Advanced High-Throughput Root Phenotyping and GWAS Identifies Key Genomic Regions in Cowpea During Vegetative Growth Stage

Improving crop production in changing environments can be achieved through selective breeding; however, limited advanced root phenotyping and genotyping in early growth stages hinder assessing root architecture variation and diversity, despite its importance. Therefore, this study utilized advanced image phenotyping on a diverse set of 222 cowpea accessions, revealing significant variations in key phenotypic traits and the genomic regions influencing them. Our study revealed a total of 55 genes linked to major root traits. Among eight root traits—total root length (TRL), surface area (SA), average diameter (AD), root volume (RV), tip number (TN), fork number (FN), primary root length (PRL), and lateral root length (LRL), analyzed, seven significant single nucleotide polymorphisms (SNPs) demonstrated particularly strong associations with three key traits, including surface area (SA), tip number (TN), and fork number (FN). SA emerged as a significant trait, exhibiting considerable variation across the studied accessions. The mean SA was 59.59 cm², with some genotypes surpassing 140.72 cm². Further analysis identified two SNPs that showed significant association with SA, located on two distinct chromosomes: 3 and 11. Similarly, two significant SNPs associated with TN were found on chromosome 3, while three SNPs associated with FN were identified on chromosomes 2, 3, and 8. These findings significantly advance our understanding of the genetic foundations underlying important phenotypic traits in cowpeas, offering a robust framework for future genetic improvement initiatives. The results strongly suggest that implementing breeding programs focused on selecting root phenotypes could significantly enhance cowpea productivity across various environments.