1
|
Samuel B, Mengistie D, Assefa E, Kang M, Park C, Dadi H, Dinka H. Genetic diversity of DGAT1 gene linked to milk production in cattle populations of Ethiopia. BMC Genom Data 2022; 23:64. [PMID: 35948865 PMCID: PMC9364525 DOI: 10.1186/s12863-022-01080-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/03/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Diacylglycerol acyl-CoA acyltransferase 1 (DGAT1) has become a promising candidate gene for milk production traits because of its important role as a key enzyme in catalyzing the final step of triglyceride synthesis. Thus use of bovine DGAT1 gene as milk production markers in cattle is well established. However, there is no report on polymorphism of the DGAT1 gene in Ethiopian cattle breeds. The present study is the first comprehensive report on diversity, evolution, neutrality evaluation and genetic differentiation of DGAT1 gene in Ethiopian cattle population. The aim of this study was to characterize the genetic variability of exon 8 region of DGAT1 gene in Ethiopian cattle breeds. RESULTS Analysis of the level of genetic variability at the population and sequence levels with genetic distance in the breeds considered revealed that studied breeds had 11, 0.615 and 0.010 haplotypes, haplotype diversity and nucleotide diversity respectively. Boran-Holstein showed low minor allele frequency and heterozygosity, while Horro showed low nucleotide and haplotype diversities. The studied cattle DGAT1 genes were under purifying selection. The neutrality test statistics in most populations were negative and statistically non-significant (p > 0.10) and consistent with a populations in genetic equilibrium or in expansion. Analysis for heterozygosity, polymorphic information content and inbreeding coefficient revealed sufficient genetic variation in DGAT1 gene. The pairwise FST values indicated significant differentiation among all the breeds (FST = 0.13; p ≤ 0.05), besides the rooting from the evolutionary or domestication history of the cattle inferred from the phylogenetic tree based on the neighbourhood joining method. There was four separated cluster among the studied cattle breeds, and they shared a common node from the constructed tree. CONCLUSION The cattle populations studied were polymorphic for DGAT1 locus. The DGAT1 gene locus is extremely crucial and may provide baseline information for in-depth understanding, exploitation of milk gene variation and could be used as a marker in selection programmes to enhance the production potential and to accelerate the rate of genetic gain in Ethiopian cattle populations exposed to different agro ecology condition.
Collapse
Affiliation(s)
- Behailu Samuel
- Department of Applied Biology, Adama Science and Technology University, P. O. Box 1888, Adama, Ethiopia
| | - Dejenie Mengistie
- Bio and Emerging Technology Institute, P. O. Box 5954, Addis Ababa, Ethiopia
| | - Ermias Assefa
- Bio and Emerging Technology Institute, P. O. Box 5954, Addis Ababa, Ethiopia
| | - Mingue Kang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - Hailu Dadi
- Bio and Emerging Technology Institute, P. O. Box 5954, Addis Ababa, Ethiopia
| | - Hunduma Dinka
- Department of Applied Biology, Adama Science and Technology University, P. O. Box 1888, Adama, Ethiopia.
| |
Collapse
|
2
|
King F, Visser C, Banga C. Genetic characterization of Mozambican Nguni cattle and their relationship with indigenous populations of South Africa. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
3
|
Dixit SP, Bhatia AK, Ganguly I, Singh S, Dash S, Sharma A, Anandkumar N, Dang AK, Jayakumar S. Genome analyses revealed genetic admixture and selection signatures in Bos indicus. Sci Rep 2021; 11:21924. [PMID: 34753978 PMCID: PMC8578574 DOI: 10.1038/s41598-021-01144-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/21/2021] [Indexed: 11/20/2022] Open
Abstract
The genomic diversity and relationship among seven diverse cattle breeds viz. Sahiwal, Tharparkar, Gir, Vechur, Ongole, Kangayam and Hariana were investigated in 132 random samples based on high density SNP array comprising > 777 K SNPs. A total of 1993 SNPs (0.25% of the total) having greater power (FST ≥ 0.20) to differentiate these cattle populations were identified, and utilized to partition genome of each animal into a predefined number of clusters. The structure of these cattle indicated shared ancestry of dairy breeds viz. Gir, Tharparkar and Sahiwal. Most of the animals (> 76%) of different populations under study except Vechur clustered into their own group of animals called breed. Vechur population retained highest rate of admixture, consistent with its crossing with other breeds. Ongole, Kangayam and Hariana shared comparatively less of their genome (≤ 15%) with other breeds. The study indicated that all seven breeds evolved from their independent ancestry but there was intermixing of these breeds in the recent past. The selection signatures identified between draft (Kangayam) and dairy breeds included several genes like FAM19A2, RAB31P, BEST3, DGKA, AHCY, PIGU and PFKP which are involved in immune response, metabolic pathway, transportation of glucose and sugars, signaling pathways, cellular processes, cell division and glycolysis regulation, respectively. Moreover, these genomic regions also harbour QTLs affecting milk performance traits. The signatures were also identified even between the dairy breeds. In comparison to large-sized cattle, there were significant differences in the number of QTLs affecting production (body weight, growth rate etc.) and morphological traits (height) in short-statured Vechur breed. The presence of HMGA2 gene in the selection signature on chromosome 5 may explain the variations in stature between these cattle.
