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Du Q, Yu H, Zhang Y, Qiao Q, Wang J, Zhang T, Xue L, Lei J. Uncovering fruit flavor and genetic diversity across diploid wild Fragaria species via comparative metabolomics profiling. Food Chem 2024; 456:140013. [PMID: 38878536 DOI: 10.1016/j.foodchem.2024.140013] [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: 02/06/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 07/24/2024]
Abstract
Wild Fragaria resources exhibit extensive genetic diversity and desirable edible traits, such as high soluble solid content and flavor compounds. However, specific metabolites in different wild strawberry fruits remain unknown. In this study, we characterized 1008 metabolites covering 11 subclasses among 13 wild diploid resources representing eight species, including F. vesca, F. nilgerrensis, F. viridis, F. nubicola, F. pentaphylla, F. mandschurica, F. chinensis, and F. emeiensis. Fifteen potential metabolite biomarkers were identified to distinguish fruit flavors among the 13 diploid wild Fragaria accessions. A total of nine distinct modules were employed to explore key metabolites related to fruit quality through weighted gene co-expression module analysis, with significant enrichment in amino acid biosynthesis pathway. Notably, the identified significantly different key metabolites highlighted the close association of amino acids, sugars, and anthocyanins with flavor formation. These findings offer valuable resources for improving fruit quality through metabolome-assisted breeding.
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Affiliation(s)
- Qiuling Du
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Haoming Yu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuanyuan Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Qin Qiao
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming 650201, China
| | - Jian Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Ticao Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Li Xue
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China.
| | - Jiajun Lei
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China.
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Wang Y, Li P, Zhu Y, Zhang F, Zhang S, He Y, Wu Y, Lin Y, Wang H, Ren W, Wang L, Yang Y, Wang R, Zheng P, Liu Y, Wang S, Yue J. Graph-Based Pangenome of Actinidia chinensis Reveals Structural Variations Mediating Fruit Degreening. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400322. [PMID: 38757662 PMCID: PMC11267314 DOI: 10.1002/advs.202400322] [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: 01/09/2024] [Revised: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Fruit ripening is associated with the degreening process (loss of chlorophyll) that occurs in most fruit species. Kiwifruit is one of the special species whose fruits may maintain green flesh by accumulating a large amount of chlorophyll even after ripening. However, little is known about the genetic variations related to the fruit degreening process. Here, a graph-based kiwifruit pangenome by analyzing 14 chromosome-scale haplotype-resolved genome assemblies from seven representative cultivars or lines in Actinidia chinensis is built. A total of 49,770 non-redundant gene families are identified, with core genes constituting 46.6%, and dispensable genes constituting 53.4%. A total of 84,591 non-redundant structural variations (SVs) are identified. The pangenome graph integrating both reference genome sequences and variant information facilitates the identification of SVs related to fruit color. The SV in the promoter of the AcBCM gene determines its high expression in the late developmental stage of fruits, which causes chlorophyll accumulation in the green-flesh fruits by post-translationally regulating AcSGR2, a key enzyme of chlorophyll catabolism. Taken together, a high-quality pangenome is constructed, unraveled numerous genetic variations, and identified a novel SV mediating fruit coloration and fruit quality, providing valuable information for further investigating genome evolution and domestication, QTL genes function, and genomics-assisted breeding.
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Affiliation(s)
- Yingzhen Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
- School of Forestry Science and TechnologyLishui Vocational and Technical CollegeLishui323000China
| | - Pengwei Li
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Yanyan Zhu
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Feng Zhang
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Sijia Zhang
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Yan He
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Ying Wu
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Yunzhi Lin
- Ministry of Education Key Laboratory for Bio‐resource and Eco‐environmentCollege of Life ScienceState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengdu610064China
| | - Hongtao Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Wangmei Ren
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Lihuan Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Ying Yang
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Runze Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Pengpeng Zheng
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Yongsheng Liu
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
- Ministry of Education Key Laboratory for Bio‐resource and Eco‐environmentCollege of Life ScienceState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengdu610064China
| | - Songhu Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Junyang Yue
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
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3
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Li WG, Li YY, Zheng CK, Li ZZ. Chromosome-level genome assembly of a cliff plant Taihangia rupestris var. ciliata provides insights into its adaptation and demographic history. BMC PLANT BIOLOGY 2024; 24:596. [PMID: 38914948 PMCID: PMC11197248 DOI: 10.1186/s12870-024-05322-y] [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: 12/14/2023] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
BACKGROUND Cliffs are recognized as one of the most challenging environments for plants, characterized by harsh conditions such as drought, infertile soil, and steep terrain. However, they surprisingly host ancient and diverse plant communities and play a crucial role in protecting biodiversity. The Taihang Mountains, which act as a natural boundary in eastern China, support a rich variety of plant species, including many unique to cliff habitats. However, it is little known how cliff plants adapt to harsh habitats and the demographic history in this region. RESULTS To better understand the demographic history and adaptation of cliff plants in this area, we analyzed the chromosome-level genome of a representative cliff plant, T. rupestris var. ciliata, which has a genome size of 769.5 Mb, with a scaffold N50 of 104.92 Mb. The rapid expansion of transposable elements may have contributed to the increasing genome and its ability to adapt to unique and challenging cliff habitats. Comparative analysis of the genome evolution between Taihangia and non-cliff plants in Rosaceae revealed a significant expansion of gene families associated with oxidative phosphorylation, which is likely a response to the abiotic stresses faced by cliff plants. This expansion may explain the long-term adaptation of Taihangia to harsh cliff environments. The effective population size of the two varieties has continuously decreased due to climatic fluctuations during the Quaternary period. Furthermore, significant differences in gene expression between the two varieties may explain the varied leaf phenotypes and adaptations to harsh conditions in different natural distributions. CONCLUSION Our study highlights the extraordinary adaptation of T. rupestris var. ciliata, shedding light on the evolution of cliff plants worldwide.
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Affiliation(s)
- Wei-Guo Li
- School of Resource and Environment, Henan Polytechnic University, Jiaozuo, Henan, 454000, China.
| | - Yuan-Yuan Li
- School of Resource and Environment, Henan Polytechnic University, Jiaozuo, Henan, 454000, China
| | - Chuan-Kun Zheng
- School of Resource and Environment, Henan Polytechnic University, Jiaozuo, Henan, 454000, China
| | - Zhi-Zhong Li
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
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Qiao Q, Cao Q, Zhang R, Wu M, Zheng Y, Xue L, Lei J, Sun H, Liston A, Zhang T. Genomic analyses provide insights into sex differentiation of tetraploid strawberry (Fragaria moupinensis). PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1552-1565. [PMID: 38184782 PMCID: PMC11123429 DOI: 10.1111/pbi.14286] [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: 09/19/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/08/2024]
Abstract
The strawberry genus, Fragaria, exhibits a wide range of sexual systems and natural ploidy variation. Nearly, all polyploid strawberry species exhibit separate sexes (dioecy). Research has identified the sex-determining sequences as roughly conserved but with repeatedly changed genomic locations across octoploid strawberries. However, it remains unclear whether tetraploid wild strawberries evolved dioecy independently or shared a common origin with octoploid strawberries. In this study, we investigated the sex determinants of F. moupinensis, a dioecious plant with heterogametic females (ZW). Utilizing a combination of haplotype-resolved genome sequencing of the female F. moupinensis, k-mer-based and coverage-based genome-wide association studies (GWAS), and transcriptomic analysis, we discovered a non-recombining, approximately 33.6 kb W-specific region on chromosome 2a. Within this region, only one candidate sex-determining gene (FmoAFT) was identified. Furthermore, an extensive resequencing of the entire Fragaria genus indicated that the W-specific region displays conservative female specificity across all tetraploid species. This observation suggests that dioecy evolved independently in tetraploid and octoploid strawberries. Moreover, employing virus-induced gene silencing (VIGS), we knocked down the expression of the FmoAFT homologue transcript in cultivated strawberries, revealing its potential role in promoting female functions during early carpel development. We also applied DNA affinity purification sequencing (DAP-seq) and yeast one-hybrid assays to identify potential direct targets of FmoAFT. These insights shed new light on the genetic basis and evolutionary history of sex determination in strawberries, thereby facilitating the formulation of strategies to manipulate sex determination in breeding programs.
