Bacterial artificial chromosome clones randomly selected for sequencing reveal genomic differences between soybean cultivars
Tingting He A , Longshu Yang A , Xianlong Ding A , Linfeng Chen A , Yanwei Li A , Tanliu Wang A , Hao Zhang A , Junyi Gai A and Shouping Yang A B
+ Author Affiliations
- Author Affiliations
A Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China.
B Corresponding author. Email: spyung@126.com
Crop and Pasture Science 69(2) 131-141 https://doi.org/10.1071/CP17204
Submitted: 2 June 2017 Accepted: 20 November 2017 Published: 29 January 2018
Abstract
This study pioneered the use of multiple technologies to combine the bacterial artificial chromosome (BAC) pooling strategy with high-throughput next- and third-generation sequencing technologies to analyse genomic difference. To understand the genetic background of the Chinese soybean cultivar N23601, we built a BAC library and sequenced 10 randomly selected clones followed by de novo assembly. Comparative analysis was conducted against the reference genome of Glycine max var. Williams 82 (2.0). Therefore, our result is an assessment of the reference genome. Our results revealed that 3517 single nucleotide polymorphisms (SNPs) and 662 insertion–deletions (InDels) occurred in ~1.2 Mb of the genomic region and that four of the 10 BAC clones contained 15 large structural variations (72 887 bp) compared with the reference genome. Gene annotation of the reference genome showed that Glyma.18g181000 was missing from the corresponding position of the 10 BAC clones. Additionally, there may be a problem with the assembly of some positions of the reference genome. Several gap regions in the reference genome could be supplemented by using the complete sequence of the 10 BAC clones. We believe that accurate and complete BAC sequence is a valuable resource that contributes to the completeness of the reference genome.
Additional keywords: BAC clones, comparative genomic analysis, gene variation, structural variation.
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