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Genomic characterization of the nucleus for conservation of the Chino Santandereano breed using SNP markers. Trop Anim Health Prod 2021; 53:492. [PMID: 34596804 DOI: 10.1007/s11250-021-02936-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/23/2021] [Indexed: 10/20/2022]
Abstract
The Chino Santandereano (CHS) creole cattle breed has undergone an adaptation process of more than 500 years to the Colombian mountainous tropics. Despite its advantages, the breed has been replaced by specialized cattle that put it at risk of extinction. The aim of this work was to estimate the genomic diversity and population structure of the nucleus of conservation of the CHS breed. Thirty-seven CHS and 20 Brahman animals were genotyped due to the possible introgression of genes with the GGP Bovine LD v3 chip. Quality control was performed, and linkage disequilibrium (LD), effective population size (Ne), ROH segments, homozygosity, and genomic inbreeding in the breed were estimated. Subsequently, 50 K genomic information of the Holstein (n = 30) and Romosinuano (n = 8) breeds were included to estimate the minor allele frequency (MAF) with common markers and constructing the graphs of the principal component analysis (PCA). Pairwise FSTs were estimated and a neighbor-joining tree was constructed using the IBS matrix. Admixture was used with k = 2 to 10 for the racial composition. LD (r2) was found up to a distance of 0.13 Mb, r2 > 0.3 at a distance of 340.3 kb, and Ne of 32 ± 1. ROH inbreeding was 5.36 ± 0.86%, with a higher contribution from recent inbreeding (4.55%). The PCA showed that the creole breeds were closer together, and the Brahman was more distant. The admixture analysis suggested k = 5 possible ancestral groups and shows that within the CHS breed, there seem to be two different groups with little Holstein and Brahman introgression. The genetic diversity parameters obtained in this work show minimal diversity in this breed and reinforce the need to protect this resource and the conservation banks.
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Genetic diversity and population structure of three native cattle populations in Mozambique. Trop Anim Health Prod 2021; 53:117. [PMID: 33438116 DOI: 10.1007/s11250-021-02562-0] [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: 06/16/2020] [Accepted: 01/05/2021] [Indexed: 12/25/2022]
Abstract
In the present work, the population diversity and structure of three populations of native Mozambican cattle were studied, to develop knowledge that is required for sound conservation and genetic improvement programs of these genetic resources. A total of 228 animals (Landim, Angone, and Tete) were genotyped using the International Dairy and Beef version three (IDBV3) SNP BeadChip array. Population parameters varied within a limited scope, with the average minor allele frequency (MAF) ranging from 0.228 ± 0.154 in the Angone to 0.245 ± 0.145 in the Tete population, while estimates of expected heterozygosities varied from 0.304 ± 0.166 in the Angone to 0.329 ± 0.148 in the Tete population. Low positive (0.065 ± 0.109) inbreeding rates were detected in the three cattle groups. Population structure and admixture analyses indicated low genetic differentiation and various degrees of admixture among the populations. The effective population size has decreased over time and at 12 generations ago ranged between 349 (Tete) and 929 (Landim). The average linkage disequilibrium (LD) of the studied populations ranged from 0.400 ± 0.213 (Tete) to 0.434 ± 0.232 (Landim). The findings of this study will be valuable for formulating management and conservation strategies for indigenous Mozambican cattle populations.
