Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India.
PLoS One. 2020 Aug 17;15(8):e0237538. doi: 10.1371/journal.pone.0237538. eCollection 2020.
Dearth of genomic resources particularly, microsatellite markers in nutritionally and commercially important fruit crop, guava necessitate the development of the novel genomic SSR markers through the library enrichment techniques. Three types of 3' -biotinylated oligonucleotide probes [(CT)14, (GT)12, and (AAC)8] were used to develop microsatellite enriched libraries. A total of 153 transformed colonies were screened of which 111 positive colonies were subjected for Sanger sequencing. The clones having more than five motif repeats were selected for primer designing and a total of 38 novel genomic simple sequence repeats could be identified. The g-SSRs had the motif groups ranging from monomer to pentamer out of which dimer group occurred the most (89.47%). Out of 38 g-SSRs markers developed, 26 were found polymorphic, which showed substantial genetic diversity among the guava genotypes including wild species. The average number of alleles per locus, major allele frequency, gene diversity, expected heterozygosity and polymorphic information content of 26 SSRs were 3.46, 0.56, 0.53, 0.29 and 0.46, respectively. The rate of cross-species transferability of the developed g-SSR loci varied from 38.46 to 80.77% among the studied wild Psidium species. Generation of N-J tree based on 26 SSRs grouped the 40 guava genotypes into six clades with two out-groups, the wild guava species showed genetic distinctness from cultivated genotypes. Furthermore, population structure analysis grouped the guava genotypes into three genetic groups, which were partly supported by PCoA and N-J tree. Further, AMOVA and PCoA deciphered high genetic diversity among the present set of guava genotypes including wild species. Thus, the developed novel g-SSRs were found efficient and informative for diversity and population structure analyses of the guava genotypes. These developed novel g-SSR loci would add to the new genomic resource in guava, which may be utilized in genomic-assisted guava breeding.
在营养和商业上重要的水果作物番石榴中，基因组资源特别是微卫星标记非常匮乏，因此需要通过文库富集技术开发新的基因组 SSR 标记。使用三种类型的 3' -生物素化寡核苷酸探针 [(CT)14、(GT)12 和 (AAC)8] 来开发微卫星富集文库。总共筛选了 153 个转化的菌落，其中 111 个阳性菌落进行了 Sanger 测序。选择具有超过五个重复基序的克隆进行引物设计，总共可以鉴定出 38 个新的基因组简单序列重复。g-SSR 具有从单体到五聚体的基序群，其中二聚体群出现的最多（89.47%）。在所开发的 38 个 g-SSR 标记中，有 26 个标记表现出多态性，这表明包括野生种在内的番石榴基因型之间存在大量遗传多样性。每个位点的等位基因数、主要等位基因频率、基因多样性、期望杂合度和多态信息含量分别为 3.46、0.56、0.53、0.29 和 0.46。在所研究的野生 Psidium 种中，开发的 g-SSR 位点的跨物种可转移性率从 38.46%到 80.77%不等。基于 26 个 SSRs 的 N-J 树将 40 个番石榴基因型分为 6 个分支，其中 2 个为外群，野生番石榴与栽培基因型具有明显的遗传差异。此外，种群结构分析将番石榴基因型分为三个遗传群，这在一定程度上得到了 PCoA 和 N-J 树的支持。进一步的 AMOVA 和 PCoA 分析表明，目前的番石榴基因型包括野生种都具有较高的遗传多样性。因此，所开发的新型 g-SSR 标记对于番石榴基因型的多样性和种群结构分析是有效和信息丰富的。这些新开发的 g-SSR 标记将增加番石榴的新基因组资源，可用于基因组辅助番石榴育种。
