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Wang J, Suo J, Yang R, Zhang CL, Li X, Han Z, Zhou W, Liu S, Gao Q. Genetic diversity, population structure, and selective signature of sheep in the northeastern Tarim Basin. Front Genet 2023; 14:1281601. [PMID: 38028584 PMCID: PMC10666172 DOI: 10.3389/fgene.2023.1281601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Local sheep in the northeastern Tarim Basin can adapt to dry and low-rainfall regional environments. In this study, three local sheep breeds in the northeastern Tarim Basin, LOP (LOP) sheep, Bayinbuluke (BYK) sheep, and Kunlun (KUN, also known as the Qiemo sheep) sheep, and three introduced sheep breeds, Suffolk (SUF) sheep, Dorset (APD) sheep, and Texel (TEX) sheep, were analyzed for genetic diversity, population structure, and selective signature using the Illumina OvineSNP50K BeadChip. We found that LOP, BYK, and KUN had lower observed heterozygosity and expected heterozygosity than TEX, SUF, and ADP, which were differentiated based on geographic distribution. We performed fixation index (FST) analysis on three local sheep breeds in the northeastern Tarim Basin (LOP, BYK, and KUN) and introduced sheep breeds (TEX, SUF, and ADP) to measure genetic differentiation. Nucleotide diversity (PI) analysis was performed on single-nucleotide polymorphism (SNP) data of LOP, BYK, and KUN. A total of 493 candidate genes were obtained by taking the intersection at a threshold of 5%. Among them, SMAD2, ESR2, and HAS2 were related to reproductive traits. PCDH15, TLE4, and TFAP2B were related to growth traits. SOD1, TSHR, and DNAJB5 were related to desert environmental adaptation. Analyzing the genetic patterns of local sheep in the northeastern Tarim Basin can protect the germplasm resources of local sheep and promote the development and utilization of sheep genetic resources.
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Affiliation(s)
- Jieru Wang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Co-Funded by Xinjiang Production and Construction Corps and The Ministry of Science and Technology, College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Jiajia Suo
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Co-Funded by Xinjiang Production and Construction Corps and The Ministry of Science and Technology, College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
| | - Ruizhi Yang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Co-Funded by Xinjiang Production and Construction Corps and The Ministry of Science and Technology, College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
| | - Cheng-Long Zhang
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Xiaopeng Li
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Zhipeng Han
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Wen Zhou
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Shudong Liu
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Qinghua Gao
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Co-Funded by Xinjiang Production and Construction Corps and The Ministry of Science and Technology, College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
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More M, Veli E, Cruz A, Gutiérrez JP, Gutiérrez G, Ponce de León FA. Genome-Wide Association Study of Fiber Diameter in Alpacas. Animals (Basel) 2023; 13:3316. [PMID: 37958071 PMCID: PMC10648856 DOI: 10.3390/ani13213316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/13/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
The aim of this study was the identification of candidate genomic regions associated with fiber diameter in alpacas. DNA samples were collected from 1011 female Huacaya alpacas from two geographical Andean regions in Peru (Pasco and Puno), and three alpaca farms within each region. The samples were genotyped using an Affymetrix Custom Alpaca genotyping array containing 76,508 SNPs. After the quality controls, 960 samples and 51,742 SNPs were retained. Three association study methodologies were performed. The GWAS based on a linear model allowed us to identify 11 and 35 SNPs (-log10(p-values) > 4) using information on all alpacas and alpacas with extreme values of fiber diameter, respectively. The haplotype and marker analysis method allowed us to identify nine haplotypes with standardized haplotype heritability higher than six standard deviations. The selection signatures based on cross-population extended haplotype homozygosity (XP-EHH) allowed us to identify