SNP Sites Developed by Specific Length Amplification Fragment Sequencing(SLAF-seq) and Genetic Analysis in Ammopitanthus mongolicus

doi:10.7525/j.issn.1673-5102.2018.01.017

Abstract

Abstract: Ten site of Ammopiptanthus mongolicus distributed in Inner Mongolia, Ningxia and Gansu Province were used as experiment materials for sequencing by specific-locus amplified fragment sequencing(SLAF-seq). The scheme of the experiment was designed based on bio-informatics technology. Taking Glycine max as the reference genome, specific size of DNA were chosen to construct the SLAF-seq library. After high-throughput sequencing, a great amount of sequences were obtained and used to obtain the polymorphism SLAF tags by software alignment, then found the distribution of specific SNP sites. In total, we obtained 374 265 SLAF tags, including 56 295 polymorphic SLAF tags. According to these conditions that integrity >0.5 and MAF>0.05 screening from all SNP, obtained 102 025 group SNP which have high consistency. Phylogenetic relationship population structure and PCA analysis of ten individuals of A.mongolicus were analyzed using mathematical statistic method based on screening SNP, from the level of the genome to reveal the genetic differentiation between different groups. The results show that these A.mongolicus in ten different sites all originate from the same ancestor, but due to these factor that geographical location make the A.mongolicus produced genetic differentiation. Therefore, A.mongolicus growing in Inner Mongolia have close relationship, and that distributed in Ningxia and Gansu Province have close relationship.

Key words: Thymus mongolicus, SLAF-seq, SNP, genetic differentiation

CLC Number:

Q941

DUAN Yi-Zhong, WANG Jian-Wu, DU Zhong-Yu, KANG Fu-Ren. SNP Sites Developed by Specific Length Amplification Fragment Sequencing(SLAF-seq) and Genetic Analysis in Ammopitanthus mongolicus[J]. Bulletin of Botanical Research, 2018, 38(1): 141-147.

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