Wang Jing, Feng Li, Mu Shuaicheng, Dong Ang, Gan Jinwen, Wen Zhenying, Meng Juan, Li Mingyu, Wu Rongling, Sun Lidan
Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
Hortic Res. 2022 May 17;9:uhac104. doi: 10.1093/hr/uhac104. eCollection 2022.
Hexaploids, a group of organisms containing three complete sets of chromosomes in a single nucleus, are of utmost importance to evolutionary studies and breeding programs. Many studies have focused on hexaploid linkage analysis and QTL mapping in controlled crosses, but little methodology has been developed to reveal how hexaploids diversify and evolve in natural populations. We formulate a general framework for studying the pattern of genetic variation in autohexaploid populations through testing deviation from Hardy-Weinberg equilibrium (HWE) at individual molecular markers. We confirm that hexaploids cannot reach exact HWE but can approach asymptotic HWE at 8-9 generations of random mating. We derive a statistical algorithm for testing HWE and the occurrence of double reduction for autopolyploids, a phenomenon that affects population variation during long evolutionary processes. We perform computer simulation to validate the statistical behavior of our test procedure and demonstrate its usefulness by analyzing a real data set for autohexaploid chrysanthemum. When extended to allohexaploids, our test procedure will provide a generic tool for illustrating the genome structure of hexaploids in the quest to infer their evolutionary status and design association studies of complex traits.
六倍体是指在单个细胞核中含有三组完整染色体的一类生物体，对进化研究和育种计划至关重要。许多研究都集中在六倍体的连锁分析和受控杂交中的数量性状位点（QTL）定位上，但很少有方法被开发出来以揭示六倍体在自然种群中是如何多样化和进化的。我们通过检测个体分子标记处偏离哈迪-温伯格平衡（HWE）的情况，制定了一个研究同源六倍体群体遗传变异模式的通用框架。我们证实六倍体无法达到精确的HWE，但在随机交配8 - 9代时可以接近渐近HWE。我们推导了一种用于检测HWE和多倍体双减数发生情况的统计算法，双减数是一种在漫长进化过程中影响种群变异的现象。我们进行计算机模拟以验证我们测试程序的统计行为，并通过分析同源六倍体菊花的真实数据集来证明其有用性。当扩展到异源六倍体时，我们的测试程序将提供一个通用工具，用于阐明六倍体的基因组结构，以推断其进化状态并设计复杂性状的关联研究。
