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Keywords = cockfighting

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17 pages, 3194 KiB  
Article
Genetic Diversity, Runs of Homozygosity, and Selection Signatures in Native Japanese Chickens: Insights from Single-Nucleotide Polymorphisms
by Vanessa V. Velasco, Masaoki Tsudzuki, Norikazu Hashimoto, Naoki Goto and Akira Ishikawa
Animals 2024, 14(22), 3341; https://doi.org/10.3390/ani14223341 - 20 Nov 2024
Cited by 3 | Viewed by 1403
Abstract
Understanding genetic diversity, runs of homozygosity (ROH), and selection signatures is critical for the conservation and breeding management of native Japanese chickens. In this study, genetic diversity, ROH, and selection signatures in 11 populations of seven native Japanese breeds and three foreign breeds [...] Read more.
Understanding genetic diversity, runs of homozygosity (ROH), and selection signatures is critical for the conservation and breeding management of native Japanese chickens. In this study, genetic diversity, ROH, and selection signatures in 11 populations of seven native Japanese breeds and three foreign breeds with different genetic and behavioral backgrounds were investigated using 11,493 SNPs identified through restriction-site-associated DNA sequencing. The Oh-Shamo (OSM), an aggressive cockfighting breed, exhibited the highest genetic diversity. Six native Japanese breeds, Ingie (IG), Ryujin-Jidori (RYU), Tosa-Jidori (TJI), Tosa-Kukin (TKU), Nagoya (NAG), and Ukkokei (UK), showed intermediate levels of genetic diversity and ROH. Population analyses grouped the 11 populations into four distinct clusters: (1) five populations comprising three foreign breeds (the Fayoumi inbred line, closed-colony G line of White Leghorn, commercial T line of WL, and White Plymouth Rock) and the IG Japanese breed; (2) OSM and two old Jidori breeds (RYU and TJI); (3) TKU and UK; and (4) the meat-type Nagoya breed. ROH and Fst analyses identified seven SNPs on chromosomes 13, 17, 20, 24, and 26, five of which were candidate genetic variants for fear-related behavior. These findings provide insights into genetic diversity and conserved genomic segments valuable for breeding and conservation in Japanese chicken breeds. Full article
(This article belongs to the Section Poultry)
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10 pages, 1911 KiB  
Article
Systematic Selection Signature Analysis of Chinese Gamecocks Based on Genomic and Transcriptomic Data
by Xufang Ren, Zi Guan, Xiurong Zhao, Xinye Zhang, Junhui Wen, Huan Cheng, Yalan Zhang, Xue Cheng, Yuchen Liu, Zhonghua Ning and Lujiang Qu
Int. J. Mol. Sci. 2023, 24(6), 5868; https://doi.org/10.3390/ijms24065868 - 20 Mar 2023
Cited by 10 | Viewed by 2987
Abstract
Selection pressures driven by natural causes or human interference are key factors causing genome variants and signatures of selection in specific regions of the genome. Gamecocks were bred for cockfighting, presenting pea-combs, larger body sizes, stronger limbs, and higher levels of aggression than [...] Read more.
Selection pressures driven by natural causes or human interference are key factors causing genome variants and signatures of selection in specific regions of the genome. Gamecocks were bred for cockfighting, presenting pea-combs, larger body sizes, stronger limbs, and higher levels of aggression than other chickens. In this study, we aimed to explore the genomic differences between Chinese gamecocks and commercial, indigenous, foreign, and cultivated breeds by detecting the regions or sites under natural or artificial selection using genome-wide association studies (GWAS), genome-wide selective sweeps based on the genetic differentiation index (FST), and transcriptome analyses. Ten genes were identified using GWAS and FST: gga-mir-6608-1, SOX5, DGKB, ISPD, IGF2BP1, AGMO, MEOX2, GIP, DLG5, and KCNMA1. The ten candidate genes were mainly associated with muscle and skeletal development, glucose metabolism, and the pea-comb phenotype. Enrichment analysis results showed that the differentially expressed genes between the Luxi (LX) gamecock and Rhode Island Red (RIR) chicken were mainly related to muscle development and neuroactive-related pathways. This study will help to understand the genetic basis and evolution of Chinese gamecocks and support the further use of gamecocks as an excellent breeding material from a genetic perspective. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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13 pages, 1891 KiB  
Article
Effects of Genetic Mutation Sites in ADR Genes on Modern Chickens Produced and Domesticated by Artificial Selection
by Tomoyoshi Komiyama
Biology 2023, 12(2), 169; https://doi.org/10.3390/biology12020169 - 20 Jan 2023
Cited by 1 | Viewed by 2988
Abstract
Associations between neurotransmitters, adrenergic receptor (ADR) mutations, and behaviors in chickens produced and domesticated by artificial selection remain unclear. This study investigates the association of neurotransmitters and ADR mutations with egg laying and cockfighting—behaviors associated with significantly different breeding backgrounds—in Shaver Brown and [...] Read more.
Associations between neurotransmitters, adrenergic receptor (ADR) mutations, and behaviors in chickens produced and domesticated by artificial selection remain unclear. This study investigates the association of neurotransmitters and ADR mutations with egg laying and cockfighting—behaviors associated with significantly different breeding backgrounds—in Shaver Brown and Shamo chickens. Accordingly, the whole sequences of nine ADR genes were determined, and nine amino acid-specific mutation sites from five genes (ADRα1A: S365G, ADRα1D: T440N, ADRα2A: D273E, ADRβ1: N443S, S445N, ADRβ3: R342C, Q404L, and P406S) were extracted. Evolutionary analysis showed that these mutations were not ancestrally derived. These results confirm that the mutations at these sites were artificially selected for domestication and are breed specific. NST population analysis confirmed a difference in the degree of genetic differentiation between the two populations in seven genes. The results further confirm differences in the degree of genetic differentiation between the two populations in Shaver Brown (ADRA1B and ADRA1D) and Shamo (ADRA1A and ADRA2B) chickens, indicating that the ADR gene differs between the two breeds. The effects of artificial selection, guided by the human-driven selection of desirable traits, are reflected in adrenaline gene mutations. Furthermore, certain gene mutations may affect domestication, while others may affect other traits in populations or individuals. Full article
(This article belongs to the Special Issue Deficiencies of Phenotype Characteristics Based on Environments, Genetics, Disease and Other Factors)
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