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Macharia JK, Kim J, Kim M, Cho E, Munyaneza JP, Lee JH. Characterisation of runs of homozygosity and inbreeding coefficients in the red-brown Korean native chickens. Anim Biosci 2024; 37:1355-1366. [PMID: 38665087 PMCID: PMC11222857 DOI: 10.5713/ab.23.0514] [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: 12/10/2023] [Revised: 02/05/2024] [Accepted: 02/27/2024] [Indexed: 07/05/2024] Open
Abstract
OBJECTIVE The analysis of runs of homozygosity (ROH) has been applied to assess the level of inbreeding and identify selection signatures in various livestock species. The objectives of this study were to characterize the ROH pattern, estimate the rate of inbreeding, and identify signatures of selection in the red-brown Korean native chickens. METHODS The Illumina 60K single nucleotide polymorphism chip data of 651 chickens was used in the analysis. Runs of homozygosity were analysed using the PLINK v1.9 software. Inbreeding coefficients were estimated using the GCTA software and their correlations were examined. Genomic regions with high levels of ROH were explored to identify selection signatures. RESULTS A total of 32,176 ROH segments were detected in this study. The majority of the ROH segments were shorter than 4 Mb. The average ROH inbreeding coefficients (FROH) varied with the length of ROH segments. The means of inbreeding coefficients calculated from different methods were also variable. The correlations between different inbreeding coefficients were positive and highly variable (r = 0.18-1). Five ROH islands harbouring important quantitative trait loci were identified. CONCLUSION This study assessed the level of inbreeding and patterns of homozygosity in Red-brown native Korean chickens. The results of this study suggest that the level of recent inbreeding is low which indicates substantial progress in the conservation of red-brown Korean native chickens. Additionally, Candidate genomic regions associated with important production traits were detected in homozygous regions.
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Affiliation(s)
- John Kariuki Macharia
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Jaewon Kim
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Minjun Kim
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Eunjin Cho
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134,
Korea
| | - Jean Pierre Munyaneza
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134,
Korea
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Cho Y, Kim JY, Kim N. Comparative genomics and selection analysis of Yeonsan Ogye black chicken with whole-genome sequencing. Genomics 2022; 114:110298. [PMID: 35134497 DOI: 10.1016/j.ygeno.2022.110298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 12/24/2021] [Accepted: 02/01/2022] [Indexed: 11/30/2022]
Abstract
Yeonsan Ogye (OGYE; Gallus gallus domesticus) is a rare indigenous chicken breed that inhabits the Korean Peninsula. This breed has completely black coloring, including plumage, skin, eyes, beak, and internal organs. Despite these unique morphological characteristics, the population of OGYE has declined without in-depth research into their genome research. Therefore, this study aimed to compare the whole genome of OGYE to 12 other chicken populations, including ancestral breed, commercial breeds, Chinese indigenous breeds, and Korean native chickens. We focused on revealing the selection signature of OGYE, which has occurred through environmental pressures in the Korean Peninsula. Genome-wide selection analysis has identified local adaptation traits, such as egg development, that contribute to fetal viability and innate immune response to prevent viral and microbes infection in OGYE. In particular, SPP1 (Secreted Phosphoprotein 1), HSP90AA1 (Heat Shock Protein 90 Alpha Family Class A Member 1), and P2RX4 (Purinergic Receptor P2X 4) could have considerable involvement in egg development and RNASEL (Ribonuclease L), BRIP1 (BRCA1 Interacting Protein C-terminal Helicase 1), and TLR4 (Toll-Like Receptor 4) are crucial for the determination of the innate immune response. This study revealed the unique genetic diversity of OGYE at the genome-wide level. Furthermore, we emphasized the sustainable management of genetic resources and formulated breeding strategies for livestock on the Korean Peninsula.
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Affiliation(s)
- Youngbeom Cho
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea
| | - Jae-Yoon Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea.
