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Ishikawa A, Takanuma T, Hashimoto N, Goto T, Tsudzuki M. New Behavioral Handling Test Reveals Temperament Differences in Native Japanese Chickens. Animals (Basel) 2023; 13:3556. [PMID: 38003175 PMCID: PMC10668715 DOI: 10.3390/ani13223556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
It is well known in the poultry industry that fear and stress experienced during the handling of day-old chicks in commercial hatcheries can have long-lasting effects on their behavior later in life. These hatchery-related stresses are more intense and complex than those encountered in traditional behavioral tests. Consequently, a single behavioral test may not be sufficient to measure hatchery stresses and chicken temperament. In this study, we developed a new behavioral handling test for day-old chickens, which incorporated concepts from established behavioral tests used with both young and adult birds. The new test assessed 10 behavioral traits, including vocalization frequency and responses to human interaction. It was conducted on 96 two-day-old chicks from seven breeds of native Japanese and Western chickens. The results of the principal component analysis classified chicken temperaments into three distinct categories: bustle, aggression, and timidity. Using these categories, the seven breeds were classified into five groups, each with distinct temperaments. This study highlights the reliability and value of the new handling test in characterizing the temperaments of various chicken breeds and provides insights into the complex behaviors of chickens.
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Affiliation(s)
- Akira Ishikawa
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Tomoka Takanuma
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Norikazu Hashimoto
- Laboratory of Poultry, Livestock Experiment Station, Wakayama Prefecture, Hidaka-Gun, Wakayama 644-1111, Japan;
| | - Tatsuhiko Goto
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Japan;
| | - Masaoki Tsudzuki
- Laboratory of Animal Breeding and Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8525, Japan;
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Romanov MN, Abdelmanova AS, Fisinin VI, Gladyr EA, Volkova NA, Anshakov DV, Stanishevskaya OI, Vakhrameev AB, Dotsev AV, Griffin DK, Zinovieva NA. Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History. BIOLOGY 2023; 12:979. [PMID: 37508409 PMCID: PMC10376169 DOI: 10.3390/biology12070979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/01/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023]
Abstract
A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th-19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool.
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Affiliation(s)
- Michael N Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK
| | - Alexandra S Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Vladimir I Fisinin
- Center "All-Russian Poultry Research and Technological Institute" of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia
| | - Elena A Gladyr
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Natalia A Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Dmitry V Anshakov
- Breeding and Genetic Center "Zagorsk Experimental Breeding Farm"-Branch of the Federal Research Centre "All-Russian Poultry Research and Technological Institute" of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia
| | - Olga I Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L. K. Ernst Federal Research Center for Animal Husbandry, Pushkin, Saint Petersburg 196601, Russia
| | - Anatoly B Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L. K. Ernst Federal Research Center for Animal Husbandry, Pushkin, Saint Petersburg 196601, Russia
| | - Arsen V Dotsev
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK
| | - Natalia A Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
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Yonezawa T, Nishibori M, Yamamoto Y, Sasaki T, Kudo K, Ogawa H, Endo H, Akishinonomiya F. Complete Mitochondrial Genome Analysis Clarifies the Enigmatic Origin of Haplogroup D in Japanese Native Chickens. J Poult Sci 2022; 59:316-322. [PMID: 36348651 PMCID: PMC9596293 DOI: 10.2141/jpsa.0220027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/09/2022] [Indexed: 11/21/2022] Open
Abstract
Japanese native chickens (JNCs) comprise approximately 50 breeds, making Japan a diversity hotspot for native chicken breeds. JNCs were established through the repeated introduction of chickens from foreign countries. Jidori, which is the generic name of JNC breeds whose ancestral morphology resembles that of their wild progenitor (red junglefowls), is generally thought to have propagated from north East Asia (Korea and north China) to ancient Japan. However, mitochondrial haplogroup D, which is abundant in Island Southeast Asia (ISEA) as well as the Pacific but relatively rare in other regions, can be observed in some Jidori breeds (e.g., Tosa-Jidori, Tokuji-Jidori) with high frequency, leading to speculation that chickens from ISEA or the Pacific also contributed genetically to JNCs. To test this hypothesis, we sequenced the mitochondrial genomes of Jidori breeds and conducted phylogeographic analysis. Our results indicate that the JNC Haplogroup D belongs to Sub-haplogroup D2, which is currently only observed in Xinjiang, northwest China, and not to Sub-haplogroup D1, which is widely distributed in the ISEA-Pacific region. The other mitochondrial haplogroups of Jidori examined in this study also showed affinity to those of chickens native to north East Asia. Therefore, our findings support the north East Asian origin hypothesis for Jidori.
