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

Abstract

Summary Although efforts have been taken to exploit diversity for yield and quality improvements, limited progress on using beneficial alleles 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 inheritance under artificial selection has been challenging. Here we sequenced Gossypium hirsutum L. cv CRI ‐12 (the cotton variety with the largest acreage in China), its parental cultivars, and progeny cultivars, which were bred by the different institutes in China. In total, 3.3 million SNP s were identified and 118, 126 and 176 genes were remarkably correlated with Verticillium wilt , 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 1029 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.

Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang

“…Based on a group of SNPs, a number of improvement‐selective sweeps involving a string of causal genes and IBD segments inherited from foundation parents have been identified, laying a foundation for germplasm resource analysis and breeding by design in the future. In recent years, an abundance studies have been performed to trace IBD segments and exploit key trait regions during the breeding process following their well‐defined genetic paths (Chen et al , ; Fang et al , ; Lai et al , ; Lu et al , ; Ma et al , ; Wu et al , ). Based on more than 2 million SNPs, the Xinjiang cotton population could be divided into two groups (Figure ), preliminarily indicating that Upland cotton populations in Xinjiang were not only spawned from DPL15, STV2B and UGDM, which are the original germplasms used for modern Upland cotton breeding in Yangtze River and Yellow River cotton‐growing regions in China (Fang et al , ), but also have a close kinship with the former Soviet Union cotton landraces.…”

“…These cultivars exhibit phenotypes commensurate with important traits (Shinada et al , ), as exemplified in the development of Kitaake, Kyowa and Huanghuazhan in rice (Shinada et al , ; Zhou et al , ), B73, Mo17, etc. in maize (Lai et al , ; Smith et al , ; Wu et al , ), and Ekangmian 9 and CRI12 in cotton (Lu et al , ; Ma et al , ). Moreover, identity‐by‐descent (IBD) regions have been demonstrated to be powerful in relatedness evaluation and mapping of genetic loci associated with phenotypic variations in many studies (Browning and Browning, ; Browning and Thompson, ; Stevens et al , ; Westerlind et al , ) .…”

EST–SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives

“…Artificial selection might influence important loci variation, affecting traits of agronomic interest. Artificially selected SNPs might be consistently linked to important agronomic traits [29]. Artificial selection of crop varieties focused on modifying factors such as plant architecture and stress resistance, as a means of increasing yield [30].…”

Genome-wide Identification and Function Analysis of HMAD Gene Family in Cotton (Gossypium Spp.)

“…HMAD highly expressed under salt condition, probably because of ROS caused by ion balance [6,7]. For example, on the one hand, gene expression in ROS way and ion balance maintenance, such as Ca 2+ signaling pathway and MAPK, MYB transcription factor [62,63,64], programmed cell death [65,66,67]. And then the GSH, as the main way to remove ROS under the condition of high concentration, can not only response to heavy metal ions [68], also can response to salt stress ion [69].…”