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Qi L, Xiao L, Fu R, Nie Q, Zhang X, Luo W. Genetic characteristics and selection signatures between Southern Chinese local and commercial chickens. Poult Sci 2024; 103:103863. [PMID: 38810566 PMCID: PMC11166977 DOI: 10.1016/j.psj.2024.103863] [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: 01/22/2024] [Revised: 04/25/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
The introduction of exotic breeds and the cultivation of new lines by breeding companies have posed challenges to native chickens in South China, including loss of breed characteristics, decreased genetic diversity, and declining purity. Understanding the population genetic structure and genetic diversity of native chickens in South China is crucial for further advancements in breeding efforts. In this study, we analyzed the population genetic structure and genetic diversity of 321 individuals from 10 different breeds in South China. By comparing commercial chickens with native ones, we identified selection signatures occurring between local chickens and commercial breeds. The analysis of population genetic structure revealed that the native chicken populations in South China exhibited a considerable level of genetic diversity. Moreover, the commercial lines of Xiaobai chicken and Huangma chicken displayed even higher levels of genetic diversity, which distinguished them from other native varieties at the clustering level. However, certain individuals within these commercial varieties showed a discernible genetic relationship with the native populations. Notably, both commercial varieties also retained a significant degree of genetic similarity to their respective native counterparts. In order to investigate the genomic changes occurring during the commercialization of native chickens, we employed 4 methods (Fst, ROD, XPCLR, and XPEHH) to identify potential candidate regions displaying selective signatures in Southern Chinese native chicken population. A total of 168 (identified by Fst and ROD) and 86 (identified by XPCLR and XPEHH) overlapping genes were discovered. Functional annotation analysis revealed that these genes may be associated with reproduction and growth (SAMSN1, HYLS1, ROBO3, FGF14, PRSS23), musculoskeletal development (DNER, MYBPC1, DGKB, ORC1, KLF10), disease resistance and environmental adaptability (PUS3, CRB2, CALD1, USP15, SGCD, LTBP1), as well as egg production (ADGRB3, ACSF3). Overall, native chickens in South China harbor numerous selective sweep regions compared to commercial chickens, enriching valuable genomic resources for future genetic research and breeding conservation.
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Affiliation(s)
- Lin Qi
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China
| | - Liangchao Xiao
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China
| | - Rong Fu
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China
| | - Qinghua Nie
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China
| | - Xiquan Zhang
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China
| | - Wen Luo
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China.
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Balog K, Mizeranschi AE, Wanjala G, Sipos B, Kusza S, Bagi Z. Application potential of chicken DNA chip in domestic pigeon species - Preliminary results. Saudi J Biol Sci 2023; 30:103594. [PMID: 36874200 PMCID: PMC9975693 DOI: 10.1016/j.sjbs.2023.103594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/12/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Introducing the SNP technology to pigeon breeding will enhance the competitiveness of a sector that produces one of the healthiest and best quality meats. The present study aimed to test the applicability of the Illumina Chicken_50K_CobbCons array on 24 domestic pigeon individuals from the Mirthys hybrids and Racing pigeon breeds. A total of 53,313 SNPs were genotyped. Principal component analysis shows a significant overlap between the two groups. The chip performed poorly in this data set, with a call rate per sample of 0.474 (49%). The low call rate was likely due to an increase in the evolutionary distance. A total of 356 SNPs were retained after a relatively strict quality control. We have demonstrated that it is technically feasible to use a chicken microarray chip on pigeon samples. Presumably, with a larger sample size and by assigning phenotypic data, efficiency would be improved, allowing more thorough analyses, such as genome-wide association studies.
