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Chen S, Mei H, Xu L, Zhan L, Yang Y, Zhao D, Bao G, Li X, Cao Z. Impact of fermented feed of soybean hulls and rapeseed cake on immunity, antioxidant capacity, and gut microbiota in Chahua chicken. Poult Sci 2024; 103:103451. [PMID: 38301497 PMCID: PMC10847688 DOI: 10.1016/j.psj.2024.103451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/25/2023] [Accepted: 01/06/2024] [Indexed: 02/03/2024] Open
Abstract
The present study investigated the effects of replacing part of the basal diet with 2-stage fermented feed (FF) (soybean hulls:rapeseed cake (2:1, m/m)) on the growth performance, immunity, antioxidant capacity, and intestinal health of Chahua chicken. A total of 160 Chahua chickens were randomly divided into 4 groups to receive a control diet or diet with 5%, 10%, or 15% of the basal diet replaced by FF, respectively for 56 d. The results showed that FF significantly improved the average daily gain (ADG) and average daily feed intake (ADFI) of Chahua chickens (P < 0.05). Furthermore, the serum immunoglobulin (Ig) A, glutathione peroxidase (GSH-Px), and superoxide dismutase (SOD) in Chahua chicken receiving the diet added with 15% FF significantly increased (P < 0.05). Chahua chicken in both the 10% and 15% groups showed increased serum IgG and IgM and decreased malondialdehyde. Serum interleukin-2 and interferon-gamma significantly increased in all FF groups. Compared with the CON group, higher ileal villus height (VH) was found in the 10% FF group. Treatment with FF significantly increased the ileal villus height/crypt depth (VH/CD) ratio, jejunal VH, and jejunal VH/CD ratio while reducing ileal and jejunal CD. The modified gut microbiota composition was observed in the Chahua chicken fed a diet containing FF, in particular, with the increased abundance of Faecalibacterium and Lactobacillus. The abundance of Lactobacillus significantly increased in the 10% and 15% FF groups (all P < 0.05). Correlation analysis revealed a positive correlation between Lactobacillus and VH (R = 0.38, P = 0.10, Figure 3B), AH/CD ratio (R = 0.63, P = 0.003), and a negative correlation with CD (R = -0.72, P = 0.001). These results indicate that FF improves immunity, antioxidant capacity, and intestinal health and consequently enhances growth performance in Chahua chicken.
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Affiliation(s)
- Shiyu Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China
| | - Huiyou Mei
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China
| | - Le Xu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China; Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Heilongtan, Kunming 650201, People's Republic of China
| | - Limei Zhan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China
| | - Yuhao Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China
| | - Dexuan Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China
| | - Guoying Bao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China
| | - Xiaoye Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China
| | - Zhenhui Cao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China; Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Heilongtan, Kunming 650201, People's Republic of China.
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Li W, Wu X, Xiang D, Zhang W, Wu L, Meng X, Huo J, Yin Z, Fu G, Zhao G. Genome-Wide Detection for Runs of Homozygosity in Baoshan Pigs Using Whole Genome Resequencing. Genes (Basel) 2024; 15:233. [PMID: 38397222 PMCID: PMC10887577 DOI: 10.3390/genes15020233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Baoshan pigs (BS) are a local breed in Yunnan Province that may face inbreeding owing to its limited population size. To accurately evaluate the inbreeding level of the BS pig population, we used whole-genome resequencing to identify runs of homozygosity (ROH) regions in BS pigs, calculated the inbreeding coefficient based on pedigree and ROH, and screened candidate genes with important economic traits from ROH islands. A total of 22,633,391 SNPS were obtained from the whole genome of BS pigs, and 201 ROHs were detected from 532,450 SNPS after quality control. The number of medium-length ROH (1-5 Mb) was the highest (98.43%), the number of long ROH (>5 Mb) was the lowest (1.57%), and the inbreeding of BS pigs mainly occurred in distant generations. The inbreeding coefficient FROH, calculated based on ROH, was 0.018 ± 0.016, and the FPED, calculated based on the pedigree, was 0.027 ± 0.028, which were positively correlated. Forty ROH islands were identified, containing 507 genes and 891 QTLs. Several genes were associated with growth and development (IGFALS, PTN, DLX5, DKK1, WNT2), meat quality traits (MC3R, ACSM3, ECI1, CD36, ROCK1, CACNA2D1), and reproductive traits (NPW, TSHR, BMP7). This study provides a reference for the protection and utilization of BS pigs.
