Maria Jurado, Carmen García-Fernández, Ana Campa & Juan Jose Ferreira

Theoretical and Applied Genetics; Published: 27 May 2024; Volume 137, article number 143

Key message

Association analysis, colocation study with previously reported QTL, and differential expression analyses allowed the identification of the consistent QTLs and main candidate genes controlling seed traits.

Abstract

Common beans show wide seed variations in shape, size, water uptake, and coat proportion. This study aimed to identify consistent genomic regions and candidate genes involved in the genetic control of seed traits by combining association and differential expression analyses. In total, 298 lines from the Spanish Diversity Panel were genotyped with 4,658 SNP and phenotyped for seven seed traits in three seasons. Thirty-eight significant SNP-trait associations were detected, which were grouped into 23 QTL genomic regions with 1,605 predicted genes. The positions of the five QTL regions associated with seed weight were consistent with previously reported QTL. HCPC analysis using the SNP that tagged these five QTL regions revealed three main clusters with significantly different seed weights. This analysis also separated groups that corresponded well with the two gene pools described: Andean and Mesoamerican. Expression analysis was performed on the seeds of the cultivar ‘Xana’ in three seed development stages, and 1,992 differentially expressed genes (DEGs) were detected, mainly when comparing the early and late seed development stages (1,934 DEGs). Overall, 91 DEGs related to cell growth, signaling pathways, and transcriptomic factors underlying these 23 QTL were identified. Twenty-two DEGs were located in the five QTL regions associated with seed weight, suggesting that they are the main set of candidate genes controlling this character. The results confirmed that seed weight is the sum of the effects of a complex network of loci, and contributed to the understanding of seed phenotype control.

See https://link.springer.com/article/10.1007/s00122-024-04638-5

Fig. 3: Chromosomal positions of genomic regions associated with seven seed traits identified by GWAS (green boxes). * Regions colocated with previously reported QTL for seed traits. Genes differentially expressed during seed development underlying those genomic regions revealed by RNA-seq analysis are shown at the right of each chromosome.