Dataset Information

Multiple ancestral haplotypes harboring regulatory mutations cumulatively contribute to a QTL affecting chicken growth traits.

ABSTRACT: In depth studies of quantitative trait loci (QTL) can provide insights to the genetic architectures of complex traits. A major effect QTL at the distal end of chicken chromosome 1 has been associated with growth traits in multiple populations. This locus was fine-mapped in a fifteen-generation chicken advanced intercross population including 1119 birds and explored in further detail using 222 sequenced genomes from 10 high/low body weight chicken stocks. We detected this QTL that, in total, contributed 14.4% of the genetic variance for growth. Further, nine mosaic precise intervals (Kb level) which contain ancestral regulatory variants were fine-mapped and we chose one of them to demonstrate the key regulatory role in the duodenum. This is the first study to break down the detail genetic architectures for the well-known QTL in chicken and provides a good example of the fine-mapping of various of quantitative traits in any species.

SUBMITTER: Wang Y

PROVIDER: S-EPMC7455696 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Multiple ancestral haplotypes harboring regulatory mutations cumulatively contribute to a QTL affecting chicken growth traits.

Wang Yuzhe Y Cao Xuemin X Luo Chenglong C Sheng Zheya Z Zhang Chunyuan C Bian Cheng C Feng Chungang C Li Jinxiu J Gao Fei F Zhao Yiqiang Y Jiang Ziqin Z Qu Hao H Shu Dingming D Carlborg Örjan Ö Hu Xiaoxiang X Li Ning N

Communications biology 20200828 1

In depth studies of quantitative trait loci (QTL) can provide insights to the genetic architectures of complex traits. A major effect QTL at the distal end of chicken chromosome 1 has been associated with growth traits in multiple populations. This locus was fine-mapped in a fifteen-generation chicken advanced intercross population including 1119 birds and explored in further detail using 222 sequenced genomes from 10 high/low body weight chicken stocks. We detected this QTL that, in total, cont ...[more]

PMID: 32859973

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Project description:The excessive accumulation of abdominal fat in chickens has resulted in a reduction in both the feed conversion efficiency and the slaughter yield. To elucidate the regulatory mechanisms and metabolic pathways affecting abdominal fat deposition in the context of broiler breeding, a cohort of 400 Qingyuan partridge chickens with varying abdominal fat deposition was established. Whole transcriptome sequencing analyses were conducted on the duodenum of 20 representative chickens to ascertain the regulatory networks at this vital digestive and absorptive organ. Consequently, 116 differentially expressed genes were identified, exhibiting a trend of increasing or decreasing expression in correlation with the accumulation of abdominal fat. A total of 36 DEmRNAs, 170 DElncRNAs, 92 DEcircRNAs and 88 DEmiRNAs were identified as differentially expressed between chickens with extremely high and low abdominal fat deposition. The functional enrichment analyses demonstrated that the differentially expressed RNA in the duodenum were involved in the regulation of chicken abdominal fat deposition by mediating a series of metabolic pathways, including the Wnt signaling pathway, the PPAR signaling pathway, the Hippo signaling pathway, the FoxO signaling pathway, the MAPK signaling pathway and other signaling pathways that are involved in fatty acid metabolism and degradation. The construction of putative interaction pairs led to the suggestion of two lncRNA-miRNA-mRNA ceRNA networks comprising two mRNAs, two miRNAs, and 29 lncRNAs, as well as two circRNA-lncRNA-miRNA-mRNA ceRNA networks comprising 26 mRNAs, 12 miRNAs, 17 lncRNAs, and nine circRNAs, as core regulatory networks in the duodenum affecting chicken abdominal fat deposition. The aforementioned genes including TMEM150C, REXO1, PIK3C2G, ppp1cb, PARP12, SERPINE2, LRAT, CYP1A1, INSR and APOA4, were proposed as candidate genes, while the miRNAs, including miR-107-y, miR-22-y, miR-25-y, miR-2404-x and miR-16-x, as well as lncRNAs such as ENSGALT00000100291, TCONS_00063508, TCONS_00061201 and TCONS_00079402 were the candidate regulators associated with chicken abdominal fat deposition. The findings of this study provide a theoretical foundation for the molecular mechanisms of mRNAs and non-coding RNAs in duodenal tissues on abdominal fat deposition in chickens.

Project description:BackgroundCrossbreeding is widely promoted as an efficient strategy to improve the productivity in agriculture. The molecular mechanism underlying heterosis for egg production is always intriguing in chicken. The transcriptional dynamic changes play a crucial role in the formation of heterosis, but little is known for the egg production traits.ResultsIn present study, we measured the continuous manifestation of heterosis ranging from 2.67% to 10.24% for egg number in the crossbreds generated by reciprocal crossing White Leghorn and Beijing You chicken. The high-quality transcriptomes of ovary for purebreds (WW and YY) and crossbreds (WY and YW) in 5 laying stages were sequenced and integrated to identify regulatory networks relevant to the heterosis. We found highly conserved transcriptional features among 4 genetic groups. By using weighted gene co-expression network analysis (WGCNA), we obtained multiple gene co-expression modules that were significantly correlated with egg number for each group. The common KEGG pathways including apelin signaling pathway, cell cycle, ribosome, spliceosome and oxidative phosphorylation, were screened for the 2 crossbreds. Then, we identified consensus co-expression modules (CMs) that showed divergent expression pattern among crossbred (WY or YW) and purebreds (WW and YY). The hub genes of CMs were again overrepresented in the cell cycle pathway, and the crossbreds exhibited temporally complementary dominance of hub genes in the 5 laying stages. These results suggested that the crossbreds inherited from both parents to maintain the ovary function by cell cycle-related genes, contributing to the persistent heterosis for egg production. Furthermore, the dominant genes including MAD2L1, CHEK2 and E2F1 were demonstrated to function in ovarian follicle development and maturation and could be the candidate genes for egg production heterosis.ConclusionOur study characterized the dynamic profile of genome-wide gene expression in ovary and highlighted the role of dominant expression of cell cycle pathway genes in heterosis. These findings provided new insights for the molecular mechanism of egg production heterosis, which would facilitate the rational choice of suitable parents for producing crossbred chickens with higher egg production.

Dataset Information

Multiple ancestral haplotypes harboring regulatory mutations cumulatively contribute to a QTL affecting chicken growth traits.

Publications

Multiple ancestral haplotypes harboring regulatory mutations cumulatively contribute to a QTL affecting chicken growth traits.

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