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Thomas WJW, Amas JC, Dolatabadian A, Huang S, Zhang F, Zandberg JD, Neik TX, Edwards D, Batley J. Recent advances in the improvement of genetic resistance against disease in vegetable crops. PLANT PHYSIOLOGY 2024; 196:32-46. [PMID: 38796840 PMCID: PMC11376385 DOI: 10.1093/plphys/kiae302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/10/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024]
Affiliation(s)
- William J W Thomas
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
| | - Junrey C Amas
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
| | - Aria Dolatabadian
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
| | - Shuanglong Huang
- Department of Plant Science, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Fangning Zhang
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Jaco D Zandberg
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
| | - Ting Xiang Neik
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Republic of Singapore
- NUS Agritech Centre, National University of Singapore, Singapore, 118258, Republic of Singapore
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
- Centre for Applied Bioinformatics, The University of Western Australia, Perth, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
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2
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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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3
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Cortinovis G, Vincenzi L, Anderson R, Marturano G, Marsh JI, Bayer PE, Rocchetti L, Frascarelli G, Lanzavecchia G, Pieri A, Benazzo A, Bellucci E, Di Vittori V, Nanni L, Ferreira Fernández JJ, Rossato M, Aguilar OM, Morrell PL, Rodriguez M, Gioia T, Neumann K, Alvarez Diaz JC, Gratias A, Klopp C, Bitocchi E, Geffroy V, Delledonne M, Edwards D, Papa R. Adaptive gene loss in the common bean pan-genome during range expansion and domestication. Nat Commun 2024; 15:6698. [PMID: 39107305 PMCID: PMC11303546 DOI: 10.1038/s41467-024-51032-2] [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: 12/15/2023] [Accepted: 07/28/2024] [Indexed: 08/10/2024] Open
Abstract
The common bean (Phaseolus vulgaris L.) is a crucial legume crop and an ideal evolutionary model to study adaptive diversity in wild and domesticated populations. Here, we present a common bean pan-genome based on five high-quality genomes and whole-genome reads representing 339 genotypes. It reveals ~234 Mb of additional sequences containing 6,905 protein-coding genes missing from the reference, constituting 49% of all presence/absence variants (PAVs). More non-synonymous mutations are found in PAVs than core genes, probably reflecting the lower effective population size of PAVs and fitness advantages due to the purging effect of gene loss. Our results suggest pan-genome shrinkage occurred during wild range expansion. Selection signatures provide evidence that partial or complete gene loss was a key adaptive genetic change in common bean populations with major implications for plant adaptation. The pan-genome is a valuable resource for food legume research and breeding for climate change mitigation and sustainable agriculture.
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Affiliation(s)
- Gaia Cortinovis
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Leonardo Vincenzi
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Robyn Anderson
- Centre for Applied Bioinformatics and School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | | | - Jacob Ian Marsh
- Centre for Applied Bioinformatics and School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Philipp Emanuel Bayer
- Centre for Applied Bioinformatics and School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Lorenzo Rocchetti
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Giulia Frascarelli
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Giovanna Lanzavecchia
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Alice Pieri
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, 44100, Ferrara, Italy
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Valerio Di Vittori
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | | | - Marzia Rossato
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
- Genartis s.r.l, 37126, Verona, Italy
| | - Orlando Mario Aguilar
- Institute of Biotechnology and Molecular Biology, UNLP-CONICET, CCT La Plata, La Plata, Argentina
| | - Peter Laurent Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108-6026, USA
| | - Monica Rodriguez
- Department of Agriculture, University of Sassari, 07100, Sassari, Italy
- CBV-Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, University of Sassari, 07041, Alghero, Italy
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, 85100, Potenza, Italy
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Seeland, Germany
| | - Juan Camilo Alvarez Diaz
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), University of Evry, University Paris-Saclay, 91405, Orsay, France
| | - Ariane Gratias
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), University of Evry, University Paris-Saclay, 91405, Orsay, France
| | - Christophe Klopp
- INRAE, Genotoul Bioinformatics Platform, Applied Mathematics and Informatics of Toulouse, Sigenae, MIAT, UR875, Castanet Tolosan, France
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Valérie Geffroy
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), University of Evry, University Paris-Saclay, 91405, Orsay, France
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
- Genartis s.r.l, 37126, Verona, Italy
| | - David Edwards
- Centre for Applied Bioinformatics and School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy.
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4
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Cai C, de Vos RC, Qian H, Bucher J, Bonnema G. Metabolomic and Transcriptomic Profiles in Diverse Brassica oleracea Crops Provide Insights into the Genetic Regulation of Glucosinolate Profiles. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:16032-16044. [PMID: 38975781 PMCID: PMC11261609 DOI: 10.1021/acs.jafc.4c02932] [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: 04/03/2024] [Revised: 06/14/2024] [Accepted: 06/24/2024] [Indexed: 07/09/2024]
Abstract
Glucosinolates (GSLs) are plant secondary metabolites commonly found in the cruciferous vegetables of the Brassicaceae family, offering health benefits to humans and defense against pathogens and pests to plants. In this study, we investigated 23 GSL compounds' relative abundance in four tissues of five different Brassica oleracea morphotypes. Using the five corresponding high-quality B. oleracea genome assemblies, we identified 183 GSL-related genes and analyzed their expression with mRNA-Seq data. GSL abundance and composition varied strongly, among both tissues and morphotypes, accompanied by different gene expression patterns. Interestingly, broccoli exhibited a nonfunctional AOP2 gene due to a conserved 2OG-FeII_Oxy domain loss, explaining the unique accumulation of two health-promoting GSLs. Additionally, transposable element (TE) insertions were found to affect the gene structure of MAM3 genes. Our findings deepen the understanding of GSL variation and genetic regulation in B. oleracea morphotypes, providing valuable insights for breeding with tailored GSL profiles in these crops.
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Affiliation(s)
- Chengcheng Cai
- Plant
Breeding, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
- State
Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology
and Genetic Improvement of Horticultural Crops of the Ministry of
Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural
Genomics, Institute of Vegetables and Flowers,
Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ric C.H. de Vos
- Bioscience, Wageningen
University and Research, Wageningen 6708 PB, The Netherlands
| | - Hao Qian
- Plant
Breeding, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
| | - Johan Bucher
- Plant
Breeding, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
| | - Guusje Bonnema
- Plant
Breeding, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
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5
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Paritosh K, Rajarammohan S, Yadava SK, Sharma S, Verma R, Mathur S, Mukhopadhyay A, Gupta V, Pradhan AK, Kaur J, Pental D. A chromosome-scale assembly of Brassica carinata (BBCC) accession HC20 containing resistance to multiple pathogens and an early generation assessment of introgressions into B. juncea (AABB). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:762-782. [PMID: 38722594 DOI: 10.1111/tpj.16794] [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: 07/01/2023] [Revised: 04/04/2024] [Accepted: 04/22/2024] [Indexed: 07/16/2024]
Abstract
Brassica carinata (BBCC) commonly referred to as Ethiopian mustard is a natural allotetraploid containing the genomes of Brassica nigra (BB) and Brassica oleracea (CC). It is an oilseed crop endemic to the northeastern regions of Africa. Although it is under limited cultivation, B. carinata is valuable as it is resistant/highly tolerant to most of the pathogens affecting widely cultivated Brassica species of the U's triangle. We report a chromosome-scale genome assembly of B. carinata accession HC20 using long-read Oxford Nanopore sequencing and Bionano optical maps. The assembly has a scaffold N50 of ~39.8 Mb and covers ~1.11 Gb of the genome. We compared the long-read genome assemblies of the U's triangle species and found extensive gene collinearity between the diploids and allopolyploids with no evidence of major gene losses. Therefore, B. juncea (AABB), B. napus (AACC), and B. carinata can be regarded as strict allopolyploids. We cataloged the nucleotide-binding and leucine-rich repeat immune receptor (NLR) repertoire of B. carinata and, identified 465 NLRs, and compared these with the NLRs in the other Brassica species. We investigated the extent and nature of early-generation genomic interactions between the constituent genomes of B. carinata and B. juncea in interspecific crosses between the two species. Besides the expected recombination between the constituent B genomes, extensive homoeologous exchanges were observed between the A and C genomes. Interspecific crosses, therefore, can be used for transferring disease resistance from B. carinata to B. juncea and broadening the genetic base of the two allotetraploid species.
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Affiliation(s)
- Kumar Paritosh
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | | | - Satish Kumar Yadava
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Sarita Sharma
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Rashmi Verma
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Shikha Mathur
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Arundhati Mukhopadhyay
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Vibha Gupta
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Akshay K Pradhan
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Jagreet Kaur
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
- Department of Genetics, University of Delhi South Campus, New Delhi, 110021, India
| | - Deepak Pental
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
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6
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Khan AW, Garg V, Sun S, Gupta S, Dudchenko O, Roorkiwal M, Chitikineni A, Bayer PE, Shi C, Upadhyaya HD, Bohra A, Bharadwaj C, Mir RR, Baruch K, Yang B, Coyne CJ, Bansal KC, Nguyen HT, Ronen G, Aiden EL, Veneklaas E, Siddique KHM, Liu X, Edwards D, Varshney RK. Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea. Nat Genet 2024; 56:1225-1234. [PMID: 38783120 DOI: 10.1038/s41588-024-01760-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 04/18/2024] [Indexed: 05/25/2024]
Abstract
Chickpea (Cicer arietinum L.)-an important legume crop cultivated in arid and semiarid regions-has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicer super-pangenome based on the de novo genome assemblies of eight annual Cicer wild species. We identified 24,827 gene families, including 14,748 core, 2,958 softcore, 6,212 dispensable and 909 species-specific gene families. The dispensable genome was enriched for genes related to key agronomic traits. Structural variations between cultivated and wild genomes were used to construct a graph-based genome, revealing variations in genes affecting traits such as flowering time, vernalization and disease resistance. These variations will facilitate the transfer of valuable traits from wild Cicer species into elite chickpea varieties through marker-assisted selection or gene-editing. This study offers valuable insights into the genetic diversity and potential avenues for crop improvement in chickpea.
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Affiliation(s)
- Aamir W Khan
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA
| | - Vanika Garg
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | | | - Saurabh Gupta
- Curtin Health Innovation Research Institute (CHIRI), Curtin Medical School, Curtin University, Perth, Western Australia, Australia
| | - Olga Dudchenko
- Department of Molecular and Human Genetics, Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | | | - Hari D Upadhyaya
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, USA
| | - Abhishek Bohra
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | | | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir,Wadura Campus, Kashmir, India
| | | | | | - Clarice J Coyne
- USDA-ARS Plant Germplasm Introduction and Testing, Washington State University, Pullman, WA, USA
| | - Kailash C Bansal
- National Academy of Agricultural Sciences (NAAS), NASC Complex, New Delhi, India
| | - Henry T Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA
| | - Gil Ronen
- NRGene Ltd, Park HaMada, Ness Ziona, Israel
| | - Erez Lieberman Aiden
- Department of Molecular and Human Genetics, Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Erik Veneklaas
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Kadambot H M Siddique
- UWA Institute of Agriculture, and School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Xin Liu
- BGI Research, Qingdao, China.
