yanli Liu
- Cangzhou Academy of Agriculture and Forestry Sciences, Cangzhou, China
| | - Bohong Tian
- Cangzhou Academy of Agriculture and Forestry Sciences, Cangzhou, China
| | - Xiaoqin Zhao
- Dingxi Academy of Agricultural Sciences, Dingxi, China
| | - Ruiling Jia
- Dingxi Academy of Agricultural Sciences, Dingxi, China
| | - Baili Feng
- College of Agronomy, Northwest A & F University, Yangling, China
| | - Jiewei Zhang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jianhua Wei
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Michael Purugganan
- Center for Genomics and Systems Biology, New York University, New York City, NY, USA.
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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38
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Li N, He Q, Wang J, Wang B, Zhao J, Huang S, Yang T, Tang Y, Yang S, Aisimutuola P, Xu R, Hu J, Jia C, Ma K, Li Z, Jiang F, Gao J, Lan H, Zhou Y, Zhang X, Huang S, Fei Z, Wang H, Li H, Yu Q. Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species. Nat Genet 2023; 55:852-860. [PMID: 37024581 PMCID: PMC10181942 DOI: 10.1038/s41588-023-01340-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/21/2023] [Indexed: 04/08/2023]
Abstract
Effective utilization of wild relatives is key to overcoming challenges in genetic improvement of cultivated tomato, which has a narrow genetic basis; however, current efforts to decipher high-quality genomes for tomato wild species are insufficient. Here, we report chromosome-scale tomato genomes from nine wild species and two cultivated accessions, representative of Solanum section Lycopersicon, the tomato clade. Together with two previously released genomes, we elucidate the phylogeny of Lycopersicon and construct a section-wide gene repertoire. We reveal the landscape of structural variants and provide entry to the genomic diversity among tomato wild relatives, enabling the discovery of a wild tomato gene with the potential to increase yields of modern cultivated tomatoes. Construction of a graph-based genome enables structural-variant-based genome-wide association studies, identifying numerous signals associated with tomato flavor-related traits and fruit metabolites. The tomato super-pangenome resources will expedite biological studies and breeding of this globally important crop.
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Grants
- the National Natural Science Foundation of China (31860555, 32260763 and 31991180), Key projects for crop traits formation and cutting-edge technologies in biological breeding (xjnkywdzc-2022001), Key Research and development task special project of Xinjiang (2022B02002), Special Incubation Project of Science & Technology Renovation of Xinjiang Academy of Agricultural Sciences (xjkcpy-2021001), China Agriculture Research System of MOF and MARA (CARS-23-G24), Guangdong Major Project of Basic and Applied Basic Research (2021B0301030004), the National Key Research and Development Program of China (2019YFA0906200 and 2021YFF1000100), Shenzhen Science and Technology Program (Grant No. KQTD2016113010482651), Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District (Grand No. RC201901-05), Shenzhen Outstanding Talents Training Fund and the US National Science Foundation (IOS-1855585).