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Genetic diversity and relationship of Korean chicken breeds using 12 microsatellite markers. JOURNAL OF ANIMAL REPRODUCTION AND BIOTECHNOLOGY 2021. [DOI: 10.12750/jarb.36.3.154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Manjula P, Fulton JE, Seo D, Lee JH. Major histocompatibility complex B variability in Korean native chicken breeds. Poult Sci 2020; 99:4704-4713. [PMID: 32988505 PMCID: PMC7598131 DOI: 10.1016/j.psj.2020.05.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 05/04/2020] [Accepted: 05/22/2020] [Indexed: 12/01/2022] Open
Abstract
Adaptive genetic variations have direct influences on the fitness traits of the animal. The major histocompatibility complex B (MHC-B) region is responsible for adaptive and innate immune responses in chickens. In native Korean chicken breeds, no information on serologically defined B haplotypes is available. We investigated the MHC-B diversity in 5 restored lines of Korean native chicken and Ogye chicken breeds using a recently described MHC-B single-nucleotide polymorphism (SNP) panel and the MHC-linked LEI0258 variable number of tandem repeat marker. High SNP haplotype diversity was observed in Korean native chicken breeds with an average of 9.7 MHC-B SNP haplotypes per line. The total number of haplotypes ranged from 6 to 12 per line, and population-specific haplotypes ranged from 3 to 4. A total of 41 BSNP haplotypes, including 26 novel population-specific haplotypes and 15 common haplotypes, were reported over all populations. The 15 common haplotypes included 7 novel and 8 previously reported standard haplotypes. Selection and breeding evidence supports the observation of common haplotypes between the Korean native chicken and exotic breeds. Similarly, the LEI0258 marker showed allele variation, between 193 bp and 474 bp having 5 to 8 alleles per population. Some of these alleles (193, 249, 309, and 443 bp) were shared and more frequently observed. Comparison between SNP haplotypes and LEI0258 allele sizes for the same samples showed that some LEI0258 allele sizes correspond to more than one BSNP haplotype. The use of the MHC-B SNP panel greatly enhances the identification of MHC diversity compared with the sole use of the LEI0258 marker in native chicken populations.
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Affiliation(s)
- Prabuddha Manjula
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | | | - Dongwon Seo
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea.
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Manjula P, Bed'Hom B, Hoque MR, Cho S, Seo D, Chazara O, Lee SH, Lee JH. Genetic diversity of MHC-B in 12 chicken populations in Korea revealed by single-nucleotide polymorphisms. Immunogenetics 2020; 72:367-379. [PMID: 32839847 DOI: 10.1007/s00251-020-01176-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/17/2020] [Indexed: 01/07/2023]
Abstract
This study used a single-nucleotide polymorphism (SNP) panel to characterise the diversity in the major histocompatibility complex B region (MHC-B) in 12 chicken populations in Korea. Samples were genotyped for 96 MHC-B SNPs using an Illumina GoldenGate genotyping assay. The MHC-B SNP haplotypes were predicted using 58 informative SNPs and a coalescence-based Bayesian algorithm implemented by the PHASE program and a manual curation process. In total, 117 haplotypes, including 24 shared and 93 unique haplotypes, were identified. The unique haplotype numbers ranged from 0 in Rhode Island Red to 32 in the Korean native commercial chicken population 2 ("Hanhyup-3ho"). Population and haplotype principal component analysis (PCA) indicated no clear population structure based on the MHC haplotypes. Three haplotype clusters (A, B, C) segregated in these populations highlighted the relationship between the haplotypes in each cluster. The sequences from two clusters (B and C) overlapped, whereas the sequences from the third cluster (A) were very different. Overall, native breeds had high genetic diversity in the MHC-B region compared with the commercial breeds. This highlights their immune capabilities and genetic potential for resistance to many different pathogens.
