Genome-Wide Introgression and Quantitative Trait Locus Mapping Reveals the Potential of Asian Cotton (Gossypium arboreum) in Improving Upland Cotton (Gossypium hirsutum)

Abstract

Gossypium arboreum (2n=2x=26, A2), the putative progenitor of the At-subgenome of Gossypium hirsutum (2n=4x=52, AD), is a repository of genes of interesting that have been eliminated during evolution/domestication of G. hirsutum. However, its valuable genes remain untapped so far due to species isolation. Here, using a synthetic amphiploid (AADDA2A2) previously reported, we developed a set of 289 G. arboreum chromosome segment introgression lines (ILs) in G. hirsutum by expanding the backcrossing population and through precise marker-assisted selection (MAS) although complex chromosomal structural variations existed between parents which severely hindered introgression. Our results showed the total coverage length of introgressed segments was 1,116.29 Mb, representing 78.48% of the At-subgenome in the G. hirsutum background, with an average segment-length of 8.69 Mb. A total of 81 co- quantitative trait loci (QTLs) for yield and fiber quality were identified by both the RSTEP-ADD-based QTL mapping and the genome-wide association study (GWAS) analysis, with 1.01–24.78% of the phenotypic variance explained. Most QTLs for boll traits showed negative additive effects, but G. arboreum still has the potential to improve boll-number traits in G. hirsutum. Most QTLs for fiber quality showed negative additive effects, implying these QTLs were domesticated in G. hirsutum compared with G. arboreum and, a small quantity of fiber quality QTLs showing positive additive effects, conversely; however, indicates that G. arboreum has the underlying genes of enhancing fiber quality of G. hirsutum. This study provides new insights into the breeding genetic potential of G. arboreum, lays the foundation for further mining favorable genes of interest, and provides guidance for inter-ploidy gene transference from relatives into cultivated crops.

Lint percentage and boll weight QTLs in three excellent upland cotton (Gossypium hirsutum): ZR014121, CCRI60, and EZ60

“…The QTLs qLP-C13-1 and qLP-C25-1 for LP explain 5.77% and 8.87% of the phenotypic variation, respectively [ 64 ]. A GWAS of a set of 289 Gossypium arboreum chromosome segment ILs in G. hirsutum indicates that co-QTLs for LP explain 1.21–10.79% of the phenotypic variation, and co-QTLs for BW explain 1.17–11.56% of the phenotypic variation [ 65 ]. Some QTLs for LP identified in this study explained nearly 10% of the phenotypic variation, and all QTLs for BW explained less than 10% of the phenotypic variation (Table S 4 ).…”

Transcriptomic and metabolomic profiling of flavonoid biosynthesis provides novel insights into petals coloration in Asian cotton (Gossypium arboreum L.)

“…Asian cotton (Gossypium arboreum L.) is one of the significant sources of natural fiber, initially introduced to China from the Indian subcontinent during the twelfth century [1]. It possesses resilience against biological and environmental stresses and is also a natural source of genetic variation for fiber-related traits [2][3][4][5].…”