Genetic variation associated with the shoot biomass of upland cotton seedlings under contrasting phosphate supplies

Abstract

As over-fertilization leads to environmental concerns, selecting cultivars that can produce high yields on phosphorus (P)-deficient soils and understanding the genetic basis underlying P-starved tolerance have become crucially important. In this study, we evaluated the variation of ten P deficiency-related traits at the seedling stage of 419 core accessions in two different environments. The results showed that the shoot dry weight (SDW) could be considered an indicator for screening P-tolerant germplasm resources. A genome-wide association study (GWAS) was performed for two SDW-related traits using 3.66 million high-quality single-nucleotide polymorphisms (SNPs). A total of 102 significantly associated SNPs were located within or near 137 genes, of which, 27 of the SNPs were consistently detected for multiple traits or multiple environments. We further identified and validated a novel candidate gene, Gh_D11G2219, by qRT-PCR analysis and virus-induced gene silencing (VIGS), and the results suggested that Gh_D11G2219 plays a role in the positive regulation of tolerance to P deficiency stress in cotton. In addition, the elite SNPs linked to tolerance to P-starved stress have undergone negative selection pressure during the cotton breeding process. This is the first GWAS of P deficiency tolerance, and the identified SNPs and candidate genes provide valuable information for breeding highly P-efficient varieties.