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Affiliation(s)
- Qin Qiao
- College of Horticulture and LandscapeYunnan Agricultural UniversityKunmingChina
| | - Qiang Cao
- College of Horticulture and LandscapeYunnan Agricultural UniversityKunmingChina
| | - Rengang Zhang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
| | - Mingzhao Wu
- School of AgricultureYunnan UniversityKunmingChina
| | | | - Li Xue
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Jiajun Lei
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
| | - Aaron Liston
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOregonUSA
| | - Ticao Zhang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
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5
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Wu H, Jia Y, Chen X, Jiang N, Zhang Z, Chai S. Novel Allelic Gene Variations in CmCLAVATA3 ( CmCLV3) Were Identified in a Genetic Population of Melon ( Cucumis melo L.). Int J Mol Sci 2024; 25:6011. [PMID: 38892198 PMCID: PMC11173160 DOI: 10.3390/ijms25116011] [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: 04/25/2024] [Revised: 05/20/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Carpel number (CN) is an important trait affecting the fruit size and shape of melon, which plays a crucial role in determining the overall appearance and market value. A unique non-synonymous single nucleotide polymorphism (SNP) in CmCLAVATA3 (CmCLV3) is responsible for the variation of CN in C. melo ssp. agrestis (hereafter agrestis), but it has been unclear in C. melo ssp. melo (hereafter melo). In this study, one major locus controlling the polymorphism of 5-CN (multi-CN) and 3-CN (normal-CN) in melo was identified using bulked segregant analysis (BSA-seq). This locus was then fine-mapped to an interval of 1.8 Mb on chromosome 12 using a segregating population containing 1451 progeny. CmCLV3 is still present in the candidate region. A new allele of CmCLV3, which contains five other nucleotide polymorphisms, including a non-synonymous SNP in coding sequence (CDS), except the SNP reported in agrestis, was identified in melo. A cis-trans test confirmed that the candidate gene, CmCLV3, contributes to the variation of CNs in melo. The qRT-PCR results indicate that there is no significant difference in the expression level of CmCLV3 in the apical stem between the multi-CN plants and the normal-CN plants. Overall, this study provides a genetic resource for melon fruit development research and molecular breeding. Additionally, it suggests that melo has undergone similar genetic selection but evolved into an independent allele.
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Affiliation(s)
| | | | | | | | | | - Sen Chai
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China; (H.W.); (Y.J.); (X.C.); (N.J.); (Z.Z.)
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Fan Z, Whitaker VM. Genomic signatures of strawberry domestication and diversification. THE PLANT CELL 2024; 36:1622-1636. [PMID: 38113879 PMCID: PMC11062436 DOI: 10.1093/plcell/koad314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023]
Abstract
Cultivated strawberry (Fragaria × ananassa) has a brief history of less than 300 yr, beginning with the hybridization of octoploids Fragaria chiloensis and Fragaria virginiana. Here we explored the genomic signatures of early domestication and subsequent diversification for different climates using whole-genome sequences of 289 wild, heirloom, and modern varieties from two major breeding programs in the United States. Four nonadmixed wild octoploid populations were identified, with recurrent introgression among the sympatric populations. The proportion of F. virginiana ancestry increased by 20% in modern varieties over initial hybrids, and the proportion of F. chiloensis subsp. pacifica rose from 0% to 3.4%. Effective population size rapidly declined during early breeding. Meanwhile, divergent selection for distinct environments reshaped wild allelic origins in 21 out of 28 chromosomes. Overlapping divergent selective sweeps in natural and domesticated populations revealed 16 convergent genomic signatures that may be important for climatic adaptation. Despite 20 breeding cycles since initial hybridization, more than half of loci underlying yield and fruit size are still not under artificial selection. These insights add clarity to the domestication and breeding history of what is now the most widely cultivated fruit in the world.
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Affiliation(s)
- Zhen Fan
- Horticultural Sciences Department, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL 33597, USA
| | - Vance M Whitaker
- Horticultural Sciences Department, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL 33597, USA
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Vondracek K, Altpeter F, Liu T, Lee S. Advances in genomics and genome editing for improving strawberry ( Fragaria ×ananassa). Front Genet 2024; 15:1382445. [PMID: 38706796 PMCID: PMC11066249 DOI: 10.3389/fgene.2024.1382445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/04/2024] [Indexed: 05/07/2024] Open
Abstract
The cultivated strawberry, Fragaria ×ananassa, is a recently domesticated fruit species of economic interest worldwide. As such, there is significant interest in continuous varietal improvement. Genomics-assisted improvement, including the use of DNA markers and genomic selection have facilitated significant improvements of numerous key traits during strawberry breeding. CRISPR/Cas-mediated genome editing allows targeted mutations and precision nucleotide substitutions in the target genome, revolutionizing functional genomics and crop improvement. Genome editing is beginning to gain traction in the more challenging polyploid crops, including allo-octoploid strawberry. The release of high-quality reference genomes and comprehensive subgenome-specific genotyping and gene expression profiling data in octoploid strawberry will lead to a surge in trait discovery and modification by using CRISPR/Cas. Genome editing has already been successfully applied for modification of several strawberry genes, including anthocyanin content, fruit firmness and tolerance to post-harvest disease. However, reports on many other important breeding characteristics associated with fruit quality and production are still lacking, indicating a need for streamlined genome editing approaches and tools in Fragaria ×ananassa. In this review, we present an overview of the latest advancements in knowledge and breeding efforts involving CRISPR/Cas genome editing for the enhancement of strawberry varieties. Furthermore, we explore potential applications of this technology for improving other Rosaceous plant species.
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Affiliation(s)
- Kaitlyn Vondracek
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL, United States
- University of Florida, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Fredy Altpeter
- University of Florida, Agronomy Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Tie Liu
- University of Florida, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Seonghee Lee
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL, United States
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Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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9
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Xu MRX, Liao ZY, Brock JR, Du K, Li GY, Chen ZQ, Wang YH, Gao ZN, Agarwal G, Wei KHC, Shao F, Pang S, Platts AE, van de Velde J, Lin HM, Teresi SJ, Bird K, Niederhuth CE, Xu JG, Yu GH, Yang JY, Dai SF, Nelson A, Braasch I, Zhang XG, Schartl M, Edger PP, Han MJ, Zhang HH. Maternal dominance contributes to subgenome differentiation in allopolyploid fishes. Nat Commun 2023; 14:8357. [PMID: 38102128 PMCID: PMC10724154 DOI: 10.1038/s41467-023-43740-y] [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: 02/16/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Teleost fishes, which are the largest and most diverse group of living vertebrates, have a rich history of ancient and recent polyploidy. Previous studies of allotetraploid common carp and goldfish (cyprinids) reported a dominant subgenome, which is more expressed and exhibits biased gene retention. However, the underlying mechanisms contributing to observed 'subgenome dominance' remains poorly understood. Here we report high-quality genomes of twenty-one cyprinids to investigate the origin and subsequent subgenome evolution patterns following three independent allopolyploidy events. We identify the closest extant relatives of the diploid progenitor species, investigate genetic and epigenetic differences among subgenomes, and conclude that observed subgenome dominance patterns are likely due to a combination of maternal dominance and transposable element densities in each polyploid. These findings provide an important foundation to understanding subgenome dominance patterns observed in teleost fishes, and ultimately the role of polyploidy in contributing to evolutionary innovations.