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Affiliation(s)
- Katalin Balog
- University of Debrecen, Doctoral School of Animal Science, Böszörményi út 138, 4032, Debrecen, Hungary.,Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
| | | | - George Wanjala
- University of Debrecen, Doctoral School of Animal Science, Böszörményi út 138, 4032, Debrecen, Hungary.,Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
| | - Bíborka Sipos
- University of Debrecen, Faculty of Agricultural and Food Sciences and Environmental Management, Böszörményi út 138, 4032, Debrecen, Hungary
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
| | - Zoltán Bagi
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
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3
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In-silico investigation of genomic regions related to ascites and identifying their pathways in broilers. WORLD POULTRY SCI J 2019. [DOI: 10.1017/s0043933919000035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Al-Zahrani K, Licknack T, Watson DL, Anthony NB, Rhoads DD. Further investigation of mitochondrial biogenesis and gene expression of key regulators in ascites- susceptible and ascites- resistant broiler research lines. PLoS One 2019; 14:e0205480. [PMID: 30870420 PMCID: PMC6417772 DOI: 10.1371/journal.pone.0205480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 02/28/2019] [Indexed: 01/02/2023] Open
Abstract
We have extended our previous survey of the association of mitochondrial prevalence in particular tissues with ascites susceptibility in broilers. We previously reported that in breast muscle of 22 week old susceptible line male birds had significantly higher mtDNA copy number relative to nuclear copy number (mtDNA/nucDNA), compared to resistant line male birds. The higher copy number correlated with higher expression of PPARGC1A mRNA gene. Ascites is a significant metabolic disease associated with fast-growing meat-type chickens (broilers) and is a terminal result of pulmonary hypertension syndrome. We now report the mtDNA/nucDNA ratio in lung, liver, heart, thigh, and breast of both genders at 3, and 20 weeks old. At 3 weeks the mtDNA/nucDNA ratio is significantly higher in lung, breast, and thigh for susceptible line males compared to the resistant line males. Conversely, we see the opposite for lung and breast in females. At 20 weeks of age the differences between males from the two lines is lost for lung, and thigh. Although there is a significant reduction in the mtDNA/nucDNA ratio of breast from 3 weeks to 20 weeks in the susceptible line males, the susceptible males remain higher than resistant line males for this specific tissue. We assessed relative expression of five genes known to regulate mitochondrial biogenesis for lung, thigh and breast muscle from males and females of both lines with no consistent pattern to explain the marked gender and line differences for these tissues. Our results indicate clear sex differences in mitochondrial biogenesis establishing a strong association between the mtDNA quantity in a tissue-specific manner and correlated with ascites-phenotype. We propose that mtDNA/nucDNA levels could serve as a potential predictive marker in breeding programs to reduce ascites.
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Affiliation(s)
- Khaloud Al-Zahrani
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, United States of America
- * E-mail:
| | - Timothy Licknack
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States of America
| | - Destiny L. Watson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, United States of America
| | - Nicholas B. Anthony
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States of America
| | - Douglas D. Rhoads
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, United States of America
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Dey S, Parveen A, Tarrant KJ, Licknack T, Kong BC, Anthony NB, Rhoads DD. Whole genome resequencing identifies the CPQ gene as a determinant of ascites syndrome in broilers. PLoS One 2018; 13:e0189544. [PMID: 29293530 PMCID: PMC5749702 DOI: 10.1371/journal.pone.0189544] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/27/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Ascites syndrome is the most severe manifestation of pulmonary hypertension in fast-growing broilers. The disease can be attributed to increased body weights of birds, where the higher metabolic load is not matched by sufficient oxygen supply to the cells and tissues. Although there are environmental components, the disease exhibits moderate to high heritability. The current study uses high throughput whole genome resequencing (WGR) to identify genes and chromosomal regions associated with ascites. RESULTS The WGR data identified the CPQ gene on chromosome 2. The association was confirmed by genotyping a large collection of DNAs from phenotyped birds from three distinct broiler lines using SNPs in intron 6 and exon 8 of the CPQ gene. By combining the genotype data for these two SNP loci, we identified three different alleles segregating in the three broiler lines. Particular genotypes could be associated with resistance to ascites. We further determined that particular genotypes most associated with resistance overexpress CPQ mRNA in three tissues which might explain the role of these alleles in contributing to resistance. CONCLUSIONS Our findings indicate CPQ is an important determinant of pulmonary hypertension syndrome leading to ascites in broilers. We identified particular SNPs that can be used for marker-assisted selection of broilers for resistance to the disease. Our findings validate WGR as a highly efficient approach to map determinants contributing to complex phenotypic or disease-related traits. The CPQ gene has been associated with pulmonary hypertension in genome-wide association studies in humans. Therefore, ascites investigations in broilers are likely to provide insights into some forms of hypertension in humans.
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Affiliation(s)
- Shatovisha Dey
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, Arkansas, United States of America
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
- * E-mail: (DDR); (SD)
| | - Alia Parveen
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, Arkansas, United States of America
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Katy J. Tarrant
- Department of Animal Sciences and Agricultural Education, California State University, Fresno, California, United States of America
| | - Timothy Licknack
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, Arkansas, United States of America
- Department of Poultry Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Byungwhi C. Kong
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, Arkansas, United States of America
- Department of Poultry Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Nicholas B. Anthony
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, Arkansas, United States of America
- Department of Poultry Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Douglas D. Rhoads
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, Arkansas, United States of America
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
- * E-mail: (DDR); (SD)
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Dey S, Krishna S, Anthony NB, Rhoads DD. Further investigation of a quantitative trait locus for ascites on chromosome 9 in broiler chicken lines. Poult Sci 2017; 96:788-797. [PMID: 28339549 DOI: 10.3382/ps/pew380] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/20/2016] [Indexed: 01/05/2023] Open
Abstract
Previously, we reported a genome wide association study (GWAS) that had shown association of a region between 11.8 and 13.6 Mbp on chromosome 9 with ascites phenotype in broilers. We had used microsatellite loci to demonstrate an association of particular genotypes for this region with ascites in experimental ascites lines and commercial broiler breeder lines. We identified two potential candidate genes, AGTR1 and UTS2D, within that chromosomal region for mediating the quantitative effect. We have now extended our analysis using SNPs for these genes to assess association with resistance or susceptibility to ascites in these same broiler lines. Surprisingly, in contrast to our previous GWAS and microsatellite data for this region, we find no association of the SNP genotypes or haplotypes in the region suggesting that the two genes might have limited association with the disease phenotype.