- BGI Research, Shenzhen, China.
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia.
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
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7
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Jiang C, Zhao G, Wang H, Zheng W, Zhang R, Wang L, Zheng Z. Comparative genomics analysis and transposon mutagenesis provides new insights into high menaquinone-7 biosynthetic potential of Bacillus subtilis natto. Gene 2024; 907:148264. [PMID: 38346457 DOI: 10.1016/j.gene.2024.148264] [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: 10/06/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
This research combined Whole-Genome sequencing, intraspecific comparative genomics and transposon mutagenesis to investigate the menaquinone-7 (MK-7) synthesis potential in Bacillus subtilis natto. First, Whole-Genome sequencing showed that Bacillus subtilis natto BN-P15-11-1 contains one single circular chromosome in size of 3,982,436 bp with a GC content of 43.85 %, harboring 4,053 predicted coding genes. Next, the comparative genomics analysis among strain BN-P15-11-1 with model Bacillus subtilis 168 and four typical Bacillus subtilis natto strains proves that the closer evolutionary relationship Bacillus subtilis natto BN-P15-11-1 and Bacillus subtilis 168 both exhibit strong biosynthetic potential. To further dig for MK-7 biosynthesis latent capacity of BN-P15-11-1, we constructed a mutant library using transposons and a high throughput screening method using microplates. We obtained a YqgQ deficient high MK-7 yield strain F4 with a yield 3.02 times that of the parent strain. Experiments also showed that the high yield mutants had defects in different transcription and translation regulatory factor genes, indicating that regulatory factor defects may affect the biosynthesis and accumulation of MK-7 by altering the overall metabolic level. The findings of this study will provide more novel insights on the precise identification and rational utilization of the Bacillus subtilis subspecies for biosynthesis latent capacity.
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Affiliation(s)
- Chunxu Jiang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China; University of Science and Technology of China, Hefei, Anhui, PR China
| | - Genhai Zhao
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Han Wang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Wenqian Zheng
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China; University of Science and Technology of China, Hefei, Anhui, PR China
| | - Rui Zhang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Li Wang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
| | - Zhiming Zheng
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
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8
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Ji G, Long Y, Cai G, Wang A, Yan G, Li H, Gao G, Xu K, Huang Q, Chen B, Li L, Li F, Nishio T, Shen J, Wu X. A new chromosome-scale genome of wild Brassica oleracea provides insights into the domestication of Brassica crops. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2882-2899. [PMID: 38421062 DOI: 10.1093/jxb/erae079] [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: 08/22/2023] [Accepted: 02/28/2024] [Indexed: 03/02/2024]
Abstract
The cultivated diploid Brassica oleracea is an important vegetable crop, but the genetic basis of its domestication remains largely unclear in the absence of high-quality reference genomes of wild B. oleracea. Here, we report the first chromosome-level assembly of the wild Brassica oleracea L. W03 genome (total genome size, 630.7 Mb; scaffold N50, 64.6 Mb). Using the newly assembled W03 genome, we constructed a gene-based B. oleracea pangenome and identified 29 744 core genes, 23 306 dispensable genes, and 1896 private genes. We re-sequenced 53 accessions, representing six potential wild B. oleracea progenitor species. The results of the population genomic analysis showed that the wild B. oleracea populations had the highest level of diversity and represents the most closely related population to modern-day horticultural B. oleracea. In addition, the WUSCHEL gene was found to play a decisive role in domestication and to be involved in cauliflower and broccoli curd formation. We also illustrate the loss of disease-resistance genes during selection for domestication. Our results provide new insights into the domestication of B. oleracea and will facilitate the future genetic improvement of Brassica crops.
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Affiliation(s)
- Gaoxiang Ji
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ying Long
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Guangqin Cai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Aihua Wang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan,China
| | - Guixin Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hao Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Guizhen Gao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Kun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Qian Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Biyun Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Lixia Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Feng Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-0845, Japan
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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9
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Kapoor C, Anamika, Mukesh Sankar S, Singh SP, Singh N, Kumar S. Omics-driven utilization of wild relatives for empowering pre-breeding in pearl millet. PLANTA 2024; 259:155. [PMID: 38750378 DOI: 10.1007/s00425-024-04423-0] [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: 12/17/2023] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
MAIN CONCLUSION Pearl millet wild relatives harbour novel alleles which could be utilized to broaden genetic base of cultivated species. Genomics-informed pre-breeding is needed to speed up introgression from wild to cultivated gene pool in pearl millet. Rising episodes of intense biotic and abiotic stresses challenge pearl millet production globally. Wild relatives provide a wide spectrum of novel alleles which could address challenges posed by climate change. Pre-breeding holds potential to introgress novel diversity in genetically narrow cultivated Pennisetum glaucum from diverse gene pool. Practical utilization of gene pool diversity remained elusive due to genetic intricacies. Harnessing promising traits from wild pennisetum is limited by lack of information on underlying candidate genes/QTLs. Next-Generation Omics provide vast scope to speed up pre-breeding in pearl millet. Genomic resources generated out of draft genome sequence and improved genome assemblies can be employed to utilize gene bank accessions effectively. The article highlights genetic richness in pearl millet and its utilization with a focus on harnessing next-generation Omics to empower pre-breeding.
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Affiliation(s)
- Chandan Kapoor
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Anamika
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S Mukesh Sankar
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, 673012, India
| | - S P Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Nirupma Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sudhir Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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10
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Lu Y, Liu D, Kong X, Song Y, Jing L. Pangenome characterization and analysis of the NAC gene family reveals genes for Sclerotinia sclerotiorum resistance in sunflower (Helianthus annuus). BMC Genom Data 2024; 25:39. [PMID: 38693490 PMCID: PMC11064331 DOI: 10.1186/s12863-024-01227-9] [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: 01/07/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024] Open
Abstract
BACKGROUND Sunflower (Helianthus annuus) is one of the most important economic crops in oilseed production worldwide. The different cultivars exhibit variability in their resistance genes. The NAC transcription factor (TF) family plays diverse roles in plant development and stress responses. With the completion of the H. annuus genome sequence, the entire complement of genes coding for NACs has been identified. However, the reference genome of a single individual cannot cover all the genetic information of the species. RESULTS Considering only a single reference genome to study gene families will miss many meaningful genes. A pangenome-wide survey and characterization of the NAC genes in sunflower species were conducted. In total, 139 HaNAC genes are identified, of which 114 are core and 25 are variable. Phylogenetic analysis of sunflower NAC proteins categorizes these proteins into 16 subgroups. 138 HaNACs are randomly distributed on 17 chromosomes. SNP-based haplotype analysis shows haplotype diversity of the HaNAC genes in wild accessions is richer than in landraces and modern cultivars. Ten HaNAC genes in the basal stalk rot (BSR) resistance quantitative trait loci (QTL) are found. A total of 26 HaNAC genes are differentially expressed in response to Sclerotinia head rot (SHR). A total of 137 HaNAC genes are annotated in Gene Ontology (GO) and are classified into 24 functional groups. GO functional enrichment analysis reveals that HaNAC genes are involved in various functions of the biological process. CONCLUSIONS We identified NAC genes in H. annuus (HaNAC) on a pangenome-wide scale and analyzed S. sclerotiorum resistance-related NACs. This study provided a theoretical basis for further genomic improvement targeting resistance-related NAC genes in sunflowers.
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Affiliation(s)
- Yan Lu
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Dongqi Liu
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiangjiu Kong
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Yang Song
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Lan Jing
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China.
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11
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Liu M, Zhang F, Lu H, Xue H, Dong X, Li Z, Xu J, Wang W, Wei C. PPanG: a precision pangenome browser enabling nucleotide-level analysis of genomic variations in individual genomes and their graph-based pangenome. BMC Genomics 2024; 25:405. [PMID: 38658835 PMCID: PMC11044437 DOI: 10.1186/s12864-024-10302-5] [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: 12/08/2023] [Accepted: 04/11/2024] [Indexed: 04/26/2024] Open
Abstract
Graph-based pangenome is gaining more popularity than linear pangenome because it stores more comprehensive information of variations. However, traditional linear genome browser has its own advantages, especially the tremendous resources accumulated historically. With the fast-growing number of individual genomes and their annotations available, the demand for a genome browser to visualize genome annotation for many individuals together with a graph-based pangenome is getting higher and higher. Here we report a new pangenome browser PPanG, a precise pangenome browser enabling nucleotide-level comparison of individual genome annotations together with a graph-based pangenome. Nine rice genomes with annotations were provided by default as potential references, and any individual genome can be selected as the reference. Our pangenome browser provides unprecedented insights on genome variations at different levels from base to gene, and reveals how the structures of a gene could differ for individuals. PPanG can be applied to any species with multiple individual genomes available and it is available at https://cgm.sjtu.edu.cn/PPanG .
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Affiliation(s)
- Mingwei Liu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Fan Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Huimin Lu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hongzhang Xue
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xiaorui Dong
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Zhikang Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Jianlong Xu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Wensheng Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China.
| | - Chaochun Wei
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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12
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Gu J, Guan Z, Jiao Y, Liu K, Hong D. The story of a decade: Genomics, functional genomics, and molecular breeding in Brassica napus. PLANT COMMUNICATIONS 2024; 5:100884. [PMID: 38494786 PMCID: PMC11009362 DOI: 10.1016/j.xplc.2024.100884] [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: 11/06/2023] [Revised: 03/01/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Rapeseed (Brassica napus L.) is one of the major global sources of edible vegetable oil and is also used as a feed and pioneer crop and for sightseeing and industrial purposes. Improvements in genome sequencing and molecular marker technology have fueled a boom in functional genomic studies of major agronomic characters such as yield, quality, flowering time, and stress resistance. Moreover, introgression and pyramiding of key functional genes have greatly accelerated the genetic improvement of important traits. Here we summarize recent progress in rapeseed genomics and genetics, and we discuss effective molecular breeding strategies by exploring these findings in rapeseed. These insights will extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture throughout the world.
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Affiliation(s)
- Jianwei Gu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Life Science and Technology, Hubei Engineering University, Xiaogan 432100 Hubei, China
| | - Zhilin Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074 Hubei, China
| | - Yushun Jiao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Yazhouwan National Laboratory, Sanya 572024 Hainan, China.
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13
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Hu H, Li R, Zhao J, Batley J, Edwards D. Technological Development and Advances for Constructing and Analyzing Plant Pangenomes. Genome Biol Evol 2024; 16:evae081. [PMID: 38669452 PMCID: PMC11058698 DOI: 10.1093/gbe/evae081] [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: 11/06/2023] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
A pangenome captures the genomic diversity for a species, derived from a collection of genetic sequences of diverse populations. Advances in sequencing technologies have given rise to three primary methods for pangenome construction and analysis: de novo assembly and comparison, reference genome-based iterative assembly, and graph-based pangenome construction. Each method presents advantages and challenges in processing varying amounts and structures of DNA sequencing data. With the emergence of high-quality genome assemblies and advanced bioinformatic tools, the graph-based pangenome is emerging as an advanced reference for exploring the biological and functional implications of genetic variations.
