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Romanov MN, Abdelmanova AS, Fisinin VI, Gladyr EA, Volkova NA, Koshkina OA, Rodionov AN, Vetokh AN, Gusev IV, Anshakov DV, Stanishevskaya OI, Dotsev AV, Griffin DK, Zinovieva NA. Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds. J Anim Sci Biotechnol 2023; 14:35. [PMID: 36829208 PMCID: PMC9951459 DOI: 10.1186/s40104-022-00813-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/27/2022] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by, and formed due to, past and current admixture events. Adaptation to diverse environments, including acclimation to harsh climatic conditions, has also left selection footprints in breed genomes. RESULTS Using the Chicken 50K_CobbCons SNP chip, we genotyped four divergently selected breeds: two aboriginal, cold tolerant Ushanka and Orloff Mille Fleur, one egg-type Russian White subjected to artificial selection for cold tolerance, and one meat-type White Cornish. Signals of selective sweeps were determined in the studied breeds using three methods: (1) assessment of runs of homozygosity islands, (2) FST based population differential analysis, and (3) haplotype differentiation analysis. Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds. In these regions, we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies. Amongst them, SOX5, ME3, ZNF536, WWP1, RIPK2, OSGIN2, DECR1, TPO, PPARGC1A, BDNF, MSTN, and beta-keratin genes can be especially mentioned as candidates for cold adaptation. Epigenetic factors may be involved in regulating some of these important genes (e.g., TPO and BDNF). CONCLUSION Based on a genome-wide scan, our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds. These include genes representing the sine qua non for adaptation to harsh environments. Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals, and this warrants further investigation.
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Affiliation(s)
- Michael N. Romanov
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia ,grid.9759.20000 0001 2232 2818School of Biosciences, University of Kent, Canterbury, UK
| | - Alexandra S. Abdelmanova
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Vladimir I. Fisinin
- grid.4886.20000 0001 2192 9124Federal State Budget Scientific Institution Federal Research Centre “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad, Moscow Region Russia
| | - Elena A. Gladyr
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Natalia A. Volkova
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Olga A. Koshkina
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Andrey N. Rodionov
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Anastasia N. Vetokh
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Igor V. Gusev
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Dmitry V. Anshakov
- grid.4886.20000 0001 2192 9124Breeding and Genetic Centre “Zagorsk Experimental Breeding Farm” – Branch of the Federal Research Centre “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad, Moscow Region Russia
| | - Olga I. Stanishevskaya
- grid.473314.6Russian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, St. Petersburg, Russia
| | - Arsen V. Dotsev
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Darren K. Griffin
- grid.9759.20000 0001 2232 2818School of Biosciences, University of Kent, Canterbury, UK
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
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Liu K, Wen YY, Liu HH, Cao HY, Dong XY, Mao HG, Yin ZZ. POMC gene expression, polymorphism, and the association with reproduction traits in chickens. Poult Sci 2020; 99:2895-2901. [PMID: 32475422 PMCID: PMC7597669 DOI: 10.1016/j.psj.2019.12.070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 10/06/2019] [Accepted: 12/31/2019] [Indexed: 01/21/2023] Open
Abstract
Reproduction trait is one of the most important economic traits in poultry industry. This study was aimed to investigate the mRNA expression levels, single nucleotide polymorphisms (SNP) of POMC gene, and the association with reproduction traits in chickens. Five SNP (g.958 G > A, g.1374 G > C, g.1393 G > A, g.1817 C > T, and g.1918G > A) were detected in introns of POMC gene in 317 Zhenning yellow chickens. Association analysis revealed that g.958 G > A and g.1817 C > T showed significantly associations with fertilization rate, hatching rate of hatching eggs, and hatching rate of fertilized eggs in chickens. Simultaneously, g.1374 G > C and g.1918G > A were both associated with egg weight at 300 D of age (P < 0.05). The SNP of g.958 G > A, g.1393 G > A, and g.1817 C > T were all associated with E2 hormone levels (P < 0.05). The result of mRNA expression levels in different tissues showed that POMC mRNA expression level in the pituitary was higher than those in the other tissues and varied in different genotypes. In conclusion, the results in this study provided new evidences that polymorphisms of the POMC gene have potential effects on reproduction traits in chickens. The 5 SNP detected in this study could be potential markers for improving reproduction traits in chickens.
