Data from: 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 hundred 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.
Data for the study, which evaluated eight seed and yield component traits in 375 accessions of the UCR Minicore collection, along with 10 checks. The experiment was conducted in 2021 at the Plant Science Research and Experimental Unit (PSREU), Citra, FL. A row-column field design was used, with two replicates, and plants were manually seeded. To ensure accurate phenotypic evaluation, three plants were harvested from the center of each plot.
Contact estebanrios@ufl.edu with any questions. This manuscript has been accepted for publication. (07/February/2025)
Habib Akinmade, Rebecca Caroline Ulbricht Ferreira, Mario Henrique Murad Leite Andrade, Claudio Fernandes, Pablo Sipowicz, María Muñoz-Amatriaín, Esteban Rios, Genome-wide association studies dissect the genetic architecture of seed and yield component traits in cowpea (Vigna unguiculata L. Walp), G3 Genes|Genomes|Genetics, 2025;, jkaf024, https://doi.org/10.1093/g3journal/jkaf024
Data file includes:
“Cowpea2021 pods and seeds.txt”
#Experimental Design Metadata
1. Plot: The unique identifier assigned to each experimental unit (3 m × 0.6 m) where cowpea plants were grown.
2. Rep: The replicate number in which each accession was planted.
3. Column: The column number where a specific plot was positioned in the row-column design.
4. Row: The row number where the plot was placed within the field.
5. Taxa: The name of the cowpea accession used in the study.
6. Accession Number (Accesion_number) :A unique identifier assigned to each accession from the UCR Minicore collection (Muñoz-Amatriaín et al. 2021) and additional checks.
#Trait Descriptions and Measurement Methods:
7. Number of Pods per Plant [N_pods_perplant]: The total number of mature pods per plant was counted and averaged across three harvested plants per plot. Measurement Method: Manual (Direct Count)
8. Pod Length (cm) [AveragePodLength_cm]: The longitudinal length of mature pods was measured. Five randomly chosen pods were selected per plant and their lengths were averaged. Measurement Method: Manual (Direct Measurement)
9. 100-Seed Weight (g) [Weight_100seed_gr]: The average weight of 100 seeds collected from three plants per plot, providing an indicator of seed size and density. Measurement Method: Manual (Weighing)
10. Grain Yield (g) [Yield_perplant_gr]: The total seed yield collected from three harvested plants at pod maturity stage, measured in grams per plot. Measurement Method: Manual (Harvested Yield)
11. Seed Area [Area(mm2)]: The total two-dimensional area covered by each seed, estimated from scanned seed images using SmartGrain software. Measurement Method: Digital Imaging (SmartGrain Software)
12. Seed Perimeter [Perimeter(mm)]: The total outer boundary length of each seed, measured through image processing software.Measurement Method: Digital Imaging (SmartGrain Software)
13. Seed Length [Length(mm)]: The longest dimension of the seed was measured using high-throughput seed image analysis.Measurement Method: Digital Imaging (SmartGrain Software)
14. Seed Width [Width(mm)]: The widest dimension of the seed, measured using SmartGrain software from scanned seed images. Measurement Method: Digital Imaging (SmartGrain Software)
Extra notes on phenotyping method:
- Pod Traits were manually measured at harvest.
- Seed Traits were assessed using high-throughput imaging and analyzed via SmartGrain software.
- Seeds were scanned using a Xerox VersaLink C405 scanner, and four background colors (red, yellow, purple, blue) were used for contrast enhancement.
This dataset provides high-throughput phenotypic data for GWAS, which allowed us to carry out the analysis of genetic factors controlling seed and yield component traits in cowpea.