Genomic variation mapping and detection of novel genes based on genome-wide survey of an elite upland cotton hybrid (Gossypium hirsutum L.)

文献类型： 外文期刊

第一作者： Zhenyu Wang;;Wei Li

作者： Zhenyu Wang;Wei Li;Guanghui Xiao;Xiaojian Zhou;Xiaoyu Pei;Yangai Liu;Kehai Zhou;Kunlun He;Junfang Liu;Ying Li;Wensheng Zhang;Zhongying Ren;Qingqin Meng;Haifeng Wang;Xiongfeng Ma;Daigang Yang

作者机构：

关键词： Cotton hybrid; genomic variation map; mutational hotspots; novel genes

期刊名称：CURRENT SCIENCE （ 影响因子：1.102； 五年影响因子：1.163 ）

ISSN： 0011-3891

年卷期： 2018 年 115 卷 4 期

页码：

收录情况： SCI

摘要： CCRI63, with the largest cultivated area among hybrids in China, is a successful promotion of elite upland cotton (Gossypium hirsutum L.) hybrid cultivar. We have constructed a detailed genomic variation map of CCRI63 by aligning whole-genome shotgun sequencing reads from CCRI63 to the TM-1 reference genome. Genomic single nucleotide polymorphism (SNP) and insertion-deletion (Indel) mutational hotspots were identified, most of which were located on chromosome D02, and associated with disease resistance and lipid glycosylation and modification. The density of heterozygous SNP sites showed 73 quantitative trait loci overlapped with peak intervals of high-density heterozygous SNPs, suggesting that the heterozygous sites in the peak are important for improvement of CCRI63 yield and fibre quality. To avoid loss of genetic components, unmapped reads were used for de novo assembly of the missing regions in the reference genome, and 153 novel functional genes were obtained. The large-scale genetic variation and novel functional genes identified in the CCRI63 genome can facilitate future gene-phenotype studies and provide an additional resource for the improvement of cotton.

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