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Affiliation(s)
- Ning Li
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Wang
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Baike Wang
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Jiantao Zhao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shaoyong Huang
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi, China
| | - Tao Yang
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yaping Tang
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Shengbao Yang
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Patiguli Aisimutuola
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Ruiqiang Xu
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi, China
| | - Jiahui Hu
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi, China
| | - Chunping Jia
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Kai Ma
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Zhiqiang Li
- Adsen Biotechnology Co., Ltd., Urumqi, China
| | - Fangling Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jie Gao
- College of Horticulture, Xinjiang Agricultural University, Urumqi, China
| | - Haiyan Lan
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Yongfeng Zhou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xinyan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
- US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Qinghui Yu
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
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39
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Huang K, Jahani M, Gouzy J, Legendre A, Carrere S, Lázaro-Guevara JM, González Segovia EG, Todesco M, Mayjonade B, Rodde N, Cauet S, Dufau I, Staton SE, Pouilly N, Boniface MC, Tapy C, Mangin B, Duhnen A, Gautier V, Poncet C, Donnadieu C, Mandel T, Hübner S, Burke JM, Vautrin S, Bellec A, Owens GL, Langlade N, Muños S, Rieseberg LH. The genomics of linkage drag in inbred lines of sunflower. Proc Natl Acad Sci U S A 2023; 120:e2205783119. [PMID: 36972449 PMCID: PMC10083583 DOI: 10.1073/pnas.2205783119] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/18/2022] [Indexed: 03/29/2023] Open
Abstract
Crop wild relatives represent valuable sources of alleles for crop improvement, including adaptation to climate change and emerging diseases. However, introgressions from wild relatives might have deleterious effects on desirable traits, including yield, due to linkage drag. Here, we analyzed the genomic and phenotypic impacts of wild introgressions in inbred lines of cultivated sunflower to estimate the impacts of linkage drag. First, we generated reference sequences for seven cultivated and one wild sunflower genotype, as well as improved assemblies for two additional cultivars. Next, relying on previously generated sequences from wild donor species, we identified introgressions in the cultivated reference sequences, as well as the sequence and structural variants they contain. We then used a ridge-regression best linear unbiased prediction (BLUP) model to test the effects of the introgressions on phenotypic traits in the cultivated sunflower association mapping population. We found that introgression has introduced substantial sequence and structural variation into the cultivated sunflower gene pool, including >3,000 new genes. While introgressions reduced genetic load at protein-coding sequences, they mostly had negative impacts on yield and quality traits. Introgressions found at high frequency in the cultivated gene pool had larger effects than low-frequency introgressions, suggesting that the former likely were targeted by artificial selection. Also, introgressions from more distantly related species were more likely to be maladaptive than those from the wild progenitor of cultivated sunflower. Thus, breeding efforts should focus, as far as possible, on closely related and fully compatible wild relatives.
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Affiliation(s)
- Kaichi Huang
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Mojtaba Jahani
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Jérôme Gouzy
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Alexandra Legendre
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Sébastien Carrere
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - José Miguel Lázaro-Guevara
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Eric Gerardo González Segovia
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Marco Todesco
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Baptiste Mayjonade
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Nathalie Rodde
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - Stéphane Cauet
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - Isabelle Dufau
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - S. Evan Staton
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Research and Development Department, NRGene Canada Inc., Saskatoon, SKS7N 3R3, Canada
| | - Nicolas Pouilly
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Marie-Claude Boniface
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Camille Tapy
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Brigitte Mangin
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Alexandra Duhnen
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Véronique Gautier
- Gentyane Genomic Platform, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Clermont Ferrand, 63000France
| | - Charles Poncet
- Gentyane Genomic Platform, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Clermont Ferrand, 63000France
| | - Cécile Donnadieu
- Plateforme Génome et Transcriptome (GeT-PlaGe), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - Tali Mandel
- MIGAL Galilee Research Institute, Tel-Hai Academic College, Upper Galilee, 11016Israel
| | - Sariel Hübner
- MIGAL Galilee Research Institute, Tel-Hai Academic College, Upper Galilee, 11016Israel
| | - John M. Burke
- Department of Plant Biology, University of Georgia, Athens, GA30602
| | - Sonia Vautrin
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - Arnaud Bellec
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - Gregory L. Owens
- Department of Biology, University of Victoria, Victoria, BCV8W 2Y2, Canada
| | - Nicolas Langlade
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Stéphane Muños
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Loren H. Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
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Yan H, Sun M, Zhang Z, Jin Y, Zhang A, Lin C, Wu B, He M, Xu B, Wang J, Qin P, Mendieta JP, Nie G, Wang J, Jones CS, Feng G, Srivastava RK, Zhang X, Bombarely A, Luo D, Jin L, Peng Y, Wang X, Ji Y, Tian S, Huang L. Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet. Nat Genet 2023; 55:507-518. [PMID: 36864101 PMCID: PMC10011142 DOI: 10.1038/s41588-023-01302-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/18/2023] [Indexed: 03/04/2023]
Abstract
Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Comparative genomics and transcriptomics analyses revealed the expansion of the RWP-RK transcription factor family and the involvement of endoplasmic reticulum (ER)-related genes in heat tolerance. The overexpression of one RWP-RK gene led to enhanced plant heat tolerance and transactivated ER-related genes quickly, supporting the important roles of RWP-RK transcription factors and ER system in heat tolerance. Furthermore, we found that some SVs affected the gene expression associated with heat tolerance and SVs surrounding ER-related genes shaped adaptation to heat tolerance during domestication in the population. Our study provides a comprehensive genomic resource revealing insights into heat tolerance and laying a foundation for generating more robust crops under the changing climate.
