Integrating Genome-wide association and whole transcriptome analysis to reveal genetic control of leaf traits in Gossypium arboreum L.

Leaves are important organs for crop photosynthesis and transpiration, and their morphological characteristics can directly reflect the growth state of plants. Accurate measurement of leaf traits and mining molecular markers are of great significance to the study of cotton growth. Here, we performed a Genome-wide association study on 7 leaf traits in 213 Asian cotton accessions. 32 significant SNPs and 44 genes were identified. A field experiment showed significant difference in leaf hair and leaf area between DPL971 and its natural mutant DPL972. We also compared the leaf transcriptome difference between DPL971 and DPL972, and found a batch of differentially expressed genes and non-coding RNAs (including lncRNAs, microRNAs, and circRNAs). After integrating the GWAS and transcriptome results, we finally selected two coding genes (Ga03G2383 and Ga05G3412) and two microRNAs (hbr-miR156, unconservative_Chr03_contig343_2364) as the candidate for leaf traits. Those findings will provide important genomic resources for cotton leaf improvement breeding.