Collapse
Affiliation(s)
- S P Dixit
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India.
| | - A K Bhatia
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Indrajit Ganguly
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Sanjeev Singh
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Soumya Dash
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Anurodh Sharma
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - N Anandkumar
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - A K Dang
- ICAR - National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - S Jayakumar
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| |
Collapse
|
4
|
Mandefro A, Sisay T, Kim KS, Edea Z, Konwarh R, Dadi H. Single nucleotide polymorphisms of leptin gene in five Ethiopian indigenous cattle breeds and the Korean Hanwoo breed. Trop Anim Health Prod 2021; 53:202. [PMID: 33694014 DOI: 10.1007/s11250-021-02642-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/01/2021] [Indexed: 10/21/2022]
Abstract
Considering the escalating number of scientific reports on the association between the leptin gene and diverse physiological traits and performance of cattle populations, this study was directed towards identifying SNPs in the leptin gene among five indigenous cattle breeds of Ethiopia. DNA samples were extracted from the nasal swabs of the Ethiopian indigenous cattle breeds: Arsi (n = 18), Horro (n = 20), Begait (n = 21), Boran (n = 19), and Fogera (n = 17) and the Korean Hanwoo (a representative taurine breed) (n = 20), followed by PCR amplification of exon 2 and exon 3 regions of the leptin gene and sequence analysis of the PCR products. Five SNPs, two (generating missense mutations) on exon 2 and three (generating silent mutations) on exon 3 regions, were explicated in this study. Allele frequency and genotype frequency distribution pertaining to the SNPs were recorded for the studied cattle breeds besides the minor allele frequency and deviation from the Hardy-Weinberg equilibrium. Positive FIS index values were recorded for all the markers except SNP2, illustrative of heterozygote deficiency. MEGA X software-based evolutionary divergence analysis of the phylogenetic tree based on the SNP data revealed that the large-sized breeds, Hanwoo, Begait, Boran, and Fogera, were more closely clustered compared to the small-sized Arsi breed. Among the seven haplotypes documented from the various breeds, sequence analysis was suggestive of haplotypes 1 and 2 to be ancestral haplotypes for the leptin gene. This study is envisaged to accelerate molecular breeding programs for the genetic improvement of the Ethiopian cattle breeds.
Collapse
Affiliation(s)
- Ayele Mandefro
- Department of Biotechnology, Addis Ababa Science and Technology University, P.O. Box 16417, Addis Ababa, Ethiopia.,Institute of Biotechnology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Tesfaye Sisay
- Institute of Biotechnology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Kwan-Suk Kim
- Department of Animal Sciences, Chungbuk National University, Cheongju, Chungbuk, 361-763, South Korea
| | - Zewdu Edea
- Department of Animal Sciences, Chungbuk National University, Cheongju, Chungbuk, 361-763, South Korea
| | - Rocktotpal Konwarh
- Department of Biotechnology, Addis Ababa Science and Technology University, P.O. Box 16417, Addis Ababa, Ethiopia.,Division of Nanobiomaterials and Nanomedicine, Uniglobe Scientific Pvt. Ltd., 7/9, Kishan Garh, Vasant Kunj, New Delhi, 110070, India
| | - Hailu Dadi
- Ethiopian Biotechnology Institute, P.O. Box 2490, Addis Ababa, Ethiopia.
| |
Collapse
|
5
|
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.
