Genetic analysis and QTL mapping of the seed hardness trait in a black common bean (Phaseolus vulgaris) recombinant inbred line (RIL) population
Citation
Sandhu, K.S., You, F.M., Conner, R.L., Balasubramanian, P.M., Hou, A. (2018). Genetic analysis and QTL mapping of the seed hardness trait in a black common bean (Phaseolus vulgaris) recombinant inbred line (RIL) population. Molecular Breeding, [online] 38(3), http://dx.doi.org/10.1007/s11032-018-0789-y
Plain language summary
Dry bean seeds are commonly used for cooking and canning for human consumption. One undesirable trait is 'hard-to-cook' or 'stone' seed. A stone seed does not absorb water even after overnight soaking. The trait is affected by both environmental and genetic factors. This study aims to identify the unknown genetic factors and associated DNA markers. A black bean variety was identified as a hard line with high percentage of stone seeds, while another line was selected as a soft line with no or very low percentage of stone seeds. A genetic population was developed with the two lines as parents for this study. The materials were grown at two locations in southern Manitoba over the past three years. Seed samples were harvested manually at maturity to test for seed hardness traits by soaking the seeds overnight at room temperature. The DNA sequence was also determined for each of the lines. This multi-year-site study shows that despite large environmental effects, seed-hardness is a highly heritable trait. Three specific regions on the chromosomes were identified, with each of the regions potentially contains a gene that controls seed hardness traits. While one of the regions confirmed previous findings, two regions were new regions. The identification of the three DNA regions and markers associated with seed hardness can be applied for common bean variety improvement and genetic exploitation of these traits.
Abstract
Seed hardness trait has a profound impact on cooking time and canning quality in dry beans. This study aims to identify the unknown genetic factors and associated molecular markers to better understand and tag this trait. An F2:7 recombinant inbred line (RIL) population was derived from a cross between the hard and soft seeded black bean parents (H68-4 and BK04-001). Eighty-five RILs and the parental lines were grown at two locations in southern Manitoba during years 2014–2016. Seed samples were harvested manually at maturity to test for seed hardness traits. The hydration capacity and stone seed count were estimated by soaking the seeds overnight at room temperature following AACC method 56-35.01. Seed samples from 2016 tests were also cooked to determine effect of seed hardness on cooking quality. For mapping of genomic regions contributing to the traits, the RIL population was genotyped using the genotype by sequencing (GBS) approach. The QTL mapping revealed that in addition to the major QTL on chromosome 7 at a genomic location previously reported to affect seed-hydration, two novel QTL with significant effects were also detected on chromosomes 1 and 2. In addition, a major QTL affecting the visual appeal of cooked bean was mapped on chromosome 4. This multi-year-site study shows that despite large environmental effects, seed hardness is an oligo-genic and highly heritable trait, which is inherited independently of the cooking quality scored as visual appeal of cooked beans. The identification of the QTLs and development of SNP markers associated with seed hardness can be applied for common bean variety improvement and genetic exploitation of these traits.