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Affiliation(s)
- Haifei Hu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Risheng Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA 6009, Australia
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14
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Tan W, Zhou P, Huang X, Liao R, Wang X, Wu Y, Ni Z, Shi T, Yu X, Zhang H, Ma C, Gao F, Ma Y, Bai Y, Hayat F, Omondi OK, Coulibaly D, Gao Z. Haplotype-resolved genome of Prunus zhengheensis provides insight into its evolution and low temperature adaptation in apricot. HORTICULTURE RESEARCH 2024; 11:uhae103. [PMID: 38689698 PMCID: PMC11059810 DOI: 10.1093/hr/uhae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 03/31/2024] [Indexed: 05/02/2024]
Abstract
Prunus zhengheensis, an extremely rare population of apricots, originated in warm South-East China and is an excellent material for genetic breeding. However, most apricots and two related species (P. sibirica, P. mandshurica) are found in the cold northern regions in China and the mechanism of their distribution is still unclear. In addition, the classification status of P. zhengheensis is controversial. Thus, we generated a high-quality haplotype-resolved genome for P. zhengheensis, exploring key genetic variations in its adaptation and the causes of phylogenetic incongruence. We found extensive phylogenetic discordances between the nuclear and organelle phylogenies of P. zhengheensis, which could be explained by incomplete lineage sorting. A 242.22-Mb pan-genome of the Armeniaca section was developed with 13 chromosomal genomes. Importantly, we identified a 566-bp insertion in the promoter of the HSFA1d gene in apricot and showed that the activity of the HSFA1d promoter increased under low temperatures. In addition, HSFA1d overexpression in Arabidopsis thaliana indicated that HSFA1d positively regulated plant growth under chilling. Therefore, we hypothesized that the insertion in the promoter of HSFA1d in apricot improved its low-temperature adaptation, allowing it to thrive in relatively cold locations. The findings help explain the weather adaptability of Armeniaca plants.
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Affiliation(s)
- Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengyu Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruyu Liao
- Institute of Fruit, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Xiaoan Wang
- Institute of Fruit, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Yaoyao Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaqing Yu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Huiqin Zhang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Chengdong Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yufan Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Faisal Hayat
- Department of Pomology, College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Ouma Kenneth Omondi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Department of Crops, Horticulture and Soils, Faculty of Agriculture, Egerton University, P.O. Box 536, Egerton 20115, Kenya
| | - Daouda Coulibaly
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Department of Agricultural Sciences and Techniques-Horticulture, Rural Polytechnic Institute for Training and Applied Research (IPR/IFRA) of Katibougou, Koulikoro B.P.224, Mali
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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15
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Jiang M, Chen M, Zeng J, Du Z, Xiao J. A comprehensive evaluation of the potential of three next-generation short-read-based plant pan-genome construction strategies for the identification of novel non-reference sequence. FRONTIERS IN PLANT SCIENCE 2024; 15:1371222. [PMID: 38567138 PMCID: PMC10986365 DOI: 10.3389/fpls.2024.1371222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
Pan-genome studies are important for understanding plant evolution and guiding the breeding of crops by containing all genomic diversity of a certain species. Three short-read-based strategies for plant pan-genome construction include iterative individual, iteration pooling, and map-to-pan. Their performance is very different under various conditions, while comprehensive evaluations have yet to be conducted nowadays. Here, we evaluate the performance of these three pan-genome construction strategies for plants under different sequencing depths and sample sizes. Also, we indicate the influence of length and repeat content percentage of novel sequences on three pan-genome construction strategies. Besides, we compare the computational resource consumption among the three strategies. Our findings indicate that map-to-pan has the greatest recall but the lowest precision. In contrast, both two iterative strategies have superior precision but lower recall. Factors of sample numbers, novel sequence length, and the percentage of novel sequences' repeat content adversely affect the performance of all three strategies. Increased sequencing depth improves map-to-pan's performance, while not affecting the other two iterative strategies. For computational resource consumption, map-to-pan demands considerably more than the other two iterative strategies. Overall, the iterative strategy, especially the iterative pooling strategy, is optimal when the sequencing depth is less than 20X. Map-to-pan is preferable when the sequencing depth exceeds 20X despite its higher computational resource consumption.
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Affiliation(s)
- Meiye Jiang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Meili Chen
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Jingyao Zeng
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Zhenglin Du
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Jingfa Xiao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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16
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Liang Q, Muñoz-Amatriaín M, Shu S, Lo S, Wu X, Carlson JW, Davidson P, Goodstein DM, Phillips J, Janis NM, Lee EJ, Liang C, Morrell PL, Farmer AD, Xu P, Close TJ, Lonardi S. A view of the pan-genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.). THE PLANT GENOME 2024; 17:e20319. [PMID: 36946261 DOI: 10.1002/tpg2.20319] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/19/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
Cowpea, Vigna unguiculata L. Walp., is a diploid warm-season legume of critical importance as both food and fodder in sub-Saharan Africa. This species is also grown in Northern Africa, Europe, Latin America, North America, and East to Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six subpopulations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. In the most complete assembly (IT97K-499-35), 26,026 core and 4963 noncore genes were identified, with 35,436 pan genes when considering all seven accessions. GO terms associated with response to stress and defense response were highly enriched among the noncore genes, while core genes were enriched in terms related to transcription factor activity, and transport and metabolic processes. Over 5 million single nucleotide polymorphisms (SNPs) relative to each assembly and over 40 structural variants >1 Mb in size were identified by comparing genomes. Vu10 was the chromosome with the highest frequency of SNPs, and Vu04 had the most structural variants. Noncore genes harbor a larger proportion of potentially disruptive variants than core genes, including missense, stop gain, and frameshift mutations; this suggests that noncore genes substantially contribute to diversity within domesticated cowpea.
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Affiliation(s)
- Qihua Liang
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
- Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Shengqiang Shu
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sassoum Lo
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Xinyi Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Joseph W Carlson
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Patrick Davidson
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David M Goodstein
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy Phillips
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nadia M Janis
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN, USA
| | - Elaine J Lee
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN, USA
| | - Chenxi Liang
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN, USA
| | | | - Pei Xu
- Key Lab of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, China Jiliang University, Hangzhou, China
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA
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17
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Hu H, Scheben A, Wang J, Li F, Li C, Edwards D, Zhao J. Unravelling inversions: Technological advances, challenges, and potential impact on crop breeding. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:544-554. [PMID: 37961986 PMCID: PMC10893937 DOI: 10.1111/pbi.14224] [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: 07/10/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023]
Abstract
Inversions, a type of chromosomal structural variation, significantly influence plant adaptation and gene functions by impacting gene expression and recombination rates. However, compared with other structural variations, their roles in functional biology and crop improvement remain largely unexplored. In this review, we highlight technological and methodological advancements that have allowed a comprehensive understanding of inversion variants through the pangenome framework and machine learning algorithms. Genome editing is an efficient method for inducing or reversing inversion mutations in plants, providing an effective mechanism to modify local recombination rates. Given the potential of inversions in crop breeding, we anticipate increasing attention on inversions from the scientific community in future research and breeding applications.
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Affiliation(s)
- Haifei Hu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor LaboratoryCold Spring HarborNew YorkUSA
| | - Jian Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| | - Fangping Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Chengdao Li
- Western Crop Genetics Alliance, Centre for Crop & Food Innovation, Food Futures Institute, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - David Edwards
- School of Biological SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
- Australia & Centre for Applied BioinformaticsUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
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18
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Li X, Wang Y, Cai C, Ji J, Han F, Zhang L, Chen S, Zhang L, Yang Y, Tang Q, Bucher J, Wang X, Yang L, Zhuang M, Zhang K, Lv H, Bonnema G, Zhang Y, Cheng F. Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea. Nat Genet 2024; 56:517-529. [PMID: 38351383 PMCID: PMC10937405 DOI: 10.1038/s41588-024-01655-4] [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: 06/16/2023] [Accepted: 01/03/2024] [Indexed: 02/21/2024]
Abstract
Brassica oleracea, globally cultivated for its vegetable crops, consists of very diverse morphotypes, characterized by specialized enlarged organs as harvested products. This makes B. oleracea an ideal model for studying rapid evolution and domestication. We constructed a B. oleracea pan-genome from 27 high-quality genomes representing all morphotypes and their wild relatives. We identified structural variations (SVs) among these genomes and characterized these in 704 B. oleracea accessions using graph-based genome tools. We show that SVs exert bidirectional effects on the expression of numerous genes, either suppressing through DNA methylation or promoting probably by harboring transcription factor-binding elements. The following examples illustrate the role of SVs modulating gene expression: SVs promoting BoPNY and suppressing BoCKX3 in cauliflower/broccoli, suppressing BoKAN1 and BoACS4 in cabbage and promoting BoMYBtf in ornamental kale. These results provide solid evidence for the role of SVs as dosage regulators of gene expression, driving B. oleracea domestication and diversification.
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Affiliation(s)
- Xing Li
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Wang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chengcheng Cai
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Jialei Ji
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fengqing Han
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shumin Chen
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingkui Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yinqing Yang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qi Tang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Xuelin Wang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Limei Yang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mu Zhuang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kang Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Honghao Lv
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Guusje Bonnema
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
| | - Yangyong Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
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19
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Cao Y, Mo W, Li Y, Xiong Y, Wang H, Zhang Y, Lin M, Zhang L, Li X. Functional characterization of NBS-LRR genes reveals an NBS-LRR gene that mediates resistance against Fusarium wilt. BMC Biol 2024; 22:45. [PMID: 38408951 PMCID: PMC10898138 DOI: 10.1186/s12915-024-01836-x] [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: 08/15/2023] [Accepted: 01/25/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND Most disease resistance (R) genes in plants encode proteins that contain leucine-rich-repeat (LRR) and nucleotide-binding site (NBS) domains, which belong to the NBS-LRR family. The sequenced genomes of Fusarium wilt-susceptible Vernicia fordii and its resistant counterpart, Vernicia montana, offer significant resources for the functional characterization and discovery of novel NBS-LRR genes in tung tree. RESULTS Here, we identified 239 NBS-LRR genes across two tung tree genomes: 90 in V. fordii and 149 in V. montana. Five VmNBS-LRR paralogous were predicted in V. montana, and 43 orthologous were detected between V. fordii and V. montana. The orthologous gene pair Vf11G0978-Vm019719 exhibited distinct expression patterns in V. fordii and V. montana: Vf11G0978 showed downregulated expression in V. fordii, while its orthologous gene Vm019719 demonstrated upregulated expression in V. montana, indicating that this pair may be responsible for the resistance to Fusarium wilt in V. montana. Vm019719 from V. montana, activated by VmWRKY64, was shown to confer resistance to Fusarium wilt in V. montana by a virus-induced gene silencing (VIGS) experiment. However, in the susceptible V. fordii, its allelic counterpart, Vf11G0978, exhibited an ineffective defense response, attributed to a deletion in the promoter's W-box element. CONCLUSIONS This study provides the first systematic analysis of NBS-LRR genes in the tung tree and identifies a candidate gene that can be utilized for marker-assisted breeding to control Fusarium wilt in V. fordii.
