Novel candidate loci for morpho-agronomic and seed quality traits detected by targeted genotyping-by-sequencing in common bean

Abstract

Phaseolus vulgaris L., known as common bean, is one of the most important grain legumes cultivated around the world for its immature pods and dry seeds, which are rich in protein and micronutrients. Common bean offers a cheap food and protein sources to ameliorate food shortage and malnutrition around the world. However, the genetic basis of most important traits in common bean remains unknown. This study aimed at identifying QTL and candidate gene models underlying twenty-six agronomically important traits in common bean. For this, we assembled and phenotyped a diversity panel of 200 P. vulgaris genotypes in the greenhouse, comprising determinate bushy, determinate climbing and indeterminate climbing beans. The panel included dry beans and snap beans from different breeding programmes, elite lines and landraces from around the world with a major focus on accessions of African, European and South American origin. The panel was genotyped using a cost-conscious targeted genotyping-by-sequencing (GBS) platform to take advantage of highly polymorphic SNPs detected in previous studies and in diverse germplasm. The detected single nucleotide polymorphisms (SNPs) were applied in marker-trait analysis and revealed sixty-two quantitative trait loci (QTL) significantly associated with sixteen traits. Gene model identification via a similarity-based approach implicated major candidate gene models underlying the QTL associated with ten traits including, flowering, yield, seed quality, pod and seed characteristics. Our study revealed six QTL for pod shattering including three new QTL potentially useful for breeding. However, the panel was evaluated in a single greenhouse environment and the findings should be corroborated by evaluations across different field environments. Some of the detected QTL and a number of candidate gene models only elucidate the understanding of the genetic nature of these traits and provide the basis for further studies. Finally, the study showed the possibility of using a limited number of SNPs in performing marker-trait association in common bean by applying a highly scalable targeted GBS approach. This targeted GBS approach is a cost-efficient strategy for assessment of the genetic basis of complex traits and can enable geneticists and breeders to identify novel loci and targets for marker-assisted breeding more efficiently.

Identification of consistent QTL and candidate genes associated with seed traits in common bean by combining GWAS and RNA-Seq

“… *(1) González et al ( 2016 ), (2) Berry et al ( 2020 ), (3) Murube et al ( 2020 ), (4) Bassett et al ( 2021 ), (5) Arriagada et al ( 2022 ), (6) Giordani et al ( 2022 ), (7) Ugwuanyi et al ( 2022 ) …”

“…Well-characterized QTL, consistent among backgrounds, well delimited and tagged, and with a significant contribution to the expression of the trait are desirable for use in breeding. A few studies have reported QTL for seed size and shape (González et al 2016 ; Murube et al 2020 ; Bassett et al 2021 ; Giordani et al 2022 ; Ugwuanyi et al 2022 ; Arriagada et al 2022 ) and seed quality traits (Berry et al 2020 ; Bassett et al 2021 ). The results allowed the identification of 13 consistent genomic regions associated with QTL that were previously reported in different genetic backgrounds and environments, indicating the relevance of such regions in the control of seed characters.…”

“…The size of QTL can depend on factors such as variation among genomes, density of markers, recombination of the region, or number of genes that contribute to the characteristics. The QTL region Seed09_23.4 was also involved in SW and SWI (Ugwuanyi et al 2022 ; Arriagada et al 2022 ). Interestingly, this delimited region annotated the genes Phvul.009G190100 and Phvul.009G202100 , which had a significant effect on yield in a set of 42 common bean genotypes evaluated at two locations (Reinprecht et al 2021 ).…”

“…Remarkably, differences were established by the QTL regions Seed01_51.9 and Seed10_39.1, 6.63 g (Clusters 2 and 3) and 6.47 g (Clusters 1 and 2) between the two extreme groups (see Table 5 ). Both regions were found to be associated with seed weight in several QTL analyses (Bassett et al 2021 ; Ugwuanyi et al 2022 ; Arriagada et al 2022 ); therefore, they are of special interest for breeding. Interestingly, the end of chromosome Pv01 is important for bean domestication and adaptation because it contains genes for determinacy ( Fin locus) and sensitivity to photoperiod ( Ppd locus; Weller et al 2019 ).…”

“…The identified blocks were named using the prefix ‘Seed,’ chromosome number, and start position in Mb. To complete the characterization of the delimited blocks revealed by GWAS, the genomic positions in the bean genome were compared with those of QTL previously reported in common bean (González et al 2016 ; Murube et al 2020 ; Berry et al 2020 ; Bassett et al 2021 ; Giordani et al 2022 ; Ugwuanyi et al 2022 ; Arriagada et al 2022 ). The list of annotated genes under the QTL was established based on those residing within the region delimited by the leftmost and rightmost flanking SNP in the defined haplotype blocks.…”