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Affiliation(s)
- Min-Rui-Xuan Xu
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Zhen-Yang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jordan R Brock
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | - Guo-Yin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | | | - Ying-Hao Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhong-Nan Gao
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Gaurav Agarwal
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Kevin H-C Wei
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University, School of Life Sciences, Chongqing, China
| | | | - Adrian E Platts
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Jozefien van de Velde
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Hong-Min Lin
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Scott J Teresi
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Kevin Bird
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Jin-Gen Xu
- Jiujiang Academy of Agricultural Sciences, Jiujiang, China
| | - Guo-Hua Yu
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Jian-Yuan Yang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Si-Fa Dai
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | | | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - Xiao-Gu Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Bayern, Germany.
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, USA.
| | - Min-Jin Han
- State Key Laboratory of Resource Insects, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China.
| | - Hua-Hao Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
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10
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Lyu K, Xiao J, Lyu S, Liu R. Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels. Int J Mol Sci 2023; 24:16935. [PMID: 38069258 PMCID: PMC10706760 DOI: 10.3390/ijms242316935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Transposable elements (TEs) make up a large portion of plant genomes and play a vital role in genome structure, function, and evolution. Cultivated strawberry (Fragaria x ananassa) is one of the most important fruit crops, and its octoploid genome was formed through several rounds of genome duplications from diploid ancestors. Here, we built a pan-genome TE library for the Fragaria genus using ten published strawberry genomes at different ploidy levels, including seven diploids, one tetraploid, and two octoploids, and performed comparative analysis of TE content in these genomes. The TEs comprise 51.83% (F. viridis) to 60.07% (F. nilgerrensis) of the genomes. Long terminal repeat retrotransposons (LTR-RTs) are the predominant TE type in the Fragaria genomes (20.16% to 34.94%), particularly in F. iinumae (34.94%). Estimating TE content and LTR-RT insertion times revealed that species-specific TEs have shaped each strawberry genome. Additionally, the copy number of different LTR-RT families inserted in the last one million years reflects the genetic distance between Fragaria species. Comparing cultivated strawberry subgenomes to extant diploid ancestors showed that F. vesca and F. iinumae are likely the diploid ancestors of the cultivated strawberry, but not F. viridis. These findings provide new insights into the TE variations in the strawberry genomes and their roles in strawberry genome evolution.
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Affiliation(s)
- Keliang Lyu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (K.L.); (S.L.)
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Jiajing Xiao
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Shiheng Lyu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (K.L.); (S.L.)
| | - Renyi Liu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
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11
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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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12
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Denoyes B, Prohaska A, Petit J, Rothan C. Deciphering the genetic architecture of fruit color in strawberry. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6306-6320. [PMID: 37386925 PMCID: PMC10627153 DOI: 10.1093/jxb/erad245] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/28/2023] [Indexed: 07/01/2023]
Abstract
Fruits of Fragaria species usually have an appealing bright red color due to the accumulation of anthocyanins, water-soluble flavonoid pigments. Octoploid cultivated strawberry (Fragaria × ananassa) is a major horticultural crop for which fruit color and associated nutritional value are main breeding targets. Great diversity in fruit color intensity and pattern is observed not only in cultivated strawberry but also in wild relatives such as its octoploid progenitor F. chiloensis or the diploid woodland strawberry F. vesca, a model for fruit species in the Rosaceae. This review examines our understanding of fruit color formation in strawberry and how ongoing developments will advance it. Natural variations of fruit color as well as color changes during fruit development or in response to several cues have been used to explore the anthocyanin biosynthetic pathway and its regulation. So far, the successful identification of causal genetic variants has been largely driven by the availability of high-throughput genotyping tools and high-quality reference genomes of F. vesca and F. × ananassa. The current completion of haplotype-resolved genomes of F. × ananassa combined with QTL mapping will accelerate the exploitation of the untapped genetic diversity of fruit color and help translate the findings into strawberry improvement.
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Affiliation(s)
- Béatrice Denoyes
- INRAE and Univ. of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Alexandre Prohaska
- INRAE and Univ. of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
- INVENIO, MIN de Brienne, Bordeaux, France
| | - Johann Petit
- INRAE and Univ. of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Christophe Rothan
- INRAE and Univ. of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
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13
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Xu P, Li X, Fan J, Tian S, Cao M, Lin A, Gao Q, Xiao K, Wang C, Kuang H, Lian H. An arginine-to-histidine mutation in flavanone-3-hydroxylase results in pink strawberry fruits. PLANT PHYSIOLOGY 2023; 193:1849-1865. [PMID: 37477940 DOI: 10.1093/plphys/kiad424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/22/2023]
Abstract
Fruit color is a very important external commodity factor for consumers. Compared to the most typical red octoploid strawberry (Fragaria × ananassa), the pink strawberry often sells for a more expensive price and has a higher economic benefit due to its outstanding color. However, few studies have examined the molecular basis of pink-colored strawberry fruit. Through an EMS mutagenesis of woodland strawberry (Fragaria vesca), we identified a mutant with pink fruits and green petioles. Bulked-segregant analysis sequencing analysis and gene function verification confirmed that the responsible mutation resides in a gene encoding flavanone-3-hydroxylase (F3H) in the anthocyanin synthesis pathway. This nonsynonymous mutation results in an arginine-to-histidine change at position 130 of F3H. Molecular docking experiments showed that the arginine-to-histidine mutation results in a reduction of intermolecular force-hydrogen bonding between the F3H protein and its substrates. Enzymatic experiments showed a greatly reduced ability of the mutated F3H protein to catalyze the conversion of the substrates and hence a blockage of the anthocyanin synthesis pathway. The discovery of a key residue in the F3H gene controlling anthocyanin synthesis provides a clear target of modification for the molecular breeding of strawberry varieties with pink-colored fruits, which may be of great commercial value.
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Affiliation(s)
- Pengbo Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinyu Li
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junmiao Fan
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuhua Tian
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Minghao Cao
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Ecology, Lishui University, Lishui 323000, China
| | - Anqi Lin
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qinhua Gao
- Shanghai Key Laboratory of Protected Horticultural Technology, Forestry and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Kun Xiao
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- College of Horticultural Science, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Chong Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huiyun Kuang
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences 201403, Shanghai, China
| | - Hongli Lian
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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14
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Liu Z, Liang T, Kang C. Molecular bases of strawberry fruit quality traits: Advances, challenges, and opportunities. PLANT PHYSIOLOGY 2023; 193:900-914. [PMID: 37399254 DOI: 10.1093/plphys/kiad376] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/25/2023] [Accepted: 06/01/2023] [Indexed: 07/05/2023]
Abstract
The strawberry is one of the world's most popular fruits, providing humans with vitamins, fibers, and antioxidants. Cultivated strawberry (Fragaria × ananassa) is an allo-octoploid and highly heterozygous, making it a challenge for breeding, quantitative trait locus (QTL) mapping, and gene discovery. Some wild strawberry relatives, such as Fragaria vesca, have diploid genomes and are becoming laboratory models for the cultivated strawberry. Recent advances in genome sequencing and CRISPR-mediated genome editing have greatly improved the understanding of various aspects of strawberry growth and development in both cultivated and wild strawberries. This review focuses on fruit quality traits that are most relevant to the consumers, including fruit aroma, sweetness, color, firmness, and shape. Recently available phased-haplotype genomes, single nucleotide polymorphism (SNP) arrays, extensive fruit transcriptomes, and other big data have made it possible to locate key genomic regions or pinpoint specific genes that underlie volatile synthesis, anthocyanin accumulation for fruit color, and sweetness intensity or perception. These new advances will greatly facilitate marker-assisted breeding, the introgression of missing genes into modern varieties, and precise genome editing of selected genes and pathways. Strawberries are poised to benefit from these recent advances, providing consumers with fruit that is tastier, longer-lasting, healthier, and more beautiful.