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Fabbri MC, Dadousis C, Bozzi R. Estimation of Linkage Disequilibrium and Effective Population Size in Three Italian Autochthonous Beef Breeds. Animals (Basel) 2020; 10:ani10061034. [PMID: 32545850 PMCID: PMC7341513 DOI: 10.3390/ani10061034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022] Open
Abstract
The objective was to investigate the pattern of linkage disequilibrium (LD) in three local beef breeds, namely, Calvana (n = 174), Mucca Pisana (n = 270), and Pontremolese (n = 44). As a control group, samples of the Italian Limousin breed (n = 100) were used. All cattle were genotyped with the GeneSeek GGP-LDv4 33k SNP chip containing 30,111 SNPs. The genotype quality control for each breed was conducted separately, and SNPs with call rate < 0.95 and minor allele frequency (MAF) > 1% were used for the analysis. LD extent was estimated in PLINK v1.9 using the squared correlation between pairs of loci (r2) across autosomes. Moreover, r2 values were used to calculate historical and contemporary effective population size (Ne) in each breed. Average r2 was similar in Calvana and Mucca Pisana (~0.14) and higher in Pontremolese (0.17); Limousin presented the lowest LD extent (0.07). LD up to 0.11-0.15 was persistent in the local breeds up to 0.75 Mbp, while in Limousin, it showed a more rapid decay. Variation of different LD levels across autosomes was observed in all the breeds. The results demonstrated a rapid decrease in Ne across generations for local breeds, and the contemporary population size observed in the local breeds, ranging from 41.7 in Calvana to 17 in Pontremolese, underlined the demographic alarming situation.
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Ghoreishifar SM, Moradi-Shahrbabak H, Parna N, Davoudi P, Khansefid M. Linkage disequilibrium and within-breed genetic diversity in Iranian Zandi sheep. Arch Anim Breed 2019; 62:143-151. [PMID: 31807624 PMCID: PMC6852851 DOI: 10.5194/aab-62-143-2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 03/08/2019] [Indexed: 12/23/2022] Open
Abstract
This research aimed to measure the extent of linkage disequilibrium (LD),
effective population size (Ne), and runs of homozygosity (ROHs)
in one of the major Iranian sheep breeds (Zandi) using 96 samples genotyped
with Illumina Ovine SNP50 BeadChip. The amount of LD (r2) for
single-nucleotide polymorphism (SNP) pairs in short distances (10–20 kb)
was 0.21±0.25 but rapidly decreased to 0.10±0.16 by increasing the
distance between SNP pairs (40–60 kb). The Ne of Zandi sheep in
past (approximately 3500 generations ago) and recent (five generations ago)
populations was estimated to be 6475 and 122, respectively. The ROH-based
inbreeding was 0.023. We found 558 ROH regions, of which 37 % were
relatively long (>10 Mb). Compared with the rate of LD
reduction in other species (e.g., cattle and pigs), in Zandi, it was reduced
more rapidly by increasing the distance between SNP pairs. According to the
LD pattern and high genetic diversity of Zandi sheep, we need to use an SNP
panel with a higher density than Illumina Ovine SNP50 BeadChip for genomic
selection and genome-wide association studies in this breed.
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Affiliation(s)
- Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Hossein Moradi-Shahrbabak
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Nahid Parna
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Pourya Davoudi
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Majid Khansefid
- Agriculture Victoria, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia
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Lwin M, Mon SLY, Yamanaka H, Nagano Y, Mannen H, Faruque MO, Kawabe K, Okamoto S, Shimogiri T. Genetic diversities and population structures of four popular Myanmar local cattle breeds. Anim Sci J 2018; 89:1648-1655. [PMID: 30318818 DOI: 10.1111/asj.13112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/20/2018] [Accepted: 09/03/2018] [Indexed: 11/30/2022]
Abstract
Local cattle breeds are popular in Myanmar because they make excellent draught animals, so it is of fundamental importance that their genetic diversities and population structures are elucidated for breeding and conservation purposes. In this study, we characterized the genetic diversities and population structures of four popular Myanmar local cattle breeds and five native cattle populations from neighboring countries (Bangladesh, Laos, Cambodia, and Vietnam) using the GGP Bovine 50K array. The mean observed and expected heterozygosity estimates using pruned datasets ranged from 0.317 and 0.322, respectively, in Cambodia to 0.448 and 0.421, respectively, in Vietnam South. The four Myanmar local breeds exhibited similar levels of genetic diversity. However, AMOVA revealed significant genetic differentiation among the nine populations (p < 0.00001), and Neighbor-Net analysis showed that Shan Ngwar Pu was distinct from the other Myanmar local breeds. Furthermore, PCA and population structure analyses revealed that the native cattle from neighboring countries genetically influenced the Myanmar local breeds to some extent and that the genetic origins could also be observed in the local breeds. These findings highlight the importance of Myanmar local breeds as genetic resources and provide useful information for the future development of breeding strategies and conservation management plans.
