1
|
Ávila G, Ceciliani F, Viala D, Dejean S, Sala G, Lecchi C, Bonnet M. Conjugated linoleic acid (CLA) modulates bovine peripheral blood mononuclear cells (PBMC) proteome in vitro. J Proteomics 2024; 304:105232. [PMID: 38909954 DOI: 10.1016/j.jprot.2024.105232] [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: 04/20/2024] [Revised: 06/16/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
Conjugated linoleic acid (CLA) is a group of natural isomers of the n-6 polyunsaturated fatty acid (PUFA) linoleic acid, exerting biological effects on cow physiology. This study assessed the impact of the mixture 50:50 (vol:vol) of CLA isomers (cis-9, trans-11 and trans-10, cis-12) on bovine peripheral blood mononuclear cells (PBMC) proteome, identifying 1608 quantifiable proteins. A supervised multivariate statistical analysis, sparse variant partial least squares - discriminant analysis (sPLS-DA) for paired data identified 407 discriminant proteins (DP), allowing the clustering between the CLA and controls. The ProteINSIDE workflow found that DP with higher abundance in the CLA group included proteins related to innate immune defenses (PLIN2, CD36, C3, C4, and AGP), with antiapoptotic (SERPINF2 and ITIH4) and antioxidant effects (HMOX1). These results demonstrated that CLA modulates the bovine PBMC proteome, supports the antiapoptotic and immunomodulatory effects observed in previous in vitro studies on bovine PBMC, and suggests a cytoprotective role against oxidative stress. SIGNIFICANCE: In this study, we report for the first time that the mixture 50:50 (vol:vol) of cis-9, trans-11, and trans-10, cis-12-CLA isomers modulates the bovine PBMC proteome. Our results support the immunomodulatory and antiapoptotic effects observed in bovine PBMC in vitro. In addition, the present study proposes a cytoprotective role of CLA mixture against oxidative stress. We suggest a molecular signature of CLA treatment based on combining a multivariate sparse discriminant analysis and a clustering method. This demonstrates the great value of sPLS-DA as an alternative option to identify discriminant proteins with relevant biological significance.
Collapse
Affiliation(s)
- G Ávila
- Department of Veterinary Medicine and Animal Science, Università Degli Studi di Milano, Via dell'Università 6, 26900 Lodi, Italy
| | - F Ceciliani
- Department of Veterinary Medicine and Animal Science, Università Degli Studi di Milano, Via dell'Università 6, 26900 Lodi, Italy.
| | - D Viala
- INRAE, Université Clermont Auvergne, Vetagro Sup, UMRH, 63122 Saint-Genès-Champanelle, France; INRAE, Metabolomic and Proteomic Exploration Facility (PFEM), F-63122 Saint-Genès-Champanelle, France
| | - S Dejean
- Institut de Mathématiques de Toulouse, Université de Toulouse, CNRS, UPS, UMR 5219, 31062 Toulouse, France
| | - G Sala
- Department of Veterinary Medicine and Animal Science, Università Degli Studi di Milano, Via dell'Università 6, 26900 Lodi, Italy
| | - C Lecchi
- Department of Veterinary Medicine and Animal Science, Università Degli Studi di Milano, Via dell'Università 6, 26900 Lodi, Italy
| | - M Bonnet
- INRAE, Université Clermont Auvergne, Vetagro Sup, UMRH, 63122 Saint-Genès-Champanelle, France
| |
Collapse
|
2
|
Saravanan KA, Rajawat D, Kumar H, Nayak SS, Bhushan B, Dutt T, Panigrahi M. Signatures of selection in riverine buffalo populations revealed by genome-wide SNP data. Anim Biotechnol 2023; 34:3343-3354. [PMID: 36384399 DOI: 10.1080/10495398.2022.2145292] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The detection of selection signatures assists in understanding domestication, evolution, and the identification of genomic regions related to adaptation and production traits in buffaloes. The emergence of high-throughput technologies like Next Generation Sequencing and SNP genotyping had expanded our ability to detect these signatures of selection. In this study, we sought to identify signatures of selection in five buffalo populations (Brazilian Murrah, Bulgarian Murrah, Indian Murrah, Nili-Ravi, and Kundi) using Axiom Buffalo 90 K Genotyping Array data. Using seven different methodologies (Tajima's D, CLR, ROH, iHS, FST, FLK and hapFLK), we identified selection signatures in 374 genomic regions, spanning a total of 381 genes and 350 quantitative trait loci (QTLs). Among these, several candidate genes were associated with QTLs for milk production, reproduction, growth and carcass traits. The genes and QTLs reported in this study provide insight into selection signals shaping the genome of buffalo breeds. Our findings can aid in further genomic association studies, genomic prediction, and the implementation of breeding programmes in Indian buffaloes.
Collapse
Affiliation(s)
- K A Saravanan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| |
Collapse
|
3
|
Turner N, Abeysinghe P, Flay H, Meier S, Sadowski P, Mitchell MD. SWATH-MS Analysis of Blood Plasma and Circulating Small Extracellular Vesicles Enables Detection of Putative Protein Biomarkers of Fertility in Young and Aged Dairy Cows. J Proteome Res 2023; 22:3580-3595. [PMID: 37830897 DOI: 10.1021/acs.jproteome.3c00406] [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] [Indexed: 10/14/2023]
Abstract
The development of biomarkers of fertility could provide benefits for the genetic improvement of dairy cows. Circulating small extracellular vesicles (sEVs) show promise as diagnostic or prognostic markers since their cargo reflects the metabolic state of the cell of origin; thus, they mirror the physiological status of the host. Here, we employed data-independent acquisition mass spectrometry to survey the plasma and plasma sEV proteomes of two different cohorts of Young (Peripubertal; n = 30) and Aged (Primiparous; n = 20) dairy cows (Bos taurus) of high- and low-genetic merit of fertility and known pregnancy outcomes (ProteomeXchange data set identifier PXD042891). We established predictive models of fertility status with an area under the curve of 0.97 (sEV; p value = 3.302e-07) and 0.95 (plasma; p value = 6.405e-08). Biomarker candidates unique to high-fertility Young cattle had a sensitivity of 0.77 and specificity of 0.67 (*p = 0.0287). Low-fertility biomarker candidates uniquely identified in sEVs from Young and Aged cattle had a sensitivity and specificity of 0.69 and 1.0, respectively (***p = 0.0005). Our bioinformatics pipeline enabled quantification of plasma and circulating sEV proteins associated with fertility phenotype. Further investigations are warranted to validate this research in a larger population, which may lead to improved classification of fertility status in cattle.