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Affiliation(s)
- Haidong Yan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Min Sun
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | | | - Yarong Jin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ailing Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Chuang Lin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Bingchao Wu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Min He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Bin Xu
- College of Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Jing Wang
- Key Laboratory of Bio-Source and Environmental Conservation, School of Life Science, Sichuan University, Chengdu, China
| | - Peng Qin
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | | | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Chris S Jones
- Feed and Forage Development, International Livestock Research Institute, Nairobi, Kenya
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Rakesh K Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Aureliano Bombarely
- Instituto de Biologia Molecular y Celular de Plantas, UPV-CSIC, Valencia, Spain
| | - Dan Luo
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Long Jin
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yang Ji
- Sichuan Animal Science Academy, Chengdu, China
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing, China.
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China.
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
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Nawae W, Naktang C, Charoensri S, U-thoomporn S, Narong N, Chusri O, Tangphatsornruang S, Pootakham W. Resequencing of durian genomes reveals large genetic variations among different cultivars. FRONTIERS IN PLANT SCIENCE 2023; 14:1137077. [PMID: 36875624 PMCID: PMC9978785 DOI: 10.3389/fpls.2023.1137077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Durian (Durio zibethinus), which yields the fruit known as the "King of Fruits," is an important economic crop in Southeast Asia. Several durian cultivars have been developed in this region. In this study, we resequenced the genomes of three popular durian cultivars in Thailand, including Kradumthong (KD), Monthong (MT), and Puangmanee (PM) to investigate genetic diversities of cultivated durians. KD, MT, and PM genome assemblies were 832.7, 762.6, and 821.6 Mb, and their annotations covered 95.7, 92.4, and 92.7% of the embryophyta core proteins, respectively. We constructed the draft durian pangenome and analyzed comparative genomes with related species in Malvales. Long terminal repeat (LTR) sequences and protein families in durian genomes had slower evolution rates than that in cotton genomes. However, protein families with transcriptional regulation function and protein phosphorylation function involved in abiotic and biotic stress responses appeared to evolve faster in durians. The analyses of phylogenetic relationships, copy number variations (CNVs), and presence/absence variations (PAVs) suggested that the genome evolution of Thai durians was different from that of the Malaysian durian, Musang King (MK). Among the three newly sequenced genomes, the PAV and CNV profiles of disease resistance genes and the expressions of methylesterase inhibitor domain containing genes involved in flowering and fruit maturation in MT were different from those in KD and PM. These genome assemblies and their analyses provide valuable resources to gain a better understanding of the genetic diversity of cultivated durians, which may be useful for the future development of new durian cultivars.