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Affiliation(s)
- Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Tong Liang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chunying Kang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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15
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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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16
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Li H, Song K, Zhang X, Wang D, Dong S, Liu Y, Yang L. Application of Multi-Perspectives in Tea Breeding and the Main Directions. Int J Mol Sci 2023; 24:12643. [PMID: 37628823 PMCID: PMC10454712 DOI: 10.3390/ijms241612643] [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: 07/03/2023] [Revised: 07/29/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Tea plants are an economically important crop and conducting research on tea breeding contributes to enhancing the yield and quality of tea leaves as well as breeding traits that satisfy the requirements of the public. This study reviews the current status of tea plants germplasm resources and their utilization, which has provided genetic material for the application of multi-omics, including genomics and transcriptomics in breeding. Various molecular markers for breeding were designed based on multi-omics, and available approaches in the direction of high yield, quality and resistance in tea plants breeding are proposed. Additionally, future breeding of tea plants based on single-cellomics, pangenomics, plant-microbe interactions and epigenetics are proposed and provided as references. This study aims to provide inspiration and guidance for advancing the development of genetic breeding in tea plants, as well as providing implications for breeding research in other crops.
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Affiliation(s)
| | | | | | | | | | | | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China
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17
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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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18
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Jin X, Du H, Zhu C, Wan H, Liu F, Ruan J, Mower JP, Zhu A. Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry. NATURE PLANTS 2023; 9:1252-1266. [PMID: 37537397 DOI: 10.1038/s41477-023-01473-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 07/03/2023] [Indexed: 08/05/2023]
Abstract
Strawberry is an emerging model for studying polyploid genome evolution and rapid domestication of fruit crops. Here we report haplotype-resolved genomes of two wild octoploids (Fragaria chiloensis and Fragaria virginiana), the progenitor species of cultivated strawberry. Substantial variation is identified between species and between haplotypes. We redefine the four subgenomes and track the genetic contributions of diploid species by additional sequencing of the diploid F. nipponica genome. We provide multiple lines of evidence that F. vesca and F. iinumae, rather than other described extant species, are the closest living relatives of these wild and cultivated octoploids. In response to coexistence with quadruplicate gene copies, the octoploid strawberries have experienced subgenome dominance, homoeologous exchanges and coordinated expression of homoeologous genes. However, some homoeologues have substantially altered expression bias after speciation and during domestication. These findings enhance our understanding of the origin, genome evolution and domestication of strawberries.
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Affiliation(s)
- Xin Jin
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haiyuan Du
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chumeng Zhu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong Wan
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jiwei Ruan
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, USA.
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA.
| | - Andan Zhu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
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19
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Zhang Y, Kan L, Hu S, Liu Z, Kang C. Roles and evolution of four LEAFY homologs in floral patterning and leaf development in woodland strawberry. PLANT PHYSIOLOGY 2023; 192:240-255. [PMID: 36732676 PMCID: PMC10152680 DOI: 10.1093/plphys/kiad067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 05/03/2023]
Abstract
The plant-specific transcription factor LEAFY (LFY), generally maintained as a single-copy gene in most angiosperm species, plays critical roles in flower development. The woodland strawberry (Fragaria vesca) possesses four LFY homologs in the genome; however, their respective functions and evolution remain unknown. Here, we identified and validated that mutations in one of the four LFY homologs, FveLFYa, cause homeotic conversion of floral organs and reiterative outgrowth of ectopic flowers. In contrast to FveLFYa, FveLFYb/c/d appear dispensable under normal growth conditions, as fvelfyc mutants are indistinguishable from wild type and FveLFYb and FveLFYd are barely expressed. Transgenic analysis and yeast one-hybrid assay showed that FveLFYa and FveLFYb, but not FveLFYc and FveLFYd, are functionally conserved with AtLFY in Arabidopsis (Arabidopsis thaliana). Unexpectedly, LFY-binding site prediction and yeast one-hybrid assay revealed that the transcriptional links between LFY and the APETALA1 (AP1) promoter/the large AGAMOUS (AG) intron are missing in F. vesca, which is due to the loss of LFY-binding sites. The data indicate that mutations in cis-regulatory elements could contribute to LFY evolution. Moreover, we showed that FveLFYa is involved in leaf development, as approximately 30% of mature leaves have smaller or fewer leaflets in fvelfya. Phylogenetic analysis indicated that LFY homologs in Fragaria species may arise from recent duplication events in their common ancestor and are undergoing convergent gene loss. Together, these results provide insight into the role of LFY in flower and leaf development in strawberry and have important implications for the evolution of LFY.
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Affiliation(s)
- Yunming Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Lijun Kan
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Shaoqiang Hu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Chunying Kang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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20
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Stull GW, Pham KK, Soltis PS, Soltis DE. Deep reticulation: the long legacy of hybridization in vascular plant evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:743-766. [PMID: 36775995 DOI: 10.1111/tpj.16142] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 05/27/2023]
Abstract
Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep evolutionary scales has been largely obscure. Over the past decade, genomic and phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, has been common throughout the evolutionary history of plants, particularly in various lineages of flowering plants. However, phylogenomic studies have also highlighted the challenges of disentangling signals of ancient hybridization from other sources of genomic conflict (in particular, incomplete lineage sorting). Here, we provide a critical review of ancient hybridization in vascular plants, outlining well-documented cases of ancient hybridization across plant phylogeny, as well as the challenges unique to documenting ancient versus recent hybridization. We provide a definition for ancient hybridization, which, to our knowledge, has not been explicitly attempted before. Further documenting the extent of deep reticulation in plants should remain an important research focus, especially because published examples likely represent the tip of the iceberg in terms of the total extent of ancient hybridization. However, future research should increasingly explore the macroevolutionary significance of this process, in terms of its impact on evolutionary trajectories (e.g. how does hybridization influence trait evolution or the generation of biodiversity over long time scales?), as well as how life history and ecological factors shape, or have shaped, the frequency of hybridization across geologic time and plant phylogeny. Finally, we consider the implications of ubiquitous ancient hybridization for how we conceptualize, analyze, and classify plant phylogeny. Networks, as opposed to bifurcating trees, represent more accurate representations of evolutionary history in many cases, although our ability to infer, visualize, and use networks for comparative analyses is highly limited. Developing improved methods for the generation, visualization, and use of networks represents a critical future direction for plant biology. Current classification systems also do not generally allow for the recognition of reticulate lineages, and our classifications themselves are largely based on evidence from the chloroplast genome. Updating plant classification to better reflect nuclear phylogenies, as well as considering whether and how to recognize hybridization in classification systems, will represent an important challenge for the plant systematics community.
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Affiliation(s)
- Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | - Kasey K Pham
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
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21
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Chen W, Wan H, Liu F, Du H, Zhang C, Fan W, Zhu A. Rapid evolution of T2/S-RNase genes in Fragaria linked to multiple transitions from self-incompatibility to self-compatibility. PLANT DIVERSITY 2023; 45:219-228. [PMID: 37069931 PMCID: PMC10105083 DOI: 10.1016/j.pld.2022.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 04/23/2022] [Indexed: 06/18/2023]
Abstract
The T2/RNase gene family is widespread in eukaryotes, and particular members of this family play critical roles in the gametophytic self-incompatibility (GSI) system in plants. Wild diploid strawberry (Fragaria) species have diversified their sexual systems via self-incompatible and self-compatible traits, yet how these traits evolved in Fragaria remains elusive. By integrating the published and de novo assembled genomes and the newly generated RNA-seq data, members of the RNase T2 gene family were systematically identified in six Fragaria species, including three self-incompatible species (Fragaria nipponica, Fragaria nubicola, and Fragaria viridis) and three self-compatible species (Fragaria nilgerrensis, Fragaria vesca, and Fragaria iinumae). In total, 115 RNase T2 genes were identified in the six Fragaria genomes and can be classified into three classes (I-III) according to phylogenetic analysis. The identified RNase T2 genes could be divided into 22 homologous gene sets according to amino acid sequence similarity and phylogenetic and syntenic relationships. We found that extensive gene loss and pseudogenization coupled with small-scale duplications mainly accounted for variations in the RNase T2 gene numbers in Fragaria. Multiple copies of homologous genes were mainly generated from tandem and segmental duplication events. Furthermore, we newly identified five S-RNase genes in three self-incompatible Fragaria genomes, including two in F. nipponica, two in F. viridis, and one in F. nubicola, which fit for typical features of a pistil determinant, including highly pistil-specific expression, highly polymorphic proteins and alkaline isoelectric point (pI), while no S-RNase genes were found in all three self-compatible Fragaria species. Surprisingly, these T2/S-RNase genes contain at least one large intron (>10 kb). This study revealed that the rapid evolution of T2/S-RNase genes within the Fragaria genus could be associated with its sexual mode, and repeated evolution of the self-compatible traits in Fragaria was convergent via losses of S-RNase.
