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Dementieva NV, Mitrofanova OV, Dysin AP, Kudinov AA, Stanishevskaya OI, Larkina TA, Plemyashov KV, Griffin DK, Romanov MN, Smaragdov MG. Assessing the effects of rare alleles and linkage disequilibrium on estimates of genetic diversity in the chicken populations. Animal 2021; 15:100171. [PMID: 33563558 DOI: 10.1016/j.animal.2021.100171] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/15/2022] Open
Abstract
Phenotypic diversity in poultry has been mainly driven by artificial selection and genetic drift. These led to the adaptation to the environment and the development of specific phenotypic traits of chickens in response to their economic use. This study evaluated genetic diversity within and between Russian breeds and populations using Illumina Chicken 60K SNP iSelect BeadChip by analysing genetic differences between populations with Hudson's fixation index (FST statistic) and heterozygosity. We estimated the effect of rare alleles and linkage disequilibrium (LD) on these measurements. To assess the effect of LD on the genetic diversity population, we carried out the LD-based pruning (LD<0.5 and LD<0.1) for seven chicken populations combined (I) or separately (II). LD pruning was specific for different dataset groups. Because of the noticeably large sample size in the Russian White RG population, pruning was substantial for Dataset I, and FST values were only positive when LD<0.1 pruning was applied. For Dataset II, the LD pruning results were confirmed by examining heterozygosity and alleles' frequency distribution. LD between single nucleotide polymorphisms was consistent across the seven chicken populations, except the Russian White RG population with the smallest r2 values and the largest effective population size. Our findings suggest to study variability in each population LD pruning has to be carried separately not after merging to avoid bias in estimates.
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Affiliation(s)
- N V Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, Russia
| | - O V Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, Russia
| | - A P Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, Russia
| | - A A Kudinov
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, Russia
| | - O I Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, Russia
| | - T A Larkina
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, Russia
| | - K V Plemyashov
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, Russia
| | - D K Griffin
- School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - M N Romanov
- School of Biosciences, University of Kent, Canterbury, Kent, UK.
| | - M G Smaragdov
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, Russia
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Traditions and local use of native Vietnamese chicken breeds in sustainable rural farming. WORLD POULTRY SCI J 2019. [DOI: 10.1017/s0043933915000380] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Xu Y, Jiang E, Chen C, Liu J, Zhu K, Zhang Z, Ning F, Du Z, Bai X. The complete mitochondrial genome sequence of Lindian Chicken ( Gallus gallus) in China. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:1228-1229. [PMID: 33474472 PMCID: PMC7800424 DOI: 10.1080/23802359.2018.1532336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In this study, the first complete mitochondrial genome of Lindian Chicken (Gallus gallus) was sequenced in order to develop the mitogenome data for genus gallus. The complete mitogenome sequence is 16,785 bp in length, containing 37 genes (13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, and one control region). The new sequenced complete mitogenome of Lindian Chicken will provide useful information for application in conservation genetics and evolution for this Near Threatened Chicken genomes.
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Affiliation(s)
- Yuan Xu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Enze Jiang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Chong Chen
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Jiayu Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Keli Zhu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Zhen Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Fangyong Ning
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Zhiheng Du
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Xiujuan Bai
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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Fathi M, El-Zarei M, Al-Homidan I, Abou-Emera O. Genetic diversity of Saudi native chicken breeds segregating for naked neck and frizzle genes using microsatellite markers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 31:1871-1880. [PMID: 29879833 PMCID: PMC6212745 DOI: 10.5713/ajas.18.0041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/07/2018] [Indexed: 11/27/2022]
Abstract
Objective Recently, there has been an increasing interest in conservation of native genetic resources of chicken on a worldwide basis. Most of the native chicken breeds are threatened by extinction or crossing with ecotypes. Methods Six Saudi native chicken breeds including black naked neck, brown frizzled, black, black barred, brown and gray were used in the current study. The aim of the current study was to evaluate genetic diversity, relationship and population structure of Saudi native chicken breeds based on 20 microsatellite markers. Results A total of 172 alleles were detected in Saudi native chicken breeds across all 20 microsatellite loci. The mean number of alleles per breed ranged from 4.35 in gray breed to 5.45 in normally feathered black with an average of 8.6 alleles. All breeds were characterized by a high degree of genetic diversity, with the lowest heterozygosity found in the brown breed (72%) and the greatest in the frizzled and black barred populations (78%). Higher estimate of expected heterozygosity (0.68) was found in both black breeds (normal and naked neck) compared to the other chicken populations. All studied breeds showed no inbreeding within breed (negative inbreeding coefficient [FIS]). The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed three main clusters, with naked neck and gray breeds in one cluster, and brown and frizzled in the second cluster leaving black barred in a separate one. Conclusion It could be concluded that the genetic information derived from the current study can be used as a guide for genetic improvement and conservation in further breeding programs. Our findings indicate that the Saudi native chicken populations have a rich genetic diversity and show a high polymorphism.
