文献类型：期刊文献

英文题名：Molecular spectrum of somaclonal variation in PLB-regenerated Oncidium revealed by SLAF-seq

作者：Wang, Caixia[1] Tian, Min[1] Zhang, Ying[1] Ouyang, Tong[1]

第一作者：王彩霞

通信作者：Tian, M[1]

机构：[1]Chinese Acad Forestry, Res Inst Subtrop Forestry, Hangzhou 311400, Zhejiang, Peoples R China

年份：2019

卷号：137

期号：3

起止页码：541-552

外文期刊名：PLANT CELL TISSUE AND ORGAN CULTURE

收录：;EI(收录号：20191106618968);Scopus(收录号：2-s2.0-85062648682);WOS:【SCI-EXPANDED(收录号:WOS:000467145200010)】；

基金：This study was funded by the National Natural Science Foundation of China (Grant No. 31301801) and the Fundamental Research Funds for the Central Non-profit Research Institution of CAF (Grant No. CAFYBB2014QB012). The authors are grateful for the assistance provided by Biomarker Technologies (Beijing, China) in data processing.

语种：英文

外文关键词：Oncidium; Protocorm-like body (PLB); Somaclonal variation; Single nucleotide polymorphism (SNP); Insertion-deletion (InDel); Specific-locus amplified fragment sequencing (SLAF-seq)

摘要：Protocorm-like body (PLB) formation is an efficient method that has been widely used in the propagation of orchids. There is little information regarding the genome-wide molecular spectrum of somaclonal variation in PLB-regenerated orchids. We used specific-locus amplified fragment sequencing (SLAF-seq) to investigate the variations of single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels) in somaclones of Oncidium Milliongolds', which was regenerated via PLB formation after in vitro culturing for 10years. A high average variation rate (1.00x10(-3)) was detected in 11 somaclones, and the most abundant variations were line specific. The average Ti/Tv ratio was 2.17, and G:C>C:G was the rarest type of SNP. The SNPs adjacent to adenine and thymine were more frequent than those adjacent to guanine and cytosine. The most prominent InDels were mononucleotide InDels. More than half of the InDels occurred within or adjacent to homopolymeric or polynucleotide repeats, and a majority of the repeats were thymine or adenine homopolymers. This study expands the current understanding of the somaclonal variation that occurs in PLB regeneration systems and long-term subcultures, which will be useful for improving the use of PLB formation in the propagation and breeding of orchids. We also confirmed that SLAF-seq is an efficient technology for genome-wide analysis of somaclonal variations for most species without reference genome sequences. Key messageWe expanded the understanding of somaclonal variation in PLB regeneration and long-term subcultures of orchids, and confirmed SLAF-seq is efficient for genome-wide analysis of somaclonal variations without reference genome sequences.