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Affiliation(s)
- Wu Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Wan
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan 650205, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Haiyuan Du
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengjun Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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22
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Song Y, Li C, Liu L, Hu P, Li G, Zhao X, Zhou H. The population genomic analyses of chloroplast genomes shed new insights on the complicated ploidy and evolutionary history in Fragaria. FRONTIERS IN PLANT SCIENCE 2023; 13:1065218. [PMID: 36874917 PMCID: PMC9975502 DOI: 10.3389/fpls.2022.1065218] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/30/2022] [Indexed: 06/18/2023]
Abstract
The genus Fragaria consists of a rich diversity of ploidy levels with diploid (2x), tetraploid (4x), pentaploid (5x), hexaploidy (6x), octoploid (8x) and decaploid (10x) species. Only a few studies have explored the origin of diploid and octoploid strawberry, and little is known about the roles of tetraploidy and hexaploidy during the evolution of octoploid strawberry. The chloroplast genome is usually a stable circular genome and is widely used in investigating the evolution and matrilineal identification. Here, we assembled the chloroplast genomes of F. x ananassa cv. 'Benihoppe' (8x) using Illumina and HiFi data seperately. The genome alignment results showed that more InDels were located in the chloroplast genomes based on the PacBio HiFi data than Illumina data. We obtain highly accurate chloroplast genomes assembled through GetOrganelle using Illumina reads. We assembled 200 chloroplast genomes including 198 Fragaria (21 species) and 2 Potentilla samples. Analyses of sequence variation, phylogenetic and PCA analyses showed that Fragaria was divided into five groups. F. iinumae, F. nilgerrensis and all octoploid accessions formed Group A, C and E separately. Species native to western China were clustered into Group B. Group D consisted of F. virdis, F. orientalis, F. moschata, and F. vesca. STRUCTURE and haplotype network confirmed that the diploid F. vesca subsp. bracteata was the last maternal donator of octoploid strawberry. The dN/dS ratio estimated for the protein-coding genes revealed that genes involved in ATP synthase and photosystem function were under positive selection. These findings demonstrate the phylogeny of totally 21 Fragaria species and the origin of octoploid species. F. vesca was the last female donator of octoploid, which confirms the hypothesis that the hexaploid species F. moschata may be an evolutionary intermediate between the diploids and wild octoploid species.
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Affiliation(s)
- Yanhong Song
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Chaochao Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Lifeng Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Panpan Hu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Gang Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Xia Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Houcheng Zhou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
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23
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Gui S, Martinez-Rivas FJ, Wen W, Meng M, Yan J, Usadel B, Fernie AR. Going broad and deep: sequencing-driven insights into plant physiology, evolution, and crop domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:446-459. [PMID: 36534120 DOI: 10.1111/tpj.16070] [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: 10/26/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Deep sequencing is a term that has become embedded in the plant genomic literature in recent years and with good reason. A torrent of (largely) high-quality genomic and transcriptomic data has been collected and most of this has been publicly released. Indeed, almost 1000 plant genomes have been reported (www.plabipd.de) and the 2000 Plant Transcriptomes Project has long been completed. The EarthBioGenome project will dwarf even these milestones. That said, massive progress in understanding plant physiology, evolution, and crop domestication has been made by sequencing broadly (across a species) as well as deeply (within a single individual). We will outline the current state of the art in genome and transcriptome sequencing before we briefly review the most visible of these broad approaches, namely genome-wide association and transcriptome-wide association studies, as well as the compilation of pangenomes. This will include both (i) the most commonly used methods reliant on single nucleotide polymorphisms and short InDels and (ii) more recent examples which consider structural variants. We will subsequently present case studies exemplifying how their application has brought insight into either plant physiology or evolution and crop domestication. Finally, we will provide conclusions and an outlook as to the perspective for the extension of such approaches to different species, tissues, and biological processes.
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Affiliation(s)
- Songtao Gui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Weiwei Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Minghui Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Björn Usadel
- IBG-4 Bioinformatics, Forschungszentrum Jülich, Wilhelm Johnen Str, BioSc, 52428, Jülich, Germany
- Institute for Biological Data Science, CEPLAS, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
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24
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Wu R, Lin X, He J, Min A, Pang L, Wang Y, Lin Y, Zhang Y, He W, Li M, Zhang Y, Luo Y, Wang X, Tang H, Chen Q. Hexokinase1: A glucose sensor involved in drought stress response and sugar metabolism depending on its kinase activity in strawberry. FRONTIERS IN PLANT SCIENCE 2023; 14:1069830. [PMID: 36778691 PMCID: PMC9911861 DOI: 10.3389/fpls.2023.1069830] [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: 10/14/2022] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
Hexokinase1 (HXK1) is a bifunctional enzyme that plays indispensable roles in plant growth, nitrogen utilization, and stress resistance. However, information on the HXK family members of strawberries and their functions in glucose sensing and metabolic regulation is scarce. In the present study, four HXKs were firstly identified in the genome of Fragaria vesca and F. pentaphylla. The conserved domains of the HXK1s were confirmed, and a site-directed mutation (S177A) was introduced into the FpHXK1. FpHXK1, which shares the highest identity with the AtHXK1 was able to restore the glucose sensitivity and developmental defects of the Arabidopsis gin2-1 mutant, but not its kinase-activity-impaired mutant (FpHXK1S177A ). The transcription of FpHXK1 was dramatically up-regulated under PEG-simulated drought stress conditions. The inhibition of the HXK kinase activity delayed the strawberry plant's responses to drought stress. Transient overexpression of the FpHXK1 and its kinase-impaired mutant differentially affected the level of glucose, sucrose, anthocyanins, and total phenols in strawberry fruits. All these results indicated that the FpHXK1, acting as a glucose sensor, was involved in drought stress response and sugar metabolism depending on its kinase activity.
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Affiliation(s)
- Runqin Wu
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ximeng Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jinwei He
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ailing Min
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Li Pang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yan Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuanxiu Lin
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yunting Zhang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Wen He
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaorong Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Haoru Tang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
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25
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Wang S, Qian YQ, Zhao RP, Chen LL, Song JM. Graph-based pan-genomes: increased opportunities in plant genomics. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:24-39. [PMID: 36255144 DOI: 10.1093/jxb/erac412] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Due to the development of sequencing technology and the great reduction in sequencing costs, an increasing number of plant genomes have been assembled, and numerous genomes have revealed large amounts of variations. However, a single reference genome does not allow the exploration of species diversity, and therefore the concept of pan-genome was developed. A pan-genome is a collection of all sequences available for a species, including a large number of consensus sequences, large structural variations, and small variations including single nucleotide polymorphisms and insertions/deletions. A simple linear pan-genome does not allow these structural variations to be intuitively characterized, so graph-based pan-genomes have been developed. These pan-genomes store sequence and structural variation information in the form of nodes and paths to store and display species variation information in a more intuitive manner. The key role of graph-based pan-genomes is to expand the coordinate system of the linear reference genome to accommodate more regions of genetic diversity. Here, we review the origin and development of graph-based pan-genomes, explore their application in plant research, and further highlight the application of graph-based pan-genomes for future plant breeding.