Collapse
Affiliation(s)
- Natalie Turner
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, Queensland 4101, Australia
| | - Pevindu Abeysinghe
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, Queensland 4101, Australia
| | - Holly Flay
- DairyNZ Limited, Private Bag 3221, Hamilton 3240, New Zealand
| | - Susanne Meier
- DairyNZ Limited, Private Bag 3221, Hamilton 3240, New Zealand
| | - Pawel Sadowski
- Central Analytical Research Facility (CARF), QUT, Gardens Point Campus, 2 George Street, Brisbane City, Queensland 4000, Australia
| | - Murray D Mitchell
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, Queensland 4101, Australia
| |
Collapse
|
4
|
Sallam AM, Reyer H, Wimmers K, Bertolini F, Aboul-Naga A, Braz CU, Rabee AE. Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds. BMC Genomics 2023; 24:573. [PMID: 37752425 PMCID: PMC10521497 DOI: 10.1186/s12864-023-09679-6] [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: 02/28/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Understanding the genomic features of livestock is essential for successful breeding programs and conservation. This information is scarce for local goat breeds in Egypt. In the current study, genomic regions with selection signatures were identified as well as runs of homozygosity (ROH), genomic inbreeding coefficients (FROH) and fixation index (FST) were detected in Egyptian Nubian, Damascus, Barki and Boer goat breeds. A total of 46,268 SNP markers and 337 animals were available for the genomic analyses. On average, 145.44, 42.02, 87.90 and 126.95 ROHs were detected per individual in the autosomal genome of the respective breeds. The mean accumulative ROH lengths ranged from 46.5 Mb in Damascus to 360 Mb in Egyptian Nubian. The short ROH segments (< 2 Mb) were most frequent in all breeds, while the longest ROH segments (> 16 Mb) were exclusively found in the Egyptian Nubian. The highest average FROH was observed in Egyptian Nubian (~ 0.12) followed by Boer (~ 0.11), while the lowest FROH was found in Damascus (~ 0.05) and Barki breed (~ 0.03). The estimated mean FST was 0.14 (Egyptian Nubian and Boer), 0.077 (Egyptian Nubian and Barki), 0.075 (Egyptian Nubian and Damascus), 0.071 (Barki and Boer), 0.064 (Damascus and Boer), and 0.015 (Damascus and Barki), for each pair of breeds. Interestingly, multiple SNPs that accounted for high FST values were observed on chromosome 6 in regions harboring ALPK1 and KCNIP4. Genomic regions overlapping both FST and ROH harbor genes related to immunity (IL4R, PHF23, GABARAP, GPS2, and CD68), reproduction (SPATA2L, TNFSF12, TMEM95, and RNF17), embryonic development (TCF25 and SOX15) and adaptation (MC1R, KDR, and KIT), suggesting potential genetic adaptations to local environmental conditions. Our results contribute to the understanding of the genetic architecture of different goat breeds and may provide valuable information for effective preservation and breeding programs of local goat breeds in Egypt.
Collapse
Affiliation(s)
- Ahmed M Sallam
- Animal and Poultry Breeding Department, Desert Research Center, Cairo, Egypt.
| | - Henry Reyer
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
- Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 6b, 18059, Rostock, Germany
| | - Francesca Bertolini
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Adel Aboul-Naga
- Animal Production Research Institute, Agricultural Research Center, Dokki, Cairo, Egypt
| | - Camila U Braz
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt
| | - Alaa Emara Rabee
- Department of Animal Sciences, University of Illinois Urbana-Champaign, 1207 Gregory Dr, Urbana, 61801, USA
| |
Collapse
|
5
|
Jalali SM, Razi Jalali M, Nikvand AA, Yazdkhasti M, Rahij Torfi H. A Study of Heavy Metal Status and its Relationship with Hematologic and Biochemical Indices in River Buffaloes in Southwest Iran. ARCHIVES OF RAZI INSTITUTE 2023; 78:1225-1237. [PMID: 38226382 PMCID: PMC10787930 DOI: 10.32592/ari.2023.78.4.1225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/20/2023] [Indexed: 01/17/2024]
Abstract
Heavy metals are among the most important environmental pollutants which accumulate in various organs and are associated with several toxic effects. This study was performed to determine the status of heavy metals in river buffaloes in Khuzestan province, Iran, and its relationship with hematologic and serum biochemical parameters. A total of 103 apparently healthy buffaloes were sampled from the region. The concentration of heavy metals, including lead (Pb), mercury (Hg), and cadmium (Cd), was determined in serum samples by atomic spectroscopy. In addition, complete blood counts and serum biochemical profiles were assessed. The serum concentration of Cd, Pb, and Hg in the sampled buffaloes, as mean±standard error, were 0.55±0.01, 6.51±0.10, and 6.28±0.09 µg/l, respectively, which are within the permissible serum levels in the livestock. Serum Cd and Hg levels showed no significant relationship with hematologic or biochemical analytes. However, there were significant negative correlations between Pb levels and phosphorus, magnesium, sodium, as well as potassium concentrations, while serum iron was positively correlated with lead (P<0.05). In addition, there was a significant positive correlation between Hg level and serum aspartate aminotransferase activity (P<0.05). Despite the fact that river buffaloes in Khuzestan spend a long time daily in the Karun River with high industrial pollution, no serum evidence of heavy metal toxicity was found in these animals. It can be suggested that river buffaloes in Khuzestan seem to be resistant to the environmental pollution caused by heavy metals. However, further studies are required to confirm this issue and identify its possible explanations.
Collapse
Affiliation(s)
- S M Jalali
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - M Razi Jalali
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - A A Nikvand
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - M Yazdkhasti
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - H Rahij Torfi
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| |
Collapse
|
6
|
Falchi L, Cesarani A, Mastrangelo S, Senczuk G, Portolano B, Pilla F, Macciotta NPP. Analysis of runs of homozygosity of cattle living in different climate zones. J Anim Sci 2023; 101:skad061. [PMID: 36802370 PMCID: PMC10066727 DOI: 10.1093/jas/skad061] [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: 09/27/2022] [Accepted: 02/16/2023] [Indexed: 02/23/2023] Open
Abstract
Aim of this study was to analyze the distribution and characteristics of runs of homozygosity in Bos taurus taurus and Bos taurus indicus breeds, as well as their crosses, farmed all around the world. With this aim in view, we used single-nucleotide polymorphisms (SNP) genotypes for 3,263 cattle belonging to 204 different breeds. After quality control, 23,311 SNPs were retained for the analysis. Animals were divided into seven different groups: 1) continental taurus, 2) temperate taurus, 3) temperate indicus, 4) temperate composite, 5) tropical taurus, 6) tropical indicus, and 7) tropical composite. The climatic zones were created according to the latitude of the breeds' country of origin: i) continental, latitude ≥ 45°; ii) temperate, 45°< Latitude >23.26°; iii) tropics, latitude ≤ 23.26°. Runs of homozygosity were computed as 15 SNPs spanning in at least 2 Mb; number of ROH per animal (nROH), average ROH length (meanMb), and ROH-based inbreeding coefficients (FROH) were also computed. Temperate indicus showed the largest nROH, whereas Temperate taurus the lowest value. Moreover, the largest meanMb was observed for Temperate taurus, whereas the lowest value for Tropics indicus. Temperate indicus breeds showed the largest FROH values. Genes mapped in the identified ROH were reported to be associated with the environmental adaptation, disease resistance, coat color determinism, and production traits. Results of the present study confirmed that runs of homozygosity could be used to identify genomic signatures due to both artificial and natural selection.