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Affiliation(s)
- Prabuddha Manjula
- Division of Animal and Dairy Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Bertrand Bed'Hom
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 75005, Paris, France
| | | | - Sunghyun Cho
- Division of Animal and Dairy Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Dongwon Seo
- Division of Animal and Dairy Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Olympe Chazara
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
- Department of Pathology and Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jun Heon Lee
- Division of Animal and Dairy Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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Roh HJ, Kim SC, Cho CY, Lee J, Jeon D, Kim DK, Kim KW, Afrin F, Ko YG, Lee JH, Batsaikhan S, Susanti T, Hegay S, Kongvongxay S, Gorkhali NA, Thi LAN, Thao TTT, Manikku L. Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2020; 33:1896-1904. [PMID: 32299162 PMCID: PMC7649407 DOI: 10.5713/ajas.19.0958] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/03/2020] [Indexed: 11/27/2022]
Abstract
Objective Estimating the genetic diversity and structures, both within and among chicken breeds, is critical for the identification and conservation of valuable genetic resources. In chickens, microsatellite (MS) marker polymorphisms have previously been widely used to evaluate these distinctions. Our objective was to analyze the genetic diversity and relationships among 22 chicken breeds in Asia based on allelic frequencies. Methods We used 469 genomic DNA samples from 22 chicken breeds from eight Asian countries (South Korea, KNG, KNB, KNR, KNW, KNY, KNO; Laos, LYO, LCH, LBB, LOU; Indonesia, INK, INS, ING; Vietnam, VTN, VNH; Mongolia, MGN; Kyrgyzstan, KGPS; Nepal, NPS; Sri Lanka, SBC) and three imported breeds (RIR, Rhode Island Red; WLG, White Leghorn; CON, Cornish). Their genetic diversity and phylogenetic relationships were analyzed using 20 MS markers. Results In total, 193 alleles were observed across all 20 MS markers, and the number of alleles ranged from 3 (MCW0103) to 20 (LEI0192) with a mean of 9.7 overall. The NPS breed had the highest expected heterozygosity (Hexp, 0.718±0.027) and polymorphism information content (PIC, 0.663±0.030). Additionally, the observed heterozygosity (Hobs) was highest in LCH (0.690±0.039), whereas WLG showed the lowest Hexp (0.372±0.055), Hobs (0.384±0.019), and PIC (0.325±0.049). Nei’s DA genetic distance was the closest between VTN and VNH (0.086), and farthest between KNG and MGN (0.503). Principal coordinate analysis showed similar results to the phylogenetic analysis, and three axes explained 56.2% of the variance (axis 1, 19.17%; 2, 18.92%; 3, 18.11%). STRUCTURE analysis revealed that the 22 chicken breeds should be divided into 20 clusters, based on the highest ΔK value (46.92). Conclusion This study provides a basis for future genetic variation studies and the development of conservation strategies for 22 chicken breeds in Asia.
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Affiliation(s)
- Hee-Jong Roh
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Seung-Chang Kim
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Chang-Yeon Cho
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Jinwook Lee
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Dayeon Jeon
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Dong-Kyo Kim
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Kwan-Woo Kim
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Fahmida Afrin
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Yeoung-Gyu Ko
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Jun-Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Solongo Batsaikhan
- Production and technology, National Centre for Livestock Genebank, Ulaanbaatar, 210349, Mongolia
| | - Triana Susanti
- Indonesia Research Institute for Animal Production, Bogor, 16720, Indonesia
| | - Sergey Hegay
- Institute of Biochemistry & Physiology, National Academy of Science of Kyrgyzstan, Bishkek, 720071, Kyrgyzstan
| | - Siton Kongvongxay
- Livestock Research Centre, Vientiane, 7170, Lao People's Democratic Republic
| | - Neena Amatya Gorkhali
- Animal Breeding Division, Nepal Agricultural Research Council, Kathmandu, 44600, Nepal
| | - Lan Anh Nguyen Thi
- Department of Animal Breeding and Genetics, Institute of Animal Sciences for Southern Vietnam, Binh Duong 75000, Vietnam
| | - Trinh Thi Thu Thao
- Department of Animal Breeding and Genetics, Institute of Animal Sciences for Southern Vietnam, Binh Duong 75000, Vietnam
| | - Lakmalie Manikku
- Department of Animal Production and Health, Veterinary Research Institute, Colombo, 20400, Sri Lanka