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Affiliation(s)
- Shuo Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yong-Qing Qian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Ru-Peng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Jia-Ming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
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26
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Cao Q, Huang L, Li J, Qu P, Tao P, Crabbe MJC, Zhang T, Qiao Q. Integrated transcriptome and methylome analyses reveal the molecular regulation of drought stress in wild strawberry (Fragaria nilgerrensis). BMC PLANT BIOLOGY 2022; 22:613. [PMID: 36575384 PMCID: PMC9795625 DOI: 10.1186/s12870-022-04006-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Fragaria nilgerrensis, which is a diploid wild strawberry with excellent drought-resistance, would provide useful candidate genes for improving drought resistance of cultivated strawberry. So far, its molecular regulatory networks involved in drought stress are unclear. We therefore investigated the drought response regulatory networks of F. nilgerrensis based on the integrated analysis of DNA methylation, transcriptome and physiological traits during four time points under drought stress. RESULTS: The most differentially expressed genes and the physiological changes were found at 8 days (T8) compared with 0 day (T0, control). Methylome analysis revealed slight dynamic changes in genome-wide mC levels under drought conditions, while the most hypomethylated and hypermethylated regions were identified at T4 and T8. Association analysis of the methylome and transcriptome revealed that unexpressed genes exhibited expected hypermethylation levels in mCHG and mCHH contexts, and highly expressed genes exhibited corresponding hypomethylation levels in the gene body, but mCG contexts showed the opposite trend. Then, 835 differentially methylated and expressed genes were identified and grouped into four clustering patterns to characterize their functions. The genes with either negative or positive correlation between methylation and gene expression were mainly associated with kinases, Reactive Oxygen Species (ROS) synthesis, scavenging, and the abscisic acid (ABA) signal pathway. Consistently, weighted gene co-expression network analysis (WGCNA) revealed Hub genes including NCED, CYP707A2, PP2Cs and others that play important roles in the ABA signaling pathway. CONCLUSION F. nilgerrensis drought is dominated by ABA-dependent pathways, possibly accompanied by ABA-independent crosstalk. DNA methylation may affect gene expression, but their correlation was more subtle and multiple types of association exist. Maintaining the balance between ROS regeneration and scavenging is an important factor in drought resistance in F. nilgerrensis. These results deepen our understanding of drought resistance and its application in breeding in strawberry plants.
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Affiliation(s)
- Qiang Cao
- School of Agriculture, Yunnan University, 650091, Kunming, China
| | - Lin Huang
- School of Agriculture, Yunnan University, 650091, Kunming, China
| | - Jiamin Li
- School of Agriculture, Yunnan University, 650091, Kunming, China
| | - Peng Qu
- School of Agriculture, Yunnan University, 650091, Kunming, China
| | - Pang Tao
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, 650205, Kunming, China
| | - M James C Crabbe
- Wolfson College, Oxford University, Oxford, OX26UD, UK
- Institute of Biomedical and Environmental Science and Technology, School of Life Sciences, University of Bedfordshire, Park Square, LU1 3JU, Luton, UK
- School of Life Science, Shanxi University, 030006, Taiyuan, Shanxi, China
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, 650500, Kunming, China.
| | - Qin Qiao
- College of Horticulture and Landscape, Yunnan Agricultural University, 650201, Kunming, China.
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27
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Liang L, Zhang J, Xiao J, Li X, Xie Y, Tan H, Song X, Zhu L, Xue X, Xu L, Zhou P, Ran J, Sun B, Huang Z, Tang Y, Lin L, Sun G, Lai Y, Li H. Genome and pan-genome assembly of asparagus bean ( Vigna unguiculata ssp. sesquipedialis) reveal the genetic basis of cold adaptation. FRONTIERS IN PLANT SCIENCE 2022; 13:1059804. [PMID: 36589110 PMCID: PMC9802904 DOI: 10.3389/fpls.2022.1059804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Asparagus bean (Vigna unguiculata ssp. sesquipedialis) is an important cowpea subspecies. We assembled the genomes of Ningjiang 3 (NJ, 550.31 Mb) and Dubai bean (DB, 564.12 Mb) for comparative genomics analysis. The whole-genome duplication events of DB and NJ occurred at 64.55 and 64.81 Mya, respectively, while the divergence between soybean and Vigna occurred in the Paleogene period. NJ genes underwent positive selection and amplification in response to temperature and abiotic stress. In species-specific gene families, NJ is mainly enriched in response to abiotic stress, while DB is primarily enriched in respiration and photosynthesis. We established the pan-genomes of four accessions (NJ, DB, IT97K-499-35 and Xiabao II) and identified 20,336 (70.5%) core genes present in all the accessions, 6,507 (55.56%) variable genes in two individuals, and 2,004 (6.95%) unique genes. The final pan genome is 616.35 Mb, and the core genome is 399.78 Mb. The variable genes are manifested mainly in stress response functions, ABC transporters, seed storage, and dormancy control. In the pan-genome sequence variation analysis, genes affected by presence/absence variants were enriched in biological processes associated with defense responses, immune system processes, signal transduction, and agronomic traits. The results of the present study provide genetic data that could facilitate efficient asparagus bean genetic improvement, especially in producing cold-adapted asparagus bean.
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Affiliation(s)
- Le Liang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jianwei Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jiachang Xiao
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaomei Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan, Chengdu, China
| | - Yongdong Xie
- Institute for Processing and Storage of Agricultural Products, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China
| | - Huaqiang Tan
- Horticulture Research Institute, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China
| | - Xueping Song
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Li Zhu
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinru Xue
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Linyu Xu
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peihan Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jianzhao Ran
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhi Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yi Tang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lijin Lin
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guochao Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yunsun Lai
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Huanxiu Li
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
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28
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Wu L, Xu H, Jian S, Gong X, Feng X. Geographic factors and climatic fluctuation drive the genetic structure and demographic history of
Cycas taiwaniana
(Cycadaceae), an endemic endangered species to Hainan Island in China. Ecol Evol 2022; 12:e9508. [DOI: 10.1002/ece3.9508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- Li‐Xin Wu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany Chinese Academy of Sciences Kunming China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany Chinese Academy of Sciences Kunming China
- University of Chinese Academy of Science Beijing China
- Plant Science Institute, School of Life Sciences Yunnan University Kunming China
| | - Hai‐Yan Xu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany Chinese Academy of Sciences Kunming China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany Chinese Academy of Sciences Kunming China
- University of Chinese Academy of Science Beijing China
| | - Shu‐Guang Jian
- CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Xun Gong
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Xiu‐Yan Feng
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany Chinese Academy of Sciences Kunming China
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Fan W, Liu F, Jia Q, Du H, Chen W, Ruan J, Lei J, Li DZ, Mower JP, Zhu A. Fragaria mitogenomes evolve rapidly in structure but slowly in sequence and incur frequent multinucleotide mutations mediated by microinversions. THE NEW PHYTOLOGIST 2022; 236:745-759. [PMID: 35731093 DOI: 10.1111/nph.18334] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Plant mitochondrial DNA has been described as evolving rapidly in structure but slowly in sequence. However, many of the noncoding portions of plant mitogenomes are not homologous among species, raising questions about the rate and spectrum of mutations in noncoding regions. Recent studies have suggested that the lack of homology in noncoding regions could be due to increased sequence divergence. We compared 30 kb of coding and 200 kb of noncoding DNA from 13 sequenced Fragaria mitogenomes, followed by analysis of the rate of sequence divergence, microinversion events and structural variations. Substitution rates in synonymous sites and nongenic sites are nearly identical, suggesting that the genome-wide point mutation rate is generally consistent. A surprisingly high number of large multinucleotide substitutions were detected in Fragaria mitogenomes, which may have resulted from microinversion events and could affect phylogenetic signal and local rate estimates. Fragaria mitogenomes preferentially accumulate deletions relative to insertions and substantial genomic arrangements, whereas mutation rates could positively associate with these sequence and structural changes among species. Together, these observations suggest that plant mitogenomes exhibit low point mutations genome-wide but exceptionally high structural variations, and our results favour a gain-and-loss model for the rapid loss of homology among plant mitogenomes.
