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Genomic region and origin for selected traits during differentiation of small-fruit cultivars in Japanese apricot (Prunus mume)

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The Japanese apricot (Prunus mume) is a popular fruit tree in Japan. However, the genetic factors associated with fruit trait variations are poorly understood. In this study, we investigated nine fruit-associated traits, including harvesting time, fruit diameter, fruit shape, fruit weight, stone (endocarp) weight, ratio of stone weight to fruit weight, and rate of fruit gumming, using 110 Japanese apricot accessions over four years. A genome-wide association study (GWAS) was performed for these traits and strong signals were detected on chromosome 6 for harvesting time and fruit diameters. These peaks were shown to undergo strong artificial selection during the differentiation of small-fruit cultivars. The genomic region defined by the GWAS and XP-nSL analyses harbored several candidate genes associated with plant hormone regulation. Furthermore, the alleles of small-fruit cultivars in this region were shown to have genetic proximity to some Chinese cultivars of P. mume. These results indicate that the small-fruit trait originated in China; after being introduced into Japan, it was preferred and selected by the Japanese people, resulting in the differentiation of small-fruit cultivars.

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Data availability

Raw FASTQ reads for Prunus mume accessions sequenced in this study were deposited in the sequence read archive (SRA) under DRA accession number DRA016343.


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We are deeply grateful to the researchers and technicians at the Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, for maintaining the Prunus mume accessions. We would like to thank Drs. R. Ishikawa and T. Ishii, Graduate School of Agricultural Science, Kobe University, for investigation support and valuable discussions. This work was supported by JSPS KAKENHI Grant Number JP18K14449 to KN and Wakayama Prefecture.

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KN and YK conceived and designed the study. KN, YK, TK, TM, and TO performed the experiments. KN, YK, and TM analyzed the data. KN, YK, and TM contributed to the bioinformatics analysis. KN and YK prepared the manuscript. All the authors have read and approved the final manuscript.

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Correspondence to Koji Numaguchi.

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Communicated by Bing Yang.

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Numaguchi, K., Kitamura, Y., Kashiwamoto, T. et al. Genomic region and origin for selected traits during differentiation of small-fruit cultivars in Japanese apricot (Prunus mume). Mol Genet Genomics 298, 1365–1375 (2023).

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