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Affiliation(s)
- Moataz Fathi
- Department of Animal Production and Breeding, College of Agriculture and Veterinary Medicine, Qassim University, Al-Qassim 51452, Saudi Arabia.,Department of Poultry Production, Faculty of Agriculture, Ain Shams University, Hadayek Shoubra 11241, Cairo, Egypt
| | - Mohamed El-Zarei
- Department of Animal Production and Breeding, College of Agriculture and Veterinary Medicine, Qassim University, Al-Qassim 51452, Saudi Arabia.,Department of Animal Production, Faculty of Agriculture, Suez Canal University 41522, Ismailia, Egypt
| | - Ibrahim Al-Homidan
- Department of Animal Production and Breeding, College of Agriculture and Veterinary Medicine, Qassim University, Al-Qassim 51452, Saudi Arabia
| | - Osama Abou-Emera
- Department of Animal Production and Breeding, College of Agriculture and Veterinary Medicine, Qassim University, Al-Qassim 51452, Saudi Arabia.,Department of Poultry Breeding, Animal Production Research Institute, Agriculture Research Center, Dokki, Giza 12618, Egypt
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Malomane DK, Reimer C, Weigend S, Weigend A, Sharifi AR, Simianer H. Efficiency of different strategies to mitigate ascertainment bias when using SNP panels in diversity studies. BMC Genomics 2018; 19:22. [PMID: 29304727 PMCID: PMC5756397 DOI: 10.1186/s12864-017-4416-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 12/22/2017] [Indexed: 12/30/2022] Open
Abstract
Background Single nucleotide polymorphism (SNP) panels have been widely used to study genomic variations within and between populations. Methods of SNP discovery have been a matter of debate for their potential of introducing ascertainment bias, and genetic diversity results obtained from the SNP genotype data can be misleading. We used a total of 42 chicken populations where both individual genotyped array data and pool whole genome resequencing (WGS) data were available. We compared allele frequency distributions and genetic diversity measures (expected heterozygosity (He), fixation index (FST) values, genetic distances and principal components analysis (PCA)) between the two data types. With the array data, we applied different filtering options (SNPs polymorphic in samples of two Gallus gallus wild populations, linkage disequilibrium (LD) based pruning and minor allele frequency (MAF) filtering, and combinations thereof) to assess their potential to mitigate the ascertainment bias. Results Rare SNPs were underrepresented in the array data. Array data consistently overestimated He compared to WGS data, however, with a similar ranking of the breeds, as demonstrated by Spearman’s rank correlations ranging between 0.956 and 0.985. LD based pruning resulted in a reduced overestimation of He compared to the other filters and slightly improved the relationship with the WGS results. The raw array data and those with polymorphic SNPs in the wild samples underestimated pairwise FST values between breeds which had low FST (<0.15) in the WGS, and overestimated this parameter for high WGS FST (>0.15). LD based pruned data underestimated FST in a consistent manner. The genetic distance matrix from LD pruned data was more closely related to that of WGS than the other array versions. PCA was rather robust in all array versions, since the population structure on the PCA plot was generally well captured in comparison to the WGS data. Conclusions Among the tested filtering strategies, LD based pruning was found to account for the effects of ascertainment bias in the relatively best way, producing results which are most comparable to those obtained from WGS data and therefore is recommended for practical use. Electronic supplementary material The online version of this article (doi: 10.1186/s12864-017-4416-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dorcus Kholofelo Malomane
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany.
| | - Christian Reimer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - Steffen Weigend
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Höltystraße 10, 31535, Neustadt, Germany
| | - Annett Weigend
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Höltystraße 10, 31535, Neustadt, Germany
| | - Ahmad Reza Sharifi
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - Henner Simianer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
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Wong J, de Bruyn J, Bagnol B, Grieve H, Li M, Pym R, Alders R. Small-scale poultry and food security in resource-poor settings: A review. GLOBAL FOOD SECURITY-AGRICULTURE POLICY ECONOMICS AND ENVIRONMENT 2017. [DOI: 10.1016/j.gfs.2017.04.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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