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Bendesky A, Brew J, Francis KX, Tello Corbetto EF, González Ariza A, Nogales Baena S, Shimmura T. The main genetic locus associated with the evolution of gamecocks is centered on ISPD. G3 (BETHESDA, MD.) 2024; 14:jkad267. [PMID: 37991999 PMCID: PMC10849328 DOI: 10.1093/g3journal/jkad267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/02/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Chickens were domesticated >4,000 years ago, probably first for fighting them and only later as a source of food. Fighting chickens, commonly known as gamecocks, continue to be bred throughout the world, but the genetic relationships among geographically diverse gamecocks and with nongame chickens are not known. Here, we sequenced the genomes of 44 geographically diverse gamecocks and 62 nongame chickens representing a variety of breeds. We combined these sequences with published genomes to generate the most diverse chicken genomes dataset yet assembled, with 307 samples. We found that gamecocks do not form a homogeneous group, yet they share genetic similarities that distinguish them from nongame chickens. Such similarities are likely the result of a common origin before their local diversification into, or mixing with nongame chickens. Particularly noteworthy is a variant in an intron of the isoprenoid synthase domain containing gene (ISPD), an extreme outlier present at a frequency of 89% in gamecocks but only 4% in nongame chickens. The ISPD locus has the strongest signal of selection in gamecocks, suggesting it is important for fighting performance. Because ISPD variants that are highly prevalent in gamecocks are still segregating in nongame chickens, selective breeding may help reduce its frequency in farm conditions in which aggression is not a desired trait. Altogether, our work provides genomic resources for agricultural genetics, uncovers a common origin for gamecocks from around the world and what distinguishes them genetically from chickens bred for purposes other than fighting, and points to ISPD as the most important locus related to fighting performance.
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Affiliation(s)
- Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, 10027-2325, USA
| | - Joseph Brew
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, 10027-2325, USA
| | - Kerel X Francis
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, 10027-2325, USA
| | | | - Antonio González Ariza
- PAIDI AGR-218 Research Group, Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain
- Diputación Provincial de Córdoba, Agropecuary Provincial Centre, 14014 Córdoba, Spain
| | - Sergio Nogales Baena
- PAIDI AGR-218 Research Group, Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain
| | - Tsuyoshi Shimmura
- Department of Biological Production, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
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Bendesky A, Brew J, Francis KX, Tello Corbetto EF, González Ariza A, Nogales Baena S, Shimmura T. Noncoding genetic variation in ISPD distinguishes gamecocks from nongame chickens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553562. [PMID: 37662209 PMCID: PMC10473654 DOI: 10.1101/2023.08.16.553562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Chickens were domesticated >4,000 years ago, probably first for fighting them and only later as a source of food. Fighting chickens, commonly known as gamecocks, continue to be bred throughout the world, but the genetic relationships among geographically diverse gamecocks and with nongame chickens are not known. Here, we sequenced the genomes of 44 geographically diverse gamecocks and of 62 nongame chickens representing a variety of breeds. We combined these sequences with published genomes to generate the most diverse chicken genomes dataset yet assembled, at 307 samples. We found that gamecocks do not form a homogeneous group, yet they share genetic similarities that distinguish them from nongame chickens. Such similarities are likely the result of a common origin before their local diversification into, or mixing with, nongame chickens. Particularly noteworthy is a variant in an intron of ISPD, an extreme outlier present at a frequency of 90% in gamecocks but only 4% in nongame chickens. The ISPD locus has the strongest signal of selection in gamecocks, suggesting it is important for fighting performance. Because ISPD variants that are highly prevalent in gamecocks are still segregating in nongame chickens, selective breeding may help reduce its frequency in farm conditions in which aggression is not a desired trait. Altogether, our work provides genomic resources for agricultural genetics, uncovers a common origin for gamecocks from around the world and what distinguishes them genetically from chickens bred for purposes other than fighting, and points to ISPD as the most important locus related to fighting performance.
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Affiliation(s)
- Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Joseph Brew
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Kerel X. Francis
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | | | - Antonio González Ariza
- PAIDI AGR-218 Research Group, Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Córdoba, Spain
- Agropecuary Provincial Centre, Diputación Provincial de Córdoba, Córdoba, Spain
| | - Sergio Nogales Baena
- PAIDI AGR-218 Research Group, Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Córdoba, Spain
| | - Tsuyoshi Shimmura
- Department of Agriculture, Tokyo University of Agriculture and Technology, Japan
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González Ariza A, Navas González FJ, León Jurado JM, Arando Arbulu A, Delgado Bermejo JV, Camacho Vallejo ME. Data Mining as a Tool to Infer Chicken Carcass and Meat Cut Quality from Autochthonous Genotypes. Animals (Basel) 2022; 12:2702. [PMID: 36230442 PMCID: PMC9559234 DOI: 10.3390/ani12192702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/26/2022] [Accepted: 10/05/2022] [Indexed: 11/29/2022] Open
Abstract
The present research aims to develop a carcass quality characterization methodology for minority chicken populations. The clustering patterns described across local chicken genotypes by the meat cuts from the carcass were evaluated via a comprehensive meta-analysis of ninety-one research documents published over the last 20 years. These documents characterized the meat quality of native chicken breeds. After the evaluation of their contents, thirty-nine variables were identified. Variables were sorted into eight clusters as follows; weight-related traits, water-holding capacity, colour-related traits, histological properties, texture-related traits, pH, content of flavour-related nucleotides, and gross nutrients. Multicollinearity analyses (VIF ≤ 5) were run to discard redundancies. Chicken sex, firmness, chewiness, L* meat 72 h post-mortem, a* meat 72 h post-mortem, b* meat 72 h post-mortem, and pH 72 h post-mortem were deemed redundant and discarded from the study. Data-mining chi-squared automatic interaction detection (CHAID)-based algorithms were used to develop a decision-tree-validated tool. Certain variables such as carcass/cut weight, pH, carcass yield, slaughter age, protein, cold weight, and L* meat reported a high explanatory potential. These outcomes act as a reference guide to be followed when designing studies of carcass quality-related traits in local native breeds and market commercialization strategies.
