摘要
为分析不同产蛋期金定鸭卵巢组织的SNPs和可变剪接,试验选取开产期和产蛋高峰期金定鸭各3只,对其卵巢转录组进行测序,得到299927852条高质量序列(Clean reads)。对筛选的SNPs进行了功能统计、位点区域统计和影响统计。功能统计结果显示,开产期共获得错义突变71276个、无义突变153个、同义突变共287148个,产蛋高峰期共获得错义突变65620个、无义突变138个、同义突变共269749个;位点区域统计结果显示,开产期外显子区域共获得401030个SNPs、内含子区域共242685个SNPs,产蛋高峰期外显子区域共获得362557个SNPs、内含子区域共219548个SNPs。影响统计结果显示,开产期共获得3141个危害程度高的SNPs,294815个危害程度低的SNPs和72772个危害程度中等的SNPs。高产期共获得2583个危害程度高的SNPs,276568个危害程度低的SNPs和67024个危害程度中等的SNPs。对开产期与产蛋高峰期进行可变剪接(AS)分类及差异AS分析。结果表明,SE事件最多涉及到15419个基因,MXE涉及到1601个基因,A5SS涉及到1211个基因,A3SS涉及到1740个基因,RI涉及到653个基因。进一步对差异AS进行显著性分析,开产期与产蛋高峰期显著差异的SE有1085个基因,MXE有219个,A5SS有199个,A3SS有288个,RI有136个。研究结果为进一步完善蛋鸭的基因组信息提供基础数据。
In this study,three Jinding ducks were selected respectively at early laying period and peak laying period,and their ovarian transcriptomes were sequenced by RNA-Seq technology.After quality control,299927852 clean reads were obtained from 6 samples.Then the functional,regional and impact statistics of SNPs were counted.Functional statistics showed that 71276 missense mutations,153 nonsense mutations and 287148 synonymous mutations were obtained at early laying period,and 65620 missense mutations,138 nonsense mutations and 269949 synonymous mutations were obtained at peak laying period.Regional statistics showed that there were 401030 SNPs in exon region,242685 SNPs in intron region at early laying period.And there were 362557 SNPs in exon region,219548 SNPs in intron regionat peak laying period.The results of impact statistics showed that 3141 SNPs with highrisk,294815 SNPs with low risk and 72772 SNPs with moderate risk were obtained at early laying period.A total of 2583 SNPs with high risk,276568 SNPs with low risk and 67024 SNPs with moderate risk were obtained at high laying period.Alternative splicing(AS)classification and differential AS analysis were carried out between early laying period and peak laying period.The results showed that Skipped exon(SE)events involved 15419 genes at most,mutually exclusive exons(MXE)involved 1601 genes,Alternative 5 splice site(A5 SS)involved 1211 genes,Alternative 3 splice site(A3 SS)involved1740 genes,retained intron(RI)involved 653 genes.Further,significant differences in AS were analyzed,there were1085 genes in SE,219 in MXE,199 in A5 SS,288 in A3 SS and 136 in RI between early laying period and peak laying period.In this study,the SNPs and alternative splicing of ovary tissue of Jinding duck was analyzed,which could provide basic data for further improving the genomic information of laying duck.
作者
朱志明
缪中纬
章琳俐
李丽
辛清武
林顺东
郑嫩珠
黄勤楼
ZHU Zhiming;MIAO Zhongwei;ZHANG Linli;LI Li;XIN Qingwu;LIN Shundong;ZHENG Nenzhu;HUANG Qinlou(Institute of Animal Husbandry and Veterinary Medicine,Fujian Academy of Agricultural Sciences,Fuzhou,Fujian 350013;Longhai Shunxing Jinding Duck Co.,Ltd.,Zhangzhou,Fujian 363100)
出处
《中国家禽》
北大核心
2020年第2期11-16,共6页
China Poultry
基金
福建省属公益类科研院所专项(2018R1023-7)
中央引导地方科技发展专项(2018L3004)
福建省发改委五新项目([2018]206)
福建省农业科学院科技创新团队(STIT2017-2-1).
关键词
转录组
金定鸭
卵巢
SNPS
可变剪接
transcriptome
Jinding duck
ovary
SNPs
alternative splicing