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Affiliation(s)
- Takahiro Yonezawa
- Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi city, Kanagawa 243-0034, Japan
| | - Masahide Nishibori
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima city, Hiroshima 739-8528, Japan
| | - Yoshio Yamamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima city, Hiroshima 739-8528, Japan
| | - Takeshi Sasaki
- Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi city, Kanagawa 243-0034, Japan
| | - Kohei Kudo
- Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi city, Kanagawa 243-0034, Japan
- The University Museum, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroshi Ogawa
- Yamashina Institute for Ornithology, Konoyama 115, Abiko city, Chiba 270-1145, Japan
| | - Hideki Endo
- The University Museum, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Fumihito Akishinonomiya
- The University Museum, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- Yamashina Institute for Ornithology, Konoyama 115, Abiko city, Chiba 270-1145, Japan
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Godinez CJP, Layos JKN, Yamamoto Y, Kunieda T, Duangjinda M, Liao LM, Huang XH, Nishibori M. Unveiling new perspective of phylogeography, genetic diversity, and population dynamics of Southeast Asian and Pacific chickens. Sci Rep 2022; 12:14609. [PMID: 36028749 PMCID: PMC9418149 DOI: 10.1038/s41598-022-18904-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
The complex geographic and temporal origins of chicken domestication have attracted wide interest in molecular phylogeny and phylogeographic studies as they continue to be debated up to this day. In particular, the population dynamics and lineage-specific divergence time estimates of chickens in Southeast Asia (SEA) and the Pacific region are not well studied. Here, we analyzed 519 complete mitochondrial DNA control region sequences and identified 133 haplotypes with 70 variable sites. We documented 82.7% geographically unique haplotypes distributed across major haplogroups except for haplogroup C, suggesting high polymorphism among studied individuals. Mainland SEA (MSEA) chickens have higher overall genetic diversity than island SEA (ISEA) chickens. Phylogenetic trees and median-joining network revealed evidence of a new divergent matrilineage (i.e., haplogroup V) as a sister-clade of haplogroup C. The maximum clade credibility tree estimated the earlier coalescence age of ancestral D-lineage (i.e., sub-haplogroup D2) of continental chickens (3.7 kya; 95% HPD 1985-4835 years) while island populations diverged later at 2.1 kya (95% HPD 1467-2815 years). This evidence of earlier coalescence age of haplogroup D ancestral matriline exemplified dispersal patterns to the ISEA, and thereafter the island clade diversified as a distinct group.
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Affiliation(s)
- Cyrill John P Godinez
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Visca, Baybay City, Leyte, 6521, Philippines.
| | - John King N Layos
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
- College of Agriculture and Forestry, Capiz State University, Burias, Mambusao, Capiz, 5807, Philippines
| | - Yoshio Yamamoto
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Tetsuo Kunieda
- Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Ehime, 794-8555, Japan
| | - Monchai Duangjinda
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Lawrence M Liao
- Laboratory of Aquatic Botany, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Xun-He Huang
- School of Life Sciences, Jiaying University, Meizhou, 514015, China
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Visca, Baybay City, Leyte, 6521, Philippines.
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Mon SLY, Lwin M, Maw AA, Htun LL, Bawm S, Kawabe K, Wada Y, Okamoto S, Shimogiri T. Phylogenetic analysis of Myanmar indigenous chickens using mitochondrial D-loop sequence reveals their characteristics as a genetic resource. Anim Sci J 2021; 92:e13647. [PMID: 34647390 DOI: 10.1111/asj.13647] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 09/15/2021] [Accepted: 09/23/2021] [Indexed: 01/16/2023]
Abstract
Myanmar indigenous chickens play important roles in food, entertainment, and farm business for the people of Myanmar. In this study, complete mitochondrial D-loop sequences (1232 bp) were analyzed using 176 chickens, including three indigenous breeds, two fighting cock populations, and three indigenous populations to elucidate genetic diversity and accomplish a phylogenetic analysis of Myanmar indigenous chickens. The average haplotype and nucleotide diversities were 0.948 ± 0.009 and 0.00814 ± 0.00024, respectively, exhibiting high genetic diversity of Myanmar indigenous chickens. Sixty-four haplotypes were classified as seven haplogroups, with the majority being haplogroup F. The breeds and populations except Inbinwa had multiple maternal haplogroups, suggesting that they experienced no recent purifying selection and bottleneck events. All breeds and populations examined shared haplogroup F. When 232 sequences belonging to haplogroup F (79 from Myanmar and 153 deposited sequences from other Asian countries/region) were analyzed together, the highest genetic diversity was observed in Myanmar indigenous chickens. Furthermore, Myanmar indigenous chickens and red junglefowls were observed in the center of the star-like median-joining network of 37 F-haplotypes, suggesting that Myanmar is one of the origins of haplogroup F. These findings revealed the unique genetic characteristic of Myanmar indigenous chickens as important genetic resources.
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Affiliation(s)
- Su Lai Yee Mon
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Moe Lwin
- Research and Development Division, Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | - Aye Aye Maw
- Department of Genetics and Animal Breeding, University of Veterinary Science, Nay Pyi Taw, Myanmar
| | - Lat Lat Htun
- Department of Pharmacology and Parasitology, University of Veterinary Science, Nay Pyi Taw, Myanmar
| | - Saw Bawm
- Department of International Relations and Information Technology, University of Veterinary Science, Nay Pyi Taw, Myanmar
| | - Kotaro Kawabe
- Education Center, Kagoshima University, Kagoshima, Japan
| | - Yasuhiko Wada
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.,Faculty of Agriculture, Saga University, Saga, Japan
| | - Shin Okamoto
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Takeshi Shimogiri
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
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