Ziya Motalebipour Elmira, Kafkas Salih, Khodaeiaminjan Mortaza, Çoban Nergiz, Gözel Hatice
Department of Horticulture, Faculty of Agriculture, University of Çukurova, 01330, Adana, Turkey.
Pistachio Research Institute, Gaziantep, Turkey.
BMC Genomics. 2016 Dec 7;17(1):998. doi: 10.1186/s12864-016-3359-x.
Pistachio (Pistacia vera L.) is one of the most important nut crops in the world. There are about 11 wild species in the genus Pistacia, and they have importance as rootstock seed sources for cultivated P. vera and forest trees. Published information on the pistachio genome is limited. Therefore, a genome survey is necessary to obtain knowledge on the genome structure of pistachio by next generation sequencing. Simple sequence repeat (SSR) markers are useful tools for germplasm characterization, genetic diversity analysis, and genetic linkage mapping, and may help to elucidate genetic relationships among pistachio cultivars and species.
To explore the genome structure of pistachio, a genome survey was performed using the Illumina platform at approximately 40× coverage depth in the P. vera cv. Siirt. The K-mer analysis indicated that pistachio has a genome that is about 600 Mb in size and is highly heterozygous. The assembly of 26.77 Gb Illumina data produced 27,069 scaffolds at N50 = 3.4 kb with a total of 513.5 Mb. A total of 59,280 SSR motifs were detected with a frequency of 8.67 kb. A total of 206 SSRs were used to characterize 24 P. vera cultivars and 20 wild Pistacia genotypes (four genotypes from each five wild Pistacia species) belonging to P. atlantica, P. integerrima, P. chinenesis, P. terebinthus, and P. lentiscus genotypes. Overall 135 SSR loci amplified in all 44 cultivars and genotypes, 41 were polymorphic in six Pistacia species. The novel SSR loci developed from cultivated pistachio were highly transferable to wild Pistacia species.
The results from a genome survey of pistachio suggest that the genome size of pistachio is about 600 Mb with a high heterozygosity rate. This information will help to design whole genome sequencing strategies for pistachio. The newly developed novel polymorphic SSRs in this study may help germplasm characterization, genetic diversity, and genetic linkage mapping studies in the genus Pistacia.
阿月浑子（Pistacia vera L.）是世界上最重要的坚果作物之一。黄连木属约有11个野生种，它们作为栽培阿月浑子和林木的砧木种子来源具有重要意义。关于阿月浑子基因组的已发表信息有限。因此，有必要通过下一代测序进行基因组调查，以了解阿月浑子的基因组结构。简单序列重复（SSR）标记是种质鉴定、遗传多样性分析和遗传连锁图谱构建的有用工具，可能有助于阐明阿月浑子品种和物种之间的遗传关系。
为了探索阿月浑子的基因组结构，在阿月浑子品种Siirt中使用Illumina平台进行了约40倍覆盖深度的基因组调查。K-mer分析表明，阿月浑子的基因组大小约为600 Mb，高度杂合。对26.77 Gb的Illumina数据进行组装，产生了27,069个支架，N50为3.4 kb，总长513.5 Mb。共检测到59,280个SSR基序，频率为8.67 kb。总共206个SSR用于鉴定24个阿月浑子品种和20个野生黄连木基因型（来自五个野生黄连木物种，每个物种四个基因型），这些野生基因型分别属于大西洋黄连木、全缘黄连木、中国黄连木、笃耨香黄连木和乳香黄连木。总体而言，所有44个品种和基因型中共扩增出135个SSR位点，其中41个在六个黄连木物种中具有多态性。从栽培阿月浑子中开发的新型SSR位点可高度转移到野生黄连木物种中。
阿月浑子基因组调查结果表明，阿月浑子基因组大小约为600 Mb，杂合率高。这些信息将有助于设计阿月浑子的全基因组测序策略。本研究新开发的新型多态性SSR可能有助于黄连木属的种质鉴定、遗传多样性和遗传连锁图谱研究。
