Genetic Control of Seed Coat Darkening in Common Bean Cultivars from Three Market Classes

Abstract

Common bean (Phaseolus vulgaris L.) cultivars with slow seed coat darkening benefit the growers by extending the seed storage period without losses in commercial quality. Seed coat darkening in pinto and carioca seeded common bean is controlled by recessive genes, but it is not known whether these genes are different or not. The objectives of this study were (i) to verify if the gene that controls seed coat darkening in common bean cultivars from different market classes is the same, and (ii) to evaluate the efficiency of the simple sequence repeat (SSR) marker Pvsd‐1158 and the single nucleotide polymorphism (SNP) marker PvbHLHp12804 linked to the Sd gene in identifying carioca and mulatinho seeded lines contrasting for seed coat darkening. Seventeen lines were used for genotypic and phenotypic evaluations in two trials, and F2:3 progenies obtained from crosses between one pinto bean line (Sd gene) and two carioca lines that have slow seed coat darkening were used in segregation tests. The result of the two markers was identical and shown 87.5% coincidence with phenotypic data. Only two lines, CNFM 11940 (mulatinho) and TAA Dama (carioca), exhibited slow seed coat darkening and marker alleles related to regular darkening. Therefore, there was recombination between the markers and the Sd gene, or there is another gene causing slow seed coat darkening in these lines. All F2:3 progenies exhibited slow seed coat darkening, indicating that there was no segregation. The two markers are efficient for assisted selection. Results of the genotypic evaluations and the segregation test indicating that the same gene (Sd) is responsible for seed coat darkening in pinto and carioca beans.

Genome-wide association mapping reveals new loci associated with light-colored seed coat at harvest and slow darkening in carioca beans

“…Considering the ΔL* to be the trait that most efficiently expresses tolerance to PHD, six QTL were mapped on four different chromosomes. This is the first study involving GWAS for tolerance to PHD, and unlike previous studies that reported monogenic control for the trait [16,21,22,32], our results showed oligogenic control. Corroborating the more complex profile of the trait, broad-sense heritability was the lowest estimated (i.e., 0.5) and the genotype × environment interaction was highly significant.…”

“…Just as for darkening in pinto, cranberry, and red bean varieties, one of the most significant factors that lead to devaluation of carioca beans after harvest is seed coat darkening, because consumers presume, they are older and more difficult to cook [31]. However, carioca beans, unlike other varieties, are devalued not only through darkening over time, but those that have low seed coat lightness (i.e., darker beans) at harvest time are devalued for the producer for the same reason mentioned above [28,32]. Therefore, Brazilian bean breeding programs have concentrated not only on developing carioca bean cultivars with tolerance to PHD, but those with the lightest colored grain possible [16], cultivars such as BRSMG-Madrepérola [33] and IAC-Polaco [34].…”

“…The GWAS showed that the QTL involved in seed coat lightness after the storage period (L30) and in tolerance to PHD (ΔL*) are different, and it is noteworthy that only the L30 had significant QTL on the Pv07 chromosome close to the sd locus (i.e., SNP ss715647732 was positioned 2.5 Mb from the Pvsd-0028 marker) reported by Felicetti et al [ 13 ] as associated with the SD trait in pinto beans. Rodrigues et al [ 32 ] found that the same locus is responsible for tolerance to PHD in carioca beans, and Alvares et al [ 23 ] validated the markers for selection of lighter-colored lines after storage. All the studies mentioned used only color after storage information, ignoring the initial color.…”

“…Previous studies classified the genotypes as SD and RD based only on evaluation of the color trait (i.e., diagrammatic scoring scale) or measurement of color (i.e., digital analysis and colorimeters) after a determined storage period, without considering the initial color of the grain [10,16,29,31,32]. Fundamentally, the SD trait should be associated with the fact that a given genotype loses little lightness of color over time, and not with the fact that it has light-colored grain after the storage period.…”

“…The CDP was validated for GWAS by Almeida et al [9] and consists of the main commercial cultivars of carioca bean in Brazil, from the first cultivar (i.e., 'Carioca comum') released in 1971 [52] to more modern cultivars, such as IAC-1850, released in 2019 [53]. The set also includes genotypes with contrasting seed coat darkening rates identified in previous studies, with the RD cultivars BRS-Cometa, BRS-Estilo, BRS-Pérola, BRS-Pontal, BRS-Requinte, IAC-Alvorada, and BRS-Majestoso [10,16,17,23,28,29,32] and the SD cultivars BRS-Madrepérola, ANFC-9, Branquinho, and TAA-Dama [28,32,33].…”