Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India.
ICFRE - Bamboo & Rattan Centre, Aizawl, 796007, Mizoram, India.
Funct Integr Genomics. 2023 Mar 27;23(2):103. doi: 10.1007/s10142-023-01033-z.
Bamboo is an important genetic resource in India, supporting rural livelihood and industries. Unfortunately, most Indian bamboo taxa are devoid of basic genomic or marker information required to comprehend the genetic processes for further conservation and management. In this study, we perform genome survey sequencing for development of de novo genomic SSRs in Dendrocalamus longispathus, a socioeconomically important bamboo species of northeast India. Using Illumina platform, 69.49 million raw reads were generated and assembled into 1,145,321 contig with GC content 43% and N50 1228 bp. In total, 46,984 microsatellite repeats were mined-out wherein di-nucleotide repeats were most abundant (54.71%) followed by mono- (31.91%) and tri-repeats (9.85%). Overall, AT-rich repeats were predominant in the genome, but GC-rich motifs were more frequent in tri-repeats. Afterwards, 21,596 SSR loci were successfully tagged with the primer pairs, and a subset of 50 were validated through polymerase chain reaction amplification. Of these, 36 SSR loci were successfully amplified, and 16 demonstrated polymorphism. Using 13 polymorphic SSRs, a moderate level of gene diversity (He = 0.480; Ar = 3.52) was recorded in the analysed populations of D. longispathus. Despite the high gene flow (Nm = 4.928) and low genetic differentiation (F = 0.119), severe inbreeding (F = 0.407) was detected. Further, genetic clustering and STRUCTURE analysis revealed that the entire genetic variability is captured under two major gene pools. Conclusively, we present a comprehensive set of novel SSR markers in D. longispathus as well as other taxa of tropical woody bamboos.
竹子是印度重要的遗传资源，支撑着农村生计和产业。不幸的是，大多数印度竹类缺乏基本的基因组或标记信息，无法理解遗传过程，从而无法进行进一步的保护和管理。在这项研究中，我们对印度东北部具有重要社会经济意义的竹种巨龙竹（Dendrocalamus longispathus）进行了基因组调查测序，以开发从头基因组 SSRs。使用 Illumina 平台，生成了 6949 万条原始读数，并组装成 1145321 个 contig，GC 含量为 43%，N50 为 1228 bp。总共挖掘出 46984 个微卫星重复序列，其中二核苷酸重复序列最为丰富（54.71%），其次是单核苷酸（31.91%）和三核苷酸重复序列（9.85%）。总的来说，富含 AT 的重复序列在基因组中占主导地位，但三核苷酸重复序列中 GC 丰富的基序更为常见。之后，用引物对成功标记了 21596 个 SSR 位点，其中 50 个的子集通过聚合酶链反应（PCR）扩增进行了验证。在这些引物中，成功扩增了 36 个 SSR 位点，其中 16 个显示出多态性。使用 13 个多态性 SSRs，分析的巨龙竹种群记录到中等水平的基因多样性（He=0.480；Ar=3.52）。尽管基因流（Nm=4.928）较高，遗传分化（F=0.119）较低，但检测到严重的近亲繁殖（F=0.407）。此外，遗传聚类和 STRUCTURE 分析表明，两个主要基因库捕获了整个遗传变异性。总之，我们在巨龙竹和其他热带木质竹类中提供了一套全面的新 SSR 标记。