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Deciphering the Patterns of Genetic Admixture and Diversity in the Ecuadorian Creole Chicken. Animals (Basel) 2019; 9:ani9090670. [PMID: 31514349 PMCID: PMC6770841 DOI: 10.3390/ani9090670] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 12/25/2022] Open
Abstract
Simple Summary In Ecuador, the production of Ecuadorian Creole chicken is of crucial importance in the economy and for the nutrition of families. These chickens represent a focal point in scientific research for three main reasons: (1) they are an unknown genetic resource derived from 500 years of environmental and human selection and represent an important reservoir of genetic variability and adaptability; (2) Ecuadorian Creole chicken production is normally familiar, in a marginal dimension, and it is an important source of economic input for medium–low income communities; and (3) being a local genetic resource, it is available to local communities without intermediary international enterprises and represents the starting point for food sovereignty. We aimed to measure the level of genetic diversity and its phylogenetic position compared with other outgroup breeds using information from microsatellite and mitochondrial markers. Our results showed that these chicken populations represent a great reservoir of genetic variability; however, the genetic fragmentation owing to the high geographical diversity of the country could compromise the conservation status and, therefore, the establishment of an official breeding program is needed for the conservation and valuation of these avian populations, with this genetic characterization being a first step. Abstract Latin American Creole chickens are generally not characterized; this is the case in Ecuador, where the lack of scientific information is contributing to their extinction. Here, we developed a characterization of the genetic resources of Ecuadorian chickens located in three continental agroecosystems (Pacific coastal, Andean, and Amazonian). Blood samples of 234 unrelated animals were collected in six provinces across Ecuador: Bolívar, Chimborazo, Cotopaxi, Guayas, Morona Santiago, and Tungurahua, in order to perform a genetic characterization and population structure assessment using the AVIANDIV project microsatellites panel (30 loci) and D-loop sequences of mitochondrial DNA and comparing with reference data from other breeds or genetic lines. The results indicate that Ecuadorian Creole chickens are the result of the admixture of different genetic groups that occurred during the last five centuries. While the influence of South Spanish breeds is demonstrated in the colonial age, genetic relationships with other breeds (Leghorn, Spanish fighter cock) cannot be discarded. The geographical configuration of the country and extreme climate variability have influenced the genetic isolation of groups constituting a homogeneous genetic status into the whole population. This is not only a source of genetic variation, but also a critical point because genetic drift produces a loss of genetic variants.
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Nunome M, Kinoshita K, Ishishita S, Ohmori Y, Murai A, Matsuda Y. Genetic diversity of 21 experimental chicken lines with diverse origins and genetic backgrounds. Exp Anim 2018; 68:177-193. [PMID: 30542001 PMCID: PMC6511517 DOI: 10.1538/expanim.18-0139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The genetic characteristics and diversity of 21 experimental chicken lines registered with the National BioResource Project of Japan were examined using mitochondrial D-loop sequences and 54 microsatellite DNA markers. A total of 12 haplotypes were detected in the 500-bp mitochondrial DNA sequences of the hypervariable segment I for 349 individuals of 21 lines. The 12 haplotypes belonged to three (A, D, and E) haplogroups, out of the eight (A‒H) common haplogroups in domestic chickens and red junglefowls. The haplogroups A and D were widely represented in indigenous chickens in the Asian and Pacific regions, and the haplogroup E was the most prevalent in domestic chickens. Genetic clustering by discriminant analysis of principal components with microsatellite markers divided 681 individuals of 21 lines into three groups that consisted of Fayoumi-, European-, and Asian- derived lines. In each of the cladograms constructed with Nei's genetic distances based on allele frequencies and the membership coefficients provided by STRUCTURE and with the genetic distance based on the proportion of shared alleles, the genetic relationships coincided well with the breeding histories of the lines. Microsatellite markers showed remarkably lower genetic heterozygosities (less than 0.1 observed heterozygosity) for eight lines (GSP, GSN/1, YL, PNP, BM-C, WL-G, BL-E, and #413), which have been maintained as closed colonies for more than 40 years (except for #413), indicating their usefulness as experimental chicken lines in laboratory animal science research.
