ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.
The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India.
PLoS One. 2016 Oct 13;11(10):e0164325. doi: 10.1371/journal.pone.0164325. eCollection 2016.
Mango (Mangifera indica L.) is called "king of fruits" due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties 'Neelam', 'Dashehari' and their hybrid 'Amrapali' using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango.
芒果（Mangifera indica L.）因其甜味、口感丰富、品种多样、产量大以及用途广泛，被誉为“水果之王”。尽管芒果具有巨大的经济重要性，但基因组资源却很稀缺，有用园艺性状的遗传也知之甚少。在这里，我们使用下一代测序技术为芒果亲本品种“Neelam”、“Dashehari”及其杂种“Amrapali”生成了深度覆盖的叶片 RNA 序列数据。从头组装生成了 27528、20771 和 35182 条转录本，分别用于这三种基因型。这些转录本进一步组装成一个非冗余的 70057 条单基因簇集合，用于 SSR 和 SNP 的鉴定和注释。在 4912 个单基因簇中鉴定出 5465 个 SSR 基因座，其中 288 个为 I 型 SSR（n≥20 bp）。随机选择了 100 个 I 型 SSR 标记，其中 43 个在第一轮验证中产生了预期大小的 PCR 扩增产物，被指定为验证的基因 SSR 标记。此外，通过将三种芒果品种的高质量序列读取与参考单基因簇集进行比对，鉴定出了 22306 个 SNP，显示杂种 Amrapali 中的 SNP 杂合性显著增强。本研究对芒果品种及其杂种的叶片 RNA 测序为芒果的遗传改良提供了有用的基因组资源。
