Abstract
SummaryBrown fibre cotton is an environmental‐friendly resource that plays a key role in the textile industry. However, the fibre quality and yield of natural brown cotton are poor, and fundamental research on brown cotton is relatively scarce. To understand the genetic basis of brown fibre cotton, we constructed linkage and association populations to systematically examine brown fibre accessions. We fine‐mapped the brown fibre region, Lc 1, and dissected it into 2 loci, qBF‐A07‐1 and qBF‐A07‐2. The qBF‐A07‐1 locus mediates the initiation of brown fibre production, whereas the shade of the brown fibre is affected by the interaction between qBF‐A07‐1 and qBF‐A07‐2. Gh_A07G2341 and Gh_A07G0100 were identified as candidate genes for qBF‐A07‐1 and qBF‐A07‐2, respectively. Haploid analysis of the signals significantly associated with these two loci showed that most tetraploid modern brown cotton accessions exhibit the introgression signature of Gossypium barbadense. We identified 10 quantitative trait loci (QTLs) for fibre yield and 19 QTLs for fibre quality through a genome‐wide association study (GWAS) and found that qBF‐A07‐2 negatively affects fibre yield and quality through an epistatic interaction with qBF‐A07‐1. This study sheds light on the genetics of fibre colour and lint‐related traits in brown fibre cotton, which will guide the elite cultivars breeding of brown fibre cotton.
Highlights
Cotton has been cultivated and domesticated for over 3000 years (Lee and Fang, 2015), and various aspects of fibre quality and yield have been domesticated and improved compared with the ancestral varieties (Fang et al, 2017)
Based on a high-density genetic map developed in our laboratory (Li et al, 2016), polymorphic markers were screened to genotype 64 recessive individuals from 243 F2 plants in 2015; 17 simple sequence repeat (SSR) markers showed loose linkage with Lc1, and one marker cosegregated with Lc1 (Figure 1a)
Three SNPs around A07_1992243 as Hap1 and two SNPs around SCAFFOLD1919_A07_226089 as Hap2 were combined to conduct a haploid analysis; the results showed that the white fibre accessions harboured a completely different haploid type compared with the brown fibre accessions
Summary
Cotton has been cultivated and domesticated for over 3000 years (Lee and Fang, 2015), and various aspects of fibre quality and yield have been domesticated and improved compared with the ancestral varieties (Fang et al, 2017). Coloured cotton serves as an environmental-friendly resource for human society because it does not require dyeing (Khatri et al, 2015). Brown and green fibre cottons are two dominant types of naturally coloured cotton (Dutt et al, 2004). Natural brown cotton exhibits a widespread origin; this type of fibre has been found in several species, including the following diploids and tetraploids: Gossypium arboreum, G. herbaceum, G. barbadense, G. hirsutum and G. tomentosum (Carvalho et al, 2014; Hutchinson, 1946; Murthy, 2001; Ware, 1932). The natural brown cotton textile market is not promising due to its low yield and quality (Feng et al, 2011). It is urgent to study the genetic basis of natural brown cotton to support the breeding of this environmental-friendly resource
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