Collapse
|
6
|
Onasanya GO, Msalya GM, Thiruvenkadan AK, Sreekumar C, Tirumurugaan GK, Sanni TM, Decampos JS, Amusan SA, Olowofeso O, Fafiolu AO, Okpeku M, Yakubu A, Ikeobi CO. Single nucleotide polymorphisms at heat shock protein 90 gene and their association with thermo-tolerance potential in selected indigenous Nigerian cattle. Trop Anim Health Prod 2020; 52:1961-1970. [PMID: 31981054 DOI: 10.1007/s11250-020-02222-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/17/2020] [Indexed: 11/24/2022]
Abstract
Heat shock protein (HSP) 90 gene provides protection and adaptation to thermal assault and certain polymorphisms have been associated to heat tolerance in humans and animals. Single nucleotide polymorphisms (SNPs) of HSP 90 gene were used to evaluate the scientific basis of heat tolerance in four zebu breeds of Nigeria. The DNA was extracted from skin tissue of 90 adult bulls representing White Fulani (WF), Sokoto Gudali (SG), Red Bororo (RB), and Ambala (AM). The SNPs were determined in DNAs using PCR, sequencing, and visualization and bio-editing by chromatogram in SeqMan Ngen tool. Subsequently, respective genotypes were constructed and genotypic and allelic frequencies were computed. Also, body parameters related to heat stress (HS) including body temperature (BT), rectal temperature (RT), and respiratory rates (RR) were taken for each animal before biological sampling and heat tolerance coefficient (HTC) was calculated. We detected four SNPs distinct/specific for each breed as follows: change from thymine (T) to guanine (G) at position 116 (T116G) in RB, G to cytosine (C) at 220 (G220C) in SG, G to adenine (A) at two positions, 346 (G346A) and 390 (G390A) in AM and WF, respectively. Heterozygous SNPs showed significantly lower values (P < 0.0001) for BT, RT, RR, and HTC than homozygous genotypes at all positions. We hypothesize that animals with heterozygous SNPs in exon 3 of HSP 90 may be tolerant to HS. These SNPs can be used as bio-markers for screening large populations of cattle for tolerance to hot tropical conditions in Nigeria and other sub-humid places.
Collapse
Affiliation(s)
- Gbolabo O Onasanya
- Department of Animal Science, Federal University Dutse, Dutse, Nigeria
- Deparment of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria
- Mecheri Sheep Research Station, Pottaneri, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
- Biotechnology Center, Postgraduate Research Institute in Animal Sciences, Kattupakkum, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - George M Msalya
- Mecheri Sheep Research Station, Pottaneri, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India.
- Department of Animal, Aquaculture and Range Sciences (DAARS), Sokoine University of Agriculture (SUA), PO Box 3004, Morogoro, Tanzania.
| | - Aranganoor K Thiruvenkadan
- Mecheri Sheep Research Station, Pottaneri, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Chirukandoth Sreekumar
- Biotechnology Center, Postgraduate Research Institute in Animal Sciences, Kattupakkum, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Gopalan K Tirumurugaan
- Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Timothy M Sanni
- Deparment of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - John S Decampos
- Department of Animal Production, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Samuel A Amusan
- Department of Animal production, Federal College of Animal Health and Production Technology, Moor Plantation, Ibadan, Nigeria
| | - Olajide Olowofeso
- Deparment of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Adeboye O Fafiolu
- Department of Animal Nutrition, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Moses Okpeku
- Department of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westvile Campus, Durban, South Africa
| | - Abdulmojeed Yakubu
- Department of Animal Science, Faculty of Agriculture, Nasarawa State University, Keffi, Shabu-Lafia Campus, Lafia, Nigeria
| | - Christian O Ikeobi
- Deparment of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria
| |
Collapse
|
7
|
Ahmad SF, Panigrahi M, Ali A, Dar RR, Narayanan K, Bhushan B. Evaluation of two bovine SNP genotyping arrays for breed clustering and stratification analysis in well-known taurine and indicine breeds. Anim Biotechnol 2019; 31:268-275. [PMID: 30857468 DOI: 10.1080/10495398.2019.1578227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The present study aimed to evaluate the efficiency of two Bovine SNP genotyping arrays (i.e., 50 K and HD) for breed clustering and stratification related studies in taurine and indicine breeds. The whole-genome SNP data at two densities were assembled into three datasets (A, B and C). Dataset A (N = 213) included 50 K genotypic data for five taurine (Holstein-Friesian, Guernsey, Brown Swiss, Angus and Jersey) and two indicine (Gir and Nellore) breeds. Dataset B (N = 241) included the same breeds with HD density data. Dataset C (N = 299) included 50 K SNP genotypic data for six taurine (Holstein-Friesian, Jersey, Guernsey, Brown Swiss, Angus and Hereford) and six indicine (Hariana, Kankrej, Brahman, Nellore, Sahiwal and Gir) breeds. The analysis was done using ADMIXTURE program (bioinformatics-based) and cross-validation errors and Principal Component Analysis (statistical analysis). The proportion of polymorphic markers and minor allele frequencies were assessed for each breed. The proportion of markers polymorphic was consistently higher in taurine breeds when compared with breeds from indicine group. Minor allele frequency estimates and ADMIXTURE results showed differential patterns for both the lineages. However, no significant increase in the accuracy of genomic clustering was found on moving from 50 K to HD density data.