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Affiliation(s)
- Antonio González Ariza
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain
- Agropecuary Provincial Centre, Diputación Provincial de Córdoba, 14071 Córdoba, Spain
| | - Francisco Javier Navas González
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain
- Institute of Agricultural Research and Training (IFAPA), Alameda del Obispo, 14004 Córdoba, Spain
| | | | - Ander Arando Arbulu
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain
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González Ariza A, Navas González FJ, Arando Arbulu A, León Jurado JM, Delgado Bermejo JV, Camacho Vallejo ME. Variability of Meat and Carcass Quality from Worldwide Native Chicken Breeds. Foods 2022; 11:1700. [PMID: 35741898 PMCID: PMC9223061 DOI: 10.3390/foods11121700] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 02/01/2023] Open
Abstract
The present research aimed to determine the differential clustering patterns of carcass and meat quality traits in local chicken breeds from around the world and to develop a method to productively characterize minority bird populations. For this, a comprehensive meta-analysis of 91 research documents that dealt with the study of chicken local breeds through the last 20 years was performed. Thirty-nine traits were sorted into the following clusters: weight-related traits, histological properties, pH, color traits, water-holding capacity, texture-related traits, flavor content-related nucleotides, and gross nutrients. Multicollinearity problems reported for pH 72 h post mortem, L* meat 72 h post mortem, a* meat 72 h post mortem, sex, firmness, and chewiness, were thus discarded from further analyses (VIF < 5). Data-mining cross-validation and chi-squared automatic interaction detection (CHAID) decision tree development allowed us to detect similarities across genotypes. Easily collectable trait, such as shear force, muscle fiber diameter, carcass/pieces weight, and pH, presented high explanatory potential of breed variability. Hence, the aforementioned variables must be considered in the experimental methodology of characterization of carcass and meat from native genotypes. This research enables the characterization of local chicken populations to satisfy the needs of specific commercial niches for poultry meat consumers.
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Affiliation(s)
- Antonio González Ariza
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Cordoba, Spain; (A.G.A.); (A.A.A.); (J.V.D.B.)
| | - Francisco Javier Navas González
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Cordoba, Spain; (A.G.A.); (A.A.A.); (J.V.D.B.)
- Institute of Agricultural Research and Training (IFAPA), 14004 Cordoba, Spain;
| | - Ander Arando Arbulu
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Cordoba, Spain; (A.G.A.); (A.A.A.); (J.V.D.B.)
| | | | - Juan Vicente Delgado Bermejo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Cordoba, Spain; (A.G.A.); (A.A.A.); (J.V.D.B.)
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Phenotypic Analysis of Growth and Morphological Traits in Miniature Breeds of Japanese Indigenous Chickens. J Poult Sci 2022; 59:38-47. [PMID: 35125911 PMCID: PMC8791770 DOI: 10.2141/jpsa.0200110] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/19/2021] [Indexed: 11/21/2022] Open
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Habimana R, Ngeno K, Okeno TO, Hirwa CDA, Keambou Tiambo C, Yao NK. Genome-Wide Association Study of Growth Performance and Immune Response to Newcastle Disease Virus of Indigenous Chicken in Rwanda. Front Genet 2021; 12:723980. [PMID: 34745207 PMCID: PMC8570395 DOI: 10.3389/fgene.2021.723980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/15/2021] [Indexed: 11/13/2022] Open
Abstract
A chicken genome has several regions with quantitative trait loci (QTLs). However, replication and confirmation of QTL effects are required particularly in African chicken populations. This study identified single nucleotide polymorphisms (SNPs) and putative genes responsible for body weight (BW) and antibody response (AbR) to Newcastle disease (ND) in Rwanda indigenous chicken (IC) using genome-wide association studies (GWAS). Multiple testing was corrected using chromosomal false detection rates of 5 and 10% for significant and suggestive thresholds, respectively. BioMart data mining and variant effect predictor tools were used to annotate SNPs and candidate genes, respectively. A total of four significant SNPs (rs74098018, rs13792572, rs314702374, and rs14123335) significantly (p ≤ 7.6E-5) associated with BW were identified on chromosomes (CHRs) 8, 11, and 19. In the vicinity of these SNPs, four genes such as pre-B-cell leukaemia homeobox 1 (PBX1), GPATCH1, MPHOSPH6, and MRM1 were identified. Four other significant SNPs (rs314787954, rs13623466, rs13910430, and rs737507850) all located on chromosome 1 were strongly (p ≤ 7.6E-5) associated with chicken antibody response to ND. The closest genes to these four SNPs were cell division cycle 16 (CDC16), zinc finger, BED-type containing 1 (ZBED1), myxovirus (influenza virus) resistance 1 (MX1), and growth factor receptor bound protein 2 (GRB2) related adaptor protein 2 (GRAP2). Besides, other SNPs and genes suggestively (p ≤ 1.5E-5) associated with BW and antibody response to ND were reported. This work offers a useful entry point for the discovery of causative genes accountable for essential QTLs regulating BW and antibody response to ND traits. Results provide auspicious genes and SNP-based markers that can be used in the improvement of growth performance and ND resistance in IC populations based on gene-based and/or marker-assisted breeding selection.
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Affiliation(s)
- Richard Habimana
- College of Agriculture, Animal Science and Veterinary Medicine, University of Rwanda, Kigali, Rwanda.,Animal Breeding and Genomics Group, Department of Animal Science, Egerton University, Egerton, Kenya
| | - Kiplangat Ngeno
- Animal Breeding and Genomics Group, Department of Animal Science, Egerton University, Egerton, Kenya
| | - Tobias Otieno Okeno
- Animal Breeding and Genomics Group, Department of Animal Science, Egerton University, Egerton, Kenya
| | | | - Christian Keambou Tiambo
- Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Nairobi, Kenya
| | - Nasser Kouadio Yao
- Biosciences Eastern and Central Africa - International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
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Nishimura K, Ijiri D, Shimamoto S, Takaya M, Ohtsuka A, Goto T. Genetic effect on free amino acid contents of egg yolk and albumen using five different chicken genotypes under floor rearing system. PLoS One 2021; 16:e0258506. [PMID: 34624067 PMCID: PMC8500412 DOI: 10.1371/journal.pone.0258506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/28/2021] [Indexed: 01/24/2023] Open
Abstract
Chicken eggs play an important role as food resources in the world. Although genetic effects on yolk and albumen contents have been reported, the number of chicken genotypes analyzed so far is still limited. To investigate the effect of genetic background on 10 egg traits, 19 yolk amino acid traits, and 19 albumen amino acid traits, we evaluated a total of 58 eggs from five genotypes: two Japanese indigenous breeds (Ukokkei and Nagoya) and three hybrids (Araucana cross, Kurohisui, and Boris Brown) under a floor rearing system. One-way ANOVA revealed significant effects of genotype on 10 egg traits, 8 yolk amino acids (Asp, Glu, Ser, Gly, Thr, Tyr, Cys, and Leu), and 11 albumen amino acids (Asp, Glu, Asn, Ser, Gln, His, Ala, Tyr, Trp, Phe, and Ile) contents. Moderate to strong positive phenotypic correlations among traits within each trait category (size and weight traits, yolk amino acid traits, and albumen amino acid traits), whereas there were basically no or weak correlations among the trait categories. However, a unique feature was found in the Araucana cross indicating moderate positive correlations of amino acids between yolk and albumen. These results suggest that genetic factors can modify not only the size and weight of the egg and eggshell color but also yolk and albumen free amino acids contents.