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Affiliation(s)
- Wanapinun Nawae
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Salisa Charoensri
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Sonicha U-thoomporn
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Nattapol Narong
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Orwintinee Chusri
- Chantaburi Horticulture Research Center, Horticulture Research Institute, Department of Agriculture, Chantaburi, Thailand
| | - Sithichoke Tangphatsornruang
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Wirulda Pootakham
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
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Shirasawa K, Moraga R, Ghelfi A, Hirakawa H, Nagasaki H, Ghamkhar K, Barrett BA, Griffiths AG, Isobe SN. An improved reference genome for Trifolium subterraneum L. provides insight into molecular diversity and intra-specific phylogeny. FRONTIERS IN PLANT SCIENCE 2023; 14:1103857. [PMID: 36875612 PMCID: PMC9975737 DOI: 10.3389/fpls.2023.1103857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Subterranean clover (Trifolium subterraneum L., Ts) is a geocarpic, self-fertile annual forage legume with a compact diploid genome (n = x = 8, 544 Mb/1C). Its resilience and climate adaptivity have made it an economically important species in Mediterranean and temperate zones. Using the cultivar Daliak, we generated higher resolution sequence data, created a new genome assembly TSUd_3.0, and conducted molecular diversity analysis for copy number variant (CNV) and single-nucleotide polymorphism (SNP) among 36 cultivars. TSUd_3.0 substantively improves prior genome assemblies with new Hi-C and long-read sequence data, covering 531 Mb, containing 41,979 annotated genes and generating a 94.4% BUSCO score. Comparative genomic analysis among select members of the tribe Trifolieae indicated TSUd 3.0 corrects six assembly-error inversion/duplications and confirmed phylogenetic relationships. Its synteny with T. pratense, T. repens, Medicago truncatula and Lotus japonicus genomes were assessed, with the more distantly related T. repens and M. truncatula showing higher levels of co-linearity with Ts than between Ts and its close relative T. pratense. Resequencing of 36 cultivars discovered 7,789,537 SNPs subsequently used for genomic diversity assessment and sequence-based clustering. Heterozygosity estimates ranged from 1% to 21% within the 36 cultivars and may be influenced by admixture. Phylogenetic analysis supported subspecific genetic structure, although it indicates four or five groups, rather than the three recognized subspecies. Furthermore, there were incidences where cultivars characterized as belonging to a particular subspecies clustered with another subspecies when using genomic data. These outcomes suggest that further investigation of Ts sub-specific classification using molecular and morpho-physiological data is needed to clarify these relationships. This upgraded reference genome, complemented with comprehensive sequence diversity analysis of 36 cultivars, provides a platform for future gene functional analysis of key traits, and genome-based breeding strategies for climate adaptation and agronomic performance. Pangenome analysis, more in-depth intra-specific phylogenomic analysis using the Ts core collection, and functional genetic and genomic studies are needed to further augment knowledge of Trifolium genomes.
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Affiliation(s)
- Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Roger Moraga
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
- Tea Break Bioinformatics Limited, Palmerston North, New Zealand
| | - Andrea Ghelfi
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
| | - Hideki Hirakawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Hideki Nagasaki
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Kioumars Ghamkhar
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Brent A. Barrett
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | | | - Sachiko N. Isobe
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
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Abstract
Over the past decade, advances in plant genotyping have been critical in enabling the identification of genetic diversity, in understanding evolution, and in dissecting important traits in both crops and native plants. The widespread popularity of single-nucleotide polymorphisms (SNPs) has prompted significant improvements to SNP-based genotyping, including SNP arrays, genotyping by sequencing, and whole-genome resequencing. More recent approaches, including genotyping structural variants, utilizing pangenomes to capture species-wide genetic diversity and exploiting machine learning to analyze genotypic data sets, are pushing the boundaries of what plant genotyping can offer. In this chapter, we highlight these innovations and discuss how they will accelerate and advance future genotyping efforts.
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Vegetable biology and breeding in the genomics era. SCIENCE CHINA. LIFE SCIENCES 2023; 66:226-250. [PMID: 36508122 DOI: 10.1007/s11427-022-2248-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize, thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.
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45
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Voelker WG, Krishnan K, Chougule K, Alexander LC, Lu Z, Olson A, Ware D, Songsomboon K, Ponce C, Brenton ZW, Boatwright JL, Cooper EA. Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes. FRONTIERS IN PLANT SCIENCE 2023; 13:1040909. [PMID: 36684744 PMCID: PMC9846640 DOI: 10.3389/fpls.2022.1040909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Introduction Sorghum (Sorghum bicolor (L.) Moench) is an agriculturally and economically important staple crop that has immense potential as a bioenergy feedstock due to its relatively high productivity on marginal lands. To capitalize on and further improve sorghum as a potential source of sustainable biofuel, it is essential to understand the genomic mechanisms underlying complex traits related to yield, composition, and environmental adaptations. Methods Expanding on a recently developed mapping population, we generated de novo genome assemblies for 10 parental genotypes from this population and identified a comprehensive set of over 24 thousand large structural variants (SVs) and over 10.5 million single nucleotide polymorphisms (SNPs). Results We show that SVs and nonsynonymous SNPs are enriched in different gene categories, emphasizing the need for long read sequencing in crop species to identify novel variation. Furthermore, we highlight SVs and SNPs occurring in genes and pathways with known associations to critical bioenergy-related phenotypes and characterize the landscape of genetic differences between sweet and cellulosic genotypes. Discussion These resources can be integrated into both ongoing and future mapping and trait discovery for sorghum and its myriad uses including food, feed, bioenergy, and increasingly as a carbon dioxide removal mechanism.
