Genetic variation underlying nitrogen-deficiency tolerance in Gossypium hirsutum during the seedling stage

As over-fertilization leads to environmental concerns, selecting high yield cotton cultivars with a high nitrogen use efficiency (NUE) has become crucially important. However, the genetic effects underlying NUE traits remain unclear. In this study, a genome-wide association study (GWAS) was performed using 2.65 million high-quality single-nucleotide polymorphisms (SNPs) based on three NUE related traits at the seedling stage of 419 core accessions in four environments. A total of 21 novel loci were detected, of which, the novel peak on D10 chromosome was consistently detected for multiple traits and selected to analyze. We further identified and validated a novel candidate gene GhERF4 by RNA-seq, RT-qPCR, virus-induced gene silencing (VIGS) and overexpression methods, and the results suggest that GhERF4 plays a negative role in the regulation of N-deficiency tolerance. The identified SNPs and candidate genes provide new insights into understanding the molecular mechanism and breeding varieties in N-efficient tolerance.