Tsumura Yoshihiko, Uchiyama Kentaro, Moriguchi Yoshinari, Kimura Megumi K, Ueno Saneyoshi, Ujino-Ihara Tokuko
Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba Ibaraki 305-8687, Japan
Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba Ibaraki 305-8687, Japan.
G3 (Bethesda). 2014 Oct 14;4(12):2389-402. doi: 10.1534/g3.114.013896.
Local adaptation of plant species is a central issue for survival during global climate change, especially for long-lived forest trees, with their lengthy regeneration time and spatially limited gene flow. Identification of loci and/or genomic regions associated with local adaptation is necessary for knowledge of both evolution and molecular breeding for climate change. Cryptomeria japonica is an important species for forestry in Japan; it has a broad natural distribution and can survive in a range of different environments. The genetic structure of 14 natural populations of this species was investigated using 3930 SNP markers. Populations on the Pacific Ocean side of Japan are clearly different from those on the Japan Sea side, as discussed in previous studies. Structure analysis and population network trees show that peripheral populations, including the most northerly and southerly ones, have unique features. We found that the genetic differentiation coefficient is low, FST = 0.05, although it must account for the presence of important genes associated with adaptation to specific environments. In total, 208 outlier loci were detected, of which 43 were associated with environmental variables. Four clumped regions of outlier loci were detected in the genome by linkage analysis. Linkage disequilibrium (LD) was quite high in these clumps of outlier loci, which were found in linkage groups (LGs) 2, 7, 10, and 11, especially between populations of two varieties, and when interchromosomal LD was also detected. The LG7 region is characteristic of the Yakushima population, which is a large, isolated, peripheral population occupying a specific environment resulting from isolation combined with volcanic activity in the region. The detected LD may provide strong evidence for selection between varieties.
植物物种的局部适应性是全球气候变化下生存的核心问题，对于寿命长、再生时间长且基因流空间有限的森林树木而言尤为如此。识别与局部适应性相关的基因座和/或基因组区域对于了解气候变化的进化和分子育种都至关重要。日本柳杉是日本林业的重要树种；它具有广泛的自然分布，能在一系列不同环境中生存。利用3930个单核苷酸多态性（SNP）标记对该物种14个自然种群的遗传结构进行了研究。正如先前研究所讨论的，日本太平洋沿岸的种群与日本海沿岸的种群明显不同。结构分析和种群网络树表明，包括最北部和最南部种群在内的边缘种群具有独特特征。我们发现遗传分化系数较低，FST = 0.05，尽管它必定解释了与适应特定环境相关的重要基因的存在。总共检测到208个异常基因座，其中43个与环境变量相关。通过连锁分析在基因组中检测到四个异常基因座的聚集区域。这些异常基因座聚集区域的连锁不平衡（LD）相当高，它们存在于连锁群（LG）2、7、10和11中，特别是在两个变种的种群之间，并且还检测到了染色体间的LD。LG7区域是屋久岛种群的特征，屋久岛种群是一个大型、孤立的边缘种群，由于该地区的隔离和火山活动而占据特定环境。检测到的LD可能为变种间的选择提供有力证据。
