Novel alleles for black and gray seed color genes in common bean

Abstract

Seed coat color is one of the most important characteristics of common bean (Phaseolus vulgaris L.). To understand the genetic basis of this trait a cross was made of two small seeded Mesoamerican bean plants from China, the varieties Longyundou 4 (Long 4) with black seed and Longyundou 5 (Long 5) with white seed. Using phenotypic classification, the genetic analysis showed that the inheritance of black, gray, and white seed color could be explained primarily by two independent genes in an addi-tive-dominant, two gene epistasis model with a significant (Ç2 = 1.65, p = 0.44) fit to the 12:3:1 segregation ratio. We also analyzed seed color as a quantitative trait to see whether significant loci aligned with any known seed color genes. To that end we developed 2357 new physically confirmed simple sequence repeat (SSR) markers (BMp series) based on the whole-genome sequences of common bean and genetically mapped 105 into the F2 bean map. Combining the results of the phenotypic analysis and the new genetic map, two major additive quantitative trait loci (QTL) were found on chromosome Pv07; near the markers BMg87, BMp7s201, and BMp7s206 that explained more than 38% of the phenotypic variation. This region may contain the Asp gene but was distal to the P gene. Several other epistatic QTL for seed color were detected on chromosome Pv08 possibly related to the V locus and on chromosome Pv11. The new linked markers would accelerate the cloning of seed coat color genes of common bean and their selection.