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High-density genotyping reveals candidate genomic regions for chicken body size in breeds of Asian origin

文献类型： 外文期刊

作者： Lyu, Shijie 1 ; Arends, Danny 1 ; Nassar, Mostafa K. 4 ; Weigend, Annett 5 ; Weigend, Steffen 5 ; Wang, Eryao 2 ; Brockmann, Gudrun A. 1 ;

作者机构： 1.Humboldt Univ, Albrecht Daniel Thaer Inst Agr & Hort Sci, D-10115 Berlin, Germany

2.Henan Acad Agr Sci, Inst Anim Sci & Vet Med, Zhengzhou 450002, Peoples R China

3.Northumbria Univ, Dept Appl Sci, Newcastle Upon Tyne, Tyne & Wear, England

4.Cairo Univ, Fac Agr, Anim Prod Dept, Giza 12613, Egypt

5.Friedrich Loeffler Inst, Inst Farm Anim Genet, D-31535 Neustadt, Germany

关键词： Asian Game type chicken; Asian Bantam type chicken; growth; GWAS; PCA

期刊名称：POULTRY SCIENCE （ 2021影响因子：4.014； 五年影响因子：4.192 ）

ISSN： 0032-5791

年卷期： 2023 年 102 卷 1 期

页码：

收录情况： SCI

摘要： Body size is one of the main selection indices in chicken breeding. Although often investigated, knowledge of the underlying genetic mechanisms is incomplete. The aim of the current study was to identify genomic regions associated with body size differences between Asian Game and Asian Bantam type chickens. In this study, 94 and 107 chickens from 4 Asian Game and 5 Asian Bantam type breeds, respectively, were genotyped using the chicken 580K single nucleotide polymorphism (SNP) array. A genome-wide association study (GWAS) and principal component analyses (PCA) were performed to identify genomic regions associated with body size related-traits such as wing length, shank length, shank thickness, keel length, and body weight. Hierarchical clustering of genotype data showed a clear genetic difference between the investigated Asian Game and Asian Bantam chicken types. GWAS identified 16 genomic regions associated with wing length (2, FDR <= 0.018), shank thickness (6, FDR <= 0.008), keel length (5, FDR <= 0.023), and body weight (3, FDR <= 0.041). PCA showed that the first principal component (PC1) separated the 2 chicken types and significantly correlated with the measured body size related-traits (P <= 2.24e-40). SNPs contributing significantly to PC1 were subjected to a more detailed investigation. This analysis identified 11 regions potentially associated with differences in body size related-traits. A region on chromosome 4 (GGA4) (17.3-21.3 Mb) was detected in both analyses GWAS and PCA. This region harbors 60 genes. Among them are myotubularin 1 (MTM1) and secreted frizzled-related protein 2 (SFPR2) which can be considered as potential candidate genes for body size related-traits. Our results clearly show that the investigated Asian Game type chicken breeds are genetically different from the Asian Bantam breeds. A region on GGA4 between 17.3 and 21.3 Mb was identified which contributes to the phenotypic difference, though further validation of candidate genes is necessary.

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