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Affiliation(s)
- Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiaoya Jia
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, China
| | - Haiyuan Du
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wu Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiwei Ruan
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Jiajun Lei
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
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30
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Sun R, Li S, Chang L, Dong J, Zhong C, Zhang H, Wei L, Gao Y, Wang G, Zhang Y, Sun J. Chromosome-level genome assembly of Fragaria pentaphylla using PacBio and Hi-C technologies. Front Genet 2022; 13:873711. [PMID: 36147512 PMCID: PMC9485601 DOI: 10.3389/fgene.2022.873711] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/12/2022] [Indexed: 11/18/2022] Open
Abstract
Fragaria pentaphylla, a wild diploid quinquefoliolate species of Fragaria, is native to Southwest China. It has two morphs of red and white fruit color in nature and has characteristics of unique fragrance and resistance, which made it not only a valuable breeding material but also a potential model plant for molecular function researches. Here, we generate a high-quality chromosome-level genome assembly of a F. pentaphylla accession, BAAFS-FP039 employing a combination of PacBio Long-Read Sequencing, Illumina Short-Read Sequencing, and Hi-C Sequencing. The assembled genome contained 256.74 Mb and a contig N50 length of 32.38 Mb, accounting for 99.9% of the estimated genome (256.77 Mb). Based on Hi-C data, seven pseudo-chromosomes of F. pentaphylla-FP039 genome were assembled, covering 99.39% of the genome assembly. The genome was composed of 44.61% repetitive sequences and 29,623 protein-coding genes, 97.62% of protein-coding genes could be functionally annotated. Phylogenetic and chromosome syntenic analysis revealed that F. pentaphylla-FP039 was closely related to F. nubicola. This high-quality genome could provides fundamental molecular resources for evolutionary studies, breeding efforts, and exploring the unique biological characteristics of F. pentaphylla.
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Affiliation(s)
- Rui Sun
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Shuangtao Li
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Linlin Chang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Jing Dong
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Chuanfei Zhong
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Hongli Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Lingzhi Wei
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Yongshun Gao
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Guixia Wang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- *Correspondence: Guixia Wang, ; Yuntao Zhang, ; Jian Sun,
| | - Yuntao Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- *Correspondence: Guixia Wang, ; Yuntao Zhang, ; Jian Sun,
| | - Jian Sun
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- *Correspondence: Guixia Wang, ; Yuntao Zhang, ; Jian Sun,
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Senger E, Osorio S, Olbricht K, Shaw P, Denoyes B, Davik J, Predieri S, Karhu S, Raubach S, Lippi N, Höfer M, Cockerton H, Pradal C, Kafkas E, Litthauer S, Amaya I, Usadel B, Mezzetti B. Towards smart and sustainable development of modern berry cultivars in Europe. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1238-1251. [PMID: 35751152 DOI: 10.1111/tpj.15876] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Fresh berries are a popular and important component of the human diet. The demand for high-quality berries and sustainable production methods is increasing globally, challenging breeders to develop modern berry cultivars that fulfill all desired characteristics. Since 1994, research projects have characterized genetic resources, developed modern tools for high-throughput screening, and published data in publicly available repositories. However, the key findings of different disciplines are rarely linked together, and only a limited range of traits and genotypes has been investigated. The Horizon2020 project BreedingValue will address these challenges by studying a broader panel of strawberry, raspberry and blueberry genotypes in detail, in order to recover the lost genetic diversity that has limited the aroma and flavor intensity of recent cultivars. We will combine metabolic analysis with sensory panel tests and surveys to identify the key components of taste, flavor and aroma in berries across Europe, leading to a high-resolution map of quality requirements for future berry cultivars. Traits linked to berry yields and the effect of environmental stress will be investigated using modern image analysis methods and modeling. We will also use genetic analysis to determine the genetic basis of complex traits for the development and optimization of modern breeding technologies, such as molecular marker arrays, genomic selection and genome-wide association studies. Finally, the results, raw data and metadata will be made publicly available on the open platform Germinate in order to meet FAIR data principles and provide the basis for sustainable research in the future.
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Affiliation(s)
- Elisa Senger
- Institute of Bio- and Geosciences, IBG-4 Bioinformatics, BioSC, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
| | - Sonia Osorio
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, Málaga, Spain
| | | | - Paul Shaw
- Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Scotland, UK
| | - Béatrice Denoyes
- Université de Bordeaux, UMR BFP, INRAE, Villenave d'Ornon, France
| | - Jahn Davik
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Stefano Predieri
- Bio-Agrofood Department, Institute for Bioeconomy, IBE-CNR, Italian National Research Council, Bologna, Italy
| | - Saila Karhu
- Natural Resources Institute Finland (Luke), Turku, Finland
| | - Sebastian Raubach
- Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Scotland, UK
| | - Nico Lippi
- Bio-Agrofood Department, Institute for Bioeconomy, IBE-CNR, Italian National Research Council, Bologna, Italy
| | - Monika Höfer
- Institute of Breeding Research on Fruit Crops, Federal Research Centre for Cultivated Plants (JKI), Dresden, Germany
| | - Helen Cockerton
- Genetics, Genomics and Breeding Department, NIAB, East Malling, UK
| | - Christophe Pradal
- CIRAD and UMR AGAP Institute, Montpellier, France
- INRIA and LIRMM, University Montpellier, CNRS, Montpellier, France
| | - Ebru Kafkas
- Department of Horticulture, Faculty of Agriculture, Çukurova University, Balcalı, Adana, Turkey
| | | | - Iraida Amaya
- Unidad Asociada deI + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain
- Laboratorio de Genómica y Biotecnología, Centro IFAPA de Málaga, Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Málaga, Spain
| | - Björn Usadel
- Institute of Bio- and Geosciences, IBG-4 Bioinformatics, BioSC, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Data Science, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Bruno Mezzetti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
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Sun M, Zhang M, Chen X, Liu Y, Liu B, Li J, Wang R, Zhao K, Wu J. Rearrangement and domestication as drivers of Rosaceae mitogenome plasticity. BMC Biol 2022; 20:181. [PMID: 35986276 PMCID: PMC9392253 DOI: 10.1186/s12915-022-01383-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/04/2022] [Indexed: 11/10/2022] Open
Abstract
Background The mitochondrion is an important cellular component in plants and that functions in producing vital energy for the cell. However, the evolution and structure of mitochondrial genomes (mitogenomes) remain unclear in the Rosaceae family. In this study, we assembled 34 Rosaceae mitogenomes and characterized genome variation, rearrangement rate, and selection signal variation within these mitogenomes. Results Comparative analysis of six genera from the Amygdaloideae and five from the Rosoideae subfamilies of Rosaceae revealed that three protein-coding genes were absent from the mitogenomes of five Rosoideae genera. Positive correlations between genome size and repeat content were identified in 38 Rosaceae mitogenomes. Twenty repeats with high recombination frequency (> 50%) provided evidence for predominant substoichiometric conformation of the mitogenomes. Variations in rearrangement rates were identified between eleven genera, and within the Pyrus, Malus, Prunus, and Fragaria genera. Based on population data, phylogenetic inferences from Pyrus mitogenomes supported two distinct maternal lineages of Asian cultivated pears. A Pyrus-specific deletion (DEL-D) in selective sweeps was identified based on the assembled genomes and population data. After the DEL-D sequence fragments originally arose, they may have experienced a subsequent doubling event via homologous recombination and sequence transfer in the Amygdaloideae; afterwards, this variant sequence may have significantly expanded to cultivated groups, thereby improving adaptation during the domestication process. Conclusions This study characterizes the variations in gene content, genome size, rearrangement rate, and the impact of domestication in Rosaceae mitogenomes and provides insights into their structural variation patterns and phylogenetic relationships. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01383-3.