Collapse
Affiliation(s)
- Sheikh Firdous Ahmad
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
| | - Ajaz Ali
- Division of Animal Reproduction, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
| | - Rouf Rashid Dar
- Division of Animal Reproduction, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
| | - Krishnaswamy Narayanan
- Division of Animal Reproduction, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Msalya G, Kim ES, Laisser ELK, Kipanyula MJ, Karimuribo ED, Kusiluka LJM, Chenyambuga SW, Rothschild MF. Determination of Genetic Structure and Signatures of Selection in Three Strains of Tanzania Shorthorn Zebu, Boran and Friesian Cattle by Genome-Wide SNP Analyses. PLoS One 2017; 12:e0171088. [PMID: 28129396 PMCID: PMC5271371 DOI: 10.1371/journal.pone.0171088] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 01/16/2017] [Indexed: 11/29/2022] Open
Abstract
Background More than 90 percent of cattle in Tanzania belong to the indigenous Tanzania Short Horn Zebu (TSZ) population which has been classified into 12 strains based on historical evidence, morphological characteristics, and geographic distribution. However, specific genetic information of each TSZ population has been lacking and has caused difficulties in designing programs such as selection, crossbreeding, breed improvement or conservation. This study was designed to evaluate the genetic structure, assess genetic relationships, and to identify signatures of selection among cattle of Tanzania with the main goal of understanding genetic relationship, variation and uniqueness among them. Methodology/Principal findings The Illumina Bos indicus SNP 80K BeadChip was used to genotype genome wide SNPs in 168 DNA samples obtained from three strains of TSZ cattle namely Maasai, Tarime and Sukuma as well as two comparative breeds; Boran and Friesian. Population structure and signatures of selection were examined using principal component analysis (PCA), admixture analysis, pairwise distances (FST), integrated haplotype score (iHS), identical by state (IBS) and runs of homozygosity (ROH). There was a low level of inbreeding (F~0.01) in the TSZ population compared to the Boran and Friesian breeds. The analyses of FST, IBS and admixture identified no considerable differentiation between TSZ trains. Importantly, common ancestry in Boran and TSZ were revealed based on admixture and IBD, implying gene flow between two populations. In addition, Friesian ancestry was found in Boran. A few common significant iHS were detected, which may reflect influence of recent selection in each breed or strain. Conclusions Population admixture and selection signatures could be applied to develop conservation plan of TSZ cattle as well as future breeding programs in East African cattle.
Collapse
Affiliation(s)
- George Msalya
- Department of Animal, Aquaculture and Range Sciences, Sokoine University of Agriculture (SUA), Morogoro, Tanzania
- * E-mail:
| | - Eui-Soo Kim
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | - Emmanuel L. K. Laisser
- Department of Animal, Aquaculture and Range Sciences, Sokoine University of Agriculture (SUA), Morogoro, Tanzania
- Ministry of Education and Vocational Training, Inspectorate Department Eastern Zone, Morogoro, Tanzania
| | | | - Esron D. Karimuribo
- Department of Veterinary Medicine and Public Health, SUA, Morogoro, Tanzania
| | - Lughano J. M. Kusiluka
- Department of Veterinary Medicine and Public Health, SUA, Morogoro, Tanzania
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Sebastian W. Chenyambuga
- Department of Animal, Aquaculture and Range Sciences, Sokoine University of Agriculture (SUA), Morogoro, Tanzania
| | - Max F. Rothschild
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| |
Collapse
|
11
|
Kim K, Kwak W, Sung SS, Cho S, Kim H, Yoon D, Lee HJ. A novel genetic variant database for Korean native cattle (Hanwoo): HanwooGDB. Genes Genomics 2015. [DOI: 10.1007/s13258-014-0224-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
12
|
Uzzaman MR, Edea Z, Bhuiyan MSA, Walker J, Bhuiyan AKFH, Kim KS. Genome-wide Single Nucleotide Polymorphism Analyses Reveal Genetic Diversity and Structure of Wild and Domestic Cattle in Bangladesh. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 27:1381-6. [PMID: 25178287 PMCID: PMC4150168 DOI: 10.5713/ajas.2014.14160] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/23/2014] [Accepted: 06/09/2014] [Indexed: 11/27/2022]
Abstract