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Affiliation(s)
- Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Keiji Kinoshita
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Satoshi Ishishita
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Yasushige Ohmori
- Laboratory of Animal Morphology, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Atsushi Murai
- Laboratory of Nutrition Science, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Yoichi Matsuda
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.,Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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Feyisa SG, Park YH, Kim YM, Lee BR, Jung KM, Choi SB, Cho CY, Han JY. Morphological defects of sperm and their association with motility, fertility, and hatchability in four Korean native chicken breeds. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 31:1160-1168. [PMID: 29268590 PMCID: PMC6043446 DOI: 10.5713/ajas.17.0626] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/07/2017] [Indexed: 11/27/2022]
Abstract
Objective This study was conducted to compare morphological defects, viability, motility (MOT), fertility (F), and hatchability (H) in four Korean native chicken breeds (KNCBs), and to evaluate whether defective segments of spermatozoa are associated with MOT, F, and H. Methods Four KNCBs, including Korean Ogye (KO), Hwangbong (HB), Hyunin Black (HH), and Hoengseong Yakdak (HY) were used. White Leghorn (WL) was used as a control. Nine cocks from each breed were randomly assigned into three groups. Semen was collected by abdominal massage method. Eosin-nigrosin staining method was used to identify live-dead spermatozoa. Different segments and specific morphological defects of spermatozoa were identified using 4′, 6-diamidino-2-phenylidole and MitoTracker Red CMXRos. F and H rates were evaluated following artificial insemination (AI). Results KO had the highest MOT rate compared to HY. Viable normal sperm rates of KO and HH were high and comparable with WL. HY spermatozoa had the highest viable abnormal sperm (VAS) or morphological defect rate followed by HB. Likewise, HB spermatozoa had the highest dead sperm (dead) rate compared to KO, HY, and WL. Bent, coiled, detached, broken, and knotted were common identified specific morphological defects for all breeds. Most morphological defects were at the head and tail in all breeds. VAS showed strong negative correlation with MOT (r = −0.697) and F (r = −0.609). Similarly, defective tail was negatively correlated with MOT (r = −0.587), F (r = −0.797), and H (r = −0.448). The F and H rates of KO and WL were comparable. Conclusion These data indicate that most identified specific morphological defects are at the head and tail. VAS and defective tail were associated with poor motility, F, and H. KNCBs showed more morphological defects than WL. Finally, these results will facilitate successful AI and semen cryopreservation.
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Affiliation(s)
- Shiferaw Garoma Feyisa
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Young Hyun Park
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Young Min Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Bo Ram Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Kyung Min Jung
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Seong Bok Choi
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Namwon 55717, Korea
| | - Chang Yeon Cho
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Namwon 55717, Korea
| | - Jae Yong Han
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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DEBNATH JOWEL, KUMAR SANJEEV, RAHIM ABDUL, YADAV RAMJI. Genetic variability in egg production-associated microsatellites in Rhode Island Red chicken. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2017. [DOI: 10.56093/ijans.v87i11.75891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Present investigation was carried out in 114 birds belonging to selected strains of Rhode Island Red chicken maintained at institute experimental layer farm with the objective to analyze polymorphism in egg production associated microsatellite loci and to determine various population genetics statistics based on allelic polymorphism. Genomic DNA samples were isolated from all experimental birds and PCR was performed using primers for ten microsatellite loci, reported to be associated with egg production traits in chicken. Alleles were separated on 3.4% MetaPhoreTM agarose and their sizes were determined by Quantity One software. Allelic data were analyzed by POPGENE. Allele numbers varied from 2 to 5 and average number of alleles per locus was 4.00±0.37 (Na). Allele sizes ranged from 99-280 bp. Allele frequency per locus ranged from 0.0225-0.8919. Nei's heterozygosity, Botstein's polymorphic information content (PIC) and Wright's fixation indices at each locus were estimated. All studied microsatellite loci were polymorphic and estimated PIC ranged from 0.19 (ADL0273) to 0.72 (MCW0110). Seven loci were moderate to highly polymorphic (PIC>0.50). Nei's heterozygosity per locus ranged from 0.20 (ADL0273) to 0.77 (MCW0110). Averaged effective number of alleles (Ne), Shannon's Information index (I) and Wright's fixation indices were 2.71±0.26, 1.0654±0.1046 and 0.5126±0.0757, respectively. Average observed (Ho) and expected (He) heterozygosities were 0.3036±0.0625 and 0.5930±0.0505, respectively. Study revealed prevalence of heterozygosity as the Ne was lesser than the Na. It further revealed that the population was under Hardy-Weinberg disequilibrium as (He) was more than (Ho).Chi square and G-square estimates were significant, which suggested that the studied microsatellite loci might have some association with ongoing selection for 40-week part-period egg production in RIR chicken.