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Affiliation(s)
- Shatovisha Dey
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701.,Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701
| | - Sriram Krishna
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701
| | - Nicholas B Anthony
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701.,Department of Poultry Sciences, University of Arkansas, Fayetteville, AR 72701
| | - Douglas D Rhoads
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701.,Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701
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Tarrant KJ, Dey S, Kinney R, Anthony NB, Rhoads DD. Multi-generational genome wide association studies identify chromosomal regions associated with ascites phenotype. Poult Sci 2017; 96:1544-1552. [PMID: 28339749 PMCID: PMC5850653 DOI: 10.3382/ps/pew478] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 12/23/2016] [Indexed: 12/29/2022] Open
Abstract
Ascites is a multi-faceted disease commonly observed in fast growing broilers, which is initiated when the body is insufficiently oxygenated. A series of events follow, including an increase in pulmonary artery pressure, right ventricle hypertrophy, and accumulation of fluid in the abdominal cavity and pericardium. Advances in management practices along with improved selection programs have decreased ascites incidence in modern broilers. However, ascites syndrome remains an economically important disease throughout the world, causing estimated losses of $100 million per year. In this study, a 60 K Illumina SNP BeadChip was used to perform a series of genome wide association studies (GWAS) on the 16th and 18th generation of our relaxed (REL) line descended from a commercial elite broiler line beginning in 1995. Regions significantly associated with ascites incidence were identified on chromosome 2 around 70 megabase pairs (Mbp) and on chromosome Z around 60 Mbp. Five candidate single nucleotide polymorphisms (SNP) were evaluated as indicators for these 2 regions in order to identify association with ascites and right ventricle to total ventricle weight (RVTV) ratios. Chromosome 2 SNP showed an association with RVTV ratios in males phenotyped as ascites resistant and ascites susceptible (P = 0.02 and P = 0.03, respectively). The chromosome Z region also indicates an association with resistant female RVTV values (P = 0.02). Regions of significance identified on chromosomes 2 and Z described in this study will be used as proposed candidate regions for further investigation into the genetics of ascites. This information will lead to a better understanding of the underlying genetics and gene networks contributing to ascites, and thus advances in ascites reduction through commercial breeding schemes.
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Affiliation(s)
- K. J. Tarrant
- Department of Animal Sciences and Agricultural Education, California State University Fresno, Fresno 93740
| | - S. Dey
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville 72701
| | - R. Kinney
- John Brown University, Siloam Springs, AR 72761
| | - N. B. Anthony
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville 72701
- Department of Poultry Sciences, University of Arkansas, Fayetteville 72701
| | - D. D. Rhoads
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville 72701
- Department of Biological Sciences, University of Arkansas, Fayetteville 72701
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Pértille F, Moreira GCM, Zanella R, Nunes JDRDS, Boschiero C, Rovadoscki GA, Mourão GB, Ledur MC, Coutinho LL. Genome-wide association study for performance traits in chickens using genotype by sequencing approach. Sci Rep 2017; 7:41748. [PMID: 28181508 PMCID: PMC5299454 DOI: 10.1038/srep41748] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/23/2016] [Indexed: 12/11/2022] Open
Abstract
Performance traits are economically important and are targets for selection in breeding programs, especially in the poultry industry. To identify regions on the chicken genome associated with performance traits, different genomic approaches have been applied in the last years. The aim of this study was the application of CornellGBS approach (134,528 SNPs generated from a PstI restriction enzyme) on Genome-Wide Association Studies (GWAS) in an outbred F2 chicken population. We have validated 91.7% of these 134,528 SNPs after imputation of missed genotypes. Out of those, 20 SNPs were associated with feed conversion, one was associated with body weight at 35 days of age (P < 7.86E-07) and 93 were suggestively associated with a variety of performance traits (P < 1.57E-05). The majority of these SNPs (86.2%) overlapped with previously mapped QTL for the same performance traits and some of the SNPs also showed novel potential QTL regions. The results obtained in this study suggests future searches for candidate genes and QTL refinements as well as potential use of the SNPs described here in breeding programs.
