Resequencing of cv CRI‐12 family reveals haplotype block inheritance and recombination of agronomically important genes in artificial selection

First author: Xuke Lu; Affiliations: Institute of Cotton Research of Chinese Academy of Agricultural Sciences (中国农业科学院棉花研究所): Anyang, China

Corresponding author: Wuwei Ye (叶武威)

Although efforts have been taken to exploit diversity for yield and quality improvements, limited progress on using beneficial alleles (有益等位基因) in domesticated and undomesticated cotton varieties is limited. Given the complexity and limited amount of genomic information since the completion of four cotton genomes, characterizing significant variations and haplotype block (单倍型域) inheritance under artificial selection has been challenging. Here we sequenced G. hirsutum L. cv CRI‐12 (the cotton variety with the largest acreage 面积 in China), its parental cultivars, and progeny cultivars, which were bred by the different institutes in China. In total, 3.3 million SNPs were identified and 118, 126 and 176 genes were remarkably correlated with Verticillium wilt (黄萎病), salinity and drought tolerance in CRI‐12, respectively. Transcriptome‐wide analyses of gene expression, and functional annotations, have provided support for the identification of genes tied to these tolerances. We totally discovered 58,116 haplotype blocks, among which 23,752 may be inherited and 1,029 may be recombined under artificial selection. This survey of genetic diversity identified loci that may have been subject to artificial selection and documented the haplotype block inheritance and recombination, shedding light on the genetic mechanism of artificial selection and guiding breeding efforts for the genetic improvement of cotton.

尽管已经有很多的研究探索了棉花的产量和质量改良，然而直接在驯化或者非驯化棉花品种改良过程中利用有益等位基因还很少。自从四个棉花基因组的测序完成以来，有关棉花的基因组信息还不够丰富，因此研究人工选择条件下的遗传变异和单倍型域遗传十分困难。本文中，作者对在中国具有最大栽培面积的棉花品种CRI‐12进行了测序，包括其亲本栽培种和子代栽培种，这些品种由不同的中国研究单位所研制。总的来说，作者共鉴定了三百三十万个SNP，并且鉴定了118个、126个和176个基因分别与CRI‐12的黄萎病、抗盐和抗干旱胁迫显著相关。转录组的基因表达分析及功能注释进一步诠释了这些抗性相关基因的功能。作者还鉴定了58116个单倍型域，其中23752个单倍型域可能是可遗传的，还有1029个单倍型域在人工选择条件下会发生重组。本文的研究鉴定了人工选择条件下的遗传多样性位点，梳理了单倍型域的遗传和重组信息，有助于人工选择遗传机理的研究，同时也为将来棉花的遗传改良提供遗传基础。

p.s. 中棉所12是以乌干达4号为母本与邢台6871杂交，经枯黄萎病圃，钵中连续定向选择，多系混合而成，为抗病高产优质棉花新品种，于1990年获国家发明一等奖。（http://www.caas.net.cn/kxyj/kjjl/gjjcg/243420.html）

通讯：叶武威  (http://www.cricaas.com.cn/rcdw/ysx_20171117175551049077/index.htm)

研究方向：棉花种质鉴定、创新利用与棉花资源生物多样性研究；抗性种质资源细胞遗传、分子遗传研究和抗性基因表达。

doi: https://doi.org/10.1111/pbi.13030

Journal: Plant Biotechnology Journal

First Published: 08 November, 2018

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