Genome-wide association studies dissect the genetic architecture of seed and yield component traits in cowpea (Vigna unguiculata L. Walp)

Abstract

The identification of loci related to seed and yield component traits in cowpea constitutes a key step for improvement through marker-assisted selection (MAS). Furthermore, seed morphology has an impact on industrial processing and influences consumer and farmer preferences. In this study, we performed genome-wide association studies (GWAS) on a mini-core collection of cowpea to dissect the genetic architecture and detect genomic regions associated with seed morphological traits and yield components. Phenotypic data were measured both manually and by high-throughput image-based approaches to test associations with 41,533 single nucleotide polymorphism markers using the FarmCPU model. From genome-associated regions, we also investigated putative candidate genes involved in the variation of the phenotypic traits. We detected 42 marker-trait associations for pod length and 100-seed weight, length, width, perimeter, and area of the seed. Candidate genes encoding leucine-rich repeat-containing (LRR) and F-box proteins, known to be associated with seed size, were identified; in addition, we identified candidate genes encoding PPR (pentatricopeptide repeat) proteins, recognized to have an important role in seed development in several crops. Our findings provide insights into natural variation in cowpea for yield-related traits and valuable information for MAS breeding strategies in this and other closely related crops.

Keywords: Vigna unguiculata; GWAS; grain yield; image-based phenotyping; seed morphology.

Fig. 1.

Cowpea seeds placed on different backgrounds used for high-throughput image-based phenotyping for seed morphology traits (one cent coin placed above for size reference).

Fig. 2.

Genetic correlation among 8 seed and yield component traits of the UCR Minicore collection in this study. PN, pod number; PL, pod length; SW, 100-seed weight; GY, grain yield; SA, seed area; SP, seed perimeter; SL, seed length; SWD, seed width.

Fig. 3.

Manhattan plots of GWAS for seed traits: seed area, seed length, seed perimeter, and seed width. Negative log₁₀(p) values are plotted against physical position on each of the 11 chromosomes (Lonardi et al. 2019). The dashed line at the higher significance threshold indicates the Bonferroni correction for genome-wide significance threshold (5.92).

Fig. 4.

Manhattan plots of GWAS for pod number, pod length, 100-seed weight, and grain yield. Negative log₁₀(p) values are plotted against physical position on each of the 11 chromosomes. The dashed line at the higher significance threshold indicates the Bonferroni correction for genome-wide significance threshold (5.92).