Mining elite loci and candidate genes for root morphology-related traits at seedling stage by genome-wide association studies in Upland Cotton (Gossypium hirsutum L.)

The root system architecture plays an essential role in water and nutrient acquisition in plants and is significantly involved in plant adaptation to various environmental stresses. In this study, a panel of 242 cotton accessions was collected to investigate six root morphological traits at the seedling stage, including main root length (MRL), root fresh weight (RFW), total root length (TRL), root surface area (RSA), root volume (RV), and root average diameter (AvgD). The correlation analysis between six root morphological traits revealed a strong positive correlation of TRL with RSA, RV with RSA and AvgD, whereas a significant negative correlation between TRL and AvgD. Subsequently, a genome-wide association study (GWAS) was performed using the root phenotypic data and genotypic data reported previously for 242 accessions using 56,010 single nucleotide polymorphisms (SNPs) from the CottonSNP80K array. A total of 41 quantitative trait loci (QTLs) were identified with 9 for MRL, 6 for RFW, 9 for TRL, 12 for RSA, 12 for RV and 2 for AvgD respectively. Among them, 8 QTLs were repeatedly detected in two or more traits. Integrated with transcriptome analysis, we identified 17 candidate genes with high transcripts of transcripts per million (TPM)≥30 in roots. Furthermore, we verified functionally a candidate gene encoding a WPP domain protein 2 in root development. Virus-induced gene silencing (VIGS) assay showed that knocking down significantly inhibited root development in cotton, indicating its positive role in root system architecture formation. Together, these results provide a theoretical basis and candidate genes for cotton root developmental biology and root-related cotton breeding.