Collapse
Affiliation(s)
- Laura Falchi
- Dipartimento di Agraria, University of Sassari, 07100 Sassari, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, 07100 Sassari, Italy
- Department of Animal and Dairy Science, University of Georgia, 30602 Athens, USA
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy
| | - Baldassare Portolano
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy
| | | |
Collapse
|
7
|
Wanjala G, Kusuma Astuti P, Bagi Z, Kichamu N, Strausz P, Kusza S. A review on the potential effects of environmental and economic factors on sheep genetic diversity: Consequences of climate change. Saudi J Biol Sci 2022; 30:103505. [DOI: 10.1016/j.sjbs.2022.103505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/17/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
|
8
|
Rahimmadar S, Ghaffari M, Mokhber M, Williams JL. Linkage Disequilibrium and Effective Population Size of Buffalo Populations of Iran, Turkey, Pakistan, and Egypt Using a Medium Density SNP Array. Front Genet 2021; 12:608186. [PMID: 34950186 PMCID: PMC8689148 DOI: 10.3389/fgene.2021.608186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/03/2021] [Indexed: 11/21/2022] Open
Abstract
Linkage disequilibrium (LD) across the genome provides information to identify the genes and variations related to quantitative traits in genome-wide association studies (GWAS) and for the implementation of genomic selection (GS). LD can also be used to evaluate genetic diversity and population structure and reveal genomic regions affected by selection. LD structure and Ne were assessed in a set of 83 water buffaloes, comprising Azeri (AZI), Khuzestani (KHU), and Mazandarani (MAZ) breeds from Iran, Kundi (KUN) and Nili-Ravi (NIL) from Pakistan, Anatolian (ANA) buffalo from Turkey, and buffalo from Egypt (EGY). The values of corrected r2 (defined as the correlation between two loci) of adjacent SNPs for three pooled Iranian breeds (IRI), ANA, EGY, and two pooled Pakistani breeds (PAK) populations were 0.24, 0.28, 0.27, and 0.22, respectively. The corrected r2 between SNPs decreased with increasing physical distance from 100 Kb to 1 Mb. The LD values for IRI, ANA, EGY, and PAK populations were 0.16, 0.23, 0.24, and 0.21 for less than 100Kb, respectively, which reduced rapidly to 0.018, 0.042, 0.059, and 0.024, for a distance of 1 Mb. In all the populations, the decay rate was low for distances greater than 2Mb, up to the longest studied distance (15 Mb). The r2 values for adjacent SNPs in unrelated samples indicated that the Affymetrix Axiom 90 K SNP genomic array was suitable for GWAS and GS in these populations. The persistency of LD phase (PLDP) between populations was assessed, and results showed that PLPD values between the populations were more than 0.9 for distances of less than 100 Kb. The Ne in the recent generations has declined to the extent that breeding plans are urgently required to ensure that these buffalo populations are not at risk of being lost. We found that results are affected by sample size, which could be partially corrected for; however, additional data should be obtained to be confident of the results.
Collapse
Affiliation(s)
- Shirin Rahimmadar
- Department of Animal Science, Faculty of Agricultural Science, Urmia University, Urmia, Iran
| | - Mokhtar Ghaffari
- Department of Animal Science, Faculty of Agricultural Science, Urmia University, Urmia, Iran
| | - Mahdi Mokhber
- Department of Animal Science, Faculty of Agricultural Science, Urmia University, Urmia, Iran
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia.,Department of Animal Science, Food and Nutrition, Università Cattolica Del Sacro Cuore, Piacenza, Italy
| |
Collapse
|
9
|
Deng TX, Ma XY, Lu XR, Duan AQ, Shokrollahi B, Shang JH. Signatures of selection reveal candidate genes involved in production traits in Chinese crossbred buffaloes. J Dairy Sci 2021; 105:1327-1337. [PMID: 34955275 DOI: 10.3168/jds.2021-21102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/03/2021] [Indexed: 12/11/2022]
Abstract
Identification of selection signature is important for a better understanding of genetic mechanisms that affect phenotypic differentiation in livestock. However, the genome-wide selection responses have not been investigated for the production traits of Chinese crossbred buffaloes. In this study, an SNP data set of 133 buffaloes (Chinese crossbred buffalo, n = 45; Chinese local swamp buffalo, n = 88) was collected from the Dryad Digital Repository database (https://datadryad.org/stash/). Population genetics analysis showed that these buffaloes were divided into the following 2 groups: crossbred buffalo and swamp buffalo. The crossbred group had higher genetic diversity than the swamp group. Using 3 complementary statistical methods (integrated haplotype score, cross population extended haplotype homozygosity, and composite likelihood ratio), a total of 31 candidate selection regions were identified in the Chinese crossbred population. Here, within these candidate regions, 25 genes were under the putative selection. Among them, several candidate genes were reported to be associated with production traits. In addition, we identified 13 selection regions that overlapped with bovine QTLs that were mainly involved in milk production and composition traits. These results can provide useful insights regarding the selection response for production traits of Chinese crossbred buffalo, as identified candidate genes influence production performance.
Collapse
Affiliation(s)
- T X Deng
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China.
| | - X Y Ma
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - X R Lu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - A Q Duan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - Borhan Shokrollahi
- Department of Animal Science, Faculty of Agriculture, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran 5595-73919
| | - J H Shang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China.
| |
Collapse
|
10
|
Zhou F, Ouyang Y, Miao Y. Peroxisome proliferator-activated receptor gamma regulates genes involved in milk fat synthesis in mammary epithelial cells of water buffalo. Anim Sci J 2021; 92:e13537. [PMID: 33682250 DOI: 10.1111/asj.13537] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 01/17/2021] [Accepted: 01/25/2021] [Indexed: 01/17/2023]
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) is a critical transcription factor regulating lipid and glucose metabolism. However, the regulatory effect of PPARγ on milk fat synthesis in buffalo mammary gland is not clear. In order to explore the role of buffalo PPARG gene in milk fat synthesis, lentivirus-mediated interference was used to knock it down and then the recombinant fusion expression vector was transfected into buffalo mammary epithelial cell (BMEC) to overexpress it. PPARG gene knockdown significantly decreased the expression of CD36, FABP3, FABP4, ACSS2, ELOVL6, DGAT2, BTN1A1, AGPAT6, LPIN1, ABCG2, PPARGC1A, INSIG1, FASN, and SREBF2 genes and significantly upregulated the expression of INSIG2 gene but had no significant effect on the expression of ACSL1, GPAM, and SREBF1 genes. PPARG overexpression significantly increased the relative mRNA abundance of CD36, FABP3, FABP4, ACSS2, ELOVL6, DGAT2, BTN1A1, AGPAT6, LPIN1, PPARGC1A, INSIG1, and SREBF2 genes and significantly downregulated the expression of INSIG2 gene but had no significant effect on the expression of ACSL1, GPAM, ABCG2, FASN, and SREBF1 genes. In addition, knockdown/overexpression of PPARG gene significantly decreased/increased triacylglycerol (TAG) content in BMECs. This study revealed that buffalo PPARG gene is a key gene regulating buffalo milk fat synthesis.
