J Integr Plant Biol ›› 2024, Vol. 66 ›› Issue (12): 2716-2735.DOI: 10.1111/jipb.13782  cstr: 32098.14.jipb.13782

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  • 收稿日期:2024-02-08 接受日期:2024-09-16 出版日期:2024-12-01 发布日期:2024-12-07

Haplotype-resolved genome of a heterozygous wild peach reveals the PdaWRKY4-PdaCYP716A1 module mediates resistance to aphids by regulating betulin biosynthesis

Jun‐Xiu Wang1,2,3,4†, Yong Li1,2,5†, Xin‐Wei Wang1,2,5†, Ke Cao1,5, Chang‐Wen Chen1,5, Jin‐Long Wu1,5, Wei‐Chao Fang1, Geng‐Rui Zhu1,2, Xue‐Jia Chen1, Dan‐Dan Guo1, Jiao Wang1, Ya‐Lin Zhao1, Jia‐Qi Fan1, Su‐Ning Liu1, Wen‐Qing Li1, Hang‐Ling Bie1, Qiang Xu3 and Li‐Rong Wang1,2,5*   

  1. 1. Zhengzhou Fruit Research Institute, National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Chinese Academy of Agricultural Sciences, Zhengzhou 451100, China
    2. Western Research Institute, Chinese Academy of Agricultural Sciences, Changji 831100, China
    3. College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
    4. Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
    5. National Horticulture Germplasm Resources Center of China (NPGRC), Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 451100, China
    †These authors contributed equally to this work.
    *Correspondence: Li‐Rong Wang (wanglirong@caas.cn)
  • Received:2024-02-08 Accepted:2024-09-16 Online:2024-12-01 Published:2024-12-07
  • Supported by:
    This study was supported by the National Key Research and Development Program (2023YFE0105400), Central Public‐interest Scientific Institution Basal Research Fund (Y2022QC23), the Agricultural Science and Technology Innovation Program (CAAS‐ASTIP‐2023‐ZFRI‐01), Natural Science Foundation of Henan (232300421042), the Crop Germplasm Resources Conservation Project (2016NWB041), the National Natural Science Foundation of China (32402492) and the National Key Research and Development Program (2019YFD1000200).

Abstract: Wild species of domesticated crops provide valuable genetic resources for resistance breeding. Prunus davidiana, a wild relative of peach with high heterozygosity and diverse stress tolerance, exhibits high resistance against aphids. However, the highly heterozygous genome of P. davidiana makes determining the underlying factors influencing resistance traits challenging. Here, we present the 501.7 Mb haplotype-resolved genome assembly of P. davidiana. Genomic comparisons of the two haplotypes revealed 18,152 structural variations, 2,699 Pda_hap1-specific and 2,702 Pda_hap2-specific genes, and 1,118 allele-specific expressed genes. Genome composition indicated 4.1% of the P. davidiana genome was non-peach origin, out of which 94.5% was derived from almond. Based on the haplotype genome, the aphid resistance quantitative trait locus (QTL) was mapped at the end of Pda03. From the aphid resistance QTL, PdaWRKY4 was identified as the major dominant gene, with a 9-bp deletion in its promoter of the resistant phenotype. Specifically, PdaWRKY4 regulates aphid resistance by promoting PdaCYP716A1-mediated anti-aphid metabolite betulin biosynthesis. Moreover, we employed a genome design to develop a breeding workflow for rapidly and precisely producing aphid-resistant peaches. In conclusion, this study identifies a novel aphid resistance gene and provides insights into genome design for the development of resistant fruit cultivars.

Key words: allele‐specific expression, aphid resistance, hap-lotype genome, PdaWRKY4, peach

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