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Affiliation(s)
- Fábio Pértille
- University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | | | - Ricardo Zanella
- College of Agronomy and Veterinary Medicine, Veterinary School, University of Passo Fundo, Rio Grande do Sul, Brazil
| | | | - Clarissa Boschiero
- University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Gregori Alberto Rovadoscki
- University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Gerson Barreto Mourão
- 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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Van Goor A, Ashwell CM, Persia ME, Rothschild MF, Schmidt CJ, Lamont SJ. Quantitative trait loci identified for blood chemistry components of an advanced intercross line of chickens under heat stress. BMC Genomics 2016; 17:287. [PMID: 27076351 PMCID: PMC4831167 DOI: 10.1186/s12864-016-2601-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/22/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Heat stress in poultry results in considerable economic losses and is a concern for both animal health and welfare. Physiological changes occur during periods of heat stress, including changes in blood chemistry components. A highly advanced intercross line, created from a broiler (heat susceptible) by Fayoumi (heat resistant) cross, was exposed to daily heat cycles for seven days starting at 22 days of age. Blood components measured pre-heat treatment and on the seventh day of heat treatment included pH, pCO2, pO2, base excess, HCO3, TCO2, K, Na, ionized Ca, hematocrit, hemoglobin, sO2, and glucose. A genome-wide association study (GWAS) for these traits and their calculated changes was conducted to identify quantitative trait loci (QTL) using a 600 K SNP panel. RESULTS There were significant increases in pH, base excess, HCO3, TCO2, ionized Ca, hematocrit, hemoglobin, and sO2, and significant decreases in pCO2 and glucose after 7 days of heat treatment. Heritabilities ranged from 0.01-0.21 for pre-heat measurements, 0.01-0.23 for measurements taken during heat, and 0.00-0.10 for the calculated change due to heat treatment. All blood components were highly correlated within measurement days, but not correlated between measurement days. The GWAS revealed 61 QTL for all traits, located on GGA (Gallus gallus chromosome) 1, 3, 6, 9, 10, 12-14, 17, 18, 21-28, and Z. A functional analysis of the genes in these QTL regions identified the Angiopoietin pathway as significant. The QTL that co-localized for three or more traits were on GGA10, 22, 26, 28, and Z and revealed candidate genes for birds' response to heat stress. CONCLUSIONS The results of this study contribute to our knowledge of levels and heritabilities of several blood components of chickens under thermoneutral and heat stress conditions. Most components responded to heat treatment. Mapped QTL may serve as markers for genomic selection to enhance heat tolerance in poultry. The Angiopoietin pathway is likely involved in the response to heat stress in chickens. Several candidate genes were identified, giving additional insight into potential mechanisms of physiologic response to high ambient temperatures.
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Affiliation(s)
| | | | - Michael E Persia
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Carl J Schmidt
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, USA
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA, USA.
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Quantitative trait loci with sex-specific effects for internal organs weights and hematocrit value in a broiler-layer cross. J Appl Genet 2015; 57:215-24. [DOI: 10.1007/s13353-015-0325-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/22/2015] [Accepted: 10/14/2015] [Indexed: 01/14/2023]
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12
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Krishnamoorthy S, Smith CD, Al-Rubaye AA, Erf GF, Wideman RF, Anthony NB, Rhoads DD. A quantitative trait locus for ascites on chromosome 9 in broiler chicken lines. Poult Sci 2014; 93:307-17. [PMID: 24570451 DOI: 10.3382/ps.2013-03359] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A genome-wide SNP survey was used to identify chromosomal regions that showed linkage disequilibrium with respect to ascites susceptibility and ventricular hypertrophy in an F2 cross between previously described ascites-resistant and -susceptible lines. Variable number tandem repeats were used to obtain genotype data to further characterize these regions. A region on chromosome 9 (12 to 13 Mbp in 2011 assembly) shows association with ascites in the ascites lines and in several commercial broiler breeder lines with a significant sex effect. There are 2 candidate genes, AGTR1 (an angiotensin II type 1 receptor) and UTS2D (urotensin 2 domain containing), in this region that have been associated with hypertension and hypoxic response in mammals.
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Colvin KL, Yeager ME. Animal Models of Pulmonary Hypertension: Matching Disease Mechanisms to Etiology of the Human Disease. ACTA ACUST UNITED AC 2014; 4. [PMID: 25705569 PMCID: PMC4334132 DOI: 10.4172/2161-105x.1000198] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recently a great deal of progress has been made in our understanding of pulmonary hypertension (PH). Research from the past 30 years has resulted in newer treatments that provide symptomatic improvements and delayed disease progression. Unfortunately, the cure for patients with this lethal syndrome remains stubbornly elusive. With the relative explosion of scientific literature regarding PH, confusion has arisen regarding animal models of the disease and their correlation to the human condition. This short review uniquely focuses on the clear and present need to better correlate mechanistic insights from existing and emerging animal models of PH to specific etiologies and histopathologies of human PH. A better understanding of the pathologic processes in various animal models and how they relate to the human disease should accelerate the development of newer and more efficacious therapies.
