Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
Molecules. 2018 Nov 13;23(11):2963. doi: 10.3390/molecules23112963.
is a fast-growing valuable indigenous tree species with multiple uses in the tropical and warm subtropical regions in South-East Asia and southern China. It has been proved to be tetraploid in most parts of its distribution in China. In the present study, next generation sequencing (NGS) technology was applied to develop numerous SSR markers for , and 64,376 contig sequences of 106,452 clean reads containing 164,357 candidate SSR loci were obtained. Among the derived SSR repeats, mono-nucleotide was the main type (77.05%), followed by di- (10.18%), tetra- (6.12%), tri- (3.56%), penta- (2.14%) and hexa-nucleotide (0.95%). The short nucleotide sequence repeats accounted for 90.79%. Among the 291 repeat motifs, AG/CT (46.33%) and AT/AT (44.15%) were the most common di-nucleotide repeats, while AAT/ATT (48.98%) was the most common tri-nucleotide repeats. A total of 2549 primer sets were designed from the identified putative SSR regions of which 900 were randomly selected for evaluation of amplification successfulness and detection of polymorphism if amplified successfully. Three hundred and ten polymorphic markers were obtained through testing with 24 individuals from natural forest in Jingxi County, Guangxi, China. The number of alleles () of each marker ranged from 2 to 19 with a mean of 5.14. The observed () and expected () heterozygosities varied from 0.04 to 1.00 and 0.04 to 0.92 with their means being 0.64 and 0.57, respectively. Shannon-Wiener diversity index () ranged from 0.10 to 2.68 with a mean of 1.12. Cross-species transferability was further examined for 96 pairs of SSR primers randomly selected, and it was found that 48.96⁻84.38% of the primer pairs could successfully amplify each of six related species. The obtained SSR markers can be used to study population genetics and molecular marker assisted breeding, particularly genome-wide association study of these species in the future.
是一种在东南亚和中国南部的热带和暖亚热带地区有多种用途的快速生长的珍贵乡土树种。在中国的分布区，它已被证明为四倍体。本研究应用新一代测序（NGS）技术开发了大量 SSR 标记，从 106,452 条清洁读长中获得了 64,376 个 contig 序列，其中包含 164,357 个候选 SSR 位点。在衍生的 SSR 重复中，单核苷酸是主要类型（77.05%），其次是二核苷酸（10.18%）、四核苷酸（6.12%）、三核苷酸（3.56%）、五核苷酸（2.14%）和六核苷酸（0.95%）。短核苷酸序列重复占 90.79%。在 291 个重复基序中，AG/CT（46.33%）和 AT/AT（44.15%）是最常见的二核苷酸重复，而 AAT/ATT（48.98%）是最常见的三核苷酸重复。从鉴定的潜在 SSR 区域中设计了 2549 对引物，其中 900 对随机选择用于评估扩增成功率和检测多态性，如果成功扩增。通过对来自中国广西靖西县天然林的 24 个个体进行测试，获得了 310 个多态性标记。每个标记的等位基因（）数范围为 2 至 19，平均值为 5.14。观察（）和预期（）杂合度范围分别为 0.04 至 1.00 和 0.04 至 0.92，平均值分别为 0.64 和 0.57。香农-威纳多样性指数（）范围为 0.10 至 2.68，平均值为 1.12。进一步对随机选择的 96 对 SSR 引物进行了种间转移能力的检验，发现 48.96-84.38%的引物对可以成功扩增 6 个相关种中的每一种。获得的 SSR 标记可用于研究种群遗传学和分子标记辅助育种，特别是这些物种的全基因组关联研究。
