Genome-wide association study identifies the loci and genes related to days to flowering, fiber length and strength in Gossypium hirsutum

Upland cotton (Gossypium hirsutum) is the most widely cultivated species, with over 90% of the global cotton production. Owing to long-term natural selection and artificial breeding under diverse climatic and cultivated conditions, plentiful germplasm resources have been produced for sustainable genetic improvement. Thus, to detect genetic factors contributing to the important traits in a genome-wide scale is indispensable based on these germplasm resources. In the present study, on the basis of approximately 3.66 million SNPs, we conducted genome-wide association study with 419 accessions in three important traits including days to flowering (FD), fiber length (FL) and strength (FS). The results showed that there were 1199, 1661 and 735 SNPs (P < 10-6) significantly associated with FD, FL and FS. We identified 528 FD, 456 FL and 301 FS genes in the 50-kb region surrounding the associated SNPs. For FD, we observed that 94.6% of the associated SNPs (1,199) were located on Dt03 with a strong peak. Among the identified FL-associated SNPs, 646 (38.9%) and 755 (45.5%) were located in At10 and Dt11 with strong association signals, respectively. For FS, 391 (53.1%) SNPs were located in At07. Therefore, we focused on these chromosomes to detect the new genes. We adopted the method that combines peak SNPs and SNP type in GWAS with transcriptome data, functional annotation of the orthologues in Arabidopsis to rapidly identify candidate genes associated with the traits. Through phenotypic significance analysis of haplotypes, qRT-PCR using two types of varieties with different haplotypes, transgenic method and VIGS technology, we found that GhCIP1 and GhUCE are the new genes contributing to FD and fiber initiation in cotton. GhFL1 in At10 and GhFL2 in Dt11 are the new genes controlling fiber elongation. Gh_A07G1769 is a causal gene underpinning the fiber strength of cotton. These results provide targets for molecular selection and genetic manipulation in cotton improvement.