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Li W, Liu J, Zhang H, Liu Z, Wang Y, Xing L, He Q, Du H. Plant pan-genomics: recent advances, new challenges, and roads ahead. J Genet Genomics 2022; 49:833-846. [PMID: 35750315 DOI: 10.1016/j.jgg.2022.06.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 10/18/2022]
Abstract
Pan-genomics can encompass most of the genetic diversity of a species or population and has proved to be a powerful tool for studying genomic evolution and the origin and domestication of species, and for providing information for plant improvement. Plant genomics has greatly progressed because of improvements in sequencing technologies and the rapid reduction of sequencing costs. Nevertheless, pan-genomics still presents many challenges, including computationally intensive assembly methods, high costs with large numbers of samples, ineffective integration of big data, and difficulty in applying it to downstream multi-omics analysis and breeding research. In this review, we summarize the definition and recent achievements of plant pan-genomics, computational technologies used for pan-genome construction, and the applications of pan-genomes in plant genomics and molecular breeding. We also discuss challenges and perspectives for future pan-genomics studies and provide a detailed pipeline for sample selection, genome assembly and annotation, structural variation identification, and construction and application of graph-based pan-genomes. The aim is to provide important guidance for plant pan-genome research and a better understanding of the genetic basis of genome evolution, crop domestication, and phenotypic diversity for future studies.
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Affiliation(s)
- Wei Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Jianan Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Hongyu Zhang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Ze Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Yu Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Longsheng Xing
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Qiang He
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Huilong Du
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China.
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Zheng D, Zhang W. Characterization of Expression and Epigenetic Features of Core Genes in Common Wheat. Genes (Basel) 2022; 13:genes13071112. [PMID: 35885895 PMCID: PMC9317296 DOI: 10.3390/genes13071112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 12/10/2022] Open
Abstract
The availability of multiple wheat genome sequences enables us to identify core genes and characterize their genetic and epigenetic features, thereby advancing our understanding of their biological implications within individual plant species. It is, however, largely understudied in wheat. To this end, we reanalyzed genome sequences from 16 different wheat varieties and identified 62,299 core genes. We found that core and non-core genes have different roles in subgenome differentiation. Meanwhile, according to their expression profiles, these core genes can be classified into genes related to tissue development and stress responses, including 3376 genes highly expressed in both spikelets and at high temperatures. After associating with six histone marks and open chromatin, we found that these core genes can be divided into eight sub-clusters with distinct epigenomic features. Furthermore, we found that ca. 51% of the expressed transcription factors (TFs) were marked with both H3K27me3 and H3K4me3, indicative of the bivalency feature, which can be involved in tissue development through the TF-centered regulatory network. Thus, our study provides a valuable resource for the functional characterization of core genes in stress responses and tissue development in wheat.
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Unraveling NPR-like Family Genes in Fragaria spp. Facilitated to Identify Putative NPR1 and NPR3/4 Orthologues Participating in Strawberry-Colletotrichum fructicola Interaction. PLANTS 2022; 11:plants11121589. [PMID: 35736739 PMCID: PMC9229442 DOI: 10.3390/plants11121589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022]
Abstract
The salicylic acid receptor NPR1 (nonexpressor of pathogenesis-related genes) and its paralogues NPR3 and NPR4 are master regulators of plant immunity. Commercial strawberry (Fragaria × ananassa) is a highly valued crop vulnerable to various pathogens. Historic confusions regarding the identity of NPR-like genes have hindered research in strawberry resistance. In this study, the comprehensive identification and phylogenic analysis unraveled this family, harboring 6, 6, 5, and 23 members in F. vesca, F. viridis, F. iinumae, and F. × ananassa, respectively. These genes were clustered into three clades, with each diploid member matching three to five homoalleles in F. × ananassa. Despite the high conservation in terms of gene structure, protein module, and functional residues/motifs/domains, substantial divergence was observed, hinting strawberry NPR proteins probably function in ways somewhat different from Arabidopsis. RT-PCR and RNAseq analysis evidenced the transcriptional responses of FveNPR1 and FxaNPR1a to Colletotrichum fructicola. Extended expression analysis for strawberry NPR-likes helped to us understand how strawberry orchestrate the NPRs-centered defense system against C. fructicola. The cThe current work supports that FveNPR1 and FxaNPR1a, as well as FveNPR31 and FxaNPR31a-c, were putative functional orthologues of AtNPR1 and AtNPR3/4, respectively. These findings set a solid basis for the molecular dissection of biological functions of strawberry NPR-like genes for improving disease resistance.
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Cao Q, Feng Y, Dai X, Huang L, Li J, Tao P, Crabbe MJC, Zhang T, Qiao Q. Dynamic Changes of DNA Methylation During Wild Strawberry ( Fragaria nilgerrensis) Tissue Culture. FRONTIERS IN PLANT SCIENCE 2021; 12:765383. [PMID: 34917103 PMCID: PMC8669611 DOI: 10.3389/fpls.2021.765383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
Tissue culture is an important tool for asexual propagation and genetic transformation of strawberry plants. In plant tissue culture, variation of DNA methylation is a potential source of phenotypic variation in regenerated plants. However, the genome wide dynamic methylation patterns of strawberry tissue culture remain unclear. In this study, we used whole-genome bisulfite sequencing (WGBS) to study genomic DNA methylation changes of a wild strawberry Fragaria nilgerrensis at six stages: from explants of shoot tips to outplanting and acclimation. Global methylation levels showed that CG sites exhibited the highest methylation level in all stages with an average of 49.5%, followed by CHG (33.2%) and CHH (12.4%). Although CHH accounted for the lowest proportion of total cytosine methylation, it showed the most obvious methylation change and the most of these changes occurred in the transposable element regions. The overall methylation levels alternately decreased and increased during the entire tissue culture process and the distribution of DNA methylation was non-uniform among different genetic regions. Furthermore, much more differentially methylated regions (DMRs) were detected in dedifferentiation and redifferentiation stages and most of them were transposable elements, suggesting these processes involved activating or silencing of amounts of transposons. The functional enrichment of the DMR-related genes indicated that genes involved in hormone metabolic processes, plant development and the stress response changed methylation throughout the tissue culture process. Finally, the quantitative real-time PCR (qRT-PCR) was conducted to examine the association of methylation and gene expression of a set of different methylated genes. Our findings give deeper insight into the epigenetic regulation of gene expression during the plant tissue cultures process, which will be useful in the efficient control of somaclonal variations and in crop improvement.
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Affiliation(s)
- Qiang Cao
- School of Agriculture, Yunnan University, Kunming, China
| | - Yuxi Feng
- School of Agriculture, Yunnan University, Kunming, China
| | - Xiongwei Dai
- School of Agriculture, Yunnan University, Kunming, China
| | - Lin Huang
- School of Agriculture, Yunnan University, Kunming, China
| | - Jiamin Li
- School of Agriculture, Yunnan University, Kunming, China
| | - Pang Tao
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - M. James C. Crabbe
- Wolfson College, Oxford University, Oxford, United Kingdom
- Institute of Biomedical and Environmental Science and Technology, School of Life Sciences, University of Bedfordshire, Luton, United Kingdom
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Qin Qiao
- School of Agriculture, Yunnan University, Kunming, China
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