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Ou JH, Rönneburg T, Carlborg Ö, Honaker CF, Siegel PB, Rubin CJ. Complex genetic architecture of the chicken Growth1 QTL region. PLoS One 2024; 19:e0295109. [PMID: 38739572 PMCID: PMC11090294 DOI: 10.1371/journal.pone.0295109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 04/05/2024] [Indexed: 05/16/2024] Open
Abstract
The genetic complexity of polygenic traits represents a captivating and intricate facet of biological inheritance. Unlike Mendelian traits controlled by a single gene, polygenic traits are influenced by multiple genetic loci, each exerting a modest effect on the trait. This cumulative impact of numerous genes, interactions among them, environmental factors, and epigenetic modifications results in a multifaceted architecture of genetic contributions to complex traits. Given the well-characterized genome, diverse traits, and range of genetic resources, chicken (Gallus gallus) was employed as a model organism to dissect the intricate genetic makeup of a previously identified major Quantitative Trait Loci (QTL) for body weight on chromosome 1. A multigenerational advanced intercross line (AIL) of 3215 chickens whose genomes had been sequenced to an average of 0.4x was analyzed using genome-wide association study (GWAS) and variance-heterogeneity GWAS (vGWAS) to identify markers associated with 8-week body weight. Additionally, epistatic interactions were studied using the natural and orthogonal interaction (NOIA) model. Six genetic modules, two from GWAS and four from vGWAS, were strongly associated with the studied trait. We found evidence of both additive- and non-additive interactions between these modules and constructed a putative local epistasis network for the region. Our screens for functional alleles revealed a missense variant in the gene ribonuclease H2 subunit B (RNASEH2B), which has previously been associated with growth-related traits in chickens and Darwin's finches. In addition, one of the most strongly associated SNPs identified is located in a non-coding region upstream of the long non-coding RNA, ENSGALG00000053256, previously suggested as a candidate gene for regulating chicken body weight. By studying large numbers of individuals from a family material using approaches to capture both additive and non-additive effects, this study advances our understanding of genetic complexities in a highly polygenic trait and has practical implications for poultry breeding and agriculture.
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Affiliation(s)
- Jen-Hsiang Ou
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Tilman Rönneburg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Örjan Carlborg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Christa Ferst Honaker
- Virginia Polytechnic Institute and State University, School of Animal Sciences, Blacksburg, Virginia, United States of America
| | - Paul B. Siegel
- Virginia Polytechnic Institute and State University, School of Animal Sciences, Blacksburg, Virginia, United States of America
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Institute of Marine Research, Bergen, Norway
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Romanov MN, Shakhin AV, Abdelmanova AS, Volkova NA, Efimov DN, Fisinin VI, Korshunova LG, Anshakov DV, Dotsev AV, Griffin DK, Zinovieva NA. 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. Genes (Basel) 2024; 15:524. [PMID: 38674458 PMCID: PMC11050503 DOI: 10.3390/genes15040524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/16/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024] Open
Abstract
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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Affiliation(s)
- Michael N. Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK;
| | - Alexey V. Shakhin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
| | - Alexandra S. Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
| | - Natalia A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
| | - Dmitry N. Efimov
- Federal State Budget Scientific Institution Federal Scientific Center “All-Russian Research and Technological Poultry Institute”, Sergiev Posad 141311, Moscow Oblast, Russia; (D.N.E.); (V.I.F.); (L.G.K.)
| | - Vladimir I. Fisinin
- Federal State Budget Scientific Institution Federal Scientific Center “All-Russian Research and Technological Poultry Institute”, Sergiev Posad 141311, Moscow Oblast, Russia; (D.N.E.); (V.I.F.); (L.G.K.)
| | - Liudmila G. Korshunova
- Federal State Budget Scientific Institution Federal Scientific Center “All-Russian Research and Technological Poultry Institute”, Sergiev Posad 141311, Moscow Oblast, Russia; (D.N.E.); (V.I.F.); (L.G.K.)
| | - Dmitry V. Anshakov
- Breeding and Genetic Center “Zagorsk Experimental Breeding Farm”—Branch of the Federal Research Center “All-Russian Poultry Research and Technological Institute”, Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Arsen V. Dotsev
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
| | | | - Natalia A. Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
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Siegel PB, Honaker CF, Andersson L. Research Note: Phenotypic trends for the multigenerational advanced intercross of the Virginia body weight lines of chickens. Poult Sci 2024; 103:103480. [PMID: 38330887 PMCID: PMC10864792 DOI: 10.1016/j.psj.2024.103480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 02/10/2024] Open
Abstract
Random samples from generation S41 of the Virginia high and low 8-week body weight lines formed the base population for producing a multigenerational reciprocal intercross population. Although genetic mapping from this intercross has been reported, lacking are phenotypic trends across multiple generations. Here, we provide phenotypic information for the parental base population, the F1 reciprocal cross, and subsequent segregating recombinant generations F2 to F17. Heterosis for the selected trait in the F1 was negative for both reciprocal crosses. Phenotypic correlations for the selected trait in the recombinant generations were essentially nil for both males and females as was percent sexual dimorphism and coefficients of variation.
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Affiliation(s)
- P B Siegel
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA.
| | - C F Honaker
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
| | - L Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, S-75123 Uppsala, Sweden; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
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Kinstler SR, Cloft SE, Siegel PB, Honaker CF, Maurer JJ, Wong EA. Early intestinal development of chickens divergently selected for high or low 8-wk body weight and a commercial broiler. Poult Sci 2024; 103:103538. [PMID: 38387293 PMCID: PMC10900922 DOI: 10.1016/j.psj.2024.103538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/31/2024] [Accepted: 02/04/2024] [Indexed: 02/24/2024] Open
Abstract
The early posthatch period is crucial to intestinal development, shaping long-term growth, metabolism, and health of the chick. The objective of this study was to determine the effect of genetic selection on morphological characteristics and gene expression during early intestinal development. Populations of White Plymouth Rocks have been selected for high weight (HWS) and low weight (LWS) for over 63 generations, and some LWS display symptoms of anorexia. Intestinal structure and function of these populations were compared to a commercial broiler Cobb 500 (Cobb) during the perihatch period. Egg weights, yolk-free embryo BW, yolk weights, and jejunal samples from HWS, LWS, and Cobb were collected on embryonic day (e) 17, e19, day of hatch, day (d) 3, d5, and d7 posthatch for histology and gene expression analysis. The RNAscope in-situ hybridization method was used to localize expression of the stem cell marker, olfactomedin 4 (Olfm4). Villus height (VH), crypt depth (CD), and VH/CD were measured from Olfm4 stained images using ImageJ. mRNA abundance for Olfm4, stem cell marker Lgr5, peptide transporter PepT1, goblet cell marker Muc2, marker of proliferation Ki67, and antimicrobial peptide LEAP2 were examined. Two-factor ANOVA was performed for measurements and Turkey's HSD was used for mean separation when appropriate. Cobb were heaviest and LWS the lightest (P < 0.01). at each timepoint. VH increased in Cobb and CD increased in HWS compared to LWS (P < 0.01). PepT1 mRNA was upregulated in LWS (P < 0.01), and Muc2 mRNA was decreased in both HWS and LWS compared to Cobb (P < 0.01). Selection for high or low 8-wk body weight has caused differences in intestinal gene expression and morphology when compared to a commercial broiler.
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Affiliation(s)
| | - Sara E Cloft
- School of Animal Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Paul B Siegel
- School of Animal Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | | | - John J Maurer
- School of Animal Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Eric A Wong
- School of Animal Sciences, Virginia Tech, Blacksburg, VA 24061, USA.
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