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Affiliation(s)
- Wenjun Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Xudong Wu
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230036, China; (X.W.); (W.Z.)
| | - Decai Xiang
- Institute of Pig and Animal Research, Yunnan Academy of Animal Husbandry and Veterinary Science, Kunming 650201, China;
| | - Wei Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230036, China; (X.W.); (W.Z.)
| | - Lingxiang Wu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Xintong Meng
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Jinlong Huo
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China;
| | - Guowen Fu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Guiying Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
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Physicochemical, Nutritional Properties and Metabolomics Analysis Fat Deposition Mechanism of Chahua Chicken No. 2 and Yao Chicken. Genes (Basel) 2022; 13:genes13081358. [PMID: 36011269 PMCID: PMC9407069 DOI: 10.3390/genes13081358] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 01/27/2023] Open
Abstract
Poultry is an important dietary source of animal protein, accounting for approximately 30% of global meat consumption. Because of its low price, low fat and cholesterol content, and no religious restrictions, chicken is considered a widely available healthy meat. Chahua chicken No. 2 is a synthetic breed of Chahua chicken derived from five generations of specialized strain breeding. In this study, Chahua chicken No. 2 (CH) and Yao chicken (Y) were used as the research objects to compare the differences in physicochemical and nutritional indicators of meat quality between the two chicken breeds, and metabolomics was used to analyze the differences in metabolites and lipid metabolism pathways and to explore the expression of genes involved in adipogenesis. The physical index and nutritional value of CH are better than that of Y, and the chemical index of Y is better than that of CH. However, the chemical index results of CH are also within the normal theoretical value range. Comprehensive comparison shows that the meat quality of CH is relatively good. Metabolomics analysis showed that CH and Y had 85 different metabolites, and the differential metabolites were mainly classified into eight categories. KEGG pathway enrichment analysis revealed 13 different metabolic pathways. The screened PPARG, FABP3, ACSL5, FASN, UCP3 and SC5D were negatively correlated with muscle fat deposition, while PPARα, ACACA and ACOX1 were positively correlated with muscle fat deposition. The meat quality of CH was better than Y. The metabolites and metabolic pathways obtained by metabonomics analysis mainly involved the metabolism of amino acids and fatty acids, which were consistent with the differences in meat quality between the two breeds and the contents of precursors affecting flavor. The screened genes were associated with fatty deposition in poultry.
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Castro Rojas LA, Gayozo E, Méndez N. Evaluación de la utilidad de marcadores microsatélites en la población avícola rustipollos. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2021. [DOI: 10.15446/rev.colomb.biote.v23n2.94961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Los marcadores moleculares son una herramienta de gran utilidad para estudios de diversidad genética, que permite identificar poblaciones con características genéticas particulares, que soportan el establecimiento de programas de conservación y mejoramiento genético. El objetivo de este estudio fue evaluar el grado de información generada por un panel de 30 marcadores microsatélites en la población avícola Rustipollos. Se obtuvieron muestras de sangre de 50 individuos, la amplificación de fragmentos se realizó mediante PCR, utilizando 30 microsatélites recomendados por la FAO-ISAG para estudios de biodiversidad en gallinas. La estimación de los tamaños de los fragmentos se realizó en un secuenciador automático ABI Prism 377. Fueron determinados el número de alelos por locus y el Contenido de Información Polimórfica (PIC), mediante el programa Microsatellite-Toolkit. El número total de alelos reportados fue de 99 en los 30 marcadores microsatélites, con un valor medio de 3.3 ±1.06 alelos por locus. La determinación del PIC registró un promedio de 0.46, con un rango de 0.18 a 0.76 en los marcadores MCW016 y ADL278, respectivamente. El 43% de los marcadores empleados resultaron altamente informativos para la población evaluada. En general, los marcadores microsatélites demostraton ser útiles para estudios genéticos en la población avícola Rustipollos.
