A. QTL identification of seed hardness traits in a diverse genetic panel of common bean (Phaseolus vulgaris)


Suo, R.Z., Mwaniki, A., Zheng, C.F., Jia, B., You, F.M., Conner, R.L., Xu, W.1 and Hou, A. QTL identification of seed hardness traits in a diverse genetic panel of common bean (Phaseolus vulgaris). Poster presentation. Bean Improvement Cooperative Biennial Meeting (Virtual), November 2-3, 2021.

Résumé en langage clair

Seed hardness in dry bean is an important trait that impacts cooking time and canning quality. Hard seeds pose negative effects such as increased processing cost, loss of nutritional values, and uneven seed germination when they are planted for crop production. It has been shown that seed hardness is a complex trait that is affected by both genetic and environmental factors. Although numerous studies have been conducted to understand the effect of environment on the hardness or cooking time of legumes, including dry beans, the assessment of its genetic mechanism is limited. The analysis of a genetic population over two years in southern Manitoba has revealed candidate chromosome loci associated with seed hydration in beans which is useful for future molecular breeding.


Seed hardness impacts cooking time and canning quality in dry beans. This study aims to identify the quantitative trait loci (QTL) and associated molecular markers to better understand and tag this trait. A diverse genetic panel consisting of 173 Mesoamerican and 15 Andean early-maturing dry bean lines was grown at two locations in southern Manitoba, Canada during 2018-2021 to evaluate seed hardness related traits. The stone seed percentage (%) (SS) was readily affected by year or location with a broad-sense heritability (H2) of 66.8%, whereas the hydration capability (%) (HC) showed relatively high H2 (80.2%). The one-hundred seed weight (SW) was a highly inheritable trait with an estimated H2 of 97.8%. Using genotyping by sequencing (GBS), a total of 1,025.8 millions of quality control passed 150bp pair-end reads were generated with an average of 5.46 millions reads per line, of which 95% of reads were mapped to the Mesoamerica type reference genome (BAT93). A total of 74,402 single nucleotide polymorphisms (SNPs) with a missing data rate less than 60% and a minimum allele frequency greater than 0.05 were identified. The principal component analysis using the SNPs revealed that all 188 accessions were distinctively grouped into two clusters of Mesoamerica and Andean types. Genome-wide association study (GWAS) was performed using the seven multi-locus statistical models implemented in the R packages rmMLM and MVP. A total of 203, 177 and 212 quantitative trait nucleotides (QTNs) were detected for HC, SS and SW, respectively. Of them, 52 QTNs were shared by HC and SS, but only one SS QTN and five HC QTNs were pleiotropic with SW, indicating weak genetic correlation between SW and seed hardness traits. All these QTNs presented significant additive effects for the traits per se, suggesting their usefulness in marker assisted or genomic selection. Further candidate genes associated with these QTNs will be screened.