Near-gapless and haplotype-resolved apple genomes provide insights into the genetic basis of rootstock-induced dwarfing

文献类型： 外文期刊

第一作者： Li, Wei

作者： Li, Wei;Li, Hui;Sun, Haochen;Wang, Shiyao;Wang, Zijun;Li, Yuqi;Zhou, Bowen;Fan, Xingqiang;Xiong, Yao;Wang, Yi;Xu, Xuefeng;Han, Zhenhai;Chu, Chong;Zhang, Hengtao;Foster, Toshi M.;Lopez-Girona, Elena;Yu, Jiaxin;Li, Yi;Ma, Yue;Zhang, Ke;Zhang, Ke;Han, Yongming;Deng, Cecilia H.

作者机构：

期刊名称：NATURE GENETICS （ 影响因子：30.8； 五年影响因子：37.4 ）

ISSN： 1061-4036

年卷期： 2024 年 56 卷 3 期

页码：

收录情况： SCI

摘要： Dwarfing rootstocks have transformed the production of cultivated apples; however, the genetic basis of rootstock-induced dwarfing remains largely unclear. We have assembled chromosome-level, near-gapless and haplotype-resolved genomes for the popular dwarfing rootstock 'M9', the semi-vigorous rootstock 'MM106' and 'Fuji', one of the most commonly grown apple cultivars. The apple orthologue of auxin response factor 3 (MdARF3) is in the Dw1 region of 'M9', the major locus for rootstock-induced dwarfing. Comparing 'M9' and 'MM106' genomes revealed a 9,723-bp allele-specific long terminal repeat retrotransposon/gypsy insertion, DwTE, located upstream of MdARF3. DwTE is cosegregated with the dwarfing trait in two segregating populations, suggesting its prospective utility in future dwarfing rootstock breeding. In addition, our pipeline discovered mobile mRNAs that may contribute to the development of dwarfed scion architecture. Our research provides valuable genomic resources and applicable methodology, which have the potential to accelerate breeding dwarfing rootstocks for apple and other perennial woody fruit trees. Near-gapless and haplotype-resolved genome assemblies of the dwarfing 'M9' and semi-vigorous 'MM106' rootstocks and a major apple cultivar 'Fuji' provide insights into the genetic basis of rootstock-induced dwarfing traits.

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