Xiong Yi, Yuan Shuai, Xiong Yanli, Li Lizuiyue, Peng Jinghan, Zhang Jin, Fan Xing, Jiang Chengzhi, Sha Li-Na, Wang Zhaoting, Peng Xue, Zhang Zecheng, Yu Qingqing, Lei Xiong, Dong Zhixiao, Liu Yingjie, Zhao Junming, Li Guangrong, Yang Zujun, Jia Shangang, Li Daxu, Sun Ming, Bai Shiqie, Liu Jianquan, Yang Yongzhi, Ma Xiao
College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
Nat Commun. 2025 Apr 1;16(1):3104. doi: 10.1038/s41467-025-58341-0.
Phylogenetic origin of the Y haplome present in allopolyploid Triticeae species remains unknown. Here, we report the 10.47 Gb chromosome-scale genome of allohexaploid Elymus nutans (StStYYHH). Phylogenomic analyses reveal that the Y haplome is sister to the clade comprising V and Jv haplomes from Dasypyrum and Thinopyum. In addition, H haplome from the Hordeum-like ancestor, St haplome from the Pseudoroegneria-like ancestor and Y haplome are placed in the successively diverged clades. Resequencing data reveal the allopolyploid origins with St, Y, and H haplome combinations in Elymus. Population genomic analyses indicate that E. nutans has expanded from medium to high/low-altitude regions. Phenotype/environmental association analyses identify MAPKKK18 promoter mutations reducing its expression, aiding UV-B adaptation in high-altitude populations. These findings enhance understanding of allopolyploid evolution and aid in breeding forage and cereal crops through intergeneric hybridization within Triticeae.
异源多倍体小麦族物种中存在的Y单倍群的系统发育起源仍然未知。在此，我们报道了异源六倍体垂穗披碱草（StStYYHH）的10.47Gb染色体水平基因组。系统发育基因组分析表明，Y单倍群是包含来自簇毛麦属和偃麦草属的V和Jv单倍群的分支的姐妹群。此外，来自类大麦属祖先的H单倍群、来自类拟鹅观草属祖先的St单倍群和Y单倍群被置于相继分化的分支中。重测序数据揭示了垂穗披碱草中St、Y和H单倍群组合的异源多倍体起源。群体基因组分析表明，垂穗披碱草已从中海拔地区扩展到高/低海拔地区。表型/环境关联分析确定了MAPKKK18启动子突变降低了其表达，有助于高海拔群体适应UV-B。这些发现增进了对异源多倍体进化的理解，并有助于通过小麦族内的属间杂交培育饲料和谷类作物。
