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

文献类型： 外文期刊

作者： Liu, Shang 1 ; Zuo, Dongyun 1 ; Cheng, Hailiang 1 ; He, Man 1 ; Wang, Qiaolian 1 ; Lv, Limin 1 ; Zhang, Youping 1 ; Ashraf, Javaria 3 ; Liu, Ji 1 ; Song, Guoli 1 ;

作者机构： 1.Chinese Acad Agr Sci, Inst Cotton Res, Anyang 455000, Peoples R China

2.Zhengzhou Univ, Zhengzhou Res Base, State Key Lab Cotton Biol, Zhengzhou 450001, Peoples R China

3.Islamia Univ Bahawalpur, Fac Agr & Environm, Dept Plant Breeding & Genet, Bahawalpur, Pakistan

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

页码：

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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