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Affiliation(s)
- Kenji Nishimura
- Department of Life and Food Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
| | - Daichi Ijiri
- Department of Biochemical Science and Technology, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Saki Shimamoto
- Department of Biochemical Science and Technology, Kagoshima University, Korimoto, Kagoshima, Japan
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Masahiro Takaya
- Department of Life and Food Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
- Hokkaido Tokachi Area Regional Food Processing Technology Center, Tokachi Foundation, Obihiro, Japan
| | - Akira Ohtsuka
- Department of Biochemical Science and Technology, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Tatsuhiko Goto
- Department of Life and Food Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
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8
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Quantitative trait loci for growth-related traits in Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing. Mol Genet Genomics 2021; 296:1147-1159. [PMID: 34251529 DOI: 10.1007/s00438-021-01806-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/16/2021] [Indexed: 10/20/2022]
Abstract
This study aimed to identify quantitative trait loci (QTLs) for growth-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers in Japanese quail. A QTL mapping population of 277 F2 birds was obtained from an intercross between a male of a large-sized strain and three females of a normal-sized strain. Body weight (BW) was measured weekly from hatching to 16 weeks of age. Non-linear regression growth models of Weibull, Logistic, Gompertz, Richards, and Brody were analyzed, and growth curve parameters of Richards was selected as the best model to describe the quail growth curve of the F2 birds. Restriction-site associated DNA sequencing developed 125 SNP markers that were informative between their parental strains. The SNP markers were distributed on 16 linkage groups that spanned 795.9 centiMorgan (cM) with an average marker interval of 7.3 cM. QTL analysis of phenotypic traits revealed four main-effect QTLs. Detected QTLs were located on chromosomes 1 and 3 and were associated with BW from 4 to 16 weeks of age and asymptotic weight of Richards model at genome-wide significant at 1% or 5% level. No QTL was detected for BW from 0 to 3 weeks of age. This is the first report identified QTLs for asymptotic weight of the Richards parameter in Japanese quail. These results highlight that the combination of QTL studies and the RAD-seq method will aid future breeding programs identify genes underlying the QTL and the application of marker-assisted selection in the poultry industry, particularly the Japanese quail.
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Mapping of Quantitative Trait Loci Controlling Egg-Quality and -Production Traits in Japanese Quail ( Coturnix japonica) Using Restriction-Site Associated DNA Sequencing. Genes (Basel) 2021; 12:genes12050735. [PMID: 34068239 PMCID: PMC8153160 DOI: 10.3390/genes12050735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 02/07/2023] Open
Abstract
This research was conducted to identify quantitative trait loci (QTL) associated with egg-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers using restriction-site associated DNA sequencing (RAD-seq) in Japanese quail. A total of 138 F2 females were produced by full-sib mating of F1 birds derived from an intercross between a male of the large-sized strain with three females of the normal-sized strain. Eggs were investigated at two different stages: the beginning stage of egg-laying and at 12 weeks of age (second stage). Five eggs were analyzed for egg weight, lengths of the long and short axes, egg shell strength and weight, yolk weight and diameter, albumen weight, egg equator thickness, and yolk color (L*, a*, and b* values) at each stage. Moreover, the age at first egg, the cumulative number of eggs laid, and egg production rate were recorded. RAD-seq developed 118 SNP markers and mapped them to 13 linkage groups using the Map Manager QTX b20 software. Markers were spanned on 776.1 cM with an average spacing of 7.4 cM. Nine QTL were identified on chromosomes 2, 4, 6, 10, 12, and Z using the simple interval mapping method in the R/qtl package. The QTL detected affected 10 egg traits of egg weight, lengths of the long and short axes of egg, egg shell strength, yolk diameter and weight, albumen weight, and egg shell weight at the beginning stage, yellowness of the yolk color at the second stage, and age at first egg. This is the first report to perform a quail QTL analysis of egg-related traits using RAD-seq. These results highlight the effectiveness of RAD-seq associated with targeted QTL and the application of marker-assisted selection in the poultry industry, particularly in the Japanese quail.
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Bibi S, Fiaz Khan M, Noreen S, Rehman A, Khan N, Mehmood S, Shah M. Morphological characteristics of native chicken of village Chhajjian, Haripur Pakistan. Poult Sci 2021; 100:100843. [PMID: 33518319 PMCID: PMC7936127 DOI: 10.1016/j.psj.2020.11.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/31/2020] [Accepted: 11/09/2020] [Indexed: 11/17/2022] Open
Abstract
The present study was conducted to describe the variations in morphological characteristics of different selected populations of indigenous chickens. Five populations of chickens in different (localities) of Chhajjian, KP, Pakistan, were studied based on qualitative traits recorded for a total of 100 chickens. Each of the study populations contains multiple variants of plumage colors and other physical features. The average flock size was observed to be 38. Predominant plumage color was grayish and other mixtures along with different percentages in different localities. Pea comb was the dominant comb type in all localities. Most of the chickens were yellow skinned. Males in all populations were heavier and taller than the females. This recorded variation in morphological traits will help in the conservation of these chickens.
