Summary: Brown 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, Lc₁, 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.

SUMMARY: The two new world tetraploid cottons, Gossypium hirsutum and Gossypium barbadense, are cultivated worldwide and are characterised by a high yield and superior fibre quality, respectively. Historical genetic introgression has been reported between them; however, the existence of introgression and its genetic effects on agronomic traits remain unclear with regard to independent breeding of G. hirsutum (Upland cotton) and G. barbadense (Pima cotton) elite cultivars. We collected 159 G. hirsutum and 70 G. barbadense cultivars developed in Xinjiang, China, along with 30 semi‐wild accessions of G. hirsutum, to perform interspecific introgression tests, intraspecific selection analyses and genome‐wide association studies (GWAS) with fibre quality and yield component traits in multiple environments. In total, we identified seven interspecific introgression events and 52 selective sweep loci in G. hirsutum, as well as 17 interspecific introgression events and 19 selective sweep loci in G. barbadense. Correlation tests between agronomic traits and introgressions showed that introgression loci were mutually beneficial for the improvement of fibre quality and yield traits in both species. In addition, the phenotypic effects of four interspecific introgression events could be detected by intraspecific GWAS, with Gb_INT13 significantly improving fibre yield in G. barbadense. The present study describes the landscape of genetic introgression and selection between the two species, and highlights the genetic effects of introgression among populations, which can be used for future improvement of fibre yield and quality in G. barbadense and G. hirsutum, respectively.

Background: The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization. Results: In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Conclusions: This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.

Background: Naturally-colored cotton has become increasingly popular because of their natural properties of coloration, UV protection, flame retardant, antibacterial activity and mildew resistance. But poor fiber quality and limited color choices are two key issues that have restricted the cultivation of naturally-colored cotton. To identify the possible pathways participating in fiber pigmentation in naturally-colored cottons, five colored cotton accessions in three different color types (with green, brown and white fiber) were chosen for a comprehensive analysis of phenylpropanoid metabolism during fiber development.Results: The expression levels of flavonoid biosynthesis pathway genes in brown cotton fibers were significantly higher than those in white and green cotton fibers. Total flavonoids and proanthocyanidin were higher in brown cotton fibers relative to those in white and green cotton fibers, which suggested that the flavonoid biosynthesis pathway might not participate in the pigmentation of green cotton fibers. Further expression analysis indicated that the genes encoding enzymes for the synthesis of caffeic acid derivatives, lignin and lignan were activated in the developing fibers of the green cotton at 10 and 15 days post-anthesis.Conclusions: Our results strengthen the understanding of phenylpropanoid metabolism and pigmentation in green and brown cotton fibers, and may improve the breeding of naturally-colored cottons.

With the promotion and popularization of machine cotton-picking, more and more attention has been paid to the selection of early-maturity varieties with compact plant architecture. The type of fruit branch is one of the most important factors affecting plant architecture and early maturity of cotton. Heredity analysis of the cotton fruit branch is beneficial to the breeding of machine-picked cotton. Phenotype analysis showed that the types of fruit branches in cotton are controlled by a single recessive gene. Using an F₂ population crossed with Huaxin102 (normal branch) and 04N-11 (nulliplex branch), BSA (Bulked Segregant Analysis) resequencing analysis and GhNB gene cloning in 04N-11, and allelic testing, showed that fruit branch type was controlled by the GhNB gene, located on chromosome D07. Ghnb5, a new recessive genotype of GhNB, was found in 04N-11. Through candidate gene association analysis, SNP 20_15811516_SNV was found to be associated with plant architecture and early maturity in the Xinjiang natural population. The GhNB gene, which is related to early maturity and the plant architecture of cotton, is a branch-type gene of cotton. The 20_15811516_SNV marker, obtained from the Xinjiang natural population, was used for the assisted breeding of machine-picked cotton varieties.