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Affiliation(s)
- Kelley L Colvin
- Deptartment of Pediatrics-Critical Care, University of Colorado Denver, USA ; Cardiovascular Pulmonary Research, USA ; Department of Bioengineering, University of Colorado Denver, USA ; Linda Crnic Institute for Down Syndrome, USA
| | - Michael E Yeager
- Deptartment of Pediatrics-Critical Care, University of Colorado Denver, USA ; Cardiovascular Pulmonary Research, USA ; Department of Bioengineering, University of Colorado Denver, USA ; Linda Crnic Institute for Down Syndrome, USA
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14
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Wideman RF, Rhoads DD, Erf GF, Anthony NB. Pulmonary arterial hypertension (ascites syndrome) in broilers: a review. Poult Sci 2013; 92:64-83. [PMID: 23243232 DOI: 10.3382/ps.2012-02745] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) syndrome in broilers (also known as ascites syndrome and pulmonary hypertension syndrome) can be attributed to imbalances between cardiac output and the anatomical capacity of the pulmonary vasculature to accommodate ever-increasing rates of blood flow, as well as to an inappropriately elevated tone (degree of constriction) maintained by the pulmonary arterioles. Comparisons of PAH-susceptible and PAH-resistant broilers do not consistently reveal differences in cardiac output, but PAH-susceptible broilers consistently have higher pulmonary arterial pressures and pulmonary vascular resistances compared with PAH-resistant broilers. Efforts clarify the causes of excessive pulmonary vascular resistance have focused on evaluating the roles of chemical mediators of vasoconstriction and vasodilation, as well as on pathological (structural) changes occurring within the pulmonary arterioles (e.g., vascular remodeling and pathology) during the pathogenesis of PAH. The objectives of this review are to (1) summarize the pathophysiological progression initiated by the onset of pulmonary hypertension and culminating in terminal ascites; (2) review recent information regarding the factors contributing to excessively elevated resistance to blood flow through the lungs; (3) assess the role of the immune system during the pathogenesis of PAH; and (4) present new insights into the genetic basis of PAH. The cumulative evidence attributes the elevated pulmonary vascular resistance in PAH-susceptible broilers to an anatomically inadequate pulmonary vascular capacity, to excessive vascular tone reflecting the dominance of pulmonary vasoconstrictors over vasodilators, and to vascular pathology elicited by excessive hemodynamic stress. Emerging evidence also demonstrates that the pathogenesis of PAH includes characteristics of an inflammatory/autoimmune disease involving multifactorial genetic, environmental, and immune system components. Pulmonary arterial hypertension susceptibility appears to be multigenic and may be manifested in aberrant stress sensitivity, function, and regulation of pulmonary vascular tissue components, as well as aberrant activities of innate and adaptive immune system components. Major genetic influences and high heritabilities for PAH susceptibility have been demonstrated by numerous investigators. Selection pressures rigorously focused to challenge the pulmonary vascular capacity readily expose the genetic basis for spontaneous PAH in broilers. Chromosomal mapping continues to identify regions associated with ascites susceptibility, and candidate genes have been identified. Ongoing immunological and genomic investigations are likely to continue generating important new knowledge regarding the fundamental biological bases for the PAH/ascites syndrome.
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Affiliation(s)
- R F Wideman
- Department of Poultry Science, University of Arkansas, FAyetteville 72701, USA.
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QTL Mapping for Meat Color Traits Using the F 2 Intercross between the Oh-Shamo (Japanese Large Game) and White Leghorn Chickens. J Poult Sci 2013. [DOI: 10.2141/jpsa.0120189] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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16
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Signatures of selection in the genomes of commercial and non-commercial chicken breeds. PLoS One 2012; 7:e32720. [PMID: 22384281 PMCID: PMC3287981 DOI: 10.1371/journal.pone.0032720] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 02/03/2012] [Indexed: 12/20/2022] Open
Abstract
Identifying genomics regions that are affected by selection is important to understand the domestication and selection history of the domesticated chicken, as well as understanding molecular pathways underlying phenotypic traits and breeding goals. While whole-genome approaches, either high-density SNP chips or massively parallel sequencing, have been successfully applied to identify evidence for selective sweeps in chicken, it has been difficult to distinguish patterns of selection and stochastic and breed specific effects. Here we present a study to identify selective sweeps in a large number of chicken breeds (67 in total) using a high-density (58 K) SNP chip. We analyzed commercial chickens representing all major breeding goals. In addition, we analyzed non-commercial chicken diversity for almost all recognized traditional Dutch breeds and a selection of representative breeds from China. Based on their shared history or breeding goal we in silico grouped the breeds into 14 breed groups. We identified 396 chromosomal regions that show suggestive evidence of selection in at least one breed group with 26 of these regions showing strong evidence of selection. Of these 26 regions, 13 were previously described and 13 yield new candidate genes for performance traits in chicken. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations.
