Abstract
Flowering is an important agronomic trait. Quantile regression (QR) can be used to fit models for all portions of a probability distribution. In Genome-wide association studies (GWAS), QR can estimate SNP (Single Nucleotide Polymorphism) effects on each quantile of interest. The objectives of this study were to estimate genetic parameters and to use QR to identify genomic regions for phenological traits (Days to first flower—DFF; Days for flowering—DTF; Days to end of flowering—DEF) in common bean. A total of 80 genotypes of common beans, with 3 replicates were raised at 4 locations and seasons. Plants were genotyped for 384 SNPs. Traditional single-SNP and 9 QR models, ranging from equally spaced quantiles (τ) 0.1 to 0.9, were used to associate SNPs to phenotype. Heritabilities were moderate high, ranging from 0.32 to 0.58. Genetic and phenotypic correlations were all high, averaging 0.66 and 0.98, respectively. Traditional single-SNP GWAS model was not able to find any SNP-trait association. On the other hand, when using QR methodology considering one extreme quantile (τ = 0.1) we found, respectively 1 and 7, significant SNPs associated for DFF and DTF. Significant SNPs were found on Pv01, Pv02, Pv03, Pv07, Pv10 and Pv11 chromosomes. We investigated potential candidate genes in the region around these significant SNPs. Three genes involved in the flowering pathways were identified, including Phvul.001G214500, Phvul.007G229300 and Phvul.010G142900.1 on Pv01, Pv07 and Pv10, respectively. These results indicate that GWAS-based QR was able to enhance the understanding on genetic architecture of phenological traits (DFF and DTF) in common bean.
Highlights
The common bean (Phaseolus vulgaris L.) is the world’s most important grain legume for human consumption [1]
Phenological traits associated with the flowering time, such as days to flowering (DTF), days to first flower (DFF), and days to end of flowering (DEF), are used in selection programs of the common bean
The goodness-of-fit for models with and without genotype-by-environmental interaction was assessed by Akaike information criterion (AIC), Bayesian information criterion (BIC), and likelihood ratio test (LRT; Table 2)
Summary
The common bean (Phaseolus vulgaris L.) is the world’s most important grain legume for human consumption [1]. Common bean is cultivated especially in African and Latin American countries, and is a key commodity for food security improvement because of the low-input agricultural systems required for production [2]. Phenological traits associated with the flowering time, such as days to flowering (DTF), days to first flower (DFF), and days to end of flowering (DEF), are used in selection programs of the common bean. Several genetic mapping studies have been performed for the common bean, improving the understanding the genetic architecture of relevant traits [4, 5, 6, 7]. The inferences on positional candidate genes associated with the identified QTL have been widely poor
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