Collapse
Affiliation(s)
- Fangting Zhou
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China.,College of Chemistry, Biology and Environment, Yuxi Normal University, Yuxi, China
| | - Yina Ouyang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China.,Herbivorous Livestock Research Institute, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Yongwang Miao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| |
Collapse
|
11
|
Strillacci MG, Moradi-Shahrbabak H, Davoudi P, Ghoreishifar SM, Mokhber M, Masroure AJ, Bagnato A. A genome-wide scan of copy number variants in three Iranian indigenous river buffaloes. BMC Genomics 2021; 22:305. [PMID: 33902439 PMCID: PMC8077898 DOI: 10.1186/s12864-021-07604-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 04/11/2021] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND In Iran, river buffalo is of great importance. It plays an important role in the economy of the Country, because its adaptation to harsh climate conditions and long productive lifespan permitting its farming across the Country and to convert low-quality feed into valuable milk. The genetic variability in Iranian buffalo breeds have been recently studied using SNPs genotyping data, but a whole genome Copy Number Variants (CNVs) mapping was not available. The aim of this study was to perform a genome wide CNV scan in 361 buffaloes of the three Iranian river breeds (Azeri, Khuzestani and Mazandarani) through the analysis of data obtained using the Axiom® Buffalo Genotyping Array 90 K. RESULTS CNVs detection resulted in a total of 9550 CNVs and 302 CNVRs identified in at least 5% of samples within breed, covering around 1.97% of the buffalo genome. and A total of 22 CNVRs were identified in all breeds and a different proportion of regions were in common among the three populations. Within the more represented CNVRs (n = 302) mapped a total of 409 buffalo genes, some of which resulted associated with morphological, healthy, milk, meat and reproductive traits, according to Animal Genome Cattle database. CONCLUSIONS This work provides a step forward in the interpretation of genomic variation within and among the buffalo populations, releasing a first map of CNVs and providing insights about their recent selection and adaptation to environment. The presence of the set of genes and QTL traits harbored in the CNVRs could be possibly linked with the buffalo's natural adaptive history together to a recent selection for milk used as primary food source from this species.
Collapse
Affiliation(s)
- Maria G. Strillacci
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy
| | - Hossein Moradi-Shahrbabak
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167 Iran
| | - Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N5E3 Canada
| | - Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167 Iran
| | - Mahdi Mokhber
- Department of Animal Science, Faculty of Agriculture and Natural resources, Urmia University, 11Km Sero Road, P. O. Box: 165, Urmia, 57561-51818 Iran
| | - Anoar Jamai Masroure
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy
| |
Collapse
|
12
|
Cesarani A, Biffani S, Garcia A, Lourenco D, Bertolini G, Neglia G, Misztal I, Macciotta NPP. Genomic investigation of milk production in Italian buffalo. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2021.1902404] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Alberto Cesarani
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Stefano Biffani
- Consiglio Nazionale delle Ricerche (CNR), Istituto di biologia e biotecnologia agraria (IBBA), Milano, Italy
| | - Andre Garcia
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Giacomo Bertolini
- Associazione Nazionale Allevatori Specie Bufalina (ANASB), Caserta, Italy
| | - Gianluca Neglia
- Dipartimento di Medicina Veterinaria e Produzioni Animali, II University of Naples, Napoli, Italy
| | - Ignacy Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | | |
Collapse
|
13
|
Macciotta NPP, Colli L, Cesarani A, Ajmone-Marsan P, Low WY, Tearle R, Williams JL. The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events. Genet Sel Evol 2021; 53:20. [PMID: 33639853 PMCID: PMC7912491 DOI: 10.1186/s12711-021-00616-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/17/2021] [Indexed: 01/03/2023] Open
Abstract
Background Water buffalo is one of the most important livestock species in the world. Two types of water buffalo exist: river buffalo (Bubalus bubalis bubalis) and swamp buffalo (Bubalus bubalis carabanensis). The buffalo genome has been recently sequenced, and thus a new 90 K single nucleotide polymorphism (SNP) bead chip has been developed. In this study, we investigated the genomic population structure and the level of inbreeding of 185 river and 153 swamp buffaloes using runs of homozygosity (ROH). Analyses were carried out jointly and separately for the two buffalo types. Results The SNP bead chip detected in swamp about one-third of the SNPs identified in the river type. In total, 18,116 ROH were detected in the combined data set (17,784 SNPs), and 16,251 of these were unique. ROH were present in both buffalo types mostly detected (~ 59%) in swamp buffalo. The number of ROH per animal was larger and genomic inbreeding was higher in swamp than river buffalo. In the separated datasets (46,891 and 17,690 SNPs for river and swamp type, respectively), 19,760 and 10,581 ROH were found in river and swamp, respectively. The genes that map to the ROH islands are associated with the adaptation to the environment, fitness traits and reproduction. Conclusions Analysis of ROH features in the genome of the two water buffalo types allowed their genomic characterization and highlighted differences between buffalo types and between breeds. A large ROH island on chromosome 2 was shared between river and swamp buffaloes and contained genes that are involved in environmental adaptation and reproduction. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00616-3.
Collapse
Affiliation(s)
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti-DIANA, Università Cattolica del Sacro Cuore, Piacenza, Italia.,Centro di Ricerca sulla Biodiversità e sul DNA Antico-BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italia
| | - Alberto Cesarani
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italia. .,Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA.
| | - Paolo Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti-DIANA, Università Cattolica del Sacro Cuore, Piacenza, Italia.,Centro di Ricerca Nutrigenomica e Proteomica-PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italia
| | - Wai Y Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Rick Tearle
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - John L Williams
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti-DIANA, Università Cattolica del Sacro Cuore, Piacenza, Italia.,The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| |
Collapse
|
14
|
Rezaei Topraggaleh T, Numan Bucak M, Shahverdi M, Koohestani Y, Furkan Batur A, Rahimizadeh P, Ili P, Gul M, Ashrafzade AM, Kazem-Allilo A, Garip M, Shahverdi A. Functional and Flow Cytometric Analysis of Buffalo Cryopreserved Spermatozoa: Comparison of Different Breeds and Incubation Times. INTERNATIONAL JOURNAL OF FERTILITY & STERILITY 2021; 15:252-257. [PMID: 34913292 PMCID: PMC8530219 DOI: 10.22074/ijfs.2021.521116.1057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/15/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND The purpose of this research was to compare the functional parameters of frozen-thawed Iranian Azari buffalo spermatozoa with imported semen samples of Italian Mediterranean buffalo (IMB) after the thawing process and 4 hours of incubation. MATERIALS AND METHODS In this experimental study, a total of twenty-four ejaculates from four Iranian Azari buffalo bulls were collected. Semen samples were diluted in AndroMed extender at a concentration of 50×106 spermatozoa/ ml. The diluted samples were filled in 0.5 ml straws and were frozen in a programmable freezer. For imported semen samples, twenty-four samples of four IMB were used, which were diluted in AndroMed extender and frozen by the same procedure. Frozen-thawed sperm motion patterns, mitochondrial activity, membrane integrity, DNA integrity, reactive oxygen species (ROS), and apoptosis status were evaluated immediately after thawing and 4 hours of incubation. RESULTS Post-thawed sperm motility, progressive motility (PM), mitochondrial activity, membrane integrity were significantly higher in imported semen samples in compare with Iranian Azari buffalo. After 4 hours of incubation, sperm velocity patterns were superior in Iranian Azari semen samples. Moreover, the percentage of sperm cells with un-damaged DNA was higher in Iranian semen samples compared to imported samples at the time 0 of incubation. Following 4 hours of incubation, a significant increase in intracellular ROS level leads to reduced membrane integrity, mitochondrial activity, and DNA integrity in both buffalo breeds. At time 4, Iranian samples showed significantly lower apoptosis and higher dead spermatozoa compared to imported semen samples. CONCLUSION Our study showed that the post-thawed quality of Iranian Azari buffalo semen was comparable with imported samples after 4 hours of incubation. Further investigations are recommended to assess the in vitro and in vivo fertility rate of both buffalo breeds.