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Affiliation(s)
- Moe Lwin
- The United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Su Lai Y Mon
- Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Hayate Yamanaka
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | - Yukio Nagano
- The United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan.,Analytical Research Center for Experimental Sciences, Saga University, Honjo, Saga, Japan
| | - Hideyuki Mannen
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | | | - Kotaro Kawabe
- Education Center, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Shin Okamoto
- The United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan.,Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Takeshi Shimogiri
- The United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan.,Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Japan
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Lashmar S, Visser C, van Marle-Köster E, Muchadeyi F. Genomic diversity and autozygosity within the SA Drakensberger beef cattle breed. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.04.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Dash S, Singh A, Bhatia AK, Jayakumar S, Sharma A, Singh S, Ganguly I, Dixit SP. Evaluation of Bovine High-Density SNP Genotyping Array in Indigenous Dairy Cattle Breeds. Anim Biotechnol 2017. [PMID: 28636460 DOI: 10.1080/10495398.2017.1329150] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In total 52 samples of Sahiwal ( 19 ), Tharparkar ( 17 ), and Gir ( 16 ) were genotyped by using BovineHD SNP chip to analyze minor allele frequency (MAF), genetic diversity, and linkage disequilibrium among these cattle. The common SNPs of BovineHD and 54K SNP Chips were also extracted and evaluated for their performance. Only 40%-50% SNPs of these arrays was found informative for genetic analysis in these cattle breeds. The overall mean of MAF for SNPs of BovineHD SNPChip was 0.248 ± 0.006, 0.241 ± 0.007, and 0.242 ± 0.009 in Sahiwal, Tharparkar and Gir, respectively, while that for 54K SNPs was on lower side. The average Reynold's genetic distance between breeds ranged from 0.042 to 0.055 based on BovineHD Beadchip, and from 0.052 to 0.084 based on 54K SNP Chip. The estimates of genetic diversity based on HD and 54K chips were almost same and, hence, low density chip seems to be good enough to decipher genetic diversity of these cattle breeds. The linkage disequilibrium started decaying (r2 < 0.2) at 140 kb inter-marker distance and, hence, a 20K low density customized SNP array from HD chip could be designed for genomic selection in these cattle else the 54K Bead Chip as such will be useful.
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Affiliation(s)
- S Dash
- a ICAR- National Dairy Research Institute , Karnal , Haryana , India
| | - A Singh
- a ICAR- National Dairy Research Institute , Karnal , Haryana , India
| | - A K Bhatia
- b ICAR- National Bureau of Animal Genetic Resources , Karnal , Haryana , India
| | - S Jayakumar
- b ICAR- National Bureau of Animal Genetic Resources , Karnal , Haryana , India
| | - A Sharma
- b ICAR- National Bureau of Animal Genetic Resources , Karnal , Haryana , India
| | - S Singh
- b ICAR- National Bureau of Animal Genetic Resources , Karnal , Haryana , India
| | - I Ganguly
- b ICAR- National Bureau of Animal Genetic Resources , Karnal , Haryana , India
| | - S P Dixit
- b ICAR- National Bureau of Animal Genetic Resources , Karnal , Haryana , India
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Estimates of linkage disequilibrium and effective population sizes in Chinese Merino (Xinjiang type) sheep by genome-wide SNPs. Genes Genomics 2017; 39:733-745. [PMID: 28706593 PMCID: PMC5486679 DOI: 10.1007/s13258-017-0539-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 03/19/2017] [Indexed: 12/14/2022]
Abstract
Knowledge of linkage disequilibrium (LD) is important for effective genome-wide association studies and accurate genomic prediction. Chinese Merino (Xinjiang type) is well-known fine wool sheep breed. However, the extent of LD across the genome remains unexplored. In this study, we calculated autosomal LD based on genome-wide SNPs of 635 Chinese Merino (Xinjiang type) sheep by Illumina Ovine SNP50 BeadChip. A moderate level of LD (r2 ≥ 0.25) across the whole genome was observed at short distances of 0–10 kb. Further, the ancestral effective population size (Ne) was analyzed by extent of LD and found that Ne increased with the increase of generations and declined rapidly within the most recent 50 generations, which is consistent with the history of Chinese Merino sheep breeding, initiated in 1971. We also noted that even when the effective population size was estimated across different single chromosomes, Ne only ranged from 140.36 to 183.33 at five generations in the past, exhibiting a rapid decrease compared with that at ten generations in the past. These results indicated that the genetic diversity in Chinese Merino sheep recently decreased and proper protective measures should be taken to maintain the diversity. Our datasets provided essential genetic information to track molecular variations which potentially contribute to phenotypic variation in Chinese Merino sheep.
