Two genomic regions associated with fiber quality traits in Chinese upland cotton under apparent breeding selection

Abstract

Fiber quality is one of the most important agronomic traits of cotton, and understanding the genetic basis of its target traits will accelerate improvements to cotton fiber quality. In this study, a panel comprising 355 upland cotton accessions was used to perform genome-wide association studies (GWASs) of five fiber quality traits in four environments. A total of 16, 10 and 7 SNPs were associated with fiber length (FL), fiber strength (FS) and fiber uniformity (FU), respectively, based on the mixed linear model (MLM). Most importantly, two major genomic regions (MGR1 and MGR2) on chromosome Dt7 and four potential candidate genes for FL were identified. Analyzing the geographical distribution of favorable haplotypes (FHs) among these lines revealed that two favorable haplotype frequencies (FHFs) were higher in accessions from low-latitude regions than in accessions from high-latitude regions. However, the genetic diversity of lines from the low-latitude regions was lower than the diversity of lines from the high-latitude regions in China. Furthermore, the FHFs differed among cultivars developed during different breeding periods. These results indicate that FHs have undergone artificial selection during upland cotton breeding in recent decades in China and provide a foundation for the further improvement of fiber quality traits.

Genome-wide identification and expression analyses of the pectate lyase (PEL) gene family in cotton (Gossypium hirsutum L.)

“…Two cultivars with significantly different fiber lengths (TM-1, with longer fibers, and kenN27–3, with shorter fibers) were chosen to explore the function of GhPELs in fiber development [ 34 ]. The expression of 7 genes ( GhPEL4_At , GhPEL48_Dt , GhPEL30_At , GhPEL68_Dt , GhPEL76_Dt , GhPEL38_At , and GhPEL53_Dt ), most of which exhibit higher expression in fiber than other organs, was analyzed in 10 DPA, 15 DPA, 20 DPA and 30 DPA fibers of TM-1 and kenN27–3.…”

QTL and genetic analysis controlling fiber quality traits using paternal backcross population in Upland Cotton

“…Using a map of single nucleotide polymorphism (SNP) markers, one fiber length hotspot on Chr 5 carrying three QTLs was observed (Li et al 2016). Additionally, four potential candidate genes for fiber length on Chr Dt7 were found using genotyping by sequencing by genome-wide association studies (GWAS) (Su et al 2016). Previous studies indicated that the RIL population and its two BCF 1 populations which derived from the same parents increased the power of QTL detection in cotton (Shang et al 2016d; Wang et al 2016).…”

Fiber Quality Improvement in Upland Cotton (Gossypium hirsutum L.): Quantitative Trait Loci Mapping and Marker Assisted Selection Application

“…For example, the development of CottonSNP63K (Hulse-Kemp et al, 2015) and CottonSNP80K (Cai et al, 2017) arrays has allowed genetic mapping, genomic selection, genome-wide association studies, and an understanding of genomic diversity among Gossypium breeding populations. Common QTLs related to fiber quality in different environments identified through SNP markers can be deployed as a priority for fine mapping and candidate genes identification Su et al, 2016;Tan et al, 2018).…”