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Affiliation(s)
- Saira Bibi
- Department of Zoology, Hazara University, Mansehra, KP, Pakistan; Department of Zoology, Women University Swabi, Haripr, KP, Pakistan.
| | | | - Shumaila Noreen
- Department of Zoology, University of Peshawar, Peshawar, KP, Pakistan
| | - Aqsa Rehman
- Department of Zoology, Hazara University, Mansehra, KP, Pakistan
| | - Nasir Khan
- Department of Zoology, Hazara University, Mansehra, KP, Pakistan
| | - Sajid Mehmood
- Department of Zoology, Hazara University, Mansehra, KP, Pakistan
| | - Muzafar Shah
- Department of Zoology, University of Swat, Swat, KP, Pakistan
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11
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Li W, Jing Z, Cheng Y, Wang X, Li D, Han R, Li W, Li G, Sun G, Tian Y, Liu X, Kang X, Li Z. Analysis of four complete linkage sequence variants within a novel lncRNA located in a growth QTL on chromosome 1 related to growth traits in chickens. J Anim Sci 2020; 98:5822640. [PMID: 32309860 DOI: 10.1093/jas/skaa122] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/16/2020] [Indexed: 12/18/2022] Open
Abstract
An increasing number of studies have shown that quantitative trait loci (QTLs) at the end of chromosome 1 identified in different chicken breeds and populations exert significant effects on growth traits in chickens. Nevertheless, the causal genes underlying the QTL effect remain poorly understood. Using an updated gene database, a novel lncRNA (named LncFAM) was found at the end of chromosome 1 and located in a growth and digestion QTL. This study showed that the expression level of LncFAM in pancreas tissues with a high weight was significantly higher than that in pancreas tissues with a low weight, which indicates that the expression level of LncFAM was positively correlated with various growth phenotype indexes, such as growth speed and body weight. A polymorphism screening identified four polymorphisms with strong linkage disequilibrium in LncFAM: a 5-bp indel in the second exon, an A/G base mutation, and 7-bp and 97-bp indels in the second intron. A study of a 97-bp insertion in the second intron using an F2 chicken resource population produced by Anka and Gushi chickens showed that the mutant individuals with genotype II had the highest values for body weight (BW) at 0 days and 2, 4, 6, 8, 10 and 12 weeks, shank girth (SG) at 4, 8 and 12 weeks, chest width (CW) at 4, 8 and 12 weeks, body slant length (BSL) at 8 and 12 weeks, and pelvic width (PW) at 4, 8 and 12 weeks, followed by ID and DD genotypes. The amplification and typing of 2,716 chickens from ten different breeds, namely, the F2 chicken resource population, dual-type chickens, including Xichuan black-bone chickens, Lushi green-shell layers, Dongxiang green-shell layers, Changshun green-shell layers, and Gushi chickens, and commercial broilers, including Ross 308, AA, Cobb and Hubbard broilers, revealed that II was the dominant genotype. Interestingly, only genotype II existed among the tested populations of commercial broilers. Moreover, the expression level in the pancreas tissue of Ross 308 chickens was significantly higher than that in the pancreas tissue of Gushi chickens (P < 0.001), which might be related to the conversion rates among different chickens. The prediction and verification of the target gene of LncFAM showed that LncFAM might regulate the expression of its target gene FAM48A through cis-expression. Our results provide useful information on the mutation of LncFAM, which can be used as a potential molecular breeding marker.
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Affiliation(s)
- Wenya Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Zhenzhu Jing
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Yingying Cheng
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiangnan Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Donghua Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Wenting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Guoxi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Xiaojun Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
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12
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Wang Y, Bu L, Cao X, Qu H, Zhang C, Ren J, Huang Z, Zhao Y, Luo C, Hu X, Shu D, Li N. Genetic Dissection of Growth Traits in a Unique Chicken Advanced Intercross Line. Front Genet 2020; 11:894. [PMID: 33033489 PMCID: PMC7509424 DOI: 10.3389/fgene.2020.00894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/20/2020] [Indexed: 12/23/2022] Open
Abstract
The advanced intercross line (AIL) that is created by successive generations of pseudo-random mating after the F2 generation is a valuable resource, especially in agricultural livestock and poultry species, because it improves the precision of quantitative trait loci (QTL) mapping compared with traditional association populations by introducing more recombination events. The growth traits of broilers have significant economic value in the chicken industry, and many QTLs affecting growth traits have been identified, especially on chromosomes 1, 4, and 27, albeit with large confidence intervals that potentially contain dozens of genes. To promote a better understanding of the underlying genetic architecture of growth trait differences, specifically body weight and bone development, in this study, we report a nine-generation AIL derived from two divergent outbred lines: High Quality chicken Line A (HQLA) and Huiyang Bearded (HB) chicken. We evaluate the genetic architecture of the F0, F2, F8, and F9 generations of AIL and demonstrate that the population of the F9 generation sufficiently randomized the founder genomes and has the characteristics of rapid linkage disequilibrium decay, limited allele frequency decline, and abundant nucleotide diversity. This AIL yielded a much narrower QTL than the F2 generations, especially the QTL on chromosome 27, which was reduced to 120 Kb. An ancestral haplotype association analysis showed that most of the dominant haplotypes are inherited from HQLA but with fluctuation of the effects between them. We highlight the important role of four candidate genes (PHOSPHO1, IGF2BP1, ZNF652, and GIP) in bone growth. We also retrieved a missing QTL from AIL on chromosome 4 by identifying the founder selection signatures, which are explained by the loss of association power that results from rare alleles. Our study provides a reasonable resource for detecting quantitative trait genes and tracking ancestor history and will facilitate our understanding of the genetic mechanisms underlying chicken bone growth.
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Affiliation(s)
- Yuzhe Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Lina Bu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xuemin Cao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hao Qu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chunyuan Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiangli Ren
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhuolin Huang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chenglong Luo
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Dingming Shu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ning Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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13
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Emrani H, Masoudi AA, Vaez Torshizi R, Ehsani A. Genome-wide association study of shank length and diameter at different developmental stages in chicken F2 resource population. Anim Genet 2020; 51:722-730. [PMID: 32662094 DOI: 10.1111/age.12981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2020] [Indexed: 01/09/2023]
Abstract
In order to find SNPs and genes affecting shank traits, we performed a GWAS in a chicken F2 population of eight half-sib families from five hatches derived from reciprocal crosses between an Arian fast-growing line and an Urmia indigenous slow-growing chicken. A total of 308 birds were genotyped using a 60K chicken SNP chip. Shank traits including shank length and diameter were measured weekly from birth to 12 weeks of age. A generalized linear model and a compressed mixed linear model (CMLM) were applied to achieve the significant regions. The value of the average genomic inflation factor (λ statistic) of the CMLM model (0.99) indicated that the CMLM was more effective than the generalized linear model in controlling the population structure. The genes surrounding significant SNPs and their biological functions were identified from NCBI, Ensembl and UniProt databases. The results indicated that 12 SNPs at 12 different ages passed the LD-adjusted 5% Bonferroni significant threshold. Two SNPs were significant for shank length and nine SNPs were significant for shank diameter. The significant SNPs were located near to or inside 11 candidate genes. The results showed that a number of significant SNPs in the middle ages were higher than the rest. The MXRA8 gene was related to the significant SNP at week 1 that promotes proliferation of growth plate chondrocytes. A unique SNP of Gga_rs16689511 located on chicken Z chromosome within the LOC101747628 gene was related to shank length at three different ages of birds (weeks 8, 9 and 11). The significant SNPs for shank diameter were found at weeks 4 and 7 (four and five SNPs respectively). The identifications of SNPs and genes here could contribute to a better understanding of the genetic control of shank traits in chicken.
