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.

由于过度施肥导致环境问题，选择能够在缺磷（P）的土壤上产生高产的栽培品种，并了解缺磷耐受性的遗传基础已变得至关重要。在这项研究中，我们评估了两种不同环境中419个核心种质在苗期的10种磷缺乏相关性状的变异。结果表明，茎干重（SDW）可以作为筛选耐磷种质资源的指标。使用366万个高质量的单核苷酸多态性（SNP）对两个与SDW相关的性状进行了全基因组关联研究（GWAS）。共有102个显着相关的SNP位于137个基因之内或附近，其中27个SNP被连续检测到具有多种性状或多种环境。Gh_D11G2219，通过qRT-PCR分析和病毒诱导的基因沉默（VIGS），结果表明，Gh_D11G2219在棉花对磷缺乏胁迫的耐受性的正调控中发挥作用。此外，在棉花育种过程中，与耐P饥饿相关的优良SNP经历了负选择压力。这是首个对磷缺乏症耐受性的GWAS，鉴定出的SNP和候选基因为育种高磷高效品种提供了有价值的信息。