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Affiliation(s)
- William G. Voelker
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
| | - Krittika Krishnan
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
| | - Kapeel Chougule
- Cold Spring Harbor Research Laboratory, Cold Spring Harbor, NY, United States
| | - Louie C. Alexander
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
| | - Zhenyuan Lu
- Cold Spring Harbor Research Laboratory, Cold Spring Harbor, NY, United States
| | - Andrew Olson
- Cold Spring Harbor Research Laboratory, Cold Spring Harbor, NY, United States
| | - Doreen Ware
- Cold Spring Harbor Research Laboratory, Cold Spring Harbor, NY, United States
- United States Department of Agriculture - Agricultural Research Service in the North Atlantic Area (USDA-ARS NAA), Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
| | - Kittikun Songsomboon
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
| | - Cristian Ponce
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
| | - Zachary W. Brenton
- Carolina Seed Systems, Darlington, SC, United States
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
| | - J. Lucas Boatwright
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Dept. of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Elizabeth A. Cooper
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
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Shi J, Tian Z, Lai J, Huang X. Plant pan-genomics and its applications. MOLECULAR PLANT 2023; 16:168-186. [PMID: 36523157 DOI: 10.1016/j.molp.2022.12.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Plant genomes are so highly diverse that a substantial proportion of genomic sequences are not shared among individuals. The variable DNA sequences, along with the conserved core sequences, compose the more sophisticated pan-genome that represents the collection of all non-redundant DNA in a species. With rapid progress in genome sequencing technologies, pan-genome research in plants is now accelerating. Here we review recent advances in plant pan-genomics, including major driving forces of structural variations that constitute the variable sequences, methodological innovations for representing the pan-genome, and major successes in constructing plant pan-genomes. We also summarize recent efforts toward decoding the remaining dark matter in telomere-to-telomere or gapless plant genomes. These new genome resources, which have remarkable advantages over numerous previously assembled less-than-perfect genomes, are expected to become new references for genetic studies and plant breeding.
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Affiliation(s)
- Junpeng Shi
- State Key Laboratory of Biocontrol, School of Agriculture, Sun Yat-sen University, Shenzhen 518107, China.
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
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47
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Cooper M, Messina CD. Breeding crops for drought-affected environments and improved climate resilience. THE PLANT CELL 2023; 35:162-186. [PMID: 36370076 PMCID: PMC9806606 DOI: 10.1093/plcell/koac321] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/01/2022] [Indexed: 05/12/2023]
Abstract
Breeding climate-resilient crops with improved levels of abiotic and biotic stress resistance as a response to climate change presents both opportunities and challenges. Applying the framework of the "breeder's equation," which is used to predict the response to selection for a breeding program cycle, we review methodologies and strategies that have been used to successfully breed crops with improved levels of drought resistance, where the target population of environments (TPEs) is a spatially and temporally heterogeneous mixture of drought-affected and favorable (water-sufficient) environments. Long-term improvement of temperate maize for the US corn belt is used as a case study and compared with progress for other crops and geographies. Integration of trait information across scales, from genomes to ecosystems, is needed to accurately predict yield outcomes for genotypes within the current and future TPEs. This will require transdisciplinary teams to explore, identify, and exploit novel opportunities to accelerate breeding program outcomes; both improved germplasm resources and improved products (cultivars, hybrids, clones, and populations) that outperform and replace the products in use by farmers, in combination with modified agronomic management strategies suited to their local environments.
