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Physical mapping and candidate gene prediction of fertility restorer gene of cytoplasmic male sterility in cotton

文献类型： 外文期刊

作者： Zhao, Cunpeng 1 ; Zhao, Guiyuan 1 ; Geng, Zhao 1 ; Wang, Zhaoxiao 1 ; Wang, Kaihui 1 ; Liu, Suen 1 ; Zhang, Hanshuang; 1 ;

作者机构： 1.Hebei Acad Agr & Forestry Sci, Minist Agr, Inst Cotton, Key Lab Biol & Genet Improvement Cotton Huanghuai, 598 Heping West, Shijiazhuang 050051, Hebei, Peoples R China

2.Hebei Acad

关键词： CMS;High-throughput sequencing;SLAF-seq;Super-BSA;Cotton

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2018 年 19 卷

页码：

收录情况： SCI

摘要： Background: Cytoplasmic male sterility (CMS) is a maternally inherited trait failing to produce functional pollen. It plays a pivotal role in the exploitation of crop heterosis. The specific locus amplified fragment sequencing (SLAF-seq) as a high-resolution strategy for the identification of new SNPs on a large-scale is gradually applied for functional gene mining. The current study combined the bulked segregant analysis (BSA) with SLAF-seq to identify the candidate genes associated with fertility restorer gene (Rf) in CMS cotton. Methods: Illumina sequencing systematically investigated the parents. A segregating population comprising of 30 + 30 F-2 individuals was developed using 3096A (female parent) as sterile and 866R (male parent) as a restorer. The original data obtained by dual-index sequencing were analyzed to obtain the reads of each sample that were compared to the reference genome in order to identify the SLAF tag with a polymorphism in parent lines and the SNP with read-associated coverage. Based on SLAF tags, SNP-index analysis, Euclidean distance (ED) correlation analysis, and whole genome resequencing, the hot regions were annotated. Results: A total of 165,007 high-quality SLAF tags, with an average depth of 47.90x in the parents and 50.78x in F-2 individuals, were sequenced. In addition, a total of 137,741 SNPs were detected: 113,311 and 98,861 SNPs in the male and female parent, respectively. A correlation analysis by SNP-index and ED initially located the candidate gene on 1.35 Mb of chrD05, and 20 candidate genes were identified. These genes were involved in genetic variations, single base mutations, insertions, and deletions. Moreover, 42 InDel markers of the whole genome resequencing were also detected. Conclusions: In this study, associated markers identified by super-BSA could accelerate the study of CMS in cotton, and as well as in other crops. Some of the 20 genes' preliminary characteristics provided useful information for further studies on CMS crops.

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