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Elferink MG, van As P, Veenendaal T, Crooijmans RPMA, Groenen MAM. Regional differences in recombination hotspots between two chicken populations. BMC Genet 2010; 11:11. [PMID: 20141624 PMCID: PMC2834597 DOI: 10.1186/1471-2156-11-11] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Accepted: 02/08/2010] [Indexed: 12/17/2022] Open
Abstract
Background Although several genetic linkage maps of the chicken genome have been published, the resolution of these maps is limited and does not allow the precise identification of recombination hotspots. The availability of more than 3.2 million SNPs in the chicken genome and the recent advances in high throughput genotyping techniques enabled us to increase marker density for the construction of a high-resolution linkage map of the chicken genome. This high-resolution linkage map allowed us to study recombination hotspots across the genome between two chicken populations: a purebred broiler line and a broiler × broiler cross. In total, 1,619 animals from the two different broiler populations were genotyped with 17,790 SNPs. Results The resulting linkage map comprises 13,340 SNPs. Although 360 polymorphic SNPs that had not been assigned to a known chromosome on chicken genome build WASHUC2 were included in this study, no new linkage groups were found. The resulting linkage map is composed of 31 linkage groups, with a total length of 3,054 cM for the sex-average map of the combined population. The sex-average linkage map of the purebred broiler line is 686 cM smaller than the linkage map of the broiler × broiler cross. Conclusions In this study, we present a linkage map of the chicken genome at a substantially higher resolution than previously published linkage maps. Regional differences in recombination hotspots between the two mapping populations were observed in several chromosomes near the telomere of the p arm; the sex-specific analysis revealed that these regional differences were mainly caused by female-specific recombination hotspots in the broiler × broiler cross.
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Affiliation(s)
- Martin G Elferink
- Animal Breeding and Genomics Centre, Wageningen University and Research Centre, Wageningen, the Netherlands.
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Polymorphisms of the IGF1R gene and their genetic effects on chicken early growth and carcass traits. BMC Genet 2008; 9:70. [PMID: 18990245 PMCID: PMC2628351 DOI: 10.1186/1471-2156-9-70] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Accepted: 11/07/2008] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The insulin-like growth factor I receptor (IGF1R) has an important effect on growth, carcass, and meat quality traits in many species. However, few studies on associations of the IGF1R gene with growth and carcass traits have been reported in chickens. The objectives of the present study were to study the associations of the IGF1R gene with chicken early growth and carcass traits using a neutral test, variation scan of the gene, genetic diversity, linkage disequilibrium and association analyses. RESULTS The tree generated from the amino acid sequences of 15 species showed that the IGF1R gene was conservative in the whole evolution among the mammalian animals and chickens. In a total of 10,818 bp of sequence, 70 single nucleotide polymorphisms were identified in the chicken IGF1R gene. The allelic and genotypic frequency distribution, genetic diversity and linkage disequilibrium of 18 single nucleotide polymorphisms (SNPs) in the Xinghua and White Recessive Rock chickens showed that six of them were possibly associated with growth traits. Association analyses showed that the A17299834G SNP was significantly associated with chicken carcass body weight, eviscerated weight with giblets, eviscerated weight, body weights at 28, 35, and 56 d of age, leg length at 56 d of age, and daily weight gain at 0-4 weeks. The haplotypes of the A17307750G and A17307494G were associated with early growth traits. The haplotypes of the A17299834G and C17293932T were significantly associated with most of the early growth traits and carcass traits. CONCLUSION There were rich polymorphisms in the chicken IGF1R gene. Several SNPs associated with chicken early growth traits and carcass traits were identified in the IGF1R gene by genetic diversity, linkage disequilibrium, and association analyses in the present study.
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Atzmon G, Blum S, Feldman M, Cahaner A, Lavi U, Hillel J. QTLs Detected in a Multigenerational Resource Chicken Population. J Hered 2008; 99:528-38. [DOI: 10.1093/jhered/esn030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Druyan S, Cahaner A. Segregation Among Test-Cross Progeny Suggests That Two Complementary Dominant Genes Explain the Difference Between Ascites-Resistant and Ascites-Susceptible Broiler Lines. Poult Sci 2007; 86:2295-300. [DOI: 10.3382/ps.2007-00018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Gordon L, Yang S, Tran-Gyamfi M, Baggott D, Christensen M, Hamilton A, Crooijmans R, Groenen M, Lucas S, Ovcharenko I, Stubbs L. Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions. Genome Res 2007; 17:1603-13. [PMID: 17921355 DOI: 10.1101/gr.6775107] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The chicken genome draft sequence has provided a valuable resource for studies of an important agricultural and experimental model species and an important data set for comparative analysis. However, some of the most gene-rich segments are missing from chicken genome draft assemblies, limiting the analysis of a substantial number of genes and preventing a closer look at regions that are especially prone to syntenic rearrangements. To facilitate the functional and evolutionary analysis of one especially gene-rich, rearrangement-prone genomic region, we analyzed sequence from BAC clones spanning chicken microchromosome GGA28; as a complement we also analyzed a gene-sparse, stable region from GGA11. In these two regions we documented the conservation and lineage-specific gain and loss of protein-coding genes and precisely mapped the locations of 31 major human-chicken syntenic breakpoints. Altogether, we identified 72 lineage-specific genes, many of which are found at or near syntenic breaks, implicating evolutionary breakpoint regions as major sites of genetic innovation and change. Twenty-two of the 31 breakpoint regions have been reused repeatedly as rearrangement breakpoints in vertebrate evolution. Compared with stable GC-matched regions, GGA28 is highly enriched in CpG islands, as are break-prone intervals identified elsewhere in the chicken genome; evolutionary breakpoints are further enriched in GC content and CpG islands, highlighting a potential role for these features in genome instability. These data support the hypothesis that chromosome rearrangements have not occurred randomly over the course of vertebrate evolution but are focused preferentially within "fragile" regions with unusual DNA sequence characteristics.
