Genome-Wide Association Study Identifies Genomic Regions for Important Morpho-Agronomic Traits in Mesoamerican Common Bean

Abstract

The population growth trend in recent decades has resulted in continuing efforts to guarantee food security in which leguminous plants, such as the common bean (Phaseolus vulgaris L.), play a particularly important role as they are relatively cheap and have high nutritional value. To meet this demand for food, the main target for genetic improvement programs is to increase productivity, which is a complex quantitative trait influenced by many component traits. This research aims to identify Quantitative Trait Nucleotides (QTNs) associated with productivity and its components using multi-locus genome-wide association studies. Ten morpho-agronomic traits [plant height (PH), first pod insertion height (FPIH), number of nodules (NN), pod length (PL), total number of pods per plant (NPP), number of locules per pod (LP), number of seeds per pod (SP), total seed weight per plant (TSW), 100-seed weight (W100), and grain yield (YLD)] were evaluated in four environments for 178 Mesoamerican common bean domesticated accessions belonging to the Brazilian Diversity Panel. In order to identify stable QTNs, only those identified by multiple methods (mrMLM, FASTmrMLM, pLARmEB, and ISIS EM-BLASSO) or in multiple environments were selected. Among the identified QTNs, 64 were detected at least thrice by different methods or in different environments, and 39 showed significant phenotypic differences between their corresponding alleles. The alleles that positively increased the corresponding traits, except PH (for which lower values are desired), were considered favorable alleles. The most influenced trait by the accumulation of favorable alleles was PH, showing a 51.7% reduction, while NN, TSW, YLD, FPIH, and NPP increased between 18 and 34%. Identifying QTNs in several environments (four environments and overall adjusted mean) and by multiple methods reinforces the reliability of the associations obtained and the importance of conducting these studies in multiple environments. Using these QTNs through molecular techniques for genetic improvement, such as marker-assisted selection or genomic selection, can be a strategy to increase common bean production.

Height to first pod: A review of genetic and breeding approaches to improve combine harvesting in legume crops

“…>10-12-15 H 2 = 0.00-0.74 r = 0.23-0.71 Martin and Wilcox, 1973;Costa et al, 2008;Ramteke et al, 2012;Kang et al, 2017;Teixeira et al, 2017;Beiküfner et al, 2019;Seferova and Bulakh, 2019;Rêbilas et al, 2020;Sobko et al, 2020;Borowska and Prusiñski, 2021;Khadka et al, 2021 Common bean (Phaseolus vulgaris L.) 15 h 2 = 0.68-0.92 r = 0.43-0.69 Bisognin et al, 2019;Nadeem et al, 2020;Delfini et al, 2021;Girgel, 2021 Chickpea (Cicer arietinum L.)…”

“…Phvul.006G098300 = BEBT, Benzyl alcohol O-benzoyltransferase. Delfini et al, 2021 Phvul.006G098200 = WD40 or WDR, WD40-repeat gene. Alternative candidate gene.…”

“…The candidate gene BEBT (benzyl alcohol O-benzoyltransferase) was identified for the HFP trait in a Brazilian diversity panel of 178 accessions of common bean using a Genotyping-by-sequencing (GBS) approach (Delfini et al, 2021) (Table 3). Four Quantitative trait nucleotides (QTNs) in total were detected as involved in HFP, but only one QTN, with the BEBT candidate gene, showed the highest LOD score (3.84-6.86) (Delfini et al, 2021).…”

Towards Heat Tolerant Runner Bean (Phaseolus coccineus L.) by Utilizing Plant Genetic Resources

“…Next generation sequencing (NGS) technologies are important elements of modern plant breeding programs but also pivotal to discovering the genetic diversity of PGRs and selecting genotypes with desired traits [21][22][23]. With regard to runner bean, studies so far have mainly focused on the elucidation of the genetic diversity and evolutionary history of this species, using mostly single sequence repeat (SSR) and inter simple sequence repeat (ISSR) markers [5,[24][25][26].…”

“…With regard to runner bean, studies so far have mainly focused on the elucidation of the genetic diversity and evolutionary history of this species, using mostly single sequence repeat (SSR) and inter simple sequence repeat (ISSR) markers [5,[24][25][26]. No research has been performed so far linking the observed genetic variability of this species to relevant agronomic traits based on state-of-the-art methods, as has been performed for the closely related common bean through genomewide association studies (GWAS) [21,27,28]. These examples highlight the importance of the combination of NGS data with GWAS to characterize genetic markers associated to (agronomic) traits of relevance, which can be used in selection and breeding programs, as reviewed in [29].…”