利用转录组测序筛选与鸭青壳性状形成相关的基因  

Identifying Genes Associated with Blue Eggshell in Ducks(Anas platyrhynchos domesticus) by Transcriptome Analysis

作　　者：陈黎[1] 黄学涛[1] 田勇[1] 陶争荣[1] 卢立志[1] 

机构地区：[1]浙江省农业科学院畜牧兽医研究所,杭州310021

出　　处：《农业生物技术学报》2016年第7期1064-1072,共9页Journal of Agricultural Biotechnology

基　　金：国家自然科学基金项目(No.31402065);"十二五"国家科技支撑计划项目(No.2012BAD39B00);国家水禽产业技术体系专项(CARS-43-2)

摘　　要：青壳性状是鸭(Anas platyrhynchos domesticus)重要的经济性状,但其遗传机制尚未揭晓。为研究鸭青壳性状形成的转录组基础,本研究通过测交法选育出基因型为纯合青壳以及纯合白壳绍兴鸭,并对两种基因型个体子宫组织进行转录组测序。本研究共获得288 008 582个高质量数据,组装出64 587个转录本,其中包括19 589个新转录本。鉴定20 302次可变剪切事件,其中外显子跳跃是最主要的可变剪切类型。表达分析发现1 768个基因在两种基因型个体间差异表达,其中包括与蛋壳主要色素物质(原卟啉、胆绿素及其螯合物)相关的基因,例如胆绿素还原酶A基因(biliverdin reductase A,BLVRA)、尿卟啉原Ⅲ合酶基因(uroporphyrinogenⅢsynthase,UROS)、血红蛋白α亚基基因(hemoglobin subunit alpha-1,HBA1)以及血红素绑定蛋白1基因(heme binding protein 1,HEBP1)等。差异基因的基因本体(Gene Ontology,GO)注释以及京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)通路分析表明这些基因涉及广泛的生物功能及通路,其中与蛋壳颜色形成密切相关的有血红素代谢功能(例如,血红素绑定以及四吡咯绑定)及胆汁代谢通路(例如,胆汁酸合成通路,胆汁分泌通路)。本研究首次探索了鸭蛋壳颜色形成的转录组基础,获得了一批差异表达基因,这些基因为进一步研究鸭蛋壳颜色形成的遗传机制提供了有价值的信息。Blue eggshell is an important economic trait in the poultry, as it presents the thicker eggshell and plays more important role in filtering solar radiation and damage resistance than the brown eggshell and the white eggshell. Now the genetic basis underlying blue eggshell in the chicken（Gus gallus） has been uncovered. However, its genetic mechanism remains unknown in ducks（Anas platyrhynchos domesticus）. In this study, to comprehensively analyze the transcriptome basis of the blue eggshell in ducks, homozygous blueshelled and homozygous white- shelled Shaoxing ducks were bred by using the test cross, and transcriptome sequencing of uterus from the 2 genotypes was performed using the Illumina Hi Seq 2500 platform with 3biological replicates per genotypes. After removing sequencing adaptors and the low-quality reads, we totallyobtained 288 008 582 clean reads, and 71.62% of them were successfully mapped to the duck genome.93.04% of the mapped reads were uniquely aligned to the duck genome. These mapped reads were assembled into 64 587 transcripts, including 19 589 novel ones. Based on these RNA- seq data 5 known alternative splicing event, including Skipped exons（SE）, Retained intron, Alternative 5＇ splicing site（A5SS）, Alternative3＇ splicing site（A3SS） and Mutually exclusive exon（MEX） were also analyzed, and 20 302 alternative splicing events were identified. Among these alternative splicing event, SE was found to be the major type,with the times of 8388, followed by 4891 A5 SS and 3649 A3 SS, and MEX was the rarest events, happening603 times. In this study, reads per kilobase per million of mapped reads（RPKM） was calculated for gene expression. Based on the RPKM value, 21 829 genes were expressed（RPKM≥1）, and most of these genes were expressed between 1 to 100 RPKM. Further differential expression analysis between the 2 genotypes showed that 1 768 genes exhibited differential expression（P〈0.05,｜fold change｜≥1.5）, including 700 upregulated and 1 068 down-regulated

关 键 词：青壳 差异表达基因 血红素 胆汁 

分 类 号：Q31[生物学—遗传学]