In spite of variation in coat color, size, and production traits among indigenous Bangladeshi cattle populations, genetic differences among most of the populations have not been investigated or exploited. In this study, we used a high-density bovine single nucleotide polymorphism (SNP) 80K Bead Chip derived from Bos indicus breeds to assess genetic diversity and population structure of 2 Bangladeshi zebu cattle populations (red Chittagong, n = 28 and non-descript deshi, n = 28) and a semi-domesticated population (gayal, n = 17). Overall, 95% and 58% of the total SNPs (69,804) showed polymorphisms in the zebu and gayal populations, respectively. Similarly, the average minor allele frequency value was as high 0.29 in zebu and as low as 0.09 in gayal. The mean expected heterozygosity varied from 0.42±0.14 in zebu to 0.148±0.14 in gayal with significant heterozygosity deficiency of 0.06 (FIS) in the latter. Coancestry estimations revealed that the two zebu populations are weakly differentiated, with over 99% of the total genetic variation retained within populations and less than 1% accounted for between populations. Conversely, strong genetic differentiation (FST = 0.33) was observed between zebu and gayal populations. Results of population structure and principal component analyses suggest that gayal is distinct from Bos indicus and that the two zebu populations were weakly structured. This study provides basic information about the genetic diversity and structure of Bangladeshi cattle and the semi-domesticated gayal population that can be used for future appraisal of breed utilization and management strategies.
Collapse
Affiliation(s)
- Md Rasel Uzzaman
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Zewdu Edea
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md Shamsul Alam Bhuiyan
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Jeremy Walker
- GeneSeek, Neogen Corporation, Lincoln, NE 68521, USA
| | - A K F H Bhuiyan
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Kwan-Suk Kim
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| |
Collapse
|
13
|
Edea Z, Dadi H, Kim SW, Dessie T, Lee T, Kim H, Kim JJ, Kim KS. Genetic diversity, population structure and relationships in indigenous cattle populations of Ethiopia and Korean Hanwoo breeds using SNP markers. Front Genet 2013; 4:35. [PMID: 23518904 PMCID: PMC3604626 DOI: 10.3389/fgene.2013.00035] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Accepted: 03/01/2013] [Indexed: 11/16/2022] Open
Abstract
In total, 166 individuals from five indigenous Ethiopian cattle populations – Ambo (n = 27), Borana (n = 35), Arsi (n = 30), Horro (n = 36), and Danakil (n = 38) – were genotyped for 8773 single nucleotide polymorphism (SNP) markers to assess genetic diversity, population structure, and relationships. As a representative of taurine breeds, Hanwoo cattle (n = 40) were also included in the study for reference. Among Ethiopian cattle populations, the proportion of SNPs with minor allele frequencies (MAFs) ≥0.05 ranged from 81.63% in Borana to 85.30% in Ambo, with a mean of 83.96% across all populations. The Hanwoo breed showed the highest proportion of polymorphism, with MAFs ≥0.05, accounting for 95.21% of total SNPs. The mean expected heterozygosity varied from 0.370 in Danakil to 0.410 in Hanwoo. The mean genetic differentiation (FST; 1%) in Ethiopian cattle revealed that within individual variation accounted for approximately 99% of the total genetic variation. As expected, FST and Reynold genetic distance were greatest between Hanwoo and Ethiopian cattle populations, with average values of 17.62 and 18.50, respectively. The first and second principal components explained approximately 78.33% of the total variation and supported the clustering of the populations according to their historical origins. At K = 2 and 3, a considerable source of variation among cattle is the clustering of the populations into Hanwoo (taurine) and Ethiopian cattle populations. The low estimate of genetic differentiation (FST) among Ethiopian cattle populations indicated that differentiation among these populations is low, possibly owing to a common historical origin and high gene flow. Genetic distance, phylogenic tree, principal component analysis, and population structure analyses clearly differentiated the cattle population according to their historical origins, and confirmed that Ethiopian cattle populations are genetically distinct from the Hanwoo breed.
Collapse
Affiliation(s)
- Zewdu Edea
- International Livestock Research Institute Addis Ababa, Ethiopia ; Department of Animal Science, Chungbuk National University Cheongju, Korea
| | | | | | | | | | | | | | | |
Collapse
|