Collapse
Affiliation(s)
- Tohid Rezaei Topraggaleh
- Department of Anatomical Sciences, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Mustafa Numan Bucak
- Department of Reproduction and Artificial Insemination, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey
| | - Maryam Shahverdi
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Yegane Koohestani
- Department of Anatomical Sciences, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Ali Furkan Batur
- Department of Urology, Selcuk University School of Medicine, Konya, Turkey
| | - Pegah Rahimizadeh
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Pinar Ili
- Department of Medical Services and Techniques, Denizli Vocational School of Health Services, Pamukkale University, Denizli, Turkey
| | - Murat Gul
- Department of Urology, Selcuk University School of Medicine, Konya, Turkey
| | - Amir Mahdi Ashrafzade
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | | | - Mustafa Garip
- Department of Animal Science, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey
| | - Abdolhossein Shahverdi
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran,Reproductive Epidemiology Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran,P.O.Box: 16635-148Department of EmbryologyReproductive Biomedicine Research CenterRoyan Institute for Reproductive BiomedicineACECRTehranIran
| |
Collapse
|
15
|
Minervino AHH, Zava M, Vecchio D, Borghese A. Bubalus bubalis: A Short Story. Front Vet Sci 2020; 7:570413. [PMID: 33335917 PMCID: PMC7736047 DOI: 10.3389/fvets.2020.570413] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022] Open
Abstract
The domestic buffalo (Bubalus bubalis), also known as water buffalo or Asian buffalo to prevent confusion with the American bison (Bison bison), wrongly named buffalo in North America, comprises two subspecies: the river buffalo (B. bubalis bubalis) and the swamp buffalo (B. bubalis kerebau). The swamp buffalo has a consistent phenotype and is considered as one type, even if many breeds are recognized within it; conversely, the river buffalo subspecies has many breeds. We found limited information available regarding the worldwide distribution of buffaloes. The best estimate is that 208,098,759 buffalo head are distributed in 77 countries in five continents. In this review, we presented the basic aspects of the water buffalo and unraveled the buffalo path followed from the origin of the species to its current global distribution. We reviewed several data sources to provide a better estimate of the world buffalo count and distribution.
Collapse
Affiliation(s)
| | - Marco Zava
- Argentine Buffalo Breeders Association, Buenos Aires, Argentina
| | - Domenico Vecchio
- Italian National Reference Centre on Water Buffalo Farming and Productions Hygiene and Technologies (CReNBuf), Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Antonio Borghese
- International Buffalo Federation - IBF, FAO/ESCORENA Buffalo Network, Animal Production Research Institute, Rome, Italy
| |
Collapse
|
16
|
Nascimento AV, Cardoso DF, Santos DJA, Romero ARS, Scalez DCB, Borquis RRA, Neto FRA, Gondro C, Tonhati H. Inbreeding coefficients and runs of homozygosity islands in Brazilian water buffalo. J Dairy Sci 2020; 104:1917-1927. [PMID: 33272579 DOI: 10.3168/jds.2020-18397] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 09/10/2020] [Indexed: 01/03/2023]
Abstract
Characterization of autozygosity is relevant to monitor genetic diversity and manage inbreeding levels in breeding programs. Identification of autozygosity hotspots can unravel genomic regions targeted by selection for economically important traits and can help identify candidate genes for selection. In this study, we estimated the inbreeding levels of a Brazilian population of Murrah buffalo undergoing selection for milk production traits, particularly milk yield. We also studied the distribution of runs of homozygosity (ROH) islands and identified putative genes and quantitative trait loci (QTL) under selection. We genotyped 422 Murrah buffalo for 51,611 SNP; 350 of these had ROH longer than 10 Mb, indicating the occurrence of inbreeding in the last 5 generations. The mean length of the ROH per animal was 4.28 ± 1.85 Mb. Inbreeding coefficients were calculated from the genomic relationship matrix, the pedigree, and the ROH, with estimates varying between 0.242 and 0.035. Inbreeding estimates from the pedigree had a low correlation with the genomic estimates, and estimates from the genomic relationship matrix were much higher than those from the pedigree or the ROH. Signatures of selection were identified in 6 genomic regions, located on chromosomes 1, 2, 3, 5, 16, and 18, encompassing a total of 190 genes and 174 QTL. Many of the genes (e.g., APRT and ACSF3) and QTL identified are related to milk production traits, such as milk yield, milk fat yield and percentage, and milk protein yield and percentage. Other genes are associated with reproduction and immune response traits as well as morphological aspects of the buffalo species. Inbreeding levels in this population are still low but are increasing due to selection and should be managed to avoid future losses due to inbreeding depression. The proximity of genes linked to milk production traits with genes associated with reproduction and immune system traits suggests the need to include these latter genes in the breeding program to avoid negatively affecting them due to selection for production traits.
Collapse
Affiliation(s)
- A V Nascimento
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, 14884900, Brazil
| | - D F Cardoso
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, 14884900, Brazil
| | - D J A Santos
- Department of Animal Science, University of Maryland, College Park 20742
| | - A R S Romero
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, 14884900, Brazil
| | - D C B Scalez
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, 14884900, Brazil
| | - R R A Borquis
- College of Agricultural Sciences, Federal University of Grande Dourados (UFGD), Dourados, 79804970, Brazil
| | - F R A Neto
- Goiano Federal Institute, Campus Rio Verde, Rio Verde, 75909120, Brazil
| | - C Gondro
- Department of Animal Science, Michigan State University, East Lansing 48824
| | - H Tonhati
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, 14884900, Brazil.
