High-density genetic variation maps reveal the correlation between asymmetric interspecific introgressions and improvement of agronomic traits in Upland and Pima cotton varieties developed in Xinjiang, China

Abstract

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.

Keywords: Gossypium barbadense; Gossypium hirsutum; GWAS; fibre traits; genetic introgression; selection.

Figure 1

Genetic variation of single nucleotide polymorphisms (SNPs) between Gh and Gb. (a) The karyotype of Gossypium hirsutum reference genome. (b) The fixed interspecific SNPs between Gh and Gb. (c) The SNPs in Gh and Gb. (d) The SNPs in Gb. (e) The SNPs in Gh. Gh, G. hirsutum cultivars; Gb, Gossypium barbadense cultivars.

Figure 2

Population structure of the interspecific panel. (a) Principal component analysis of 259 cotton accessions. (b) Phylogenetic tree of 259 cotton accessions. (c) Population structure of 259 cotton accessions when K (number of groups) = 2 and K = 3. Gh, Gossypium hirsutum cultivars; Gb, Gossypium barbadense cultivars; Gh‐race, G. hirsutum races.

Figure 3

Population differentiation, introgression and selection. (a) The population differentiation with and without introgression events among Gh, Gb and Gh‐race groups. The solid lines represent the groups with introgression loci; the dotted lines represent groups without introgression loci. Gh, Gossypium hirsutum cultivars; Gb, Gossypium barbadense cultivars; Gh‐race, G. hirsutum races. (b) Genetic introgressions in genome‐wide scale. Gb‐INT, introgression event from Gh to Gb; Gh‐INT, introgression event from Gb to Gh. (c) Selective sweeps and co‐selected loci in Gh and Gb panels.

Figure 4

The fibre yield quantitative trait locus introgressed from Gh to Gb. (a) Genome‐wide associated locus of fibre yield traits in Gb on chromosome D03. (b) The genetic effects of two fibre yield traits between the introgression and non‐introgression groups in the Gb panel. SCW, seed cotton weight; LW, lint weight; Gh, Gossypium hirsutum cultivars; Gb, Gossypium barbadense cultivars.

Figure 5

Fibre traits and gene expressions of N139 and N178 in the introgression locus. (a) Introgression diagram of N139 compared with N178 and N179 on chromosome D03. (b) Box‐plot of six fibre traits in N139 and N178. (c) Gene expressions of N139 and N178 in the introgression locus. N139, a chromosome segment substitution line (CSSL); N178, Gossypium hirsutum cv. E22; N179, Gossypium barbadense acc. 3‐79; FE, fibre elongation; FL, fibre length; FS, fibre strength; FU, fibre uniformity; MV, micronaire value; SFC, short fibre content.