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Yang X, Liu CL, Yang BG, Hu HQ, Ying G, Yi G, Chen BE, Yuan Y, Yong-Meng H, Zhang WY, Zhang DP, E GX, Li MH. Investigating genetic diversity and population phylogeny of five Chongqing local chicken populations autosomal using microsatellites. Anim Biotechnol 2021; 33:1190-1197. [PMID: 33635178 DOI: 10.1080/10495398.2021.1880421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The genetic diversity and population structures of five Chongqing local chicken populations were investigated using by 24 microsatellite markers. Results revealed that the mean number of alleles (NA) ranged from 7.08 (Daninghe chicken, DN) to 8.46 (Nanchuan chicken, NC). The highest observed heterozygosity (HO) and expected heterozygosity (HE) were observed in DN (HO = 0.7252; HE = 0.7409) and the lowest HO and HE were observed in XS (Xiushan native chicken [XS], HO = 0.5910 and HE = 0.6697). The inbreeding coefficient (FIS) within population ranged from 0.022 (DN) to 0.119 (XS). Among the 24 microsatellite markers, four loci (MCW0111, MCW0016, ADL0278, and MCW0104) deviated from the Hardy-Weinberg equilibrium in all the studied populations. The results of population polygenetic analysis based on Nei's genetic distance and STRUCTURE software showed that the clustering of the five populations was incomplete consistent with geographical distribution. Moreover, a large number of gene flows were widespread among different populations, suggesting that genetic material exchanges occurred due to human activities and migration which was also verified by PCoA. In summary, this study preliminarily showed that Chongqing local chicken populations had rich genetic diversity and remarkable genetic divergence, but still high risk in conversion. These findings would be useful to the management of conservation strategies and the utilization of local chicken populations in further.
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Affiliation(s)
- Xue Yang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Cheng-Li Liu
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Bai-Gao Yang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Hai-Qiang Hu
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Gong Ying
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Guo Yi
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Bo-Er Chen
- Chongqing Agriculture and Rural Affairs Committee of Tongnan, Chongqing, China
| | - Ying Yuan
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - He Yong-Meng
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Wei-Yi Zhang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Dan-Ping Zhang
- Dazhou Animal Husbandry Technology Extension Station, Dazhou, China
| | - Guang-Xin E
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Ming-Hui Li
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
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Comparative transcriptomic and proteomic analyses provide insights into functional genes for hypoxic adaptation in embryos of Tibetan chickens. Sci Rep 2020; 10:11213. [PMID: 32641697 PMCID: PMC7343830 DOI: 10.1038/s41598-020-68178-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/22/2020] [Indexed: 12/11/2022] Open
Abstract
The Tibetan chicken is a unique breed that has adapted to the high-altitude hypoxic conditions of the Tibetan plateau. A number of positively selected genes have been reported in these chickens; however, the mechanisms of gene expression for hypoxia adaptation are not fully understood. In the present study, eggs from Tibetan and Chahua chickens were incubated under hypoxic and normoxic conditions, and vascularization in the chorioallantoic membrane (CAM) of embryos was observed. We found that the vessel density index in the CAM of Tibetan chickens was lower than in Chahua chickens under hypoxia conditions. Transcriptomic and proteomic analyses of CAM tissues were performed in Tibetan and Chahua chicken embryos under hypoxic incubation using RNA-Seq and iTRAQ. We obtained 160 differentially expressed genes and 387 differentially expressed proteins that were mainly enriched in angiogenesis, vasculature development, blood vessel morphogenesis, blood circulation, renin-angiotensin system, and HIF-1 and VEGF signaling pathways. Twenty-six genes involved in angiogenesis and blood circulation, two genes involved in ion transport, and six genes that regulated energy metabolism were identified as candidate functional genes in regulating hypoxic adaptation of chicken embryos. This research provided insights into the molecular mechanism of hypoxia adaptation in Tibetan chickens.