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Affiliation(s)
- H Emrani
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, PO Box 14115-336, Tehran, Iran
| | - A A Masoudi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, PO Box 14115-336, Tehran, Iran
| | - R Vaez Torshizi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, PO Box 14115-336, Tehran, Iran
| | - A Ehsani
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, PO Box 14115-336, Tehran, Iran
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14
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Guo J, Qu L, Dou TC, Shen MM, Hu YP, Ma M, Wang KH. Genome-wide association study provides insights into the genetic architecture of bone size and mass in chickens. Genome 2019; 63:133-143. [PMID: 31794256 DOI: 10.1139/gen-2019-0022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Bone size is an important trait for chickens because of its association with osteoporosis in layers and meat production in broilers. Here, we employed high density genotyping platforms to detect candidate genes for bone traits. Estimates of the narrow heritabilities ranged from 0.37 ± 0.04 for shank length to 0.59 ± 0.04 for tibia length. The dominance heritability was 0.12 ± 0.04 for shank length. Using a linear mixed model approach, we identified a promising locus within NCAPG on chromosome 4, which was associated with tibia length and mass, femur length and area, and shank length. In addition, three other loci were associated with bone size or mass at a Bonferroni-corrected genome-wide significance threshold of 1%. One region on chicken chromosome 1 between 168.38 and 171.82 Mb harbored HTR2A, LPAR6, CAB39L, and TRPC4. A second region that accounted for 2.2% of the phenotypic variance was located around WNT9A on chromosome 2, where allele substitution was predicted to be associated with tibia length. Four candidate genes identified on chromosome 27 comprising SPOP, NGFR, GIP, and HOXB3 were associated with tibia length and mass, femur length and area, and shank length. Genome partitioning analysis indicated that the variance explained by each chromosome was proportional to its length.
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Affiliation(s)
- Jun Guo
- Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China.,Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China
| | - Liang Qu
- Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China.,Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China
| | - Tao-Cun Dou
- Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China.,Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China
| | - Man-Man Shen
- Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China.,Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China
| | - Yu-Ping Hu
- Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China.,Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China
| | - Meng Ma
- Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China.,Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China
| | - Ke-Hua Wang
- Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China.,Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China
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15
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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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16
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Ono T, Kouguchi T, Ishikawa A, Nagano AJ, Takenouchi A, Igawa T, Tsudzuki M. Quantitative trait loci mapping for the shear force value in breast muscle of F2 chickens. Poult Sci 2019; 98:1096-1101. [PMID: 30329107 DOI: 10.3382/ps/pey493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 10/10/2018] [Indexed: 12/18/2022] Open
Abstract
The shear force value is one of the major traits that determine meat quality. In the present study, we performed QTL analysis for chicken breast muscle shear force value at 7 wk of age using 545 single nucleotide polymorphism (SNP) markers developed via restriction-site associated DNA sequencing (RAD-seq). An F2 resource family was generated by mating Oh-Shamo, a native Japanese chicken breed, and the White Plymouth Rock chicken breed. A total of 215 F2 birds were produced. Simple interval mapping revealed one significant main-effect QTL between 6.28 and 8.10 Mb SNPs on the chromosome Z with a logarithm of odds score of 5.53 at the genome-wide 5% level. At this QTL, the confidence interval, phenotypic variance explained, and additive effect were 26 cM, 12.24%, and -0.31 in males and -0.34 in females, respectively. No QTL with epistatic interaction effects were detected. To our knowledge, this is the first report on a QTL affecting the shear force value in the chicken breast muscle, using SNP markers derived from RAD-seq.
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Affiliation(s)
- Takashi Ono
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | | | - Akira Ishikawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan.,Japanese Avian Bioresource Project Research Center, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga 520-2194, Japan
| | - Atsushi Takenouchi
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Takeshi Igawa
- Japanese Avian Bioresource Project Research Center, Higashi-Hiroshima, Hiroshima 739-8528, Japan.,Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Masaoki Tsudzuki
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan.,Japanese Avian Bioresource Project Research Center, Higashi-Hiroshima, Hiroshima 739-8528, Japan
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17
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Mapping of Quantitative Trait Loci for Growth and Carcass-Related Traits in Chickens Using a Restriction-Site Associated DNA Sequencing Method. J Poult Sci 2019; 56:166-176. [PMID: 32055211 PMCID: PMC7005382 DOI: 10.2141/jpsa.0180066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In the present study, quantitative trait loci (QTLs) analysis was performed to identify the chromosomal positions of growth and carcass-related trait QTLs using 319 F2 chickens obtained from intercrosses of an Oh-Shamo male and four White Plymouth Rock females. Body weight was measured weekly until the birds were 7 weeks old. Carcass-related traits were also measured at this timepoint. A genetic linkage map was constructed using 545 single nucleotide polymorphism (SNP) markers that were developed using a restriction-site associated DNA sequencing method. The linkage map included the 23 autosomes and the Z chromosome. Using simple interval QTL mapping, we were able to identify 10 significant and suggestive main-effect QTLs for growth and carcass-related traits present on chromosomes 1, 2, 3, 5, 8, 19, 24, and Z. These loci explained 5.60–16.52% of the phenotypic variances. The chromosomal positions of the 10 QTLs overlapped with those of previously reported QTLs, whereas the targeted traits varied. Our QTLs will aid future breeding programs in improving growth and meat yield of chickens (e.g., via marker-assisted selection), particularly in the Japanese brand chicken industry.