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Affiliation(s)
- K Liu
- Animal Science College, Zhejiang University, Zijingang Campus, Hangzhou, China 310058
| | - Y Y Wen
- Animal Science College, Zhejiang University, Zijingang Campus, Hangzhou, China 310058
| | - H H Liu
- Animal Science College, Zhejiang University, Zijingang Campus, Hangzhou, China 310058
| | - H Y Cao
- Animal Science College, Zhejiang University, Zijingang Campus, Hangzhou, China 310058
| | - X Y Dong
- Animal Science College, Zhejiang University, Zijingang Campus, Hangzhou, China 310058
| | - H G Mao
- Animal Science College, Zhejiang University, Zijingang Campus, Hangzhou, China 310058
| | - Z Z Yin
- Animal Science College, Zhejiang University, Zijingang Campus, Hangzhou, China 310058.
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Zou A, Nadeau K, Wang PW, Lee JY, Guttman DS, Sharif S, Korver DR, Brumell JH, Parkinson J. Accumulation of genetic variants associated with immunity in the selective breeding of broilers. BMC Genet 2020; 21:5. [PMID: 31952471 PMCID: PMC6969402 DOI: 10.1186/s12863-020-0807-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/03/2020] [Indexed: 12/19/2022] Open
Abstract
Background To satisfy an increasing demand for dietary protein, the poultry industry has employed genetic selection to increase the growth rate of broilers by over 400% in the past 50 years. Although modern broilers reach a marketable weight of ~ 2 kg in a short span of 35 days, a speed twice as fast as a broiler 50 years ago, the expedited growth has been associated with several negative detrimental consequences. Aside from heart and musculoskeletal problems, which are direct consequences of additional weight, the immune response is also thought to be altered in modern broilers. Results Given that identifying the underlying genetic basis responsible for a less sensitive innate immune response would be economically beneficial for poultry breeding, we decided to compare the genomes of two unselected meat control strains that are representative of broilers from 1957 and 1978, and a current commercial broiler line. Through analysis of genetic variants, we developed a custom prioritization strategy to identify genes and pathways that have accumulated genetic changes and are biologically relevant to immune response and growth performance. Our results highlight two genes, TLR3 and PLIN3, with genetic variants that are predicted to enhance growth performance at the expense of immune function. Conclusions Placing these new genomes in the context of other chicken lines, reveal genetic changes that have specifically arisen in selective breeding programs that were implemented in the last 50 years.
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Affiliation(s)
- Angela Zou
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, ON, Canada.,Program in Molecular Medicine, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
| | - Kerry Nadeau
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Pauline W Wang
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, 25 Willcocks Street, Toronto, M5S 3G5, ON, Canada
| | - Jee Yeon Lee
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, 25 Willcocks Street, Toronto, M5S 3G5, ON, Canada
| | - David S Guttman
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, 25 Willcocks Street, Toronto, M5S 3G5, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, M5S 3G5, ON, Canada
| | - Shayan Sharif
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, N1G 2W1, ON, Canada
| | - Doug R Korver
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - John H Brumell
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, ON, Canada.,Program in Cell Biology, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
| | - John Parkinson
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, ON, Canada. .,Program in Molecular Medicine, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, ON, Canada.
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Liu K, Cao H, Dong X, Liu H, Wen Y, Mao H, Lu L, Yin Z. Polymorphisms of pro-opiomelanocortin gene and the association with reproduction traits in chickens. Anim Reprod Sci 2019; 210:106196. [PMID: 31635770 DOI: 10.1016/j.anireprosci.2019.106196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 09/17/2019] [Accepted: 09/24/2019] [Indexed: 12/16/2022]
Abstract
Pro-opiomelanocortin (POMC) is a member of prohormone family and has important functions in stress response, skin pigmentation, thermoregulation and reproduction. In this study, the single nucleotide polymorphisms (SNPs) of POMC gene exons were detected by direct sequencing in 317 Zhenning yellow chickens. The sequencing results indicated there were seven mutation sites (g.1140C > T, g.1185 T > C, g.2085 T > C, g.3566A > C, g.3572 G > A, g.3594 G > A and g.3628 G > A) and all of these were synonymous. Furthermore, seven haplotypes were formed and sixteen diplotypes were obtained. The associations between the POMC gene polymorphisms or diplotypes and reproduction traits were also analyzed. The association analysis results indicated that the SNP of g.1140C > T was associated with egg production at 300 d of age (E300), fertilization rate (FR), hatching rate of hatching eggs (HEHR) and hatching rate of fertilized eggs (FEHR; P < 0.05). The SNP of g.3566A>C was associated with FR (P < 0.05), SNP of g.3594G>A was associated with egg weight at 300d of age (EW300; P < 0.05), and SNP of g.3628G>A was associated with HEHR and FEHR (P < 0.01), respectively. Furthermore, chickens with H2H3 diplotype had greater EW300 and FR than those with H1H7 and H3H4 diplotypes (P < 0.05). These results indicate the expression of the POMC gene had significant genotype effects on the reproduction traits of Zhenning yellow chickens, and that the H2H3 diplotype could be used as a potential genetic marker to improve the reproduction traits in chicken breeding.
