Hao Wei, Wang Shengji, Liu Huajing, Zhou Boru, Wang Xinwang, Jiang Tingbo
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China; College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, China.
PLoS One. 2015 Apr 29;10(4):e0125235. doi: 10.1371/journal.pone.0125235. eCollection 2015.
In order to study genetic diversity of white birch (Betula platyphylla), 544 primer pairs were designed based on the genome-wide Solexa sequences. Among them, 215 primer pairs showed polymorphism between five genotypes and 111 primer pairs that presented clear visible bands in genotyping 41 white birch plants that were collected from 6 different geographical regions. A total of 717 alleles were obtained at 111 loci with a range of 2 to 12 alleles per locus. The results of statistic analysis showed that polymorphic frequency of the alleles ranged from 17% to 100% with a mean of 55.85%; polymorphism information content (PIC) of the loci was from 0.09 to 0.58 with a mean of 0.30; and gene diversity between the tested genotypes was from 0.01 to 0.66 with a mean of 0.36. The results also indicated that major allele frequency ranged from 0.39 to 1.00 with an mean of 0.75; expected heterozygosity from 0.22 to 0.54 with a mean of 0.46; observed heterozygosity from 0.02 to 0.95 with a mean of 0.26; Nei's index from 0.21 to 0.54 with a mean of 0.46; and Shannon's Information from 0.26 to 0.87 with a mean of 0.66. The 41 white birch genotypes at the 111 selected SSR loci showed low to moderate similarity (0.025-0.610), indicating complicated genetic diversity among the white birch collections. The UPGMA-based clustering analysis of the allelic constitution of 41 white birch genotypes at 111 SSR loci suggested that the six different geographical regions can be further separated into four clusters at a similarity coefficient of 0.22. Genotypes from Huanren and Liangshui provenances were grouped into Cluster I, genotypes from Xiaobeihu and Qingyuan provenances into Cluster II, genotypes from Finland provenance into Cluster III, and genotypes from Maoershan into Cluster IV. The information provided in this study could help for genetic improvement and germplasm conservation, evaluation and utilization in white birch tree breeding program.
为研究白桦（Betula platyphylla）的遗传多样性，基于全基因组Solexa序列设计了544对引物。其中，215对引物在5个基因型间表现出多态性，111对引物在对从6个不同地理区域收集的41株白桦进行基因分型时呈现出清晰可见的条带。在111个位点共获得717个等位基因，每个位点的等位基因数在2至12个之间。统计分析结果表明，等位基因的多态频率在17%至100%之间，平均为55.85%；位点的多态信息含量（PIC）在0.09至0.58之间，平均为0.30；测试基因型间的基因多样性在0.01至0.66之间，平均为0.36。结果还表明，主要等位基因频率在0.39至1.00之间，平均为0.75；期望杂合度在0.22至0.54之间，平均为0.46；观察杂合度在0.02至0.95之间，平均为0.26；Nei指数在0.21至0.54之间，平均为0.46；Shannon信息在0.26至0.87之间，平均为0.66。在111个选定的SSR位点上，41个白桦基因型表现出低到中等的相似性（0.025 - 0.610），表明白桦收集品之间的遗传多样性复杂。基于UPGMA对41个白桦基因型在111个SSR位点的等位基因构成进行聚类分析表明，在相似系数为0.22时，6个不同地理区域可进一步分为4个类群。桓仁和凉水种源的基因型归为类群I，小北湖和清原种源的基因型归为类群II，芬兰种源的基因型归为类群III，帽儿山的基因型归为类群IV。本研究提供的信息有助于白桦树育种计划中的遗传改良以及种质资源的保存、评估和利用。
