摘要
为探索岩鸽(Columba livia)产蛋数相关基因及其遗传标记,利用STAR对高产蛋数和低产蛋数岩鸽卵巢组织转录组数据高质量序列与参考基因组进行比对,去除重复序列后利用GATK进行单核苷酸多态性(SNP)筛选,利用VCFtools对SNP质控后进行主成分分析、进化树构建和Fst计算,利用KEGG富集分析SNP所在基因.结果显示,高产蛋组共有SNP数为298 957个,低产蛋组共有SNP数为296 137个,高产蛋组、低产蛋组共有SNP数为254 118个,KEGG分析结果发现,SNP所在基因显著富集在孕酮调节的卵母细胞成熟、卵母细胞减数分裂和代谢等信号通路;高产蛋组和低产蛋组的102个特异SNP分布在14个注释基因上(LOC110357454、KDM5A、PIGS、BNC2、GBF1、SLAIN2、FGD4、DIAPH2、KIF3B、NFIB、EPG5、OSTF1、EMB、ST3GAL3),且富集的信号通路可能与其产蛋能力密切相关.
Abstract
In order to explore the genes and genetic markers related to egg production in Columba livia,STAR was used to compare high-quality transcriptome sequences of ovarian tissue transcriptome data from high and low egg production Columba livia with the ref-erence genome,after removing duplicate sequences,single nucleotide polymorphism(SNP)screening was performed using GATK.Af-ter controlling SNP quality using VCFtools,principal component analysis,evolutionary tree construction,and Fst calculation were performed.KEGG enrichment analysis was used to identify the gene where the SNP was located.The results showed that the high-yielding egg group had a total of 298 957 SNPs,the low yielding egg group had a total of 296 137 SNPs,and the high-yielding and low-yielding egg groups had a total of 254 118 SNPs.The KEGG analysis results showed that the SNP gene was significantly enriched in the progesterone regulated signaling pathways of oocyte maturation,meiosis,and metabolism;102 specific SNPs were distributed on 14 annotation genes(LOC110357454,KDM5A,PIGS,BNC2,GBF1,SLAIN2,FGD4,DIAPH2,KIF3B,NFIB,EPG5,OSTF1,EMB,and ST3GAL3)in the high and low egg production groups,and the enriched signaling pathways may be closely related to their egg production ability.
基金项目
河北省农业农村厅畜禽育种创新能力提升基金()
河北省现代农业产业技术体系建设项目创新团队蛋鸡肉鸡良繁体系与品种培育岗位基金(HBCT2023210205)
NETL
NSTL
万方数据