Genome-wide association mapping for early maturity in kintoki bean (Phaseolus vulgaris L.)

Japanese red or white common bean (Phaseolus vulgaris L.) cultivars, used to make sweetened boiled beans, are called "kintoki" beans. Kintoki beans are planted to precede winter wheat for crop rotation in Hokkaido, northern Japan. Therefore, early maturity is an important trait for them. The aim of this study was to map the genomic region associated with days to maturity in kintoki beans by genome-wide association study (GWAS). Significant single nucleotide polymorphisms associated with days to maturity were detected on chromosome 1 (Pv01) by GWAS in 3 years, and the candidate region for early maturity was mapped to a 473-kb region. Sequencing analysis indicated that Phvul.001G221100, a phytochrome A3 gene, is likely to be responsible for early maturity in kintoki cultivars: the insertion of a cytosine in exon 1 at position 47 644 850 on Pv01 causes a frameshift that creates an early stop codon. Our findings suggest that the loss-of-function mutation of Phvul.001G221100 is derived from a leading cultivar, 'Taisho-Kintoki', and is originated from a spontaneous mutation in the oldest kintoki cultivar, 'Hon-Kintoki'. The DNA markers targeting the functional insertion of phytochrome A3 will be useful for marker-assisted selection in kintoki bean breeding.