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.

棉花是一种宝贵的纤维作物，为 50 多个行业提供原材料，在全球 70 多个国家生产。棉纤维相对于其他作物的优越性主要取决于其质量。然而，现代加工技术和棉花需要进一步提高纤维长度和强度，以保持其在全球市场的地位。关联作图能够鉴定控制纤维质量相关性状的 QTL，这可用于棉花育种。在本研究中，我们对 157 G. hirsutum进行了遗传多样性、连锁不平衡和关联作图分析使用总共 102 个 SSR 标记的多亲重组自交系。由于现代棉花基因型近亲繁殖，该种群的遗传变异性降低（14%）。尽管如此，我们还是确定了 11 个与籽棉产量、皮棉百分比、纤维长度和纤维强度相关的显着且稳定的标记-性状关联 ( p  < 0.005)。我们还检测到具有正负标记累加效应的 QTL 共定位。我们的结果表明，针对阴性等位基因的选择可能与针对阳性等位基因的选择一样重要。等位基因组合对不同 QTL 的影响分析揭示了显着且稳定的标记簇，可以选择支持或反对这些标记簇，以提供棉纤维质量的最大质量增益。