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Affiliation(s)
- Yunpeng Cao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- School of Health and Nursing, Wuchang University of Technology, Wuhan, China.
- Forestry College, Central South University of Forestry and Technology, Changsha, 410004, China.
| | - Wanzhen Mo
- Forestry College, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Yanli Li
- Forestry College, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Yao Xiong
- Forestry College, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Han Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yingjie Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Mengfei Lin
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, 330224, China.
| | - Lin Zhang
- School of Health and Nursing, Wuchang University of Technology, Wuhan, China.
- Hubei Shizhen Laboratory, School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, 430065, China.
| | - Xiaoxu Li
- Beijing Life Science Academy, Beijing, 102209, China.
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20
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Liu X, Zheng J, Ding J, Wu J, Zuo F, Zhang G. When Livestock Genomes Meet Third-Generation Sequencing Technology: From Opportunities to Applications. Genes (Basel) 2024; 15:245. [PMID: 38397234 PMCID: PMC10888458 DOI: 10.3390/genes15020245] [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: 12/23/2023] [Revised: 01/30/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Third-generation sequencing technology has found widespread application in the genomic, transcriptomic, and epigenetic research of both human and livestock genetics. This technology offers significant advantages in the sequencing of complex genomic regions, the identification of intricate structural variations, and the production of high-quality genomes. Its attributes, including long sequencing reads, obviation of PCR amplification, and direct determination of DNA/RNA, contribute to its efficacy. This review presents a comprehensive overview of third-generation sequencing technologies, exemplified by single-molecule real-time sequencing (SMRT) and Oxford Nanopore Technology (ONT). Emphasizing the research advancements in livestock genomics, the review delves into genome assembly, structural variation detection, transcriptome sequencing, and epigenetic investigations enabled by third-generation sequencing. A comprehensive analysis is conducted on the application and potential challenges of third-generation sequencing technology for genome detection in livestock. Beyond providing valuable insights into genome structure analysis and the identification of rare genes in livestock, the review ventures into an exploration of the genetic mechanisms underpinning exemplary traits. This review not only contributes to our understanding of the genomic landscape in livestock but also provides fresh perspectives for the advancement of research in this domain.
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Affiliation(s)
- Xinyue Liu
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
| | - Junyuan Zheng
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
| | - Jialan Ding
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
| | - Jiaxin Wu
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
| | - Fuyuan Zuo
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
- Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing 402460, China
| | - Gongwei Zhang
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
- Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing 402460, China
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21
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Guo N, Wang S, Wang T, Duan M, Zong M, Miao L, Han S, Wang G, Liu X, Zhang D, Jiao C, Xu H, Chen L, Fei Z, Li J, Liu F. A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification. PLANT COMMUNICATIONS 2024; 5:100791. [PMID: 38168637 PMCID: PMC10873912 DOI: 10.1016/j.xplc.2023.100791] [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: 10/25/2023] [Revised: 12/08/2023] [Accepted: 12/30/2023] [Indexed: 01/05/2024]
Abstract
The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development. Here we report a graph-based pan-genome of B. oleracea constructed from high-quality genome assemblies of different morphotypes. The pan-genome harbors over 200 structural variant hotspot regions enriched in auxin- and flowering-related genes. Population genomic analyses revealed that early domestication of B. oleracea focused on leaf or stem development. Gene flows resulting from agricultural practices and variety improvement were detected among different morphotypes. Selective-sweep and pan-genome analyses identified an auxin-responsive small auxin up-regulated RNA gene and a CLAVATA3/ESR-RELATED family gene as crucial players in leaf-stem differentiation during the early stage of B. oleracea domestication and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels sprouts. Our pan-genome and functional analyses further revealed that variations in the BoFLC2 gene play key roles in the divergence of vernalization and flowering characteristics among different morphotypes, and variations in the first intron of BoFLC3 are involved in fine-tuning the flowering process in cauliflower. This study provides a comprehensive understanding of the pan-genome of B. oleracea and sheds light on the domestication and differential organ development of this globally important crop species.
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Affiliation(s)
- Ning Guo
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Shenyun Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Vegetable Research Institute, Jiangsu Academy of Agricultural Science, Nanjing, Jiangsu, China
| | - Tianyi Wang
- Smartgenomics Technology Institute, Tianjin 301700, China
| | - Mengmeng Duan
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Mei Zong
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Liming Miao
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Shuo Han
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Guixiang Wang
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Xin Liu
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Deshuang Zhang
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Chengzhi Jiao
- Smartgenomics Technology Institute, Tianjin 301700, China
| | - Hongwei Xu
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Liyang Chen
- Smartgenomics Technology Institute, Tianjin 301700, China.
| | | | - Jianbin Li
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Vegetable Research Institute, Jiangsu Academy of Agricultural Science, Nanjing, Jiangsu, China.
| | - Fan Liu
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China.
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22
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Singh A, Ramakrishna G, Singh NK, Abdin MZ, Gaikwad K. Genomic insight into variations associated with flowering-time and early-maturity in pigeonpea mutant TAT-10 and its wild type parent T21. Int J Biol Macromol 2024; 257:128559. [PMID: 38061506 DOI: 10.1016/j.ijbiomac.2023.128559] [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: 09/13/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023]
Abstract
Pigeonpea [Cajanus cajan (L.) Millspaugh] is an important grain legume crop with a broad range of 90 to 300 days for maturity. To identify the genomic variations associated with the early maturity, we conducted whole-genome resequencing of an early-maturing pigeonpea mutant TAT-10 and its wild type parent T21. A total of 135.67 and 146.34 million sequencing reads were generated for T21 and TAT-10, respectively. From this resequencing data, 1,397,178 and 1,419,904 SNPs, 276,741 and 292,347 InDels, and 87,583 and 92,903 SVs were identified in T21 and TAT-10, respectively. We identified 203 genes in the pigeonpea genome that are homologs of flowering-related genes in Arabidopsis and found 791 genomic variations unique to TAT-10 linked to 94 flowering-related genes. We identified three candidate genes for early maturity in TAT-10; Suppressor of FRI 4 (SUF4), Early Flowering In Short Days (EFS), and Probable Lysine-Specific Demethylase ELF6. The variations in ELF6 were predicted to be possibly damaging and the expression profiles of EFS and ELF6 also supported their probable role during early flowering in TAT-10. The present study has generated information on genomic variations associated with candidate genes for early maturity, which can be further studied and exploited for developing the early-maturing pigeonpea cultivars.
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Affiliation(s)
- Anupam Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | | | | | - Malik Zainul Abdin
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India.
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India.
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23
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Wang K, Hua G, Li J, Yang Y, Zhang C, Yang L, Hu X, Scheben A, Wu Y, Gong P, Zhang S, Fan Y, Zeng T, Lu L, Gong Y, Jiang R, Sun G, Tian Y, Kang X, Hu H, Li W. Duck pan-genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution. IMETA 2024; 3:e154. [PMID: 38868520 PMCID: PMC10989122 DOI: 10.1002/imt2.154] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/07/2023] [Indexed: 06/14/2024]
Abstract
Structural variations (SVs) are a major source of domestication and improvement traits. We present the first duck pan-genome constructed using five genome assemblies capturing ∼40.98 Mb new sequences. This pan-genome together with high-depth sequencing data (∼46.5×) identified 101,041 SVs, of which substantial proportions were derived from transposable element (TE) activity. Many TE-derived SVs anchoring in a gene body or regulatory region are linked to duck's domestication and improvement. By combining quantitative genetics with molecular experiments, we, for the first time, unraveled a 6945 bp Gypsy insertion as a functional mutation of the major gene IGF2BP1 associated with duck bodyweight. This Gypsy insertion, to our knowledge, explains the largest effect on bodyweight among avian species (27.61% of phenotypic variation). In addition, we also examined another 6634 bp Gypsy insertion in MITF intron, which triggers a novel transcript of MITF, thereby contributing to the development of white plumage. Our findings highlight the importance of using a pan-genome as a reference in genomics studies and illuminate the impact of transposons in trait formation and livestock breeding.
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Affiliation(s)
- Kejun Wang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Guoying Hua
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Jingyi Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Intelligent Husbandry Department, College of Animal Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yu Yang
- Wuhan Academy of Agricultural ScienceWuhanChina
| | - Chenxi Zhang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Lan Yang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Xiaoyu Hu
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Armin Scheben
- Simons Center for Quantitative BiologyCold Spring Harbor LaboratoryCold Spring HarborNew YorkUSA
| | - Yanan Wu
- Department of preventive veterinary medicine, College of Veterinary MedicineHenan Agricultural UniversityZhengzhouChina
- International Joint Research Center for National Animal ImmunologyZhengzhouHenanChina
| | - Ping Gong
- Wuhan Academy of Agricultural ScienceWuhanChina
| | - Shuangjie Zhang
- Quality Safety and Processing LaboratoryJiangsu Institute of Poultry SciencesYangzhouChina
| | - Yanfeng Fan
- Quality Safety and Processing LaboratoryJiangsu Institute of Poultry SciencesYangzhouChina
| | - Tao Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Animal Husbandry and Veterinary ScienceZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Lizhi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Animal Husbandry and Veterinary ScienceZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Yanzhang Gong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Intelligent Husbandry Department, College of Animal Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Ruirui Jiang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Guirong Sun
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Yadong Tian
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Xiangtao Kang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Haifei Hu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding and Guangdong Rice Engineering LaboratoryGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Wenting Li
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
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24
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Li Y, Yao J, Sang H, Wang Q, Su L, Zhao X, Xia Z, Wang F, Wang K, Lou D, Wang G, Waterhouse RM, Wang H, Luo S, Sun C. Pan-genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees. Mol Ecol Resour 2024; 24:e13905. [PMID: 37996991 DOI: 10.1111/1755-0998.13905] [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: 07/07/2023] [Revised: 10/20/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
The Asian honeybee, Apis cerana, is an ecologically and economically important pollinator. Mapping its genetic variation is key to understanding population-level health, histories and potential capacities to respond to environmental changes. However, most efforts to date were focused on single nucleotide polymorphisms (SNPs) based on a single reference genome, thereby ignoring larger scale genomic variation. We employed long-read sequencing technologies to generate a chromosome-scale reference genome for the ancestral group of A. cerana. Integrating this with 525 resequencing data sets, we constructed the first pan-genome of A. cerana, encompassing almost the entire gene content. We found that 31.32% of genes in the pan-genome were variably present across populations, providing a broad gene pool for environmental adaptation. We identified and characterized structural variations (SVs) and found that they were not closely linked with SNP distributions; however, the formation of SVs was closely associated with transposable elements. Furthermore, phylogenetic analysis using SVs revealed a novel A. cerana ecological group not recoverable from the SNP data. Performing environmental association analysis identified a total of 44 SVs likely to be associated with environmental adaptation. Verification and analysis of one of these, a 330 bp deletion in the Atpalpha gene, indicated that this SV may promote the cold adaptation of A. cerana by altering gene expression. Taken together, our study demonstrates the feasibility and utility of applying pan-genome approaches to map and explore genetic feature variations of honeybee populations, and in particular to examine the role of SVs in the evolution and environmental adaptation of A. cerana.