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18
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A longitudinal quantitative trait locus mapping of chicken growth traits. Mol Genet Genomics 2018; 294:243-252. [PMID: 30315370 DOI: 10.1007/s00438-018-1501-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 09/28/2018] [Indexed: 10/28/2022]
Abstract
Since the growth traits of chickens are largely related to the production of meat and eggs, it is definitely important to understand genetic basis of growth traits. Although many quantitative trait loci (QTLs) that affect growth traits have recently been reported in chickens, little is known about genetic architecture of growth traits across all growth stages. Therefore, we conducted a longitudinal QTL study of growth traits measured from 0 to 64 weeks of age using 134 microsatellite DNA markers on 26 autosomes from 406 F2 females, which resulted from an intercross of Oh-Shamo and White Leghorn chicken breeds. We found 27 and 21 independent main-effect QTLs for body weight and shank length, respectively. Moreover, 15 and 4 pairs of epistatic QTLs were found for body weight and shank length, respectively. Taken together, the present study revealed 48 QTLs for growth traits on 21 different autosomes, and these loci clearly have age-specific effects on phenotypes throughout stages that are important for meat and egg productions. Approximately 60% of Oh-Shamo-derived alleles increased the phenotypic values, corresponding to the fact that Oh-Shamo traits were higher than those of White Leghorn. On the other hand, remaining Oh-Shamo alleles decreased the phenotypic values. Our results clearly indicated that the growth traits of chickens are regulated by several main and epistatic QTLs that are widely distributed in the chicken genome, and that the QTLs have age-dependent manners of controlling the traits. This study implies importance of not only cross-sectional but also longitudinal growth data for further understanding of the complex genetic architecture in animal.
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19
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Goto T, Tsudzuki M. Genetic Mapping of Quantitative Trait Loci for Egg Production and Egg Quality Traits in Chickens: a Review. J Poult Sci 2017; 54:1-12. [PMID: 32908402 PMCID: PMC7477176 DOI: 10.2141/jpsa.0160121] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/24/2016] [Indexed: 12/11/2022] Open
Abstract
Chickens display a wide spectrum of phenotypic variations in quantitative traits such as egg-related traits. Quantitative trait locus (QTL) analysis is a statistical method used to understand the relationship between phenotypic (trait measurements) and genotypic data (molecular markers). We have performed QTL analyses for egg-related traits using an original resource population based on the Japanese Large Game (Oh-Shamo) and the White Leghorn breeds of chickens. In this article, we summarize the results of our extensive QTL analyses for 11 and 66 traits for egg production and egg quality, respectively. We reveal that at least 30 QTL regions on 17 different chromosomes affect phenotypic variation in egg-related traits. Each locus had an age-specific effect on traits, and a variety in effects was also apparent, such as additive, dominance, and epistatic-interaction effects. Although genome-wide association study (GWAS) is suitable for gene-level resolution mapping of GWAS loci with additive effects, QTL mapping studies enable us to comprehensively understand genetic control, such as chromosomal regions, genetic contribution to phenotypic variance, mode of inheritance, and age-specificity of both common and rare alleles. QTL analyses also describe the relationship between genotypes and phenotypes in experimental populations. Accumulation of QTL information, including GWAS loci, is also useful for studies of population genomics approached without phenotypic data in order to validate the identified genomic signatures of positive selection. The combination of QTL studies and next-generation sequencing techniques with uncharacterized genetic resources will enhance current understanding of the relationship between genotypes and phenotypes in livestock animals.
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Affiliation(s)
- Tatsuhiko Goto
- Genetics, Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
- Present address: Department of Life Science and Agriculture, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido 080-8555, Japan
| | - Masaoki Tsudzuki
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
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20
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Cahyadi M, Park HB, Seo DW, Jin S, Choi N, Heo KN, Kang BS, Jo C, Lee JH. Variance Component Quantitative Trait Locus Analysis for Body Weight Traits in Purebred Korean Native Chicken. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:43-50. [PMID: 26732327 PMCID: PMC4698688 DOI: 10.5713/ajas.15.0193] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 04/24/2015] [Accepted: 06/02/2015] [Indexed: 11/27/2022]
Abstract
Quantitative trait locus (QTL) is a particular region of the genome containing one or more genes associated with economically important quantitative traits. This study was conducted to identify QTL regions for body weight and growth traits in purebred Korean native chicken (KNC). F1 samples (n = 595) were genotyped using 127 microsatellite markers and 8 single nucleotide polymorphisms that covered 2,616.1 centi Morgan (cM) of map length for 26 autosomal linkage groups. Body weight traits were measured every 2 weeks from hatch to 20 weeks of age. Weight of half carcass was also collected together with growth rate. A multipoint variance component linkage approach was used to identify QTLs for the body weight traits. Two significant QTLs for growth were identified on chicken chromosome 3 (GGA3) for growth 16 to18 weeks (logarithm of the odds [LOD] = 3.24, Nominal p value = 0.0001) and GGA4 for growth 6 to 8 weeks (LOD = 2.88, Nominal p value = 0.0003). Additionally, one significant QTL and three suggestive QTLs were detected for body weight traits in KNC; significant QTL for body weight at 4 weeks (LOD = 2.52, nominal p value = 0.0007) and suggestive QTL for 8 weeks (LOD = 1.96, Nominal p value = 0.0027) were detected on GGA4; QTLs were also detected for two different body weight traits: body weight at 16 weeks on GGA3 and body weight at 18 weeks on GGA19. Additionally, two suggestive QTLs for carcass weight were detected at 0 and 70 cM on GGA19. In conclusion, the current study identified several significant and suggestive QTLs that affect growth related traits in a unique resource pedigree in purebred KNC. This information will contribute to improving the body weight traits in native chicken breeds, especially for the Asian native chicken breeds.
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Affiliation(s)
- Muhammad Cahyadi
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764 Korea ; Department of Animal Science, Faculty of Agriculture, Sebelas Maret University, Surakarta 57126, Indonesia
| | - Hee-Bok Park
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764 Korea
| | - Dong-Won Seo
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764 Korea
| | - Shil Jin
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764 Korea
| | - Nuri Choi
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764 Korea
| | - Kang-Nyeong Heo
- Poultry Science Division, National Institute of Animal Science, RDA, Cheonan 331-801, Korea
| | - Bo-Seok Kang
- Poultry Science Division, National Institute of Animal Science, RDA, Cheonan 331-801, Korea
| | - Cheorun Jo
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea
| | - Jun-Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764 Korea
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21
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Nassar MK, Goraga ZS, Brockmann GA. Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: IV. Growth performance. Anim Genet 2015; 46:441-6. [PMID: 25908024 DOI: 10.1111/age.12298] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2015] [Indexed: 11/29/2022]
Abstract
Reciprocal crosses between the inbred lines New Hampshire (NHI) and White Leghorn (WL77) comprising 579 F2 individuals were used to map QTL for body weight and composition. Here, we examine the growth performance until 20 weeks of age. Linkage analysis provided evidence for highly significant QTL on GGA1, 2, 4, 10 and 27 which had specific effects on early or late growth. The highest QTL effects, accounting for 4.6-25.6% of the phenotypic F2 variance, were found on the distal region of GGA4 between 142 and 170 cM (F ≥ 13.68). The NHI QTL allele increased body mass by 141.86 g at 20 weeks. Using body weight as a covariate in the analysis of body composition traits provided evidence for genes in the GGA4 QTL region affecting fat mass independently of body mass. The QTL effect size differed between sexes and depended on the direction of cross. TBC1D1, CCKAR and PPARGC1A are functional candidate genes in the QTL peak region. Our study confirmed the importance of the distal GGA4 region for chicken growth performance. The strong effect of the GGA4 QTL makes fine mapping and gene discovery feasible.