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Affiliation(s)
- Mark Cooper
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Queensland 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Carlos D Messina
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, USA
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48
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Wang S, Qian YQ, Zhao RP, Chen LL, Song JM. Graph-based pan-genomes: increased opportunities in plant genomics. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:24-39. [PMID: 36255144 DOI: 10.1093/jxb/erac412] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Due to the development of sequencing technology and the great reduction in sequencing costs, an increasing number of plant genomes have been assembled, and numerous genomes have revealed large amounts of variations. However, a single reference genome does not allow the exploration of species diversity, and therefore the concept of pan-genome was developed. A pan-genome is a collection of all sequences available for a species, including a large number of consensus sequences, large structural variations, and small variations including single nucleotide polymorphisms and insertions/deletions. A simple linear pan-genome does not allow these structural variations to be intuitively characterized, so graph-based pan-genomes have been developed. These pan-genomes store sequence and structural variation information in the form of nodes and paths to store and display species variation information in a more intuitive manner. The key role of graph-based pan-genomes is to expand the coordinate system of the linear reference genome to accommodate more regions of genetic diversity. Here, we review the origin and development of graph-based pan-genomes, explore their application in plant research, and further highlight the application of graph-based pan-genomes for future plant breeding.
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Affiliation(s)
- Shuo Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yong-Qing Qian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Ru-Peng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Jia-Ming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
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Daware A, Malik A, Srivastava R, Das D, Ellur RK, Singh AK, Tyagi AK, Parida SK. Rice Pangenome Genotyping Array: an efficient genotyping solution for pangenome-based accelerated genetic improvement in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:26-46. [PMID: 36377929 DOI: 10.1111/tpj.16028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/13/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
The advent of the pangenome era has unraveled previously unknown genetic variation existing within diverse crop plants, including rice. This untapped genetic variation is believed to account for a major portion of phenotypic variation existing in crop plants. However, the use of conventional single reference-guided genotyping often fails to capture a large portion of this genetic variation leading to a reference bias. This makes it difficult to identify and utilize novel population/cultivar-specific genes for crop improvement. Thus, we developed a Rice Pangenome Genotyping Array (RPGA) harboring probes assaying 80K single-nucleotide polymorphisms (SNPs) and presence-absence variants spanning the entire 3K rice pangenome. This array provides a simple, user-friendly and cost-effective (60-80 USD per sample) solution for rapid pangenome-based genotyping in rice. The genome-wide association study (GWAS) conducted using RPGA-SNP genotyping data of a rice diversity panel detected a total of 42 loci, including previously known as well as novel genomic loci regulating grain size/weight traits in rice. Eight of these identified trait-associated loci (dispensable loci) could not be detected with conventional single reference genome-based GWAS. A WD repeat-containing PROTEIN 12 gene underlying one of such dispensable locus on chromosome 7 (qLWR7) along with other non-dispensable loci were subsequently detected using high-resolution quantitative trait loci mapping confirming authenticity of RPGA-led GWAS. This demonstrates the potential of RPGA-based genotyping to overcome reference bias. The application of RPGA-based genotyping for population structure analysis, hybridity testing, ultra-high-density genetic map construction and chromosome-level genome assembly, and marker-assisted selection was also demonstrated. A web application (http://www.rpgaweb.com) was further developed to provide an easy to use platform for the imputation of RPGA-based genotyping data using 3K rice reference panel and subsequent GWAS.
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Affiliation(s)
- Anurag Daware
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ankit Malik
- Division of Genetics, Rice Section, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Rishi Srivastava
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Durdam Das
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ranjith K Ellur
- Division of Genetics, Rice Section, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Ashok K Singh
- Division of Genetics, Rice Section, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
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Kovaka S, Ou S, Jenike KM, Schatz MC. Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing. Nat Methods 2023; 20:12-16. [PMID: 36635537 PMCID: PMC10068675 DOI: 10.1038/s41592-022-01716-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The year 2022 will be remembered as the turning point for accurate long-read sequencing, which now establishes the gold standard for speed and accuracy at competitive costs. We discuss the key bioinformatics techniques needed to power long reads across application areas and close with our vision for long-read sequencing over the coming years.
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Affiliation(s)
- Sam Kovaka
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Shujun Ou
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Molecular Genetics, Ohio State University, Columbus, OH, USA
| | - Katharine M Jenike
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
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