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Habimana R, Okeno TO, Ngeno K, Mboumba S, Assami P, Gbotto AA, Keambou CT, Nishimwe K, Mahoro J, Yao N. Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers. PLoS One 2020; 15:e0225084. [PMID: 32240167 PMCID: PMC7117670 DOI: 10.1371/journal.pone.0225084] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 03/08/2020] [Indexed: 11/19/2022] Open
Abstract
Rwanda has about 4.5 million of indigenous chicken (IC) that are very low in productivity. To initiate any genetic improvement programme, IC needs to be accurately characterized. The key purpose of this study was to ascertain the genetic diversity of IC in Rwanda using microsatellite markers. Blood samples of IC sampled from 5 agro-ecological zones were collected from which DNA was extracted, amplified by PCR and genotyped using 28 microsatellite markers. A total of 325 (313 indigenous and 12 exotic) chickens were genotyped and revealed a total number of 305 alleles varying between 2 and 22 with a mean of 10.89 per locus. One hundred eighty-six (186) distinct alleles and 60 private alleles were also observed. The frequency of private alleles was highest in samples from the Eastern region, whereas those from the North West had the lowest. The influx of genes was lower in the Eastern agro-ecological zone than the North West. The mean observed heterozygosity was 0.6155, whereas the average expected heterozygosity was 0.688. The overall inbreeding coefficient among the population was 0.040. Divergence from the Hardy-Weinberg equilibrium was significant (p<0.05) in 90% of loci in all the populations. The analysis of molecular variance revealed that about 92% of the total variation originated from variation within populations. Additionally, the study demonstrated that IC in Rwanda could be clustered into four gene groups. In conclusion, there was considerable genetic diversity in IC in Rwanda, which represents a crucial genetic resource that can be conserved or optimized through genetic improvement.
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Affiliation(s)
- Richard Habimana
- Animal Science and Veterinary Medicine, University of Rwanda, College of Agriculture, Nyagatare, Rwanda
- Department of Animal Science, Animal Breeding and Genomics Group, Egerton University, Nakuru, Kenya
| | - Tobias Otieno Okeno
- Department of Animal Science, Animal Breeding and Genomics Group, Egerton University, Nakuru, Kenya
| | - Kiplangat Ngeno
- Department of Animal Science, Animal Breeding and Genomics Group, Egerton University, Nakuru, Kenya
| | - Sylvere Mboumba
- Faculty of Agronomy and Biotechnologies, Masuku University of Science and Techniques, Franceville, Gabon
| | - Pauline Assami
- Biosciences eastern and central Africa, International Livestock Research Institute Hub, Nairobi, Kenya
| | - Anique Ahou Gbotto
- Laboratoire de genomique Fonctionnelle et Amélioration Génétique Université Nangui Abrogoua, Abidjan, Cote d'Ivoire
| | - Christian Tiambo Keambou
- Biosciences eastern and central Africa, International Livestock Research Institute Hub, Nairobi, Kenya
- Faculty of Agriculture and Veterinary medicine, University of Buea, Buea, Cameroon
| | - Kizito Nishimwe
- Animal Science and Veterinary Medicine, University of Rwanda, College of Agriculture, Nyagatare, Rwanda
| | - Janvier Mahoro
- Animal Science and Veterinary Medicine, University of Rwanda, College of Agriculture, Nyagatare, Rwanda
| | - Nasser Yao
- Biosciences eastern and central Africa, International Livestock Research Institute Hub, Nairobi, Kenya
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Zhang C, Lin D, Wang Y, Peng D, Li H, Fei J, Chen K, Yang N, Hu X, Zhao Y, Li N. Widespread introgression in Chinese indigenous chicken breeds from commercial broiler. Evol Appl 2019; 12:610-621. [PMID: 30828377 PMCID: PMC6383742 DOI: 10.1111/eva.12742] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 10/17/2018] [Accepted: 11/15/2018] [Indexed: 12/17/2022] Open
Abstract
Chinese indigenous chickens (CICs) constitute world-renowned genetic resources due to their excellent traits, including early puberty, good meat quality and strong resistance to disease. Unfortunately, the introduction of a large number of commercial chickens in the past two decades has had an adverse effect on CICs. Using the chicken 60 K single nucleotide polymorphism chip, we assessed the genetic diversity and population structure of 1,187 chickens, representing eight Chinese indigenous chicken breeds, two hybrid chicken breeds, two ancestral chicken breeds, two commercial populations and additional red jungle fowl. By investigating haplotype similarity, we found extensive gene introgression from commercial broiler to almost all CICs. Approximately 15% of the genome, on average, of CICs was introgressed, ranging from 0.64% for Tibetan chicken to 21.52% for Huiyang Bearded chicken. Further analysis revealed signals consistent with positive selection in the introgression loci. For the first time, we systematically mapped and quantified introgression from commercial broiler to CICs at the whole genome level. Our data provided a usable resource for chicken genetic diversity, and our findings indicated a dire need for protecting the genetic resources of CICs.
