Cotton pedigree genome reveals restriction of cultivar-driven strategy in cotton breeding

文献类型： 外文期刊

第一作者： Liu, Shang

作者： Liu, Shang;Zuo, Dongyun;Cheng, Hailiang;He, Man;Wang, Qiaolian;Lv, Limin;Zhang, Youping;Liu, Ji;Song, Guoli;Liu, Shang;Zuo, Dongyun;Cheng, Hailiang;Wang, Qiaolian;Lv, Limin;Zhang, Youping;Song, Guoli;Ashraf, Javaria

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关键词： Cotton pedigree; Nanopore long read; Graphical genome; Cultivar-driven strategy

期刊名称：GENOME BIOLOGY （ 影响因子：12.3； 五年影响因子：17.4 ）

ISSN： 1474-760X

年卷期： 2023 年 24 卷 1 期

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收录情况： SCI

摘要： BackgroundMany elite genes have been identified from the available cotton genomic data, providing various genetic resources for gene-driven breeding. However, backbone cultivar-driven breeding is the most widely applied strategy. Revealing the genetic basis of cultivar-driven strategy's restriction is crucial for transition of cotton breeding strategy.ResultCRI12 is a backbone cultivar in cultivar-driven breeding. Here we sequence the pedigree of CRI12 using Nanopore long-read sequencing. We construct a graphical pedigree genome using the high-quality CRI12 genome and 13,138 structural variations within 20 different pedigree members. We find that low hereditary stability of elite segments in backbone cultivars is a drawback of cultivar-driven strategy. We also identify 623 functional segments in CRI12 for multiple agronomic traits in presence and absence variation-based genome-wide association study on three cohorts. We demonstrate that 25 deleterious segments are responsible for the geographical divergence of cotton in pathogen resistance. We also characterize an elite pathogen-resistant gene (GhKHCP) utilized in modern cotton breeding. In addition, we identify 386 pedigree fingerprint segments by comparing the segments of the CRI12 pedigree with those of a large cotton population.ConclusionWe characterize the genetic patterns of functional segments in the pedigree of CRI12 using graphical genome method, revealing restrictions of cultivar-driven strategies in cotton breeding. These findings provide theoretical support for transitioning from cultivar-driven to gene-driven strategy in cotton breeding.

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