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Affiliation(s)
- Ke Liu
- College of Animal Sciences, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Haiyue Cao
- College of Animal Sciences, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Xinyang Dong
- College of Animal Sciences, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Honghua Liu
- College of Animal Sciences, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yaya Wen
- College of Animal Sciences, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Haiguang Mao
- College of Animal Sciences, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Lei Lu
- Ningbo Zhenning Animal Husbandry Co. Ltd, Ningbo 315000, China
| | - Zhaozheng Yin
- College of Animal Sciences, Zhejiang University, Zijingang Campus, Hangzhou 310058, China.
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5
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Quantitative trait loci and candidate genes for the economic traits in meat-type chicken. WORLD POULTRY SCI J 2019. [DOI: 10.1017/s0043933914000348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Almeida OAC, Moreira GCM, Rezende FM, Boschiero C, de Oliveira Peixoto J, Ibelli AMG, Ledur MC, de Novais FJ, Coutinho LL. Identification of selection signatures involved in performance traits in a paternal broiler line. BMC Genomics 2019; 20:449. [PMID: 31159736 PMCID: PMC6547531 DOI: 10.1186/s12864-019-5811-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/20/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Natural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be identified using different methodologies, of which some are based on detecting contiguous sequences of homozygous identical-by-descent haplotypes, called runs of homozygosity (ROH), or estimating fixation index (FST) of genomic windows that indicates genetic differentiation. This study aimed to identify selection signatures in a paternal broiler TT line at generations 7th and 16th of selection and to investigate the genes annotated in these regions as well as the biological pathways involved. For such purpose, ROH and FST-based analysis were performed using whole genome sequence of twenty-eight chickens from two different generations. RESULTS ROH analysis identified homozygous regions of short and moderate size. Analysis of ROH patterns revealed regions commonly shared among animals and changes in ROH abundance and size between the two generations. Results also suggest that whole genome sequencing (WGS) outperforms SNPchip data avoiding overestimation of ROH size and underestimation of ROH number; however, sequencing costs can limited the number of animals analyzed. FST-based analysis revealed genetic differentiation in several genomic windows. Annotation of the consensus regions of ROH and FST windows revealed new and previously identified genes associated with traits of economic interest, such as APOB, IGF1, IGFBP2, POMC, PPARG, and ZNF423. Over-representation analysis of the genes resulted in biological terms of skeletal muscle, matrilin proteins, adipose tissue, hyperglycemia, diabetes, Salmonella infections and tyrosine. CONCLUSIONS Identification of ROH and FST-based analyses revealed selection signatures in TT line and genes that have important role in traits of economic interest. Changes in the genome of the chickens were observed between the 7th and 16th generations showing that ancient and recent selection in TT line may have acted over genomic regions affecting diseases and performance traits.
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Affiliation(s)
| | | | | | | | | | | | | | - Francisco José de Novais
- University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo Brazil
| | - Luiz Lehmann Coutinho
- University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo Brazil
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Matias JA, Gilbert ER, Denbow DM, Cline MA. Effects of intracerebroventricular injection of rosiglitazone on appetite-associated parameters in chicks. Gen Comp Endocrinol 2017; 246:99-104. [PMID: 26723189 DOI: 10.1016/j.ygcen.2015.12.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/25/2015] [Accepted: 12/22/2015] [Indexed: 11/22/2022]
Abstract
Rosiglitazone, a thiazolidinedione, is a peroxisome proliferator-activated receptor gamma (PPAR-γ) agonist that increases insulin sensitivity. A documented side effect of this diabetes drug is increased appetite, although the mechanism mediating this response is unknown. To better understand effects on food intake regulation, we evaluated the appetite-associated effects of rosiglitazone in an alternative vertebrate and agriculturally-relevant model, the domesticated chick. Four day-old chicks received intracerebroventricular (ICV) injections of 0, 5, 10 or 20nmol rosiglitazone and food and water intake were measured. Chicks that received 5 and 10nmol rosiglitazone increased food intake during the 2h observation period, with no effect on water intake. In the next experiment, chicks were ICV-injected with 10nmol rosiglitazone and hypothalamus was collected at 1h post-injection for total RNA isolation. Real-time PCR was performed to measure mRNA abundance of appetite- and glucose regulation-associated factors. Neuropeptide Y (NPY) and proopiomelanocortin (POMC) mRNA decreased while NPY receptor 1 (NPYr1) mRNA increased in rosiglitazone-injected chicks compared to the controls. Results show that central effects of rosiglitazone on appetite are conserved between birds and mammals, and that increases in food intake might be mediated through NPY and POMC neurons in the hypothalamus.
