State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China.
Southern Swedish Forest Research Center, Swedish University of Agricultural Sciences, SE-230 53 Alnarp, Sweden.
Genes (Basel). 2020 May 2;11(5):500. doi: 10.3390/genes11050500.
has significant economic and ecological value in Northeast China. However, due to the lack of suitable molecular markers, only a few available microsatellite markers were developed for further population genetics studies. In this study, for the first time we developed expressed sequence tag-simple sequence repeat (EST-SSR) markers from the cold-stressed transcriptome of using Illumina Sequencing. We identified a total of 7,235 EST-SSRs from 97,376 sequences, and we tested their transferability among seven related Pinus species. The results showed that trinucleotides were the most abundant type of repeat (1287, 18.74%) excluding mononucleotides, followed by dinucleotides (1284, 18.7%) and tetranucleotides (72, 1.05%). The most dominant dinucleotides and trinucleotide repeat motifs were AT/AT (535, 7.79%) and AAT/ATT (103, 1.5%). The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.002 to 0.986 and 0.017 to 0.743, respectively, and the polymorphism information content (PIC) values and number of alleles (Na) varied from 0.029 to 0.794 and 2 to 23, respectively. A total of 8 natural populations were divided into two main genetic clusters. Furthermore, nine of twenty polymorphic primer pairs were successfully amplified in seven Pinus species, and at least 80% of the successful EST-SSR primers could be amplified in more than four species (16, 80%). Combined results for the development of EST-SSR markers in and transferability among related species would contribute to improved studies on the genetic diversity and population structure in and phylogenetic relationships among Pinus species. They would also provide a significant source for quantitative trait locus analysis.
在中国东北地区具有重要的经济和生态价值。然而，由于缺乏合适的分子标记，仅开发了少数可用的微卫星标记用于进一步的种群遗传研究。在这项研究中，我们首次使用 Illumina 测序从冷胁迫转录组中开发了表达序列标签-简单重复序列（EST-SSR）标记。我们从 97376 个序列中总共鉴定出 7235 个 EST-SSR，并测试了它们在 7 个相关松属物种中的可转移性。结果表明，三核苷酸是最丰富的重复类型（1287，18.74%），不包括单核昔酸，其次是二核苷酸（1284，18.7%）和四核苷酸（72，1.05%）。最主要的二核苷酸和三核苷酸重复基序是 AT/AT（535，7.79%）和 AAT/ATT（103，1.5%）。观察杂合度（Ho）和期望杂合度（He）范围分别为 0.002-0.986 和 0.017-0.743，多态信息含量（PIC）值和等位基因数（Na）范围分别为 0.029-0.794 和 2-23。总共 8 个自然种群分为两个主要遗传群。此外，在七个松属物种中成功扩增了 20 个多态性引物对中的 9 对，至少有 80%的成功 EST-SSR 引物可以在四个以上物种中扩增（16，80%）。在 和相关物种之间的可转移性方面，EST-SSR 标记的开发综合结果将有助于提高对 的遗传多样性和种群结构以及松属物种系统发育关系的研究。它们还将为数量性状基因座分析提供重要来源。
