Integration of transcriptome sequencing and whole genome resequencing reveal candidate genes in egg production of upright and pendulous-comb chickens

文献类型： 外文期刊

第一作者： Cai, Danfeng

作者： Cai, Danfeng;Wang, Zhijun;Zhou, Zhen;Lin, Duo;Ju, Xing;Nie, Qinghua;Cai, Danfeng;Zhou, Zhen;Lin, Duo;Ju, Xing;Nie, Qinghua;Cai, Danfeng;Zhou, Zhen;Lin, Duo;Ju, Xing;Nie, Qinghua;Wang, Zhijun

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关键词： transcriptome sequencing; whole genome resequencing; upright and pendulous-comb; egg production performance

期刊名称：POULTRY SCIENCE （ 影响因子：4.4； 五年影响因子：4.4 ）

ISSN： 0032-5791

年卷期： 2023 年 102 卷 4 期

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收录情况： SCI

摘要： Egg production performance plays an important role in the poultry industry across the world. Previous studies have shown a great difference in egg production performance between pendulous-comb (PC) and upright-comb (UC) chickens. How-ever, there are no reports to identify potential candi-date genes for egg production in PC and UC chickens. In the present study, 1,606 laying chickens were raised, and the egg laid by individual chicken was collected for 100 d. Moreover, the expression level of estrogen and progesterone hormones was measured at the start-lay-ing and peak-laying periods of hens. Besides, 4 PC and 4 UC chickens were selected at 217 d of age to perform transcriptome sequencing (RNA-seq) and whole genome resequencing (WGS) to screen the potential candidate genes of egg production. The results showed that PC chicken demonstrated better egg production performance (P < 0.05) and higher estrogen and pro-gesterone hormone expression levels than UC chicken (P < 0.05). RNA-seq analysis showed that 341 upregu-lated and 1,036 downregulated differentially expressed genes (DEGs) were identified in the ovary tissues of PC and UC chickens. These DEGs were mainly enriched in protein-related, lipid-related, and nucleic acids-related biological processes including ribosome, peptide biosynthetic process, lipid transport terms, and catalytic activity acting on RNA which can signifi-cantly affect egg production in chicken. The enrich-ment results of WGS analysis were consistent with RNA-seq. Further, joint analysis of WGS and RNA-seq data was utilized to screen 30 genes and CAMK1D, CLSTN2, MAST2, PIK3C2G, TBC1D1, STK3, ADGRB3, and PPARGC1A were identified as poten-tial candidate genes for egg production in PC and UC chickens. In summary, our study provides a wealth of information for a better understanding of the genetic and molecular mechanism for the future breeding of PC and UC chickens for egg production.

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