Division of Genetics and Tree Improvement, Forest Research Institute, Dehradun 248 195, India.
J Genet. 2021;100.
(Nees) Keng f. is one of the most widely distributed shrubby bamboo species in the temperate region of northwest (NW) Himalayas. Along with the other three temperate bamboo species, namely , and , commonly called as 'ringal', and utilized for making various articles of household and commercial purpose by local artisans. Despite huge ecological and socio-economic importance, they are least studied and lacks baseline genetic information. In this study, ~10 Gb genome sequence data with 70.68 million reads were generated for , through genome skimming approach based on high throughput next-generation sequencing technology with Illumina protocol. The high-quality reads were assembled into 31,997 contigs, which comprised 1943 microsatellite repeats. The dinucleotide and trinucleotide repeats were most abundantly distributed in the genome with 52.95 and 41.17%, respectively. Depending on the sufficient flanking sequence, only 1123 repeats were successfully tagged with primer pairs and these sites were designated as sequence-tagged microsatellite (STMS) markers. Further, a subset of 106 STMS markers were validated through PCR amplification; 77 marker loci were successfully amplified, and 48 of these showed polymorphism. Same set of marker loci were also tested for their cross-amplification in other three temperate bamboo species of the NW Himalayas, which revealed good level of transferability (27-48%) but lesser polymorphism (4-12%). In addition, the genomewide in silico cross-amplification revealed poor cross-transferability in other bamboo taxa representing four different phylogenetic lineages, namely (10.2%), (3.03%), (1.60%), (0.89%) and (0.36%). Ten polymorphic markers were further used to estimate the measures of genetic diversity in two natural populations, which revealed high genetic diversity (polymorphic information content, PIC = 0.889; expected heterozygosity, = 0.756) and low genetic differentiation (=0.061; = 5.445). To the best of our knowledge, this is one of the pioneer studies carried out for the development of genomic STMS markers through genome skimming approach in Indian bamboo species. The marker information generated here is novel and of paramount importance for future genetic studies in as well as other temperate bamboo species through cross-transferability.
（Nees）Keng f. 是温带喜马拉雅西北部分布最广的灌木状竹种之一。与其他三种温带竹种，即 、 和 ，通常称为“ringal”，被当地工匠用于制作各种家居和商业用途的物品。尽管具有巨大的生态和社会经济重要性，但它们研究最少，缺乏基线遗传信息。在这项研究中，通过基于高通量下一代测序技术的 Illumina 方案的基因组掠过方法，为 生成了约 10 Gb 基因组序列数据，具有 7068 万条读数。高质量的读数组装成 31997 个重叠群，其中包含 1943 个微卫星重复。二核苷酸和三核苷酸重复在基因组中分布最多，分别为 52.95%和 41.17%。根据足够的侧翼序列，只有 1123 个重复成功标记了引物对，这些位点被指定为序列标记的微卫星 (STMS) 标记。此外，通过 PCR 扩增验证了 106 个 STMS 标记的子集；成功扩增了 77 个标记位点，其中 48 个显示多态性。同一组标记位点也在喜马拉雅山脉西北部的其他三种温带竹种中进行了交叉扩增测试，结果显示出较好的可转移性（27-48%），但多态性较低（4-12%）。此外，全基因组的计算机交叉扩增显示，在代表四个不同进化谱系的其他竹类分类群中，可转移性较差（10.2%）、（3.03%）、（1.60%）、（0.89%）和（0.36%）。进一步使用 10 个多态性标记来估计两个自然种群的遗传多样性，结果显示出高遗传多样性（多态性信息含量，PIC=0.889；预期杂合度，=0.756）和低遗传分化（=0.061；=5.445）。据我们所知，这是在印度竹种中通过基因组掠过方法开发基因组 STMS 标记的先驱研究之一。生成的标记信息是新颖的，对未来通过可转移性在 以及其他温带竹种中的遗传研究具有至关重要的意义。
