{"title":"杂合野生桃的单倍型基因组显示,PdaWRKY4-PdaCYP716A1模块通过调节甜菜素的生物合成来介导对蚜虫的抗性。","authors":"Jun-Xiu Wang, Yong Li, Xin-Wei Wang, Ke Cao, Chang-Wen Chen, Jin-Long Wu, Wei-Chao Fang, Geng-Rui Zhu, Xue-Jia Chen, Dan-Dan Guo, Jiao Wang, Ya-Lin Zhao, Jia-Qi Fan, Su-Ning Liu, Wen-Qing Li, Hang-Ling Bie, Qiang Xu, Li-Rong Wang","doi":"10.1111/jipb.13782","DOIUrl":null,"url":null,"abstract":"<div>\n \n <p>Wild species of domesticated crops provide valuable genetic resources for resistance breeding. <i>Prunus davidiana</i>, a wild relative of peach with high heterozygosity and diverse stress tolerance, exhibits high resistance against aphids. However, the highly heterozygous genome of <i>P. davidiana</i> makes determining the underlying factors influencing resistance traits challenging. Here, we present the 501.7 Mb haplotype-resolved genome assembly of <i>P. davidiana</i>. 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 <i>P. davidiana</i> 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, <i>PdaWRKY4</i> was identified as the major dominant gene, with a 9-bp deletion in its promoter of the resistant phenotype. Specifically, <i>PdaWRKY4</i> regulates aphid resistance by promoting <i>PdaCYP716A1</i>-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.</p></div>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"66 12","pages":"2716-2735"},"PeriodicalIF":9.3000,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.13782","citationCount":"0","resultStr":"{\"title\":\"Haplotype-resolved genome of a heterozygous wild peach reveals the PdaWRKY4-PdaCYP716A1 module mediates resistance to aphids by regulating betulin biosynthesis\",\"authors\":\"Jun-Xiu Wang, Yong Li, Xin-Wei Wang, Ke Cao, Chang-Wen Chen, Jin-Long Wu, Wei-Chao Fang, Geng-Rui Zhu, Xue-Jia Chen, Dan-Dan Guo, Jiao Wang, Ya-Lin Zhao, Jia-Qi Fan, Su-Ning Liu, Wen-Qing Li, Hang-Ling Bie, Qiang Xu, Li-Rong Wang\",\"doi\":\"10.1111/jipb.13782\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div>\\n \\n <p>Wild species of domesticated crops provide valuable genetic resources for resistance breeding. <i>Prunus davidiana</i>, a wild relative of peach with high heterozygosity and diverse stress tolerance, exhibits high resistance against aphids. However, the highly heterozygous genome of <i>P. davidiana</i> makes determining the underlying factors influencing resistance traits challenging. Here, we present the 501.7 Mb haplotype-resolved genome assembly of <i>P. davidiana</i>. 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 <i>P. davidiana</i> 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, <i>PdaWRKY4</i> was identified as the major dominant gene, with a 9-bp deletion in its promoter of the resistant phenotype. Specifically, <i>PdaWRKY4</i> regulates aphid resistance by promoting <i>PdaCYP716A1</i>-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.</p></div>\",\"PeriodicalId\":195,\"journal\":{\"name\":\"Journal of Integrative Plant Biology\",\"volume\":\"66 12\",\"pages\":\"2716-2735\"},\"PeriodicalIF\":9.3000,\"publicationDate\":\"2024-10-25\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.13782\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Integrative Plant Biology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1111/jipb.13782\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Integrative Plant Biology","FirstCategoryId":"99","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1111/jipb.13782","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
Haplotype-resolved genome of a heterozygous wild peach reveals the PdaWRKY4-PdaCYP716A1 module mediates resistance to aphids by regulating betulin biosynthesis
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.
期刊介绍:
Journal of Integrative Plant Biology is a leading academic journal reporting on the latest discoveries in plant biology.Enjoy the latest news and developments in the field, understand new and improved methods and research tools, and explore basic biological questions through reproducible experimental design, using genetic, biochemical, cell and molecular biological methods, and statistical analyses.