Genome-Wide Association Analysis and Prediction of Candidate Genes for Chlorophyll Content in Gossypium barbadense

Chlorophyll, as the core pigment of plant photosynthesis, directly affects the photosynthetic efficiency and yield of plants. By mining molecular markers and candidate genes related to chlorophyll in Sea-island cotton, we can provide a theoretical basis for the improvement of Sea-island cotton varieties.

Using 203 sea-island cotton varieties as research objects, the chlorophyll content of sea-island cotton in three stages (budding stage, flowering stage, and boll stage) was measured in 4 environments (2 points in 2 years), and the chlorophyll content of sea-island cotton in 4 environments was measured. Correlation analysis was performed on the chlorophyll content, and the whole-genome resequencing data and the BLUP value of the chlorophyll content were used for genome-wide correlation analysis to screen candidate genes related to chlorophyll content.

Descriptive statistics of chlorophyll content in the four environments showed that the chlorophyll content at bud stage, flowering stage and bell stage were normally distributed across years and locations, indicating that the trait is a quantitative trait controlled by multiple genes. Chlorophyll content varied significantly across growth periods and was significantly affected by environment, with correlation coefficients of 0.021-0.287 for chlorophyll content at bud stage, 0.017-0.180 at flowering stage and -0.118-0.212 at bell stage. GWAS research results screened out a total of 52 significant SNPs sites. Among them, 20, 20 and 12 significant SNP sites were screened in the bud stage, flowering stage and boll stage respectively, mainly distributed on chromosomes such as A05, A06, D05, D06 and D10. By annotating significant sites, a total of 80 candidate genes were annotated, including GB_A05G0103, GB_A05G0104, GB_A05G0105, GB_A05G0106, GB_A05G0107, GB_A05G0108, GB_A05G0109, GB_A05G0110, GB_A05G0111 and GB_A 05G0112 and other 10 genes are in type I (4 environments) The flowering stage and the flowering stage of type Ⅱ (two environments in northern Xinjiang) are all annotated. GB_A06G1512 and GB_A06G1513 are annotated in the flowering stage and boll stage of typeⅠand the flowering stage of typeⅡ. GB_D09G0836, GB_D09G0837 and GB_D09G0838 are annotated in the florescence and boll stage of typeⅠand typeⅡ. The flowering stages are all annotated. Nine genes related to chlorophyll content were identified through relative expression analysis. Among them, genes such as GB_A05G0097, GB_A05G0093 and GB_D05G0109 play important roles in chlorophyll metabolism, photosynthesis and plant stress resistance.

There are significant differences in the chlorophyll content of sea-island cotton at different growth stages, and are significantly affected by the environment. A total of 52 loci related to the chlorophyll content of sea-island cotton were detected, and nine genes were found to be candidate genes for chlorophyll in sea-island cotton.