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Affiliation(s)
- Laurie Gordon
- Genome Biology Group, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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22
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Tsudzuki M, Onitsuka S, Akiyama R, Iwamizu M, Goto N, Nishibori M, Takahashi H, Ishikawa A. Identification of quantitative trait loci affecting shank length, body weight and carcass weight from the Japanese cockfighting chicken breed, Oh-Shamo (Japanese Large Game). Cytogenet Genome Res 2007; 117:288-95. [PMID: 17675870 DOI: 10.1159/000103190] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Accepted: 09/11/2006] [Indexed: 11/19/2022] Open
Abstract
We performed a quantitative trait locus (QTL) analysis to map QTLs controlling shank length, body weight, and carcass weight in a resource family of 245 F(2) birds developed from a cross of the large-sized, native, Japanese cockfighting breed, Oh-Shamo (Japanese Large Game), and the White Leghorn breed of chickens. Interval mapping revealed three significant QTLs for shank length on chromosomes 1, 4 and 24 at the experiment-wise 5% level, and a suggestive shank length QTL on chromosome 27 at the experiment-wise 10% level. For body weight two QTLs, one significant and the other suggestive, were identified on chromosomes 4 and 24, respectively. As expected, QTLs for carcass weight, which was highly correlated with body weight (r = 0.95), were detected at the same chromosomal locations as the detected body weight QTLs. Interestingly, the chromosomal locations containing these body weight and carcass weight QTLs coincided with those of two of the four shank length QTLs detected. No QTL with an epistatic interaction effect was discovered for any trait. The total contribution of all detected QTLs to genetic variance was 98.4%, 27.0% and 25.9% for shank length, body weight and carcass weight, respectively, indicating that most shank length QTLs have been identified but many body weight and carcass weight QTLs have been overlooked by the present analysis because of a low coverage rate of the 88 microsatellite markers used here (approximately 46% of the whole genome).
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Affiliation(s)
- M Tsudzuki
- Laboratory of Animal Breeding and Genetics, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan.
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Tan X, Hu SH, Wang XL. Possible role of nitric oxide in the pathogenesis of pulmonary hypertension in broilers: a synopsis. Avian Pathol 2007; 36:261-7. [PMID: 17620170 DOI: 10.1080/03079450701460765] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) produced by vascular endothelial cells is an important determinant of the basal tone of small arteries and arterioles. Impaired endothelial NO production has been implicated in the pathophysiology of pulmonary hypertension in humans. Available data suggest that reduction of endothelial NO synthesis, with evidence of reduced endothelial NO synthase expression in pulmonary arterioles, is associated with increased pulmonary vasomotor tone and vascular remodelling in hypertensive broilers. Supplemental l-arginine, a precursor of NO, has been shown to induce flow-dependent pulmonary vasodilation, to prevent reduced endothelial NO synthase expression and to inhibit vascular remodelling in broilers with pulmonary hypertension. Nevertheless, its effect on pulmonary hypertension syndrome incidence is limited. It appears that impaired production of NO is a secondary rather than a causative factor in the pathogenesis of pulmonary hypertension in broilers.
