Abstract
BackgroundCytoplasmic 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.MethodsIllumina sequencing systematically investigated the parents. A segregating population comprising of 30 + 30 F2 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.ResultsA total of 165,007 high-quality SLAF tags, with an average depth of 47.90× in the parents and 50.78× in F2 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.ConclusionsIn 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.
Highlights
Cytoplasmic male sterility (CMS) is a maternally inherited trait failing to produce functional pollen
The sterile nature of the Trilobum cotton could be restored by either Rf2 of the Trilobum restorer gene or Rf1 of the Harknessii restorer gene; Rf2 is not able to restore the CMS-D2–2 of Harknessii
Yin et al constructed accurate genetic and physical maps of 15 molecular markers closely linked to the restorer gene that was located on chromosome 19 (LGD08 linkage group) with a genetic distance of
Summary
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 current studies suggest that CMS is caused by mutations in the correlated genes in the mitochondrial genome and inhibited by fertility restorer genes in the nuclear genome [1]. The fertility restoration of upland cotton CMS line is regulated by two pairs of independent recovery genes: Rf1 completely dominant and Rf2 partially dominant. Fine positioning and finding new restorer gene candidates in upland cotton are essential
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