水生生物学报2016，Vol.40Issue(6)：1128-1134,7.DOI:10.7541/2016.146
大口黑鲈转录组SNPs筛选及其与生长的关联分析
SNPS IDENTIFICATION IN RNA-SEQ DATA OF LARGEMOUTH BASS (MICROPTERUS SALMOIDES) FED ON FORMULATED FEED AND ASSOCIATION ANALYSIS WITH GROWTH TRAIT
摘要
Abstract
It is a hot research area to substitute frozen trash fish (FF) with artificial compound diet (CD) in feeding the carnivorous economic fish. Largemouth bass (Micropterus salmoides) is one of the important aquaculture species with an annual output of about 340000 tons in fresh water in China. Effect of artificial compound diet at the transcriptome level of largemouth bass is rare reported. The current study utilized RNA-Seq (RNA sequencing) technology on the Il-lumina sequencing platform (Illumina HiSeqTM 2000) to screen polymorphic SNP (single nucleotide polymorphism) markers of largemouth bass in two diets and analyzed the association of SNPs with growth trait. As a result, a total of 174M reads were assembled to generate 95024 unigenes. We used BWA (http://sourceforge.net/projects/bio-bwa/) and SamTools (http://source forge.net/projects/samtools/) to detect SNPs. Several filtering steps were performed to reduce the false positive of SNPs, 8681 SNPs met the selection criteria. 50 SNPs sequences in different genes were validated by PCR amplification and genotyped by the SNaPshot assay. 39 out of 50 SNPs were confirmed. Of these, 4 SNPs were monomorphic for all individuals and 35 SNPs were polymorphic. Validation of selected SNPs was 70%. 327 large-mouth bass with marketable sizes fed by CD were used to evaluate the correlation between these validated SNPs and growth traits including body mass, total length, head length, body width, withers height and caudal peduncle length. Genotyping data were computed and analyzed by SPSS 19.0 statistical software package. Two SNPs were associated with body mass, total length and withers height, which could be used as important candidate molecular markers for breeding selection of largemouth bass. This study shows that RNA-Seq is an efficient approach to uncover gene-asso-ciated SNPs, which could facilitate genetic and functional genomics research in the artificial domestication of formu-lated feeding of largemouth bass.关键词
转录组测序(RNA-Seq)/大口黑鲈/单核苷酸多态(SNPs)/生长性状Key words
RNA sequencing (RNA-Seq)/Largemouth bass/Single nucleotide polymorphisms (SNPs)/Growth trait分类
生物科学引用本文复制引用
全迎春,马冬梅,白俊杰,刘浩,李胜杰,刘海涌..大口黑鲈转录组SNPs筛选及其与生长的关联分析[J].水生生物学报,2016,40(6):1128-1134,7.基金项目
农业部948项目(2011-G12) （2011-G12）
广东省省级科技计划(2015A020209035) （2015A020209035）
国家自然科学基金(31001107,31201985)资助[Supported by the “948” Project of Ministry of Agriculture of China (2011-G12) （31001107,31201985）
Science and Technology Planning Project of Guangdong Province (2015A020209035) （2015A020209035）
National Natural Science Foundation of China (31001107,31201985) （31001107,31201985）
