Crop and Pasture Science Crop and Pasture Science Society
Plant sciences, sustainable farming systems and food quality

Just Accepted

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BAC clones randomly selected for sequencing reveal genomic differences between soybean cultivars

Shouping Yang , Tingting He , Longshu Yang , Xianlong Ding , Linfeng Chen , Yanwei Li , Tanliu Wang , Hao Zhang , Junyi Gai

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 analyze genomic difference. To understand the genetic background of N23601 (a Chinese soybean cultivar), we built a BAC library and sequenced ten randomly selected clones followed by de novo assembly. The 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 3,517 single nucleotide polymorphisms (SNPs) and 662 insertion-deletions (InDels) occurred in ca. 1.2 Mb of the genomic region and that four of the ten 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 ten BAC clones. Additionally, there may be problem with the assembly of some positions of the reference genome. A number of gap regions in the reference genome could be supplemented using the complete sequence of the ten BAC clones. We believe that accurate and complete BAC sequence is valuable resource that contributes to the completeness of the reference genome.

CP17204  Accepted 20 November 2017

© CSIRO 2017