Genetic Diversity Analysis of 96 Gossypium hirsutum-Gossypium barbadense Introgression Lines and Early Maturing Northern China Cotton Lines Using a 40K Liquid-Phase Chip

Background: Genetic diversity and genetic differentiation between Gossypium hirsutum-Gossypium barbadense introgression lines (ILs) and early-maturing upland cotton lines are critical for resolving the core breeding contradiction in Xinjiang cotton region: narrow genetic basis of early-maturing cultivars and late maturity of ILs with superior fiber quality. Xinjiang is one of the major cotton-producing regions in China, and breeding high-quality early-maturing upland cotton adapted to local ecological conditions is essential for improving cotton yield and quality. However, the genetic relationship and differentiation between the two types of cotton germplasm remain unclear, which hinders the efficient utilization of germplasm resources in breeding. Therefore, this study aimed to clarify the genetic diversity and differentiation between the two germplasm types and identify key candidate loci related to early maturity and fiber quality, providing support for cotton breeding. Results: Here, we used a 40K Single Nucleotide Polymorphism chip to genotype core cotton germplasm in northern Xinjiang, and analyzed their population structure, genetic diversity and functional SNP loci associated with early maturity and fiber quality. The tested materials were clearly divided into two subgroups (ILs and early-maturing lines). Genetic diversity analysis revealed a significantly narrow genetic basis in the early-maturing subgroup, while the IL subgroup had higher genetic diversity. Specifically, the early-maturing subgroup showed lower nucleotide diversity and polymorphism information content compared with the IL subgroup, indicating that the genetic variation of early-maturing cotton germplasm in northern Xinjiang is relatively limited. A total of 25 non-synonymous SNPs were identified, among which the c.A613G:p.T205A mutation in GH_D09G1484 (mRNA-decapping enzyme 1, DCP1) was a characteristic variation of early-maturing cotton, and a possible non-synonymous mutation in GH_A09G2400 (Heat shock transcription factor A6b, HSFA6B) was associated with fiber development. These two candidate genes were annotated to be involved in plant growth and development, further supporting their potential roles in regulating cotton early maturity and fiber quality. Conclusions: This study clarified the genetic differentiation between the two types of germplasms and identified key candidate loci for early maturity and fiber quality, providing precise molecular markers and theoretical support for breeding high-quality early-maturing upland cotton adapted to Xinjiang’s ecological conditions. The results also highlight the value of Gossypium hirsutum–Gossypium barbadense introgression lines in enriching the genetic basis of early-maturing cotton, which can be further utilized to solve the core breeding contradiction in the Xinjiang cotton region.