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Affiliation(s)
- Yancan Li
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, China
| | - Jun Yao
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiling Sang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Quangui Wang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Su
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiaomeng Zhao
- College of Animal Science, Shanxi Agricultural University, Shanxi, China
| | - Zhenyu Xia
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Feiran Wang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, China
| | - Kai Wang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Delong Lou
- Shandong Provincial Animal Husbandry Station, Jinan, China
| | - Guizhi Wang
- Department of Animal Science, Shandong Agricultural University, Taian, China
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Huihua Wang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shudong Luo
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, China
| | - Cheng Sun
- College of Life Sciences, Capital Normal University, Beijing, China
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25
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Edwards D, Batley J. Teatime for pangenomics. NATURE PLANTS 2023; 9:1944-1945. [PMID: 38012347 DOI: 10.1038/s41477-023-01566-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Affiliation(s)
- David Edwards
- Centre for Applied Bioinformatics and School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia.
| | - Jacqueline Batley
- Centre for Applied Bioinformatics and School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia.
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26
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Sen S, Woodhouse MR, Portwood JL, Andorf CM. Maize Feature Store: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications. Database (Oxford) 2023; 2023:baad078. [PMID: 37935586 PMCID: PMC10634621 DOI: 10.1093/database/baad078] [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: 11/27/2022] [Revised: 09/16/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023]
Abstract
The big-data analysis of complex data associated with maize genomes accelerates genetic research and improves agronomic traits. As a result, efforts have increased to integrate diverse datasets and extract meaning from these measurements. Machine learning models are a powerful tool for gaining knowledge from large and complex datasets. However, these models must be trained on high-quality features to succeed. Currently, there are no solutions to host maize multi-omics datasets with end-to-end solutions for evaluating and linking features to target gene annotations. Our work presents the Maize Feature Store (MFS), a versatile application that combines features built on complex data to facilitate exploration, modeling and analysis. Feature stores allow researchers to rapidly deploy machine learning applications by managing and providing access to frequently used features. We populated the MFS for the maize reference genome with over 14 000 gene-based features based on published genomic, transcriptomic, epigenomic, variomic and proteomics datasets. Using the MFS, we created an accurate pan-genome classification model with an AUC-ROC score of 0.87. The MFS is publicly available through the maize genetics and genomics database. Database URL https://mfs.maizegdb.org/.
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Affiliation(s)
- Shatabdi Sen
- Department of Plant Pathology & Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg, 2213 Pammel Dr, Ames, IA 50011, USA
| | - Margaret R Woodhouse
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, 819 Wallace Road, Ames, IA 50011, USA
| | - John L Portwood
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, 819 Wallace Road, Ames, IA 50011, USA
| | - Carson M Andorf
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, 819 Wallace Road, Ames, IA 50011, USA
- Department of Computer Science, Iowa State University, Atanasoff Hall, 2434 Osborn Dr, Ames, IA 50011, USA
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27
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Shuang LS, Cuevas H, Lemke C, Kim C, Shehzad T, Paterson AH. Genetic dissection of morphological variation between cauliflower and a rapid cycling Brassica oleracea line. G3 (BETHESDA, MD.) 2023; 13:jkad163. [PMID: 37506262 PMCID: PMC10627287 DOI: 10.1093/g3journal/jkad163] [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: 10/08/2022] [Revised: 08/10/2022] [Accepted: 03/14/2023] [Indexed: 07/30/2023]
Abstract
To improve resolution to small genomic regions and sensitivity to small-effect loci in the identification of genetic factors conferring the enlarged inflorescence and other traits of cauliflower while also expediting further genetic dissection, 104 near-isogenic introgression lines (NIILs) covering 78.56% of the cauliflower genome, were selected from an advanced backcross population using cauliflower [Brassica oleracea var. botrytis L., mutant for Orange gene (ORG)] as the donor parent and a rapid cycling line (TO1434) as recurrent parent. Subsets of the advanced backcross population and NIILs were planted in the field for 8 seasons, finding 141 marker-trait associations for 15 leaf-, stem-, and flower-traits. Exemplifying the usefulness of these lines, we delineated the previously known flower color gene to a 4.5 MB interval on C3; a gene for small plant size to a 3.4 MB region on C8; and a gene for large plant size and flowering time to a 6.1 MB region on C9. This approach unmasked closely linked QTL alleles with opposing effects (on chr. 8) and revealed both alleles with expected phenotypic effects and effects opposite the parental phenotypes. Selected B. oleracea NIILs with short generation time add new value to widely used research and teaching materials.
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Affiliation(s)
- Lan Shuan Shuang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Hugo Cuevas
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Cornelia Lemke
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Tariq Shehzad
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
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28
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Yocca AE, Platts A, Alger E, Teresi S, Mengist MF, Benevenuto J, Ferrão LFV, Jacobs M, Babinski M, Magallanes-Lundback M, Bayer P, Golicz A, Humann JL, Main D, Espley RV, Chagné D, Albert NW, Montanari S, Vorsa N, Polashock J, Díaz-Garcia L, Zalapa J, Bassil NV, Munoz PR, Iorizzo M, Edger PP. Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts. HORTICULTURE RESEARCH 2023; 10:uhad202. [PMID: 38023484 PMCID: PMC10673653 DOI: 10.1093/hr/uhad202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/01/2023] [Indexed: 12/01/2023]
Abstract
Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures), as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium-a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.
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Affiliation(s)
- Alan E Yocca
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, United States
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, United States
| | - Adrian Platts
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, United States
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, United States
| | - Elizabeth Alger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, United States
| | - Scott Teresi
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, United States
- Genetics and Genome Sciences, Michigan State University, East Lansing, MI, 48824, United States
| | - Molla F Mengist
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC United States
| | - Juliana Benevenuto
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, United States
| | - Luis Felipe V Ferrão
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, United States
| | - MacKenzie Jacobs
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, United States
| | - Michal Babinski
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, United States
| | | | - Philipp Bayer
- University of Western Australia, Perth 6009Australia
| | | | - Jodi L Humann
- Department of Horticulture, Washington State University, Pullman, WA, 99163, United States
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, 99163, United States
| | - Richard V Espley
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston, New Zealand
| | - Nick W Albert
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston, New Zealand
| | - Sara Montanari
- The New Zealand Institute for Plant and Food Research Limited (PFR), Motueka, New Zealand
| | - Nicholi Vorsa
- SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019United States
| | - James Polashock
- SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019United States
| | - Luis Díaz-Garcia
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, United States
| | - Juan Zalapa
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, United States
| | - Nahla V Bassil
- National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR 97333, United States
| | - Patricio R Munoz
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, United States
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NCUnited States
- Department of Horticulture, North Carolina State University, Kannapolis, NCUnited States
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, United States
- Genetics and Genome Sciences, Michigan State University, East Lansing, MI, 48824, United States
- MSU AgBioResearch, Michigan State University, East Lansing, MI, 48824, United States
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29
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Aylward AJ, Petrus S, Mamerto A, Hartwick NT, Michael TP. PanKmer: k-mer-based and reference-free pangenome analysis. Bioinformatics 2023; 39:btad621. [PMID: 37846049 PMCID: PMC10603592 DOI: 10.1093/bioinformatics/btad621] [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: 03/31/2023] [Revised: 08/29/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023] Open
Abstract
SUMMARY Pangenomes are replacing single reference genomes as the definitive representation of DNA sequence within a species or clade. Pangenome analysis predominantly leverages graph-based methods that require computationally intensive multiple genome alignments, do not scale to highly complex eukaryotic genomes, limit their scope to identifying structural variants (SVs), or incur bias by relying on a reference genome. Here, we present PanKmer, a toolkit designed for reference-free analysis of pangenome datasets consisting of dozens to thousands of individual genomes. PanKmer decomposes a set of input genomes into a table of observed k-mers and their presence-absence values in each genome. These are stored in an efficient k-mer index data format that encodes SNPs, INDELs, and SVs. It also includes functions for downstream analysis of the k-mer index, such as calculating sequence similarity statistics between individuals at whole-genome or local scales. For example, k-mers can be "anchored" in any individual genome to quantify sequence variability or conservation at a specific locus. This facilitates workflows with various biological applications, e.g. identifying cases of hybridization between plant species. PanKmer provides researchers with a valuable and convenient means to explore the full scope of genetic variation in a population, without reference bias. AVAILABILITY AND IMPLEMENTATION PanKmer is implemented as a Python package with components written in Rust, released under a BSD license. The source code is available from the Python Package Index (PyPI) at https://pypi.org/project/pankmer/ as well as Gitlab at https://gitlab.com/salk-tm/pankmer. Full documentation is available at https://salk-tm.gitlab.io/pankmer/.
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Affiliation(s)
- Anthony J Aylward
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, United States
| | - Semar Petrus
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, United States
| | - Allen Mamerto
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, United States
| | - Nolan T Hartwick
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, United States
| | - Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, United States
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30
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Amas JC, Bayer PE, Hong Tan W, Tirnaz S, Thomas WJW, Edwards D, Batley J. Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs). PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2100-2112. [PMID: 37431308 PMCID: PMC10502758 DOI: 10.1111/pbi.14116] [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: 02/22/2023] [Revised: 06/11/2023] [Accepted: 06/22/2023] [Indexed: 07/12/2023]
Abstract
Brassica rapa is grown worldwide as economically important vegetable and oilseed crop. However, its production is challenged by yield-limiting pathogens. The sustainable control of these pathogens mainly relies on the deployment of genetic resistance primarily driven by resistance gene analogues (RGAs). While several studies have identified RGAs in B. rapa, these were mainly based on a single genome reference and do not represent the full range of RGA diversity in B. rapa. In this study, we utilized the B. rapa pangenome, constructed from 71 lines encompassing 12 morphotypes, to describe a comprehensive repertoire of RGAs in B. rapa. We show that 309 RGAs were affected by presence-absence variation (PAV) and 223 RGAs were missing from the reference genome. The transmembrane leucine-rich repeat (TM-LRR) RGA class had more core gene types than variable genes, while the opposite was observed for nucleotide-binding site leucine-rich repeats (NLRs). Comparative analysis with the B. napus pangenome revealed significant RGA conservation (93%) between the two species. We identified 138 candidate RGAs located within known B. rapa disease resistance QTL, of which the majority were under negative selection. Using blackleg gene homologues, we demonstrated how these genes in B. napus were derived from B. rapa. This further clarifies the genetic relationship of these loci, which may be useful in narrowing-down candidate blackleg resistance genes. This study provides a novel genomic resource towards the identification of candidate genes for breeding disease resistance in B. rapa and its relatives.
