Integrated GWAS, BSA-seq, and RNA-seq analyses to identify candidate genes associated with male fertility trait in peach

Zhenyu Huang; Hangling Bie; Ming Li; Lehan Xia; Long Chen; Yuling Chen; Lirong Wang; Zengyu Gan; Ke Cao

doi:10.1016/j.plaphy.2025.109525

Integrated GWAS, BSA-seq, and RNA-seq analyses to identify candidate genes associated with male fertility trait in peach

Plant Physiol Biochem. 2025 Jan 17:220:109525. doi: 10.1016/j.plaphy.2025.109525. Online ahead of print.

Authors

Zhenyu Huang¹, Hangling Bie², Ming Li¹, Lehan Xia³, Long Chen³, Yuling Chen³, Lirong Wang⁴, Zengyu Gan⁵, Ke Cao⁶

Affiliations

¹ National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China; Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang, 453500, China.
² National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
³ National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
⁴ National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China; Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, 831100, China. Electronic address: [email protected].
⁵ Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China. Electronic address: [email protected].
⁶ National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China; Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang, 453500, China. Electronic address: [email protected].

PMID: 39837212
DOI: 10.1016/j.plaphy.2025.109525

Abstract

Male sterility in peach (Prunus persica L.), characterized by the absence of fertile pollen grains in the anther, is determined by a recessive allele in homozygosis of the major gene located on chromosome 6. Developing tightly linked molecular markers can help identify appropriate peach parents or male-sterile plants for early culling in segregating progenies, thereby increasing breeding efficiency. In this study, we performed comprehensive research integrating genome-wide association study, bulked segregant analysis, and tissue-specific transcriptome sequencing for precisely characterizing the genes associated with male sterility and fertility in peach. We identified the candidate gene Prupe.6G027000, which encodes an ATP-binding cassette transporter G family member 26 (ABCG26), as a reliable candidate for controlling the targeted traits, as indicated by gene expression profiling and validated by quantitative real-time polymerase chain reaction, in situ hybridization, and virus-induced gene silencing. Prupe.6G027000 was transcribed preferentially on the tapetum and microspore surface, and its transient silencing caused severe pollen abortion in peach. The genotypes of nonsynonymous single-nucleotide variation (T > C) harbored in the coding region of Prupe.6G027000 exhibited approximately 96.2% consistency with male fertile or sterile phenotype in 579 peach accessions. These findings lay the foundation for dissecting the genetic basis of male fertility traits, and facilitating the establishment of a marker-assisted selection system in peaches.

Keywords: ABC transporter G family; Gene mining; Male fertility; Pollen development; Prunus persica L.