Development of an InDel polymorphism database for jute via comparative transcriptome analysis
Development of an InDel polymorphism database for jute via comparative transcriptome analysis
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通过比较转录组分析开发黄麻 InDel 多态性数据库
DOI：
10.1139/gen-2017-0191
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发表时间：
2018
期刊：
影响因子：
3.1
通讯作者：
Su Jianguang
中科院分区：
文献类型：
--
作者：
Yang Zemao;Dai Zhigang;Xie Dongwei;Chen Jiquan;Tang Qing;Cheng Chaohua;Xu Ying;Wang Tingzhang;Su Jianguang
黄麻（Corchorusspp.）是世界上最具商业价值的韧皮纤维作物之一。然而，与其他作物相比，黄麻仍然缺乏分子标记和高密度遗传图谱。插入/缺失（InDel）标记是植物基因组中最丰富的DNA/RNA变异来源之一，利用高通量测序可以很容易地区分不同的种质。使用三个转录组数据集，我们确定和开发的InDel标记。在18 800个单基因中共检测到51 172个InDel位点，每个单基因的InDel位点数为1 ~ 31个。此外，我们发现了94种InDel类型，从1到159 bp不等;最常见的是单核苷酸（23 028），二核苷酸（9824）和三核苷酸（9182）。结果表明，在18 445个转录本中，TC和YG共检测到49 563个InDels;在18 408个转录本中，NY和YG共检测到48 934个InDels;在2701个单基因中，NY和TC共检测到3570个InDels。此外，在1129个单基因中，有1273个InDel位点在3份材料中的任何两份材料之间存在多态性。29对引物（58%）与黄麻种质相比表现出多态性，PIC变化范围为0.340 - 0.680，平均为0.491。
Jute (Corchorusspp.) is one of the most commercially important bast fiber crops in the world. However, molecular markers and high-density genetic maps are still lacking on jute compared with other crops. Insertion/deletion (InDel) markers, one of the most abundant sources of DNA/RNA variations in plant genomes, can easily be distinguished among different accessions using high-throughput sequencing. Using three transcriptome datasets, we identified and developed InDel markers. Altogether, 51 172 InDel sites in 18 800 unigenes were discovered, and the number of InDel loci per unigene varied from 1 to 31. Further, we found 94 InDel types, varying from 1 to 159 bp; the most common were single-nucleotide (23 028), binucleotide (9824), and trinucleotide (9182). In total, 49 563 InDels in 18 445 transcripts were discovered in the comparison between TC and YG, followed by 48 934 InDels in 18 408 transcripts between NY and YG, and 3570 InDels in 2701 unigenes between NY and TC. Additionally, there were 1273 InDel sites in 1129 unigenes with polymorphisms between any two of the three accessions. Twenty-nine (58%) primer pairs represented polymorphisms when compared to the jute accessions, and PIC varied from 0.340 to 0.680, with an average of 0.491.