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Affiliation(s)
- Xun Tan
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, PR China
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Identification of QTL controlling meat quality traits in an F2 cross between two chicken lines selected for either low or high growth rate. BMC Genomics 2007; 8:155. [PMID: 17559654 PMCID: PMC1899504 DOI: 10.1186/1471-2164-8-155] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Accepted: 06/08/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Meat technological traits (i.e. meat pH, water retention and color) are important considerations for improving further processing of chicken meat. These quality traits were originally characterized in experimental lines selected for high (HG) and low (LG) growth. Presently, quantitative trait loci (QTL) for these traits were analyzed in an F2 population issued from the HG x LG cross. A total of 698 animals in 50 full-sib families were genotyped for 108 microsatellite markers covering 21 linkage groups. RESULTS The HG and LG birds exhibit large differences in body weight and abdominal fat content. Several meat quality traits [pH at 15 min post-slaughter (pH15) and ultimate pH (pHu), breast color-redness (BCo-R) and breast color-yellowness (BCo-Y)] were lower in HG chickens. In contrast, meat color-lightness (BCo-L) was higher in HG chickens, whereas meat drip loss (DL) was similar in both lines. HG birds were more active on the shackle line. Association analyses were performed using maximum-likelihood interval mapping in QTLMAP. Five genome-wide significant QTLs were revealed: two for pH15 on GGA1 and GGA2, one for DL on GGA1, one for BCo-R and one for BCo-Y both on GGA11. In addition, four suggestive QTLs were identified by QTLMAP for BCo-Y, pHu, pH15 and DL on GGA1, GGA4, GGA12 and GGA14, respectively. The QTL effects, averaged on heterozygous families, ranged from 12 to 31% of the phenotypic variance. Further analyses with QTLExpress confirmed the two genome-wide QTLs for meat color on GGA11, failed to identify the genome-wide QTL for pH15 on GGA2, and revealed only suggestive QTLs for pH15 and DL on GGA1. However, QTLExpress qualified the QTL for pHu on GGA4 as genome-wide. CONCLUSION The present study identified genome-wide significant QTLs for all meat technological traits presently assessed in these chickens, except for meat lightness. This study highlights the effects of divergent selection for growth rate on some behavioral traits, muscle biochemistry and ultimately meat quality traits. Several QTL regions were identified that are worthy of further characterization. Some QTLs may in fact co-localize, suggesting pleiotropic effects for some chromosomal regions.
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Druyan S, Ben-David A, Cahaner A. Development of Ascites-Resistant and Ascites-Susceptible Broiler Lines. Poult Sci 2007; 86:811-22. [PMID: 17435013 DOI: 10.1093/ps/86.5.811] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The rapid growth of modern broilers is associated with enhanced appetite and high metabolic rate and, consequently, high O(2) demand. Ascites syndrome (AS) develops in individuals that fail to fully supply the increasing demand for O(2) in their bodies under ascites-inducing conditions (AIC) such as high altitude or low temperatures. The tendency of broilers to develop AS is heritable, but efficacious selection against AS susceptibility (without affecting the normal expression of other important traits) requires identification of indirect selection criteria. In the present study, divergent AS-susceptible (AS-S) and AS-resistant (AS-R) lines were developed to confirm the heritability of AS and to facilitate future detection of criteria for indirect selection against AS susceptibility. The base population consisted of 85 sire families with a mean of 73 progeny per sire, reared in a commercial broiler house under low-challenge AIC (cold environment and pelleted feed). Chicks dying with AS manifestations were designated AS-susceptible, whereas the surviving birds were designated AS-resistant. By the end of the trial (d 48), AS mortality had accumulated to 17.2%, but AS incidence per family (%ASF) ranged from 0 to 49%, with a high heritability (0.57). Parents of 7 families with very high %ASF produced the first generation (S(1)) of the AS-S line, and parents of 7 families with very low %ASF produced the S(1) of the AS-R line. The S(1) males and females reproduced generation S(2) of the selected lines, whereas additional S(1) males were tested under high-challenge AIC (individual cages, cool wind, and pelleted feed). Progeny testing under this high-challenge AIC, followed by sib selection, was repeated in generations S(2) and S(3), resulting in a divergence of 86.6% in the incidence of AS between the AS-S (91.3%) and AS-R (4.7%) lines. The rapid genetic divergence, and family analysis of %ASF suggested that a single or few major genes are responsible for the difference between the 2 selected lines. These lines may facilitate more sensitive and effective genomic research aimed at detecting these genes or identifying the primary physiological cause of AS.
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Affiliation(s)
- S Druyan
- Faculty of Agricultural, Food and Environmental Quality Sciences, Hebrew University, Rehovot 76100, Israel
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Abasht B, Dekkers JCM, Lamont SJ. Review of Quantitative Trait Loci Identified in the Chicken. Poult Sci 2006; 85:2079-96. [PMID: 17135661 DOI: 10.1093/ps/85.12.2079] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Methods for mapping QTL are actively used in the chicken to identify chromosomal regions contributing to variation in traits related to growth, disease resistance, egg production, behavior, and metabolic parameters. However, higher-resolution mapping and better knowledge of the genetic architecture underlying QTL are needed for successful application of this information into breeding programs. Therefore, this paper summarizes and integrates original, primary QTL studies in the chicken to identify basic information on the genetic architecture of quantitative traits in chickens. The results of this review show several instances of consensus of QTL locations for similar traits from independent studies. Furthermore, the consensus of QTL location for different traits and evidence for QTL with parent-of-origin effect, transgressive alleles, epistatic QTL, and QTL x sex interaction in chicken are presented and discussed. This information can be helpful in identifying genes or mutations underlying the QTL and in the application of genomic information in marker-assisted breeding programs.
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Affiliation(s)
- B Abasht
- Department of Animal Science, Iowa State University, Ames 50011, USA
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