The chromosome-level assembly of the wild diploid alfalfa genome provides insights into the full landscape of genomic variations between cultivated and wild alfalfa

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dc.contributor.authorShi, Kun
dc.contributor.authorDong, Hongbin
dc.contributor.authorDu, Huilong
dc.contributor.authorLi, Yuxian
dc.contributor.authorZhou, Le
dc.contributor.authorLiang, Chengzhi
dc.contributor.authorSakiroglu, Muhammet
dc.date.accessioned2025-01-06T17:36:12Z
dc.date.available2025-01-06T17:36:12Z
dc.date.issued2024
dc.description.abstractAlfalfa (Medicago sativa L.) is one of the most important forage legumes in the world, including autotetraploid (M. sativa ssp. sativa) and diploid alfalfa (M. sativa ssp. caerulea, progenitor of autotetraploid alfalfa). Here, we reported a high-quality genome of ZW0012 (diploid alfalfa, 769 Mb, contig N50 = 5.5 Mb), which was grouped into the Northern group in population structure analysis, suggesting that our genome assembly filled a major gap among the members of M. sativa complex. During polyploidization, large phenotypic differences occurred between diploids and tetraploids, and the genetic information underlying its massive phenotypic variations remains largely unexplored. Extensive structural variations (SVs) were identified between ZW0012 and XinJiangDaYe (an autotetraploid alfalfa with released genome). We identified 71 ZW0012-specific PAV genes and 1296 XinJiangDaYe-specific PAV genes, mainly involved in defence response, cell growth, and photosynthesis. We have verified the positive roles of MsNCR1 (a XinJiangDaYe-specific PAV gene) in nodulation using an Agrobacterium rhizobia-mediated transgenic method. We also demonstrated that MsSKIP23_1 and MsFBL23_1 (two XinJiangDaYe-specific PAV genes) regulated leaf size by transient overexpression and virus-induced gene silencing analysis. Our study provides a high-quality reference genome of an important diploid alfalfa germplasm and a valuable resource of variation landscape between diploid and autotetraploid, which will facilitate the functional gene discovery and molecular-based breeding for the cultivars in the future.
dc.description.sponsorshipChinese Universities Scientific Fund; National Natural Science Foundation of China [31761143013]; Beijing Municipal Natural Science Foundation [6212015, 2005DKA21003]; [2022RC025]
dc.description.sponsorshipThis research was supported by the National Natural Science Foundation of China (No. 31761143013), Beijing Municipal Natural Science Foundation (6212015), National Center for Forestry Grassland Genetic Resources (2005DKA21003), and Chinese Universities Scientific Fund (2022RC025). We thank Wen Wang and Haitao Chen for providing the sequenced plantlet and the sequencing data of XinJiangDaYe.
dc.identifier.doi10.1111/pbi.14300
dc.identifier.endpage1772
dc.identifier.issn1467-7644
dc.identifier.issn1467-7652
dc.identifier.issue6
dc.identifier.pmid38288521
dc.identifier.scopus2-s2.0-85183860107
dc.identifier.scopusqualityQ1
dc.identifier.startpage1757
dc.identifier.urihttps://doi.org/10.1111/pbi.14300
dc.identifier.urihttps://hdl.handle.net/20.500.14669/1803
dc.identifier.volume22
dc.identifier.wosWOS:001152127800001
dc.identifier.wosqualityN/A
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.language.isoen
dc.publisherWiley
dc.relation.ispartofPlant Biotechnology Journal
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.snmzKA_20241211
dc.subjectalfalfa
dc.subjectgenome assembly
dc.subjectstructural variants
dc.subjectnodule-specific cysteine-rich peptides
dc.subjectpopulation structure
dc.titleThe chromosome-level assembly of the wild diploid alfalfa genome provides insights into the full landscape of genomic variations between cultivated and wild alfalfa
dc.typeArticle

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