1. Genetic Architecture and Genomic Prediction of Cooking Time in Common Bean (Phaseolus vulgaris L.)
- Author
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Nirmala Arunachalam, Santiago Diaz, Hans-Peter Piepho, Bodo Raatz, Henry Ruiz, Harold Diaz, Johan Aparicio, Raisa Ramdeen, Carlos Hernandez, and Daniel Ariza-Suarez
- Subjects
0106 biological sciences ,0301 basic medicine ,Germplasm ,QTL ,Population ,Plant Science ,lcsh:Plant culture ,Biology ,Quantitative trait locus ,01 natural sciences ,03 medical and health sciences ,Genetic variation ,lcsh:SB1-1110 ,education ,Selection (genetic algorithm) ,Original Research ,Molecular breeding ,education.field_of_study ,cooking ,business.industry ,food and beverages ,prediction ,Genetic architecture ,Biotechnology ,030104 developmental biology ,Trait ,bean ,business ,genome-wide association mapping (GWAS) ,010606 plant biology & botany - Abstract
Cooking time of the common bean is an important trait for consumer preference, with implications for nutrition, health, and environment. For efficient germplasm improvement, breeders need more information on the genetics to identify fast cooking sources with good agronomic properties and molecular breeding tools. In this study, we investigated a broad genetic variation among tropical germplasm from both Andean and Mesoamerican genepools. Four populations were evaluated for cooking time (CKT), water absorption capacity (WAC), and seed weight (SdW): a bi-parental RIL population (DxG), an eight-parental Mesoamerican MAGIC population, an Andean (VEF), and a Mesoamerican (MIP) breeding line panel. A total of 922 lines were evaluated in this study. Significant genetic variation was found in all populations with high heritabilities, ranging from 0.64 to 0.89 for CKT. CKT was related to the color of the seed coat, with the white colored seeds being the ones that cooked the fastest. Marker trait associations were investigated by QTL analysis and GWAS, resulting in the identification of 10 QTL. In populations with Andean germplasm, an inverse correlation of CKT and WAC, and also a QTL on Pv03 that inversely controls CKT and WAC (CKT3.2/WAC3.1) were observed. WAC7.1 was found in both Mesoamerican populations. QTL only explained a small part of the variance, and phenotypic distributions support a more quantitative mode of inheritance. For this reason, we evaluated how genomic prediction (GP) models can capture the genetic variation. GP accuracies for CKT varied, ranging from good results for the MAGIC population (0.55) to lower accuracies in the MIP panel (0.22). The phenotypic characterization of parental material will allow for the cooking time trait to be implemented in the active germplasm improvement programs. Molecular breeding tools can be developed to employ marker-assisted selection or genomic selection, which looks to be a promising tool in some populations to increase the efficiency of breeding activities.
- Published
- 2021