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Affiliation(s)
- Justin A Matias
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061, United States
| | - Elizabeth R Gilbert
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061, United States
| | - D Michael Denbow
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061, United States
| | - Mark A Cline
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061, United States.
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Gholami M, Reimer C, Erbe M, Preisinger R, Weigend A, Weigend S, Servin B, Simianer H. Genome Scan for Selection in Structured Layer Chicken Populations Exploiting Linkage Disequilibrium Information. PLoS One 2015; 10:e0130497. [PMID: 26151449 PMCID: PMC4494984 DOI: 10.1371/journal.pone.0130497] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 05/20/2015] [Indexed: 01/02/2023] Open
Abstract
An increasing interest is being placed in the detection of genes, or genomic regions, that have been targeted by selection because identifying signatures of selection can lead to a better understanding of genotype-phenotype relationships. A common strategy for the detection of selection signatures is to compare samples from distinct populations and to search for genomic regions with outstanding genetic differentiation. The aim of this study was to detect selective signatures in layer chicken populations using a recently proposed approach, hapFLK, which exploits linkage disequilibrium information while accounting appropriately for the hierarchical structure of populations. We performed the analysis on 70 individuals from three commercial layer breeds (White Leghorn, White Rock and Rhode Island Red), genotyped for approximately 1 million SNPs. We found a total of 41 and 107 regions with outstanding differentiation or similarity using hapFLK and its single SNP counterpart FLK respectively. Annotation of selection signature regions revealed various genes and QTL corresponding to productions traits, for which layer breeds were selected. A number of the detected genes were associated with growth and carcass traits, including IGF-1R, AGRP and STAT5B. We also annotated an interesting gene associated with the dark brown feather color mutational phenotype in chickens (SOX10). We compared FST, FLK and hapFLK and demonstrated that exploiting linkage disequilibrium information and accounting for hierarchical population structure decreased the false detection rate.
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Affiliation(s)
- Mahmood Gholami
- Animal Breeding and Genetics Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, Germany
- * E-mail:
| | - Christian Reimer
- Animal Breeding and Genetics Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, Germany
| | - Malena Erbe
- Animal Breeding and Genetics Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, Germany
| | | | - Annett Weigend
- Institute of Farm Animal Genetics (ING), Friedrich-Loeffler-Institut (FLI), Neustadt, Germany
| | - Steffen Weigend
- Institute of Farm Animal Genetics (ING), Friedrich-Loeffler-Institut (FLI), Neustadt, Germany
| | - Bertrand Servin
- Laboratoire Génétique, Physiologie et Systèmes d’Elevage, Institut National de la Recherche Agronomique, Castanet-Tolosan, France
| | - Henner Simianer
- Animal Breeding and Genetics Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, Germany
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Identification of QTL for live weight and growth rate using DNA markers on chromosome 3 in an F2 population of Japanese quail. Mol Biol Rep 2014; 41:1049-57. [PMID: 24385302 DOI: 10.1007/s11033-013-2950-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 12/20/2013] [Indexed: 01/29/2023]
Abstract
The Japanese quail (Coturnix japonica) is an important agricultural species and is an animal model for genetic researches. This study was conducted to identify quantitative trait loci (QTL) affecting live weight and growth rate on chromosome 3 in quail. Two strains of Japanese quail including wild and white were crossed reciprocally and F1 generation was created. The birds from F2 generation were measured for growth traits and all of 472 birds (8 pairs from the parental strains, 34 F1 birds and 422 F2 birds) were genotyped for microsatellite markers on chromosome 3. The results indicated chromosome wide significant QTL for hatching weight (P < 0.01) and weight at 1, 2, 3 and 4 weeks of age, average daily gain from hatch to 1, 1-2 and 3-4 weeks of age and Kleiber ratio (P < 0.05), an indirect criterion of feed efficiency. The highest QTL additive and imprinting effects (2.72 and 0.79 % of the trait variation in the F2 population, respectively) were related to hatching weight. The identified QTL for this trait (at 7 cM relative to the centromeric region of the chromosome) had significant interaction with sex and hatch (P < 0.01). The dominance effect of QTL was significant (P < 0.05) for bodyweight at one week of age accounting for 1.69 % of the trait variation in the F2 population.