| |
Collapse
|
17
|
Rafiepour M, Ebrahimie E, Vahidi MF, Salekdeh GH, Niazi A, Dadpasand M, Liang D, Si J, Ding X, Han J, Zhang Y, Qanbari S. Whole-Genome Resequencing Reveals Adaptation Prior to the Divergence of Buffalo Subspecies. Genome Biol Evol 2020; 13:5976760. [PMID: 33179728 DOI: 10.1093/gbe/evaa231] [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] [Accepted: 10/28/2020] [Indexed: 01/30/2023] Open
Abstract
The application of high-throughput genotyping or sequencing data helps us to understand the genomic response to natural and artificial selection. In this study, we scanned the genomes of five indigenous buffalo populations belong to three recognized breeds, adapted to different geographical and agro-ecological zones in Iran, to unravel the extent of genomic diversity and to localize genomic regions and genes underwent past selection. A total of 46 river buffalo whole genomes, from West and East Azerbaijan, Gilan, Mazandaran, and Khuzestan provinces, were resequenced. Our sequencing data reached to a coverage above 99% of the river buffalo reference genome and an average read depth around 9.2× per sample. We identified 20.55 million SNPs, including 63,097 missense, 707 stop-gain, and 159 stop-loss mutations that might have functional consequences. Genomic diversity analyses showed modest structuring among Iranian buffalo populations following frequent gene flow or admixture in the recent past. Evidence of positive selection was investigated using both differentiation (Fst) and fixation (Pi) metrics. Analysis of fixation revealed three genomic regions in all three breeds with aberrant polymorphism contents on BBU2, 20, and 21. Fixation signal on BBU2 overlapped with the OCA2-HERC2 genes, suggestive of adaptation to UV exposure through pigmentation mechanism. Further validation using resequencing data from other five bovine species as well as the Axiom Buffalo Genotyping Array 90K data of river and swamp buffaloes indicated that these fixation signals persisted across river and swamp buffaloes and extended to taurine cattle, implying an ancient evolutionary event occurred before the speciation of buffalo and taurine cattle. These results contributed to our understanding of major genetic switches that took place during the evolution of modern buffaloes.
Collapse
Affiliation(s)
- Mostafa Rafiepour
- Institute of Biotechnology, School of Agriculture, Shiraz University, Iran.,Department of System Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, Agricultural University, Beijing, China
| | - Esmaeil Ebrahimie
- Institute of Biotechnology, School of Agriculture, Shiraz University, Iran.,Genomics Research Platform, School of Life Sciences, Melbourne, Victoria, Australia.,School of Animal and Veterinary Sciences, The University of Adelaide, South Australia, Australia
| | - Mohammad Farhad Vahidi
- Department of Animal Biotechnology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Ghasem Hosseini Salekdeh
- Department of System Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Ali Niazi
- Institute of Biotechnology, School of Agriculture, Shiraz University, Iran
| | - Mohammad Dadpasand
- Department of Animal Science, School of Agriculture, Shiraz University, Iran
| | - Dong Liang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, Agricultural University, Beijing, China
| | - Jingfang Si
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, Agricultural University, Beijing, China
| | - Xiangdong Ding
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, Agricultural University, Beijing, China
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,International Livestock Research Institute (ILR), Nairobi, Kenya
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, Agricultural University, Beijing, China
| | - Saber Qanbari
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| |
Collapse
|
18
|
|
19
|
Fallahi MH, Shahrbabak HM, Shahrbabak MM, Arpanahi RA, Gholami S. Assessment of Genetic Diversity in Azerbaijani Buffalo Population in Iran Based on Runs of Homozygosity Stretches. RUSS J GENET+ 2020. [DOI: 10.1134/s102279542010004x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
20
|
Genome-Wide Detection of Selection Signatures in Duroc Revealed Candidate Genes Relating to Growth and Meat Quality. G3-GENES GENOMES GENETICS 2020; 10:3765-3773. [PMID: 32859686 PMCID: PMC7534417 DOI: 10.1534/g3.120.401628] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
With the development of high-throughput genotyping techniques, selection signatures in the genome of domestic pigs have been extensively interrogated in the last decade. The Duroc, a major commercial pig breed famous for its fast growth rate and high lean ratio, has not been extensively studied focusing on footprints of intensively artificial selection in their genomes by a lot of re-sequencing data. The goal of this study was to investigate genomic regions under artificial selection and their contribution to the unique phenotypic traits of the Duroc using whole-genome resequencing data from 97 pigs. Three complementary methods (di, CLR, and iHH12) were implemented for selection signature detection. In Total, 464 significant candidate regions were identified, which covered 46.4 Mb of the pig genome. Within the identified regions, 709 genes were annotated, including 600 candidate protein-coding genes (486 functionally annotated genes) and 109 lncRNA genes. Genes undergoing selective pressure were significantly enriched in the insulin resistance signaling pathway, which may partly explain the difference between the Duroc and other breeds in terms of growth rate. The selection signatures identified in the Duroc population demonstrated positive pressures on a set of important genes with potential functions that are involved in many biological processes. The results provide new insights into the genetic mechanisms of fast growth rate and high lean mass, and further facilitate follow-up studies on functional genes that contribute to the Duroc's excellent phenotypic traits.
Collapse
|
21
|
Sun T, Huang GY, Wang ZH, Teng SH, Cao YH, Sun JL, Hanif Q, Chen NB, Lei CZ, Liao YY. Selection signatures of Fuzhong Buffalo based on whole-genome sequences. BMC Genomics 2020; 21:674. [PMID: 32993537 PMCID: PMC7526191 DOI: 10.1186/s12864-020-07095-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Fuzhong buffalo, a native breed of Guangxi Zhuang Autonomous Region, is traditionally used as a draft animal to provide farm power in the rice cultivation. In addition, the Fuzhong buffalo also prepared for the bullfighting festival organized by the locals. The detection of the selective signatures in its genome can help in elucidating the selection mechanisms in its stamina and muscle development of a draft animal. RESULTS In this study, we analyzed 27 whole genomes of buffalo (including 15 Fuzhong buffalo genomes and 12 published buffalo genomes from Upper Yangtze region). The ZHp, ZFst, π-Ratio, and XP-EHH statistics were used to identify the candidate signatures of positive selection in Fuzhong buffalo. Our results detected a set of candidate genes involving in the pathways and GO terms associated with the response to exercise (e.g., ALDOA, STAT3, AKT2, EIF4E2, CACNA2D2, TCF4, CDH2), immunity (e.g., PTPN22, NKX2-3, PIK3R1, ITK, TMEM173), nervous system (e.g., PTPN21, ROBO1, HOMER1, MAGI2, SLC1A3, NRG3, SNAP47, CTNNA2, ADGRL3). In addition, we also identified several genes related to production and growth traits (e.g., PHLPP1, PRKN, MACF1, UCN3, RALGAPA1, PHKB, PKD1L). Our results depicted several pathways, GO terms, and candidate genes to be associated with response to exercise, immunity, nervous system, and growth traits. CONCLUSIONS The selective sweep analysis of the Fuzhong buffalo demonstrated positive selection pressure on potential target genes involved in behavior, immunity, and growth traits, etc. Our findings provided a valuable resource for future research on buffalo breeding and an insight into the mechanisms of artificial selection.