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Affiliation(s)
- Junrey C. Amas
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Philipp E. Bayer
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Wei Hong Tan
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Soodeh Tirnaz
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - William J. W. Thomas
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- School of Biological Sciences and the Centre for Applied BioinformaticsThe University of Western AustraliaCrawleyWAAustralia
| | - Jacqueline Batley
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
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31
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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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32
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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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33
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Atta K, Mondal S, Gorai S, Singh AP, Kumari A, Ghosh T, Roy A, Hembram S, Gaikwad DJ, Mondal S, Bhattacharya S, Jha UC, Jespersen D. Impacts of salinity stress on crop plants: improving salt tolerance through genetic and molecular dissection. FRONTIERS IN PLANT SCIENCE 2023; 14:1241736. [PMID: 37780527 PMCID: PMC10540871 DOI: 10.3389/fpls.2023.1241736] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/14/2023] [Indexed: 10/03/2023]
Abstract
Improper use of water resources in irrigation that contain a significant amount of salts, faulty agronomic practices such as improper fertilization, climate change etc. are gradually increasing soil salinity of arable lands across the globe. It is one of the major abiotic factors that inhibits overall plant growth through ionic imbalance, osmotic stress, oxidative stress, and reduced nutrient uptake. Plants have evolved with several adaptation strategies at morphological and molecular levels to withstand salinity stress. Among various approaches, harnessing the crop genetic variability across different genepools and developing salinity tolerant crop plants offer the most sustainable way of salt stress mitigation. Some important major genetic determinants controlling salinity tolerance have been uncovered using classical genetic approaches. However, its complex inheritance pattern makes breeding for salinity tolerance challenging. Subsequently, advances in sequence based breeding approaches and functional genomics have greatly assisted in underpinning novel genetic variants controlling salinity tolerance in plants at the whole genome level. This current review aims to shed light on physiological, biochemical, and molecular responses under salt stress, defense mechanisms of plants, underlying genetics of salt tolerance through bi-parental QTL mapping and Genome Wide Association Studies, and implication of Genomic Selection to breed salt tolerant lines.
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Affiliation(s)
- Kousik Atta
- ICAR-Indian Agricultural Research Institute, New Delhi, India
- Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, India
| | - Saptarshi Mondal
- Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
| | - Shouvik Gorai
- Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, India
| | - Aditya Pratap Singh
- Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, India
- School of Agriculture, GIET University, Gunupur, Rayagada, Odisha, India
| | - Amrita Kumari
- Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, India
| | - Tuhina Ghosh
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Arkaprava Roy
- ICAR-Indian Agricultural Research Institute, New Delhi, India
- ICAR- National Institute of Biotic Stress Management, Raipur, India
| | - Suryakant Hembram
- WBAS (Research), Government of West Bengal, Field Crop Research Station, Burdwan, India
| | | | - Subhasis Mondal
- Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, India
| | | | | | - David Jespersen
- Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
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34
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Tay Fernandez CG, Bayer PE, Petereit J, Varshney R, Batley J, Edwards D. The conservation of gene models can support genome annotation. THE PLANT GENOME 2023; 16:e20377. [PMID: 37602500 DOI: 10.1002/tpg2.20377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023]
Abstract
Many genome annotations include false-positive gene models, leading to errors in phylogenetic and comparative studies. Here, we propose a method to support gene model prediction based on evolutionary conservation and use it to identify potentially erroneous annotations. Using this method, we developed a set of 15,345 representative gene models from 12 legume assemblies that can be used to support genome annotations for other legumes.
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Affiliation(s)
- Cassandria G Tay Fernandez
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | - Jakob Petereit
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | - Rajeev Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
- Centre of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
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Yocca AE, Platts A, Alger E, Teresi S, Mengist MF, Benevenuto J, Ferrão LFV, Jacobs M, Babinski M, Magallanes-Lundback M, Bayer P, Golicz A, Humann JL, Main D, Espley RV, Chagné D, Albert NW, Montanari S, Vorsa N, Polashock J, Díaz-Garcia L, Zalapa J, Bassil NV, Munoz PR, Iorizzo M, Edger PP. Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551392. [PMID: 37577683 PMCID: PMC10418200 DOI: 10.1101/2023.07.31.551392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures) as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium - a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.
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Affiliation(s)
- Alan E. Yocca
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Adrian Platts
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Elizabeth Alger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Scott Teresi
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Genetics and Genome Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Molla F. Mengist
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
| | - Juliana Benevenuto
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Luis Felipe V. Ferrão
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - MacKenzie Jacobs
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Michal Babinski
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Philipp Bayer
- University of Western Australia, Perth 6009 Australia
| | | | - Jodi L Humann
- Department of Horticulture, Washington State University, Pullman, WA, 99163, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, 99163, USA
| | - Richard V. Espley
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston, New Zealand
| | - Nick W. Albert
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston, New Zealand
| | - Sara Montanari
- The New Zealand Institute for Plant and Food Research Limited (PFR), Motueka, New Zealand
| | - Nicholi Vorsa
- SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019 USA
| | - James Polashock
- SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019 USA
| | - Luis Díaz-Garcia
- USDA-ARS, VCRU, Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Juan Zalapa
- USDA-ARS, VCRU, Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nahla V. Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR 97333, USA
| | - Patricio R. Munoz
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
- Department of Horticulture, North Carolina State University, Kannapolis, NC USA
| | - Patrick P. Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Genetics and Genome Sciences, Michigan State University, East Lansing, MI, 48824, USA
- MSU AgBioResearch, Michigan State University, East Lansing, MI, 48824, USA
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Ruperao P, Rangan P, Shah T, Thakur V, Kalia S, Mayes S, Rathore A. The Progression in Developing Genomic Resources for Crop Improvement. Life (Basel) 2023; 13:1668. [PMID: 37629524 PMCID: PMC10455509 DOI: 10.3390/life13081668] [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: 06/15/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Sequencing technologies have rapidly evolved over the past two decades, and new technologies are being continually developed and commercialized. The emerging sequencing technologies target generating more data with fewer inputs and at lower costs. This has also translated to an increase in the number and type of corresponding applications in genomics besides enhanced computational capacities (both hardware and software). Alongside the evolving DNA sequencing landscape, bioinformatics research teams have also evolved to accommodate the increasingly demanding techniques used to combine and interpret data, leading to many researchers moving from the lab to the computer. The rich history of DNA sequencing has paved the way for new insights and the development of new analysis methods. Understanding and learning from past technologies can help with the progress of future applications. This review focuses on the evolution of sequencing technologies, their significant enabling role in generating plant genome assemblies and downstream applications, and the parallel development of bioinformatics tools and skills, filling the gap in data analysis techniques.
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Affiliation(s)
- Pradeep Ruperao
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Parimalan Rangan
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi 110012, India;
| | - Trushar Shah
- International Institute of Tropical Agriculture (IITA), Nairobi 30709-00100, Kenya;
| | - Vivek Thakur
- Department of Systems & Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India;
| | - Sanjay Kalia
- Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi 110003, India;
| | - Sean Mayes
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Abhishek Rathore
- Excellence in Breeding, International Maize and Wheat Improvement Center (CIMMYT), Hyderabad 502324, India
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Wang D, Wang H, Xu X, Wang M, Wang Y, Chen H, Ping F, Zhong H, Mu Z, Xie W, Li X, Feng J, Zhang M, Fan Z, Yang T, Zhao J, Liu B, Ruan Y, Zhang G, Liu C, Liu Z. Two complementary genes in a presence-absence variation contribute to indica-japonica reproductive isolation in rice. Nat Commun 2023; 14:4531. [PMID: 37507369 PMCID: PMC10382596 DOI: 10.1038/s41467-023-40189-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Understanding the evolutionary forces in speciation is a central goal in evolutionary biology. Asian cultivated rice has two subspecies, indica and japonica, but the underlying mechanism of the partial reproductive isolation between them remains obscure. Here we show a presence-absence variation (PAV) at the Se locus functions as an indica-japonica reproductive barrier by causing hybrid sterility (HS) in indica-japonica crosses. The locus comprises two adjacent genes: ORF3 encodes a sporophytic pollen killer, whereas ORF4 protects pollen in a gametophytic manner. In F1 of indica-japonica crosses, pollen with the japonica haplotype, which lacks the sequence containing the protective ORF4, is aborted due to the pollen-killing effect of ORF3 from indica. Evolutionary analysis suggests ORF3 is a gene associated with the Asian cultivated rice species complex, and the PAV has contributed to the reproductive isolation between the two subspecies of Asian cultivated rice. Our analyses provide perspectives on rice inter-subspecies post-zygotic isolation, and will promote efforts to overcome reproductive barriers in indica-japonica hybrid rice breeding.
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Affiliation(s)
- Daiqi Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Hongru Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomic Insitute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China
| | - Xiaomei Xu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Man Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yahuan Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Hong Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Fei Ping
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Huanhuan Zhong
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Zhengkun Mu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Wantong Xie
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Xiangyu Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jingbin Feng
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Milan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Zhilan Fan
- National Field Genebank for Wild Rice (Guangzhou), Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Tifeng Yang
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Junliang Zhao
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Bin Liu
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Ying Ruan
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Chunlin Liu
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Ziqiang Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
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Glick L, Mayrose I. The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes. Genome Biol Evol 2023; 15:evad121. [PMID: 37401440 PMCID: PMC10340445 DOI: 10.1093/gbe/evad121] [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: 01/29/2023] [Revised: 06/21/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023] Open
Abstract
Pan-genomics is an emerging approach for studying the genetic diversity within plant populations. In contrast to common resequencing studies that compare whole genome sequencing data with a single reference genome, the construction of a pan-genome (PG) involves the direct comparison of multiple genomes to one another, thereby enabling the detection of genomic sequences and genes not present in the reference, as well as the analysis of gene content diversity. Although multiple studies describing PGs of various plant species have been published in recent years, a better understanding regarding the effect of the computational procedures used for PG construction could guide researchers in making more informed methodological decisions. Here, we examine the effect of several key methodological factors on the obtained gene pool and on gene presence-absence detections by constructing and comparing multiple PGs of Arabidopsis thaliana and cultivated soybean, as well as conducting a meta-analysis on published PGs. These factors include the construction method, the sequencing depth, and the extent of input data used for gene annotation. We observe substantial differences between PGs constructed using three common procedures (de novo assembly and annotation, map-to-pan, and iterative assembly) and that results are dependent on the extent of the input data. Specifically, we report low agreement between the gene content inferred using different procedures and input data. Our results should increase the awareness of the community to the consequences of methodological decisions made during the process of PG construction and emphasize the need for further investigation of commonly applied methodologies.