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Sudrajad P, Seo DW, Choi TJ, Park BH, Roh SH, Jung WY, Lee SS, Lee JH, Kim S, Lee SH. Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds. Anim Genet 2016; 48:85-89. [PMID: 27642108 DOI: 10.1111/age.12488] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2016] [Indexed: 12/01/2022]
Abstract
The routine collection and use of genomic data are useful for effectively managing breeding programs for endangered populations. Linkage disequilibrium (LD) using high-density DNA markers has been widely used to determine population structures and predict the genomic regions that are associated with economic traits in beef cattle. The extent of LD also provides information about historical events, including past effective population size (Ne ), and it allows inferences on the genetic diversity of breeds. The objective of this study was to estimate the LD and Ne in three Korean cattle breeds that are genetically similar but have different coat colors (Brown, Brindle and Jeju Black Hanwoo). Brindle and Jeju Black are endangered breeds with small populations, whereas Brown Hanwoo is the main breeding population in Korea. DNA samples from these cattle breeds were genotyped using the Illumina BovineSNP50 Bead Chip. We examined 13 cattle breeds, including European taurines, African taurines and indicines, and hybrids to compare their LD values. Brown Hanwoo consistently had the lowest mean LD compared to Jeju Black, Brindle and the other 13 cattle breeds (0.13, 0.19, 0.21 and 0.15-0.22 respectively). The high LD values of Brindle and Jeju Black contributed to small Ne values (53 and 60 respectively), which were distinct from that of Brown Hanwoo (531) for 11 generations ago. The differences in LD and Ne for each breed reflect the breeding strategy applied. The Ne for these endangered cattle breeds remain low; thus, effort is needed to bring them back to a sustainable tract.
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Affiliation(s)
- P Sudrajad
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, 305-764, Korea.,Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Jakarta, 12540, Indonesia
| | - D W Seo
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, 305-764, Korea
| | - T J Choi
- Animal Breeding and Genetics Division, National Institute of Animal Science, Seonghwan, 31000, Korea
| | - B H Park
- Animal Breeding and Genetics Division, National Institute of Animal Science, Seonghwan, 31000, Korea
| | - S H Roh
- Hanwoo Genetic Improvement Center, National Agricultural Cooperative Federation, Chungnam, 356-831, Korea
| | - W Y Jung
- Hanwoo Genetic Improvement Center, National Agricultural Cooperative Federation, Chungnam, 356-831, Korea
| | - S S Lee
- Hanwoo Genetic Improvement Center, National Agricultural Cooperative Federation, Chungnam, 356-831, Korea
| | - J H Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, 305-764, Korea
| | - S Kim
- Animal Breeding and Genetics Division, National Institute of Animal Science, Seonghwan, 31000, Korea
| | - S H Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, 305-764, Korea
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