Collapse
Affiliation(s)
- Ting Sun
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning, 530001, China.,College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Guang-Yun Huang
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning, 530001, China
| | - Zi-Hao Wang
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning, 530001, China
| | - Shao-Hua Teng
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning, 530001, China
| | - Yan-Hong Cao
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning, 530001, China
| | - Jun-Li Sun
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning, 530001, China
| | - Quratulain Hanif
- Computational Biology Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Ning-Bo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chu-Zhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Yu-Ying Liao
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning, 530001, China.
| |
Collapse
|
22
|
Zhou F, Zhang Y, Teng X, Miao Y. Identification, molecular characteristics, and tissue differential expression of DGAT2 full-CDS cDNA sequence in Binglangjiang buffalo ( Bubalus bubalis). Arch Anim Breed 2020; 63:81-90. [PMID: 32232120 PMCID: PMC7096739 DOI: 10.5194/aab-63-81-2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/06/2020] [Indexed: 11/21/2022] Open
Abstract
It has been found that diacylglycerol acyltransferase-2 (DGAT2)
plays a crucial role in the synthesis of triglycerides (TGs) in some mammals,
but its role in buffalo lactation is unclear. In the present study, the DGAT2
full-CDS cDNA sequence of Binglangjiang buffalo was isolated, and the
physicochemical characteristics and structure of its encoding protein were
characterized. Furthermore, the differential expressions of this gene in 10
tissues of lactating and non-lactating buffalo were analyzed by real-time
quantitative PCR (RT-qPCR). The results showed that the coding region (CDS)
of this gene was 1086 bp in length, encoding a peptide composed of 361 amino
acid residues. The deduced amino acid sequence shared more than 98.6 %
identity with that of cattle, zebu, yak, and bison in the Bovidae family. Buffalo
DGAT2 protein is a slightly hydrophobic protein with a transmembrane region,
which functions in membrane of endoplasmic reticulum. Besides, this protein
belongs to the LPLAT_MGAT-like family and contains a conserved
domain of DAGAT that has a function in the synthesis of TGs. The
multi-tissue differential expression analysis demonstrated that
DGAT2 was expressed in the heart, liver, mammary gland, and muscle in both non-lactating and lactating buffalo. And its expression level in the heart,
liver, and mammary gland during lactation was significantly higher than that during non-lactation.
The results indicate that buffalo DGAT2 may be involved in
milk fat synthesis. This study can establish a foundation for further
elucidating mechanisms of the buffalo DGAT2 gene in milk fat synthesis.
Collapse
Affiliation(s)
- Fangting Zhou
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Yongyun Zhang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China.,Teaching Demonstration Center of the Basic Experiments of Agricultural Majors, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Xiaohong Teng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Yongwang Miao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| |
Collapse
|
23
|
Lu XR, Duan AQ, Li WQ, Abdel-Shafy H, Rushdi HE, Liang SS, Ma XY, Liang XW, Deng TX. Genome-wide analysis reveals genetic diversity, linkage disequilibrium, and selection for milk production traits in Chinese buffalo breeds. J Dairy Sci 2020; 103:4545-4556. [PMID: 32147265 DOI: 10.3168/jds.2019-17364] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/13/2020] [Indexed: 11/19/2022]
Abstract
The water buffalo is an important dual-purpose livestock that is widespread throughout central and southern China. However, there has been no characterization of the population genetics of Chinese buffalo. Using an Axiom buffalo genotyping array (Thermo Fisher Scientific, Wilmington, DE), we analyzed the genetic diversity, linkage disequilibrium pattern, and signature of selection in 176 Chinese buffaloes from 13 breeds. A total of 35,547 SNP passed quality control and were used for further analyses. Population genetic analysis revealed a clear separation between swamp and river types. Ten Chinese indigenous breeds were clustered into the swamp group, the Murrah and Nili-Ravi breeds were clustered into the river group, and the crossbred breed was closer to the river group. Genetic diversity analysis showed that the swamp group had a lower average expected heterozygosity. Linkage disequilibrium decay distance was much shorter in the swamp group compared with the river group, with an average square of correlation coefficient value of 0.2 of approximately 50 kb. Analysis of runs of homozygosity indicated extensive remote and recent inbreeding within swamp and river groups, respectively. Moreover, one genomic region under selection was detected between the river and swamp groups. Our findings contribute to our understanding of the characterization of population genetics in Chinese buffaloes, which in turn may be used in buffalo breeding programs.
Collapse
Affiliation(s)
- X R Lu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - A Q Duan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - W Q Li
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - H Abdel-Shafy
- Department of Animal Production, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - H E Rushdi
- Department of Animal Production, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - S S Liang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - X Y Ma
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - X W Liang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - T X Deng
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China.
| |
Collapse
|
24
|
Ghoreishifar SM, Moradi-Shahrbabak H, Fallahi MH, Jalil Sarghale A, Moradi-Shahrbabak M, Abdollahi-Arpanahi R, Khansefid M. Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis. BMC Genet 2020; 21:16. [PMID: 32041535 PMCID: PMC7011551 DOI: 10.1186/s12863-020-0824-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 02/04/2020] [Indexed: 01/06/2023] Open
Abstract
Background Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~ 65,000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results In this study, 9102 ROH were identified, with an average number of 21.2 ± 13.1 and 33.2 ± 15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8 ± 120.3 Mb), and in KHZ, 5.96% (149.1 ± 107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P ≤ 0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.
Collapse
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.
| | - Mohammad Hossein Fallahi
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Ali Jalil Sarghale
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Mohammad Moradi-Shahrbabak
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Rostam Abdollahi-Arpanahi
- Departments of Animal and Poultry Science, College of Aburaihan, University of Tehran, Pakdasht, 33916-53755, Iran
| | - Majid Khansefid
- AgriBio Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, 3083, Australia
| |
Collapse
|
25
|
Wang S, Zhang Y, Cheng Y, Lu G, Yang R, Geng H, Wang C, Li H, Feng T, Liu S, Hao L. Association of SNPs in GnRH gene with sperm quality traits of Chinese water buffalo. Reprod Domest Anim 2020; 55:384-392. [PMID: 31945221 DOI: 10.1111/rda.13634] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/03/2020] [Indexed: 12/11/2022]
Abstract
Hypothalamic gonadotropin-releasing hormone (GnRH) controls the activity of hypothalamic-pituitary-gonadal axis and plays a key role in the reproductive performance of animals. In this study, five single nucleotide polymorphisms (SNPs), namely g.991T > C, g.1041T > C g.3424T > C, g.3462C > A and g.3463Inde A, were detected in the GnRH gene of 162 water buffaloes by Sanger sequencing. Each SNP was associated with more than two sperm quality traits of ejaculate volume, sperm concentration, post-thaw sperm motility and sperm abnormality. g.3424T > C and g.3462C > A were related to these four traits and had a remarkable effect on ejaculate volume. The three other SNPs were related to sperm concentration, post-thaw sperm motility and sperm abnormality. Moreover, six haplotypes (H1: TCCAI, H2: CTTC-, H3: TCCCI, H4: CTTA-, H5: CCTA- and H6: CTCC-) composed of five SNPs comprising seven different combined genotypes were generated by linkage disequilibrium analysis. Statistics followed by one-way ANOVA indicated that water buffaloes with the haplotype combination H1H1 had the highest genotypic frequency, and those with the H4H4 haplotype combination had the highest ejaculate volume. The sperm concentration of those with haplotype combination H1H5 was higher than that of the other genotypes. In summary, our study showed a remarkable association between the SNPs of GnRH and sperm quality traits of Chinese water buffalo.
