Abstract
Cotton is a valuable fiber crop which supplies raw material to more than 50 industries and is produced in more than 70 countries worldwide. The superiority of cotton fiber over other crops is primarily dependent on its quality. However, further improvements in fiber length and strength are required for modern processing technology and for cotton to maintain its position in the global market. Association mapping enables identification of QTLs controlling fiber quality-related traits which can be useful in cotton breeding. In the present study, we performed genetic diversity, linkage disequilibrium and association mapping analyses in 157 G. hirsutum multi-parent recombinant inbred lines using a total of 102 SSR markers. The population had depressed genetic variability (14%), a result of inbreeding of modern cotton genotypes. Despite this, we identified 11 significant and stable marker-trait associations for seed cotton yield, lint percentage, fiber length and fiber strength (p < 0.005). We also detected QTL co-localizations with positive and negative marker additive effects. Our results indicate that selection against negative alleles may be as important as selection for positive alleles. Analysis of the effects of allelic combinations at different QTLs revealed significant and stable marker clusters that can be selected for or against to provide maximum quality gains in cotton fiber quality.
Highlights
Gossypium is a complex and highly variable genus consisting of species with different ploidies
Conventional breeding has encountered many challenges in the development of elite varieties such as inbreeding depression, unpredictable interaction of genotype versus environment and the complex nature of quantitative traits that do not follow the laws of Mendelian genetics
We clearly detected the depression of genetic variability that has resulted from inbreeding of modern cotton genotypes indicating that genetic diversity must be urgently broadened
Summary
Gossypium is a complex and highly variable genus consisting of species with different ploidies. Gossypium species have been used as a source of desired traits and cotton fiber for thousands of years (since 800-700 BC); only four species are domesticated and cultivated: the New World cottons, G. hirsutum L. and G. barbadense L. G. barbadense has good fiber features such as long, stable, fine fibers while G. hirsutum does not. G. barbadense has narrow adaptability due to its requirement for a long growing season while G. hirsutum is adapted to a wider range of environments and produces higher yields (May and Lege 1999). G. barbadense has a small market share along with the other domesticated cottons in various parts of the world (Jenkins 2003; Lee 1984)
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