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Affiliation(s)
- Lior Glick
- Department of Life Sciences, School of Plant Sciences and Food Security, Tel-Aviv University, Tel Aviv, Israel
| | - Itay Mayrose
- Department of Life Sciences, School of Plant Sciences and Food Security, Tel-Aviv University, Tel Aviv, Israel
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Thatcher S, Jung M, Panangipalli G, Fengler K, Sanyal A, Li B, Llaca V, Habben J. The NLRomes of Zea mays NAM founder lines and Zea luxurians display presence-absence variation, integrated domain diversity, and mobility. MOLECULAR PLANT PATHOLOGY 2023; 24:742-757. [PMID: 36929631 PMCID: PMC10257044 DOI: 10.1111/mpp.13319] [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: 05/31/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 06/11/2023]
Abstract
Plant pathogens cause significant crop loss worldwide, and new resistance genes deployed to combat diseases can be overcome quickly. Understanding the existing resistance gene diversity within the germplasm of major crops, such as maize, is crucial for the development of new disease-resistant varieties. We analysed the nucleotide-binding leucine-rich repeat receptors (NLRs) of 26 recently sequenced diverse founder lines from the maize nested association mapping (NAM) population and compared them to the R gene complement present in a wild relative of maize, Zea luxurians. We found that NLRs in both species contain a large diversity of atypical integrated domains, including many domains that have not previously been found in the NLRs of other species. Additionally, the single Z. luxurians genome was found to have greater integrated atypical domain diversity than all 26 NAM founder lines combined, indicating that this species may represent a rich source of novel resistance genes. NLRs were also found to have very high sequence diversity and presence-absence variation among the NAM founder lines, with a large NLR cluster on Chr10 representing a diversity hotspot. Additionally, NLRs were shown to be mobile within maize genomes, with several putative interchromosomal translocations identified.
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Ma X, Zhu M, Liu W, Li J, Liao Y, Liu D, Jin M, Fu C, Wang F. Bulk segregant analysis coupled with transcriptomics and metabolomics revealed key regulators of bacterial leaf blight resistance in rice. BMC PLANT BIOLOGY 2023; 23:332. [PMID: 37349684 DOI: 10.1186/s12870-023-04347-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 06/14/2023] [Indexed: 06/24/2023]
Abstract
BACKGROUND Bacterial leaf blight (BLB) is a highly destructive disease, causing significant yield losses in rice (Oryza sativa). Genetic variation is contemplated as the most effective measure for inducing resistance in plants. The mutant line T1247 derived from R3550 (BLB susceptible) was highly resistant to BLB. Therefore, by utilizing this valuable source, we employed bulk segregant analysis (BSA) and transcriptome profiling to identify the genetic basis of BLB resistance in T1247. RESULTS The differential subtraction method in BSA identified a quantitative trait locus (QTL) on chromosome 11 spanning a 27-27.45 Mb region with 33 genes and 4 differentially expressed genes (DEGs). Four DEGs (P < 0.01) with three putative candidate genes, OsR498G1120557200, OsR498G1120555700, and OsR498G1120563600,0.01 in the QTL region were identified with specific regulation as a response to BLB inoculation. Moreover, transcriptome profiling identified 37 resistance analogs genes displaying differential regulation. CONCLUSIONS Our study provides a substantial addition to the available information regarding QTLs associated with BLB, and further functional verification of identified candidate genes can broaden the scope of understanding the BLB resistance mechanism in rice.
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Affiliation(s)
- Xiaozhi Ma
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Manshan Zhu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Wuge Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Jinhua Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Yilong Liao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Dilin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Mengya Jin
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Chongyun Fu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China.
- Guangdong Rice Engineering Laboratory, Guangzhou, China.
| | - Feng Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China.
- Guangdong Rice Engineering Laboratory, Guangzhou, China.
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Sun Y, Kou DR, Li Y, Ni JP, Wang J, Zhang YM, Wang QN, Jiang B, Wang X, Sun YX, Xu XT, Tan XJ, Zhang YJ, Kong XD. Pan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection. BMC Genomics 2023; 24:332. [PMID: 37322453 DOI: 10.1186/s12864-023-09443-w] [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: 01/19/2023] [Accepted: 06/11/2023] [Indexed: 06/17/2023] Open
Abstract
The rich genetic diversity in Citrullus lanatus and the other six species in the Citrullus genus provides important sources in watermelon breeding. Here, we present the Citrullus genus pan-genome based on the 400 Citrullus genus resequencing data, showing that 477 Mb contigs and 6249 protein-coding genes were absent in the Citrullus lanatus reference genome. In the Citrullus genus pan-genome, there are a total of 8795 (30.5%) genes that exhibit presence/absence variations (PAVs). Presence/absence variation (PAV) analysis showed that a lot of gene PAV were selected during the domestication and improvement, such as 53 favorable genes and 40 unfavorable genes were identified during the C. mucosospermus to C. lanatus landrace domestication. We also identified 661 resistance gene analogs (RGAs) in the Citrullus genus pan-genome, which contains 90 RGAs (89 variable and 1 core gene) located on the pangenome additional contigs. By gene PAV-based GWAS, 8 gene presence/absence variations were found associated with flesh color. Finally, based on the results of gene PAV selection analysis between watermelon populations with different fruit colors, we identified four non-reference candidate genes associated with carotenoid accumulation, which had a significantly higher frequency in the white flesh. These results will provide an important source for watermelon breeding.
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Affiliation(s)
- Yang Sun
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.
| | - Dou-Rong Kou
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Yan Li
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
- Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | | | - Jing Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
- Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yong-Mei Zhang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Qing-Nan Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Bin Jiang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Xu Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Yue-Xin Sun
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Xin-Tong Xu
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Xiao-Juan Tan
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Yong-Jun Zhang
- Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Abdul Aziz M, Masmoudi K. Insights into the Transcriptomics of Crop Wild Relatives to Unravel the Salinity Stress Adaptive Mechanisms. Int J Mol Sci 2023; 24:9813. [PMID: 37372961 DOI: 10.3390/ijms24129813] [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: 04/19/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/29/2023] Open
Abstract
The narrow genomic diversity of modern cultivars is a major bottleneck for enhancing the crop's salinity stress tolerance. The close relatives of modern cultivated plants, crop wild relatives (CWRs), can be a promising and sustainable resource to broaden the diversity of crops. Advances in transcriptomic technologies have revealed the untapped genetic diversity of CWRs that represents a practical gene pool for improving the plant's adaptability to salt stress. Thus, the present study emphasizes the transcriptomics of CWRs for salinity stress tolerance. In this review, the impacts of salt stress on the plant's physiological processes and development are overviewed, and the transcription factors (TFs) regulation of salinity stress tolerance is investigated. In addition to the molecular regulation, a brief discussion on the phytomorphological adaptation of plants under saline environments is provided. The study further highlights the availability and use of transcriptomic resources of CWR and their contribution to pangenome construction. Moreover, the utilization of CWRs' genetic resources in the molecular breeding of crops for salinity stress tolerance is explored. Several studies have shown that cytoplasmic components such as calcium and kinases, and ion transporter genes such as Salt Overly Sensitive 1 (SOS1) and High-affinity Potassium Transporters (HKTs) are involved in the signaling of salt stress, and in mediating the distribution of excess Na+ ions within the plant cells. Recent comparative analyses of transcriptomic profiling through RNA sequencing (RNA-Seq) between the crops and their wild relatives have unraveled several TFs, stress-responsive genes, and regulatory proteins for generating salinity stress tolerance. This review specifies that the use of CWRs transcriptomics in combination with modern breeding experimental approaches such as genomic editing, de novo domestication, and speed breeding can accelerate the CWRs utilization in the breeding programs for enhancing the crop's adaptability to saline conditions. The transcriptomic approaches optimize the crop genomes with the accumulation of favorable alleles that will be indispensable for designing salt-resilient crops.
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Affiliation(s)
- Mughair Abdul Aziz
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Khaled Masmoudi
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
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Xu L, Wang Y, Dong J, Zhang W, Tang M, Zhang W, Wang K, Chen Y, Zhang X, He Q, Zhang X, Wang K, Wang L, Ma Y, Xia K, Liu L. A chromosome-level genome assembly of radish (Raphanus sativus L.) reveals insights into genome adaptation and differential bolting regulation. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:990-1004. [PMID: 36648398 PMCID: PMC10106849 DOI: 10.1111/pbi.14011] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 11/29/2022] [Accepted: 01/03/2023] [Indexed: 05/04/2023]
Abstract
High-quality radish (Raphanus sativus) genome represents a valuable resource for agronomical trait improvements and understanding genome evolution among Brassicaceae species. However, existing radish genome assembly remains fragmentary, which greatly hampered functional genomics research and genome-assisted breeding. Here, using a NAU-LB radish inbred line, we generated a reference genome of 476.32 Mb with a scaffold N50 of 56.88 Mb by incorporating Illumina, PacBio and BioNano optical mapping techniques. Utilizing Hi-C data, 448.12 Mb (94.08%) of the assembled sequences were anchored to nine radish chromosomes with 40 306 protein-coding genes annotated. In total, 249.14 Mb (52.31%) comprised the repetitive sequences, among which long terminal repeats (LTRs, 30.31%) were the most abundant class. Beyond confirming the whole-genome triplication (WGT) event in R. sativus lineage, we found several tandem arrayed genes were involved in stress response process, which may account for the distinctive phenotype of high disease resistance in R. sativus. By comparing against the existing Xin-li-mei radish genome, a total of 2 108 573 SNPs, 7740 large insertions, 7757 deletions and 84 inversions were identified. Interestingly, a 647-bp insertion in the promoter of RsVRN1 gene can be directly bound by the DOF transcription repressor RsCDF3, resulting into its low promoter activity and late-bolting phenotype of NAU-LB cultivar. Importantly, introgression of this 647-bp insertion allele, RsVRN1In-536 , into early-bolting genotype could contribute to delayed bolting time, indicating that it is a potential genetic resource for radish late-bolting breeding. Together, this genome resource provides valuable information to facilitate comparative genomic analysis and accelerate genome-guided breeding and improvement in radish.
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Affiliation(s)
- Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Junhui Dong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Wei Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Mingjia Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Weilan Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Kai Wang
- School of Life SciencesNantong UniversityNantongChina
| | - Yinglong Chen
- The UWA Institute of Agriculture, and School of Agriculture and EnvironmentThe University of Western AustraliaPerthWAAustralia
| | - Xiaoli Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Qing He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Xinyu Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Kai Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Lun Wang
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Yinbo Ma
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Kai Xia
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
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Kenchanmane Raju SK, Ledford M, Niederhuth CE. DNA methylation signatures of duplicate gene evolution in angiosperms. PLANT PHYSIOLOGY 2023:kiad220. [PMID: 37061825 PMCID: PMC10400039 DOI: 10.1093/plphys/kiad220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/03/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
Abstract
Gene duplication is a source of evolutionary novelty. DNA methylation may play a role in the evolution of duplicate genes (paralogs) through its association with gene expression. While this relationship has been examined to varying extents in a few individual species, the generalizability of these results at either a broad phylogenetic scale with species of differing duplication histories or across a population remains unknown. We applied a comparative epigenomics approach to 43 angiosperm species across the phylogeny and a population of 928 Arabidopsis (Arabidopsis thaliana) accessions, examining the association of DNA methylation with paralog evolution. Genic DNA methylation was differentially associated with duplication type, the age of duplication, sequence evolution, and gene expression. Whole genome duplicates were typically enriched for CG-only gene-body methylated or unmethylated genes, while single-gene duplications were typically enriched for non-CG methylated or unmethylated genes. Non-CG methylation, in particular, was characteristic of more recent single-gene duplicates. Core angiosperm gene families differentiated into those which preferentially retain paralogs and 'duplication-resistant' families, which convergently reverted to singletons following duplication. Duplication-resistant families that still have paralogous copies were, uncharacteristically for core angiosperm genes, enriched for non-CG methylation. Non-CG methylated paralogs had higher rates of sequence evolution, higher frequency of presence-absence variation, and more limited expression. This suggests that silencing by non-CG methylation may be important to maintaining dosage following duplication and be a precursor to fractionation. Our results indicate that genic methylation marks differing evolutionary trajectories and fates between paralogous genes and have a role in maintaining dosage following duplication.
