Quantitative genomics-enabled selection for simultaneous improvement of lint yield and seed traits in cotton (Gossypium hirsutum L.)

Abstract: Improving cotton seed and oil yields has become increasingly important while continuing to breed for higher lint
yield. In this study, a novel Bayesian linkage disequilibrium-based multiple-locus mixed model was developed for QTL
identification and genomic prediction (GP). A multi-parent population consisting of 256 recombinant inbred lines, derived
from four elite cultivars with distinct combinations of traits, was used in the analysis of QTLs for lint percentage, seed index,
lint index and seed oil content and their interrelations. All four traits were moderately heritable and correlated but with no
large influence of genotype × environment interactions across multiple seasons. Seven to ten major QTLs were identified
for each trait with many being adjacent or overlapping for different trait pairs. A fivefold cross-validation of the model
indicated prediction accuracies of 0.46–0.62. GP results based on any two-season phenotypes were strongly correlated with
phenotypic means of a pooled analysis of three-season experiments (r = 0.83–0.92). When used for selection of improvement
in lint, seed and oil yields, GP captured 40–100% of individuals with comparable lint yields of those selected based on
the three-season phenotypic results. Thus, this quantitative genomics-enabled approach can not only decipher the genomic
variation underlying lint, seed and seed oil traits and their interrelations, but can provide predictions for their simultaneous
improvement. We discuss future breeding strategies in cotton that will enhance the entire value of the crop, not just its fibre.

Data Description:

"Genotype data.txt": The genotype data of 256 Australian cotton MAGIC lines. Row represent individuals, and column represents SNPs (in total 6523 SNPs).The matrices are coded as -1, 0 and 1 for genotypes AA, AB and BB, respectively.

“Genetic map.txt”: The physical genetic map of the 6523 SNPs (order is one-to-one corresponded to the SNPs in “genotype data.txt”).

“Phenotype data.txt”: The phenotype records over three seasons for the 256 Australian cotton MAGIC lines.