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Fan WL, Ng CS, Chen CF, Lu MYJ, Chen YH, Liu CJ, Wu SM, Chen CK, Chen JJ, Mao CT, Lai YT, Lo WS, Chang WH, Li WH. Genome-wide patterns of genetic variation in two domestic chickens. Genome Biol Evol 2013; 5:1376-92. [PMID: 23814129 PMCID: PMC3730349 DOI: 10.1093/gbe/evt097] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Domestic chickens are excellent models for investigating the genetic basis of phenotypic diversity, as numerous phenotypic changes in physiology, morphology, and behavior in chickens have been artificially selected. Genomic study is required to study genome-wide patterns of DNA variation for dissecting the genetic basis of phenotypic traits. We sequenced the genomes of the Silkie and the Taiwanese native chicken L2 at ∼23- and 25-fold average coverage depth, respectively, using Illumina sequencing. The reads were mapped onto the chicken reference genome (including 5.1% Ns) to 92.32% genome coverage for the two breeds. Using a stringent filter, we identified ∼7.6 million single-nucleotide polymorphisms (SNPs) and 8,839 copy number variations (CNVs) in the mapped regions; 42% of the SNPs have not found in other chickens before. Among the 68,906 SNPs annotated in the chicken sequence assembly, 27,852 were nonsynonymous SNPs located in 13,537 genes. We also identified hundreds of shared and divergent structural and copy number variants in intronic and intergenic regions and in coding regions in the two breeds. Functional enrichments of identified genetic variants were discussed. Radical nsSNP-containing immunity genes were enriched in the QTL regions associated with some economic traits for both breeds. Moreover, genetic changes involved in selective sweeps were detected. From the selective sweeps identified in our two breeds, several genes associated with growth, appetite, and metabolic regulation were identified. Our study provides a framework for genetic and genomic research of domestic chickens and facilitates the domestic chicken as an avian model for genomic, biomedical, and evolutionary studies.
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Affiliation(s)
- Wen-Lang Fan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Sun G, Li M, Li H, Tian Y, Chen Q, Bai Y, Kang X. Molecular cloning and SNP association analysis of chicken PMCH gene. Mol Biol Rep 2013; 40:5049-55. [PMID: 23670042 DOI: 10.1007/s11033-013-2606-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 04/29/2013] [Indexed: 11/26/2022]
Abstract
The pre-melanin-concentrating hormone (PMCH) gene is an important gene functionally concerning the regulations of body fat content, feeding behavior and energy balance. In this study, the full-length cDNA of chicken PMCH gene was amplified by SMART RACE method. The single nucleotide polymorphisms (SNPs) in the PMCH gene were screened by comparative sequence analysis. The obtained non-synonymous coding SNPs (ncSNPs) were designed for genotyping firstly. Its effects on growth, carcass characteristics and meat quality traits were investigated employing the F2 resource population of Gushi chicken crossed with Anak broiler by AluI CRS-PCR-RFLP. Our results indicated that the cDNA of chicken PMCH shared 67.25 and 66.47% homology with that of human and bovine PMCH, respectively. The deduced amino acid sequence of chicken PMCH (163 amino acids) were 52.07 and 50.89% identical to those of human and bovine PMCH, respectively. The PMCH protein sequence is predicted to have several functional domains, including pro-MCH, CSP, IL7, XPGI and some low complexity sequence. It has 8 phosphorylation sites and no signal peptide sequence. gga-miR-18a, gga-miR-18b, gga-miR-499 microRNA targeting site was predicted in the 3' untranslated region of chicken PMCH mRNA. In addition, a total of seven SNPs including an ncSNP and a synonymous coding SNP, were identified in the PMCH gene. The ncSNP c.81 A>T was found to be in moderate polymorphic state (polymorphic index=0.365), and the frequencies for genotype AA, AB and BB were 0.3648, 0.4682 and 0.1670, respectively. Significant associations between the locus and shear force of breast and leg were observed. This polymorphic site may serve as a useful target for the marker assisted selection of the growth and meat quality traits in chicken.
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Affiliation(s)
- Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Innovative Engineering Research Center of Poultry Germplasm Resource, No. 95 Wenhua Road, Zhengzhou, 450002, People's Republic of China
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