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Affiliation(s)
- M K Nassar
- Albrecht Daniel Thaer-Institut for Agricultural and Horticultural Sciences, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Z S Goraga
- Debre Zeit Agricultural Research Center, Debre Zeit, Ethiopia
| | - G A Brockmann
- Albrecht Daniel Thaer-Institut for Agricultural and Horticultural Sciences, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
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22
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González-Cerón F, Rekaya R, Aggrey SE. Genetic analysis of bone quality traits and growth in a random mating broiler population. Poult Sci 2015; 94:883-9. [PMID: 25784765 DOI: 10.3382/ps/pev056] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/26/2014] [Indexed: 11/20/2022] Open
Abstract
We report the genetic relationship between growth and bone quality traits in a random mating broiler control population. Traits studied were growth rates from week 0 to 4 [body weight gain (BWG) 0 to 4], from week 0 to 6 (BWG 0 to 6), and residual feed intake (RFI) from week 5 to 6 (RFI 5 to 6). Bone quality traits were obtained at 6 weeks of age. These traits were shank weight (SW), shank length (SL), shank diameter (SDIAM), tibia weight (TW), tibia length (TL), and tibia diameter (TDIAM). Likewise, tibia was used to obtain the tibia density (TDEN), tibia breaking strength (TBS), tibia mineral density (TMD), tibia mineral content (TMC), and tibia ash content (TAC). At the phenotypic level, growth traits were positively correlated with most of the bone quality traits except with TDEN and TAC which tended to show unfavorable associations (-0.04 to -0.31). Heritability of bone quality traits ranged from 0.08 to 0.54. The additive genetic associations of growth traits with weight, length, and diameter of shank and tibia were positive (0.37 to 0.80). A similar pattern was observed with TMD and TMC (0.06 to 0.65). In contrast, growth traits showed unfavorable genetic associations with TDEN, TBS, and TAC (-0.03 to -0.18). It was concluded that bone quality traits have an additive genetic background and they can be improved by means of genetic tools. It appears that selection for growth is negatively correlated with some traits involved in the integrity, health, and maturity of leg bones.
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Affiliation(s)
- F González-Cerón
- NutriGenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, GA 30602
| | - R Rekaya
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602
| | - S E Aggrey
- NutriGenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, GA 30602
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23
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Characteristics of Egg-related Traits in the Onagadori (Japanese Extremely Long Tail) Breed of Chickens. J Poult Sci 2015. [DOI: 10.2141/jpsa.0140109] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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24
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25
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Mapping of Main-Effect and Epistatic Quantitative Trait Loci for Internal Egg Traits in an F 2 Resource Population of Chickens. J Poult Sci 2014. [DOI: 10.2141/jpsa.0140030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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26
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Paswan C, Bhattacharya T, Nagaraj C, Chaterjee R, Jayashankar M. SNPs in minimal promoter of myostatin (GDF-8) gene and its association with body weight in broiler chicken. JOURNAL OF APPLIED ANIMAL RESEARCH 2013. [DOI: 10.1080/09712119.2013.846859] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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27
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Dunn IC, Meddle SL, Wilson PW, Wardle CA, Law AS, Bishop VR, Hindar C, Robertson GW, Burt DW, Ellison SJH, Morrice DM, Hocking PM. Decreased expression of the satiety signal receptor CCKAR is responsible for increased growth and body weight during the domestication of chickens. Am J Physiol Endocrinol Metab 2013; 304:E909-21. [PMID: 23443924 PMCID: PMC3651647 DOI: 10.1152/ajpendo.00580.2012] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 02/22/2013] [Indexed: 12/05/2022]
Abstract
Animal domestication has resulted in changes in growth and size. It has been suggested that this may have involved selection for differences in appetite. Divergent growth between chickens selected for egg laying or meat production is one such example. The neurons expressing AGRP and POMC in the basal hypothalamus are important components of appetite regulation, as are the satiety feedback pathways that carry information from the intestine, including CCK and its receptor CCKAR (CCK1 receptor). Using 16 generations of a cross between a fast and a relatively slow growing strain of chicken has identified a region on chromosome 4 downstream of the CCKAR gene, which is responsible for up to a 19% difference in body weight at 12 wk of age. Animals possessing the high-growth haplotype at the locus have lower expression of mRNA and immunoreactive CCKAR in the brain, intestine, and exocrine organs, which is correlated with increased levels of orexigenic AGRP in the hypothalamus. Animals with the high-growth haplotype are resistant to the anorectic effect of exogenously administered CCK, suggesting that their satiety set point has been altered. Comparison with traditional breeds shows that the high-growth haplotype has been present in the founders of modern meat-type strains and may have been selected early in domestication. This is the first dissection of the physiological consequences of a genetic locus for a quantitative trait that alters appetite and gives us an insight into the domestication of animals. This will allow elucidation of how differences in appetite occur in birds and also mammals.
