A functional variant in the promoter region of IGF1 gene is associated with chicken abdominal fat deposition

Wang, W.J.; Guo, Yongli; Xie, Kaipeng; Li, Y.D.; Li, Z.W.; Wang, N.; Fan, Xiaoxi; Guo, Huaishun; Li, H.; Wang, S.Z.

doi:10.1016/j.domaniend.2020.106584

Cited by 6 publications

(3 citation statements)

References 35 publications

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“…For instance, Qanbari et al [ 38 , 40 ] reported signals of selective sweeps for the following candidate genes in laying hens (with respective chromosome of their location indicated in the parentheses): ANKH (ANKH inorganic pyrophosphate transport regulator; GGA1), IGF1 (insulin-like growth factor 1; GGA1), BMPR1B (bone morphogenetic protein receptor type 1B; GGA4), TSHR (thyroid stimulating hormone receptor; GGA5), and IGSF10 (immunoglobulin superfamily member 10; GGA9). Among these, IGF1 is also an important growth factor [ 40 ] associated with abdominal fat weight/deposition, body weight, and other traits in chickens [ 113 , 114 ], and BMPR1B is a candidate gene for low methylation related to hypoxic adaptation in Tibetan chickens [ 115 ]. The BMPR1B gene was also found within a feed intake-associated QTL [ 68 ] ( Table 6 ).…”

Section: Discussionmentioning

confidence: 99%

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Abdelmanova

Dotsev

Romanov

et al. 2021

Biology

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Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by FST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.

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Section: Discussionmentioning

confidence: 99%

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Abdelmanova

Dotsev

Romanov

et al. 2021

Biology

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“…Zhu et al found that Sp1 is involved in the transcriptional regulation of IGF-1 in rats and that IGF-1 expression is decreased in cells with a mutation in the Sp1 binding site, indicating the importance of Sp1 in activating IGF-1 expression [ 74 ]. Wang et al found that IGF-1 c.-366 A > C is associated with fat deposition in chickens and that this SNP affects IGF-1 expression through differences in transcription factor binding [ 75 ]. Tang et al found different levels of IGF-1 expression in goose breeds of different sizes, with significantly higher levels in large geese compared with that in small geese [ 76 ].…”

Section: Discussionmentioning

confidence: 99%

Origins, timing and introgression of domestic geese revealed by whole genome data

Wen

Wang

et al. 2023

J Animal Sci Biotechnol

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Background Geese are among the most important poultry species in the world. The current generally accepted hypothesis is that the European domestic geese originated from greylag geese (Anser anser), and Chinese domestic geese have two origins, most of which originated from swan geese (Anser cygnoides), and the Yili goose originated from greylag geese. To explain the origin and demographic history of geese, we selected 14 goose breeds from Europe and China and wild populations of swan and greylag geese, and whole genome sequencing data were obtained for 74 samples. Results Population structure analysis and phylogenetic trees showed that the wild ancestor of Chinese domestic geese, except for Yili, is the swan geese, and the wild ancestor of Chinese Yili and European domestic geese is greylag geese. Analysis of the demographic history suggests that the domestication of Chinese geese occurred ~ 3499 years ago and that of the European geese occurred ~ 7552 years ago. Furthermore, gene flow was observed between domestic geese and their wild ancestors. Analysis of introgression showed that Yili geese had been introgressed by Chinese domestic geese, and the body size of Yili geese may be influenced by introgression events of some growth-related genes, including IGF-1. Conclusions Our study provides evidence for the origin of geese at the genome-wide level and advances the understanding of the history of goose domestication and the traits affected by introgression events.

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“…On GGA1, we also identified another important growth and development candidate factor, IGF1 (insulin like growth factor 1). Previously, it was linked to a signal of selective sweeps, being associated with abdominal fat weight/deposition, body weight, and other traits in chickens [153][154][155][156]. Its human homolog was recognized by a broad expression in various tissues [149].…”

Section: Gga1mentioning

confidence: 99%

Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka

Romanov,

Shakhin,

Abdelmanova

et al. 2024

Genes

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Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZFST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits.

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A functional variant in the promoter region of IGF1 gene is associated with chicken abdominal fat deposition

Cited by 6 publications

References 35 publications

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Origins, timing and introgression of domestic geese revealed by whole genome data

Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka

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