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Affiliation(s)
- Chunyuan Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthChina Agricultural UniversityBeijingChina
- State Key Laboratory for Agrobiotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Deng Lin
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthChina Agricultural UniversityBeijingChina
| | - Yuzhe Wang
- State Key Laboratory for Agrobiotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Dezhi Peng
- State Key Laboratory for Agrobiotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Huifang Li
- Institute of Poultry ScienceChinese Academy of Agricultural SciencesYangzhouChina
| | - Jing Fei
- State Key Laboratory for Agrobiotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Kuanwei Chen
- Institute of Poultry ScienceChinese Academy of Agricultural SciencesYangzhouChina
| | - Ning Yang
- National Engineering Laboratory for Animal BreedingChina Agricultural UniversityBeijingChina
| | - Xiaoxiang Hu
- State Key Laboratory for Agrobiotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yiqiang Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthChina Agricultural UniversityBeijingChina
- State Key Laboratory for Agrobiotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Ning Li
- State Key Laboratory for Agrobiotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
- National Engineering Laboratory for Animal BreedingChina Agricultural UniversityBeijingChina
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Azimu W, Manatbay B, Li Y, Kaimaerdan D, Wang HE, Reheman A, Muhatai G. Genetic diversity and population structure analysis of eight local chicken breeds of Southern Xinjiang. Br Poult Sci 2018; 59:629-635. [DOI: 10.1080/00071668.2018.1523537] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- W. Azimu
- College of Animal Science, Tarim University, Alar, Aksu, China
| | - B. Manatbay
- Xinjiang Entry-Exit Inspections and Quarantine Bureau Technology Center, Urumqi, China
| | - Y. Li
- Institutes of Arid Ecology and Geography, Xinjiang University, Urumqi, China
| | - D. Kaimaerdan
- Autonomous Regional Animal Husbandry Station Down, Urumqi, Xinjiang, China
| | - H. E. Wang
- College of Animal Science, Tarim University, Alar, Aksu, China
| | - A. Reheman
- College of Animal Science, Tarim University, Alar, Aksu, China
| | - G. Muhatai
- College of Animal Science, Tarim University, Alar, Aksu, China
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Global genomic diversity and conservation priorities for domestic animals are associated with the economies of their regions of origin. Sci Rep 2018; 8:11677. [PMID: 30076315 PMCID: PMC6076285 DOI: 10.1038/s41598-018-30061-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 07/18/2018] [Indexed: 12/03/2022] Open
Abstract
Domestic animals play a key role in human survival and the development of civilization. However, the genetic resources of domestic animals are facing an alarming rate of erosion due to socioeconomic changes, economic globalization and financial constraints. In this study, through genome-wide SNP analysis, we estimated the heterozygosity, inbreeding coefficient, effective population size, and runs of homozygosity to identify the breeds facing the risk of extinction for sheep and cattle across the world. In particular, we quantified the contribution of 97 sheep breeds and 53 cattle breeds to genomic diversity (within-breed, between-breed and total) and prioritized the breeds for conservation. Additionally, we compared the average values of genomic diversity between breeds from regions (or countries) in different economic categories (underdeveloped, developing and developed), and found that breeds in developed regions exhibit significantly higher levels of total genomic diversity than those in underdeveloped and developing regions. Altogether, our results suggested that conservation priority should be given to breeds in developed regions to secure the future genomic diversity hotspots of domestic animal resources.
