GSE159374
Recognition and fine genetic mapping of the golden pod gene (pv-ye) from the common bean (Phaseolus vulgaris L.)
The pod is the main edible part of Phaseolus vulgaris L. (common bean). The commercial use of the pods is mainly affected by their color. Consumers seem to prefer golden pods. However, planters suffer economic losses because of pod color instability. The aim of the present study was to identify the gene responsible for the golden pod trait in the common bean. 'A18-1' (a golden bean line) and 'Renaya' (a green bean line) were chosen as the experimental materials. Genetic analysis indicated that a single recessive gene, pv-ye, controls the golden pod trait. A candidate region of 4.24-Mb was mapped to chromosome A02 using bulked-segregant analysis coupled to whole genome sequencing. In this region, linkage analysis in an F2 population localized the pv-ye gene to an interval of 182.9-kb between the simple sequence repeat markers SSR77 and SSR93. This region comprised 16 genes in this region, comprising 12 annotated genes from the P. vulgaris database, and 4 functionally unknown genes. Combined with transcriptome sequencing, we identified Phvul.002G006200 as the potential candidate gene for pv-ye. Sequencing of Phvul.002G006200 identified a single nucleotide polymorphism (SNP) in pv-ye. This SNP is located in the coding region and is responsible for substituting a glutamic acid with an glutamine at position 416 of the pv-ye protein (E416Q). A pair of primers covering the SNP was designed and the fragment was sequenced to screen 316 F2 plants with the 'A18-1' phenotype, based on the different site. Our findings showed that the among the 316 mapped individuals, the SNP cosegregated with the 'A18-1' phenotype. The findings presented here could form the basis to reveal the mechanism of the golden pod trait in the common bean at the molecular level. Overall design: The present study identified the pv-ye gene, which is responsible for the golden pod trait of line 'A18-1' of the common bean. The pod color of A18-1 changes gradually from green to gold as the tender pods develop into mature commercial pods, and Renaya (R), whose pod color remains green until ripening. From lines R (Renaya) and A (A18-1), pod walls were collected at 10, 14, and 18 (A10, A14, A18) DAF as RNA-seq materials, with three independent biological repeats.