Collapse
Affiliation(s)
- Siyao Wang
- College of Animal Science, Jilin University, Changchun, China
| | - Yining Zhang
- Endocrinology and Genetics Department of Pediatrics, The First Hospital of Jilin University, Changchun, China
| | - Yunyun Cheng
- College of Animal Science, Jilin University, Changchun, China
| | - Guanhong Lu
- College of Animal Science, Jilin University, Changchun, China
| | - Rui Yang
- College of Animal Science, Jilin University, Changchun, China
| | - Hongwei Geng
- College of Animal Science, Jilin University, Changchun, China
| | - Chunli Wang
- College of Animal Science, Jilin University, Changchun, China
| | - Haoyang Li
- College of Animal Science, Jilin University, Changchun, China
| | - Tianqi Feng
- College of Animal Science, Jilin University, Changchun, China
| | - Songcai Liu
- College of Animal Science, Jilin University, Changchun, China.,Five-Star Animal Health Pharmaceutical Factory of Jilin Province, Changchun, China
| | - Linlin Hao
- College of Animal Science, Jilin University, Changchun, China
| |
Collapse
|
26
|
Gonzalez Guzman JL, Lázaro SF, do Nascimento AV, de Abreu Santos DJ, Cardoso DF, Becker Scalez DC, Galvão de Albuquerque L, Hurtado Lugo NA, Tonhati H. Genome-wide association study applied to type traits related to milk yield in water buffaloes (Bubalus bubalis). J Dairy Sci 2019; 103:1642-1650. [PMID: 31759604 DOI: 10.3168/jds.2019-16499] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 10/07/2019] [Indexed: 01/13/2023]
Abstract
This research aimed to estimate genetic parameters for milk yield and type traits [withers height (WH), croup height (CH), body length (BL), croup length (CL), iliac width (ILW), ischial width (ISW), and thoracic circumference] in Murrah buffaloes and to identify genomic regions related to type traits by applying a single-step genome-wide association study. Data used to estimate the genetic parameters consisted of 601 records of milk yield in the first lactation and the aforementioned type traits. For the single-step genome-wide association study, 322 samples genotyped with a 90K Axiom Buffalo Genotyping array (Thermo Fisher Scientific, Santa Clara, CA) were used. Bivariate analysis revealed that heritability for milk yield (kg) at 305 d was 0.31 ± 0.11, whereas it ranged from 0.22 ± 0.07 to 0.34 ± 0.09 for the studied conformation traits. Based on the percentages of genetic variance explained by windows of 10 markers, there were 16 genomic regions explaining more than 0.5% of the variance for WH, CH, BL, CL, ILW, ISW, and thoracic circumference. Between those regions, 4 were associated with more than 1 trait, suggesting pleiotropic roles for some genes of Bos taurus autosome (BTA) 12 on CL and WH, BTA13 on ISW and ILW, BTA23 on CH and BL, and BTA28 on ISW and BL. Most of these regions coincide with known quantitative trait loci for milk traits. Thus, further studies based on sequence data will help to validate the association of this region with type traits and likely identify the causal mutations.
Collapse
Affiliation(s)
- Jessica Lorena Gonzalez Guzman
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo 14884-900, Brazil
| | - Sirlene Fernandes Lázaro
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo 14884-900, Brazil
| | - André Vieira do Nascimento
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo 14884-900, Brazil
| | | | - Diercles Francisco Cardoso
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo 14884-900, Brazil
| | - Daiane Cristina Becker Scalez
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo 14884-900, Brazil
| | - Lúcia Galvão de Albuquerque
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo 14884-900, Brazil
| | - Naudin Alejandro Hurtado Lugo
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo 14884-900, Brazil
| | - Humberto Tonhati
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo 14884-900, Brazil.
| |
Collapse
|
27
|
Bioinformatics analysis of candidate genes for milk production traits in water buffalo (Bubalus bubalis). Trop Anim Health Prod 2019; 52:63-69. [DOI: 10.1007/s11250-019-01984-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/19/2019] [Indexed: 12/11/2022]
|
28
|
Mokhber M, Shahrbabak MM, Sadeghi M, Shahrbabak HM, Stella A, Nicolzzi E, Williams JL. Study of whole genome linkage disequilibrium patterns of Iranian water buffalo breeds using the Axiom Buffalo Genotyping 90K Array. PLoS One 2019; 14:e0217687. [PMID: 31150486 PMCID: PMC6544294 DOI: 10.1371/journal.pone.0217687] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 05/16/2019] [Indexed: 01/21/2023] Open
Abstract
Accuracy of genome-wide association studies, and the successful implementation of genomic selection depends on the level of linkage disequilibrium (LD) across the genome and also the persistence of LD phase between populations. In the present study LD between adjacent SNPs and LD decay between SNPs was calculated in three Iranian water buffalo populations. Persistence of LD phase was evaluated across these populations and effective population size (Ne) was estimated from corrected r2 information. A set of 404 individuals from three Iranian buffalo populations were genotyped with the Axiom Buffalo Genotyping 90K Array. Average r2 and |D'| between adjacent SNP pairs across all chromosomes was 0.27 and 0.66 for AZI, 0.29 and 0.68 for KHU, and 0.32 and 0.72 for MAZ. The LD between the SNPs decreased with increasing physical distance from 100Kb to 1Mb between markers, from 0.234 to 0.018 for AZI, 0.254 to 0.034 for KHU, and 0.297 to 0.119 for MAZ, respectively. These results indicate that a density of 90K SNP is sufficient for genomic analyses relying on long range LD (e.g. GWAS and genomic selection). The persistence of LD phase decreased with increasing marker distances across all the populations, but remained above 0.8 for AZI and KHU for marker distances up to 100Kb. For multi-breed genomic evaluation, the 90K SNP panel is suitable for AZI and KHU buffalo breeds. Estimated effective population sizes for AZI, KHU and MAZ were 477, 212 and 32, respectively, for recent generations. The estimated effective population sizes indicate that the MAZ is at risk and requires careful management.
Collapse
Affiliation(s)
- Mahdi Mokhber
- Department of Animal Science, Faculty of Agriculture, Urmia University, Urmia, Iran
- * E-mail:
| | - Mohammad Moradi Shahrbabak
- Department of Animal Science, Faculty of Agricultural Science and Engineering, University College of Agriculture and Natural Resources (UTCAN), University of Tehran, Karaj, Iran
| | - Mostafa Sadeghi
- Department of Animal Science, Faculty of Agricultural Science and Engineering, University College of Agriculture and Natural Resources (UTCAN), University of Tehran, Karaj, Iran
| | - Hossein Moradi Shahrbabak
- Department of Animal Science, Faculty of Agricultural Science and Engineering, University College of Agriculture and Natural Resources (UTCAN), University of Tehran, Karaj, Iran
| | | | | | - John L. Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, South Australia, Australia
| |
Collapse
|