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Nunome M, Nakano M, Tadano R, Kawahara-Miki R, Kono T, Takahashi S, Kawashima T, Fujiwara A, Nirasawa K, Mizutani M, Matsuda Y. Genetic Divergence in Domestic Japanese Quail Inferred from Mitochondrial DNA D-Loop and Microsatellite Markers. PLoS One 2017; 12:e0169978. [PMID: 28107483 PMCID: PMC5249226 DOI: 10.1371/journal.pone.0169978] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 12/25/2016] [Indexed: 12/25/2022] Open
Abstract
To assess the genetic diversity of domestic Japanese quail (Coturnix japonica) populations, and their genetic relationships, we examined mitochondrial DNA (mtDNA) D-loop sequences and microsatellite markers for 19 Japanese quail populations. The populations included nine laboratory lines established in Japan (LWC, Quv, RWN, WE, AWE, AMRP, rb-TKP, NIES-L, and W), six meat-type quail lines reimported from Western countries (JD, JW, Estonia, NIES-Br, NIES-Fr, and NIES-Hn), one commercial population in Japan, and three wild quail populations collected from three Asian areas. The phylogenetic tree of mtDNA D-loop sequences revealed two distinct haplotype groups, Dloop-Group1 and Dloop-Group2. Dloop-Group1 included a dominant haplotype representing most of the quail populations, including wild quail. Dloop-Group2 was composed of minor haplotypes found in several laboratory lines, two meat-type lines, and a few individuals in commercial and wild quail populations. Taking the breeding histories of domestic populations into consideration, these results suggest that domestic quail populations may have derived from two sources, i.e., domestic populations established before and after World War II in Japan. A discriminant analysis of principal components and a Bayesian clustering analysis with microsatellite markers indicated that the domestic populations are clustered into four genetic groups. The two major groups were Microsat-Group1, which contained WE, and four WE-derived laboratory lines (LWC, Quv, RWN, and AWE), and Microsat-Group2 consisting of NIES-L, JD, JW, Estonia, NIES-Br, NIES-Fr, NIES-Hn, W, and commercial and wild populations. The remaining two lines (AMRP and rb-TKP) were each clustered into a separate clade. This hierarchical genetic difference between domestic quail populations is attributed to the genetic background derived from two different genetic sources-the pre-war and post-war populations-which is well supported by their breeding histories.
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Affiliation(s)
- Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Mikiharu Nakano
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Ryo Tadano
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Ryoka Kawahara-Miki
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan
| | - Tomohiro Kono
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Shinji Takahashi
- General Affairs Department, National Institute for Environmental Studies, Tsukuba, Japan
| | - Takaharu Kawashima
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba 305–8506, Japan
| | - Akira Fujiwara
- Laboratory Animal Research Station, Nippon Institute for Biological Science, Hokuto, Japan
| | - Keijiro Nirasawa
- Animal Breeding and Reproduction Research Division, NARO Institute of Livestock and Grassland Science, Tsukuba, Japan
| | - Makoto Mizutani
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yoichi Matsuda
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Laboratory of Animal Genetics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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12
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Yaro M, Munyard KA, Stear MJ, Groth DM. Molecular identification of livestock breeds: a tool for modern conservation biology. Biol Rev Camb Philos Soc 2016; 92:993-1010. [DOI: 10.1111/brv.12265] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 02/14/2016] [Accepted: 02/18/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Mohammed Yaro
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
| | - Kylie A. Munyard
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
| | - Michael J. Stear
- Institute of Biodiversity, Animal Health and Comparative Medicine; University of Glasgow; Bearsden Road Glasgow G61 1QH U.K
| | - David M. Groth
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
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