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Özdemir D, Cassandro M. Assessment of the population structure and genetic diversity of Denizli chicken subpopulations using SSR markers. ITALIAN JOURNAL OF ANIMAL SCIENCE 2017. [DOI: 10.1080/1828051x.2017.1384336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Demir Özdemir
- Teknik Bilimler Meslek Yüksekokulu, University of Akdeniz, Antalya, Turkey
| | - Martino Cassandro
- Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente, University of Padova, Padova, Italy
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Rudresh BH, Murthy HNN, Jayashankar MR, Nagaraj CS, Kotresh AM, Byregowda SM. Microsatellite based genetic diversity study in indigenous chicken ecotypes of Karnataka. Vet World 2015; 8:970-6. [PMID: 27047184 PMCID: PMC4774763 DOI: 10.14202/vetworld.2015.970-976] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/30/2015] [Accepted: 07/08/2015] [Indexed: 11/16/2022] Open
Abstract
Aim: The current study was the first of its kind taken upon indigenous ecotypes of the Karnataka in order to unravel the diversity details at 20 chicken microsatellite regions. Materials and Methods: 210 indigenous chicken belonging to six districts of Bangalore and Mysore division formed the target sample for the present study. The genomic deoxyribonucleic acid was isolated by phenol chloroform isoamyl alcohol method. A panel of 20 microsatellite regions, including 14 recommended by FAO and six identified from published scientific literature became the targeted chicken genomic region. 27-33 samples were successfully genotyped in each of the six ecotypes through simplex or multiplex polymerase chain reactions, polyacrylamide gel electrophoresis and silver staining for the selected microsatellite panel. Results: The chickens of Ramanagara and Chamrajnagara were most distant with a Nei’s genetic distance value of 0.22. The chickens of Bangalore rural and Mysore were least distant with a value of 0.056. The Ramanagara and Chamrajnagara pair had Nei’s genetic identity value of 0.802, which is least among all pairs of ecotypes. There were five main nodes from which the six ecotypes evolved on the basis 20 microsatellite markers used in this study. This study indicates that the four ecotypes Ramnagara, Bangalore Rural, Chickaballapura and Mysore are genetically identical due to their common ancestral evolution while, Mandya and Chamrajnagara ecotypes formed a relatively different cluster due to a separate common ancestral chicken population and less number of generations since drifting from bifurcation node. Conclusion: Twenty microsatellite markers based genetic diversity study on six indigenous ecotypes indicated lower genetic distances as well as lower FST values compared to the distinguished breeds reported. There were two main clusters, which differentiated into six ecotypes. They may differentiate into more distinct varieties if bred in isolation for a longer number of generations.
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Affiliation(s)
- B H Rudresh
- Department of Animal Genetics and Breeding, Veterinary College, Karnataka Veterinary, Animal and Fisheries Sciences University, Shimoga, Karnataka, India
| | - H N N Murthy
- Department of Livestock Production and Management, Veterinary College, Karnataka Veterinary, Animal and Fisheries Sciences University, Bangalore, Karnataka, India
| | - M R Jayashankar
- Department of Animal Genetics and Breeding, Veterinary College, Karnataka Veterinary, Animal and Fisheries sciences University, Bangalore, Karnataka, India
| | - C S Nagaraj
- All India Coordinated Research Project on Poultry Meat, Karnataka Veterinary, Animal and Fisheries Sciences University, Veterinary College, Bangalore, Karnataka, India
| | - A M Kotresh
- Department of Veterinary Physiology and Biochemistry, Veterinary College, Karnataka Veterinary, Animal and Fisheries sciences University, Shimoga, Karnataka, India
| | - S M Byregowda
- Institute of Animal Health & Veterinary Biologicals, Bangalore, Karnataka Veterinary, Animal and Fisheries Sciences University, Karnataka, India
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