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Affiliation(s)
- Ian C Dunn
- University of Edinburgh, Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush, United Kingdom
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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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Nassar MK, Goraga ZS, Brockmann GA. Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: II. Muscle weight and carcass composition. Anim Genet 2012; 43:739-45. [DOI: 10.1111/j.1365-2052.2012.02344.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2011] [Indexed: 11/28/2022]
Affiliation(s)
- M. K. Nassar
- Breeding Biology and Molecular Genetics; Department of Crop and Animal Sciences; Humboldt-Universität zu Berlin; Invalidenstraβe 42; D-10115; Berlin; Germany
| | - Z. S. Goraga
- Breeding Biology and Molecular Genetics; Department of Crop and Animal Sciences; Humboldt-Universität zu Berlin; Invalidenstraβe 42; D-10115; Berlin; Germany
| | - G. A. Brockmann
- Breeding Biology and Molecular Genetics; Department of Crop and Animal Sciences; Humboldt-Universität zu Berlin; Invalidenstraβe 42; D-10115; Berlin; Germany
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Detection of a Polymorphism Associated with Shank Length and Body Weight in Japanese Quail (Coturnix japonica) by AFLP. J Poult Sci 2012. [DOI: 10.2141/jpsa.011047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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31
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Genome-wide association study of body weight in chicken F2 resource population. PLoS One 2011; 6:e21872. [PMID: 21779344 PMCID: PMC3136483 DOI: 10.1371/journal.pone.0021872] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 06/10/2011] [Indexed: 11/19/2022] Open
Abstract
Chicken body weight is an economically important trait and great genetic progress has been accomplished in genetic selective for body weight. To identify genes and chromosome regions associated with body weight, we performed a genome-wide association study using the chicken 60 k SNP panel in a chicken F2 resource population derived from the cross between Silky Fowl and White Plymouth Rock. A total of 26 SNP effects involving 9 different SNP markers reached 5% Bonferroni genome-wide significance. A chicken chromosome 4 (GGA4) region approximately 8.6 Mb in length (71.6-80.2 Mb) had a large number of significant SNP effects for late growth during weeks 7-12. The LIM domain-binding factor 2 (LDB2) gene in this region had the strongest association with body weight for weeks 7-12 and with average daily gain for weeks 6-12. This GGA4 region was previously reported to contain body weight QTL. GGA1 and GGA18 had three SNP effects on body weight with genome-wide significance. Some of the SNP effects with the significance of "suggestive linkage" overlapped with previously reported results.
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Gao Y, Feng CG, Song C, Du ZQ, Deng XM, Li N, Hu XX. Mapping quantitative trait loci affecting chicken body size traits via genome scanning. Anim Genet 2011; 42:670-4. [DOI: 10.1111/j.1365-2052.2011.02193.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Goto T, Ishikawa A, Onitsuka S, Goto N, Fujikawa Y, Umino T, Nishibori M, Tsudzuki M. Mapping quantitative trait loci for egg production traits in an F2 intercross of Oh-Shamo and White Leghorn chickens. Anim Genet 2011; 42:634-41. [PMID: 22035005 DOI: 10.1111/j.1365-2052.2011.02190.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We performed quantitative trait locus (QTL) analyses for egg production traits, including age at first egg (AFE) and egg production rates (EPR) measured every 4 weeks from 22 to 62 weeks of hen age, in a population of 421 F(2) hens derived from an intercross between the Oh-Shamo (Japanese Large Game) and White Leghorn breeds of chickens. Simple interval mapping revealed a main-effect QTL for AFE on chromosome 1 and four main-effect QTL for EPR on chromosomes 1 and 11 (three on chromosome 1 and one on chromosome 11) at the genome-wide 5% levels. Among the three EPR QTL on chromosome 1, two were identified at the early stage of egg laying (26-34 weeks of hen age) and the remaining one was discovered at the late stage (54-58 weeks). The alleles at the two EPR QTL derived from the Oh-Shamo breed unexpectedly increased the trait values, irrespective of the Oh-Shamo being inferior to the White Leghorn in the trait. This suggests that the Oh-Shamo, one of the indigenous Japanese breeds, is an untapped resource that is important for further improvement of current elite commercial laying chickens. In addition, six epistatic QTL were identified on chromosomes 2, 4, 7, 8, 17 and 19, where none of the above main-effect QTL were located. This is the first example of detection of epistatic QTL affecting egg production traits. The main and epistatic QTL identified accounted for 4-8% of the phenotypic variance. The total contribution of all QTL detected for each trait to the phenotypic and genetic variances ranged from 4.1% to 16.9% and from 11.5% to 58.5%, respectively.
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Affiliation(s)
- T Goto
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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Ankra-Badu GA, Bihan-Duval EL, Mignon-Grasteau S, Pitel F, Beaumont C, Duclos MJ, Simon J, Carré W, Porter TE, Vignal A, Cogburn LA, Aggrey SE. Mapping QTL for growth and shank traits in chickens divergently selected for high or low body weight. Anim Genet 2010; 41:400-5. [DOI: 10.1111/j.1365-2052.2009.02017.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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35
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Gao Y, Du ZQ, Feng CG, Deng XM, Li N, Da Y, Hu XX. Identification of quantitative trait loci for shank length and growth at different development stages in chicken. Anim Genet 2009; 41:101-4. [PMID: 19917046 DOI: 10.1111/j.1365-2052.2009.01962.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Shank length affects chicken leg health and longer shanks are a source of leg problems in heavy-bodied chickens. Identification of quantitative trait loci (QTL) affecting shank length traits may be of value to genetic improvement of these traits in chickens. A genome scan was conducted on 238 F(2) chickens from a reciprocal cross between the Silky Fowl and the White Plymouth Rock breeds using 125 microsatellite markers to detect static and developmental QTL affecting weekly shank length and growth (from 1 to 12 weeks) in chickens. Static QTL affected shank length from birth to time t, while developmental QTL affected shank growth from time t-1 to time t. Seven static QTL on six chromosomes (GGA2, GGA3, GGA4, GGA7, GGA9 and GGA23) were detected at ages of 2, 3, 4, 5, 6, 7, 9 and 12 weeks, and six developmental QTL on five chromosomes (GGA1, GGA2, GGA4, GGA5 and GGA23) were detected for five shank growth periods, weeks 2-3, 4-5, 5-6, 10-11 and 11-12. A static QTL and a developmental QTL (SQSL1 and DQSL2) were identified at GGA2 (between ADL0190 and ADL0152). SQSL1 explained 2.87-5.30% of the phenotypic variation in shank length from 3 to 7 weeks. DQSL2 explained 2.70% of the phenotypic variance of shank growth between 2 and 3 weeks. Two static and two developmental QTL were involved chromosome 4 and chromosome 23. Two chromosomes (GGA7 and GGA9) had static QTL but no developmental QTL and another two chromosomes (GGA1 and GGA5) had developmental QTL but no static QTL. The results of this study show that shank length and shank growth at different developmental stages involve different QTL.
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Affiliation(s)
- Y Gao
- China Agricultural University, Beijing, China
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36
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Mutations of Japanese Quail ( Coturnix japonica) and Recent Advances of Molecular Genetics for This Species. J Poult Sci 2008. [DOI: 10.2141/jpsa.45.159] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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