a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China.
b Zhejiang Institute of Microbiology, Hangzhou, 310012, China.
Genome. 2018 May;61(5):323-327. doi: 10.1139/gen-2017-0191. Epub 2018 Feb 8.
Jute (Corchorus spp.) 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.
黄麻（Corchorus spp.）是世界上最重要的商业用韧皮纤维作物之一。然而，与其他作物相比，黄麻在分子标记和高密度遗传图谱方面仍然缺乏。插入/缺失（InDel）标记是植物基因组中 DNA/RNA 变异最丰富的来源之一，可使用高通量测序轻松区分不同的材料。利用三个转录组数据集，我们鉴定并开发了 InDel 标记。总共在 18800 个非编码基因中发现了 51172 个 InDel 位点，每个非编码基因的 InDel 位点数量从 1 到 31 不等。此外，我们发现了 94 种 InDel 类型，长度从 1 到 159bp；最常见的是单核苷酸（23028）、双核苷酸（9824）和三核苷酸（9182）。在 TC 和 YG 之间的比较中，总共发现了 49563 个 InDels 在 18445 个转录本中，其次是 NY 和 YG 之间的 48934 个 InDels 在 18408 个转录本中，NY 和 TC 之间的 3570 个 InDels 在 2701 个非编码基因中。此外，在三个材料中的任意两个之间有 1273 个 InDel 位点在 1129 个非编码基因中存在多态性。29 对（58%）引物对与黄麻材料相比表现出多态性，PIC 从 0.340 到 0.680 不等，平均值为 0.491。