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Affiliation(s)
| | | | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- AgBioResearch, Michigan State University, East Lansing, MI 48824, USA
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Yamamoto M, Ishii T, Ogura M, Akanuma T, Zhu XY, Kitashiba H. S haplotype collection in Brassicaceae crops-an updated list of S haplotypes. BREEDING SCIENCE 2023; 73:132-145. [PMID: 37404351 PMCID: PMC10316313 DOI: 10.1270/jsbbs.22091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/07/2023] [Indexed: 07/06/2023]
Abstract
Self-incompatibility is the system that inhibits pollen germination and pollen tube growth by self-pollen. This trait is important for the breeding of Brassica and Raphanus species. In these species, self-incompatibility is governed by the S locus, which contains three linked genes (a set called the S haplotype), i.e., S-locus receptor kinase, S-locus cysteine-rich protein/S-locus protein 11, and S-locus glycoprotein. A large number of S haplotypes have been identified in Brassica oleracea, B. rapa, and Raphanus sativus to date, and the nucleotide sequences of their many alleles have also been registered. In this state, it is important to avoid confusion between S haplotypes, i.e., an identical S haplotype with different names and a different S haplotype with an identical S haplotype number. To mitigate this issue, we herein constructed a list of S haplotypes that are easily accessible to the latest nucleotide sequences of S-haplotype genes, together with revisions to and an update of S haplotype information. Furthermore, the histories of the S-haplotype collection in the three species are reviewed, the importance of the collection of S haplotypes as a genetic resource is discussed, and the management of information on S haplotypes is proposed.
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Affiliation(s)
- Masaya Yamamoto
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba Aobaku, Sendai, Miyagi 980-8572, Japan
| | - Tomoko Ishii
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba Aobaku, Sendai, Miyagi 980-8572, Japan
| | - Marina Ogura
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba Aobaku, Sendai, Miyagi 980-8572, Japan
| | - Takashi Akanuma
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba Aobaku, Sendai, Miyagi 980-8572, Japan
| | - Xing-Yu Zhu
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba Aobaku, Sendai, Miyagi 980-8572, Japan
| | - Hiroyasu Kitashiba
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba Aobaku, Sendai, Miyagi 980-8572, Japan
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Amas JC, Thomas WJW, Zhang Y, Edwards D, Batley J. Key Advances in the New Era of Genomics-Assisted Disease Resistance Improvement of Brassica Species. PHYTOPATHOLOGY 2023:PHYTO08220289FI. [PMID: 36324059 DOI: 10.1094/phyto-08-22-0289-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Disease resistance improvement remains a major focus in breeding programs as diseases continue to devastate Brassica production systems due to intensive cultivation and climate change. Genomics has paved the way to understand the complex genomes of Brassicas, which has been pivotal in the dissection of the genetic underpinnings of agronomic traits driving the development of superior cultivars. The new era of genomics-assisted disease resistance breeding has been marked by the development of high-quality genome references, accelerating the identification of disease resistance genes controlling both qualitative (major) gene and quantitative resistance. This facilitates the development of molecular markers for marker assisted selection and enables genome editing approaches for targeted gene manipulation to enhance the genetic value of disease resistance traits. This review summarizes the key advances in the development of genomic resources for Brassica species, focusing on improved genome references, based on long-read sequencing technologies and pangenome assemblies. This is further supported by the advances in pathogen genomics, which have resulted in the discovery of pathogenicity factors, complementing the mining of disease resistance genes in the host. Recognizing the co-evolutionary arms race between the host and pathogen, it is critical to identify novel resistance genes using crop wild relatives and synthetic cultivars or through genetic manipulation via genome-editing to sustain the development of superior cultivars. Integrating these key advances with new breeding techniques and improved phenotyping using advanced data analysis platforms will make disease resistance improvement in Brassica species more efficient and responsive to current and future demands.
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Affiliation(s)
- Junrey C Amas
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - William J W Thomas
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - Yueqi Zhang
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - David Edwards
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - Jacqueline Batley
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
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Neik TX, Siddique KHM, Mayes S, Edwards D, Batley J, Mabhaudhi T, Song BK, Massawe F. Diversifying agrifood systems to ensure global food security following the Russia–Ukraine crisis. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2023.1124640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
The recent Russia–Ukraine conflict has raised significant concerns about global food security, leaving many countries with restricted access to imported staple food crops, particularly wheat and sunflower oil, sending food prices soaring with other adverse consequences in the food supply chain. This detrimental effect is particularly prominent for low-income countries relying on grain imports, with record-high food prices and inflation affecting their livelihoods. This review discusses the role of Russia and Ukraine in the global food system and the impact of the Russia–Ukraine conflict on food security. It also highlights how diversifying four areas of agrifood systems—markets, production, crops, and technology can contribute to achieving food supply chain resilience for future food security and sustainability.
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Carballo J, Bellido AM, Selva JP, Zappacosta D, Gallo CA, Albertini E, Caccamo M, Echenique V. From tetraploid to diploid, a pangenomic approach to identify genes lost during synthetic diploidization of Eragrostis curvula. FRONTIERS IN PLANT SCIENCE 2023; 14:1133986. [PMID: 36993842 PMCID: PMC10040859 DOI: 10.3389/fpls.2023.1133986] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/24/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION In Eragrostis curvula, commonly known as weeping lovegrass, a synthetic diploidization event of the facultative apomictic tetraploid Tanganyika INTA cv. originated from the sexual diploid Victoria cv. Apomixis is an asexual reproduction by seeds in which the progeny is genetically identical to the maternal plant. METHODS To assess the genomic changes related to ploidy and to the reproductive mode occurring during diploidization, a mapping approach was followed to obtain the first E. curvula pangenome assembly. In this way, gDNA of Tanganyika INTA was extracted and sequenced in 2x250 Illumina pair-end reads and mapped against the Victoria genome assembly. The unmapped reads were used for variant calling, while the mapped reads were assembled using Masurca software. RESULTS The length of the assembly was 28,982,419 bp distributed in 18,032 contigs, and the variable genes annotated in these contigs rendered 3,952 gene models. Functional annotation of the genes showed that the reproductive pathway was differentially enriched. PCR amplification in gDNA and cDNA of Tanganyika INTA and Victoria was conducted to validate the presence/absence variation in five genes related to reproduction and ploidy. The polyploid nature of the Tanganyika INTA genome was also evaluated through the variant calling analysis showing the single nucleotide polymorphism (SNP) coverage and allele frequency distribution with a segmental allotetraploid pairing behavior. DISCUSSION The results presented here suggest that the genes were lost in Tanganyika INTA during the diploidization process that was conducted to suppress the apomictic pathway, affecting severely the fertility of Victoria cv.
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Affiliation(s)
- Jose Carballo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
| | - Andrés Martin Bellido
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
| | - Juan Pablo Selva
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - Diego Zappacosta
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - Cristian Andres Gallo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
| | - Emidio Albertini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | | | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
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Christine TD, Clothilde C, Mathieu B, Laurence A, Valentin K, Cédric M, Wing Rod A, Yves V, Francois S. FrangiPANe, a tool for creating a panreference using left behind reads. NAR Genom Bioinform 2023; 5:lqad013. [PMID: 36814455 PMCID: PMC9940456 DOI: 10.1093/nargab/lqad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/21/2022] [Accepted: 02/02/2023] [Indexed: 02/22/2023] Open
Abstract
We present here FrangiPANe, a pipeline developed to build panreference using short reads through a map-then-assemble strategy. Applying it to 248 African rice genomes using an improved CG14 reference genome, we identified an average of 8 Mb of new sequences and 5290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1 306 676 contigs, were assembled. We validated 97.7% of the contigs of the TOG5681 cultivar individual assembly from short reads on a newly long reads genome assembly of the same TOG5681 cultivar. FrangiPANe also allowed the anchoring of 31.5% of the new contigs within the CG14 reference genome, with a 92.5% accuracy at 2 kb span. We annotated in addition 3252 new genes absent from the reference. FrangiPANe was developed as a modular and interactive application to simplify the construction of a panreference using the map-then-assemble approach. It is available as a Docker image containing (i) a Jupyter notebook centralizing codes, documentation and interactive visualization of results, (ii) python scripts and (iii) all the software and libraries requested for each step of the analysis. We foreseen our approach will help leverage large-scale illumina dataset for pangenome studies in GWAS or detection of selection.
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Affiliation(s)
| | | | - Blaison Mathieu
- DIADE, Univ Montpellier, CIRAD, IRD, 911 Avenue Agropolis 34934, 34830 Montpellier Cedex 5, France
| | - Albar Laurence
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Klein Valentin
- DIADE, Univ Montpellier, CIRAD, IRD, 911 Avenue Agropolis 34934, 34830 Montpellier Cedex 5, France
| | - Mariac Cédric
- DIADE, Univ Montpellier, CIRAD, IRD, 911 Avenue Agropolis 34934, 34830 Montpellier Cedex 5, France
| | - A. Wing Rod
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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Gao Y, Xu J, Li Z, Zhang Y, Riera N, Xiong Z, Ouyang Z, Liu X, Lu Z, Seymour D, Zhong B, Wang N. Citrus genomic resources unravel putative genetic determinants of Huanglongbing pathogenicity. iScience 2023; 26:106024. [PMID: 36824272 PMCID: PMC9941208 DOI: 10.1016/j.isci.2023.106024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/08/2022] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
Citrus HLB caused by Candidatus Liberibacter asiaticus is a pathogen-triggered immune disease. Here, we identified putative genetic determinants of HLB pathogenicity by integrating citrus genomic resources to characterize the pan-genome of accessions that differ in their response to HLB. Genome-wide association mapping and analysis of allele-specific expression between susceptible, tolerant, and resistant accessions further refined candidates underlying the response to HLB. We first developed a phased diploid assembly of Citrus sinensis 'Newhall' genome and produced resequencing data for 91 citrus accessions that differ in their response to HLB. These data were combined with previous resequencing data from 356 accessions for genome-wide association mapping of the HLB response. Genes determinants for HLB pathogenicity were associated with host immune response, ROS production, and antioxidants. Overall, this study has provided a significant resource of citrus genomic data and identified candidate genes to be further explored to understand the genetic determinants of HLB pathogenicity.
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Affiliation(s)
- Yuxia Gao
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Zhilong Li
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Yunzeng Zhang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Nadia Riera
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Zhiwei Xiong
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Zhigang Ouyang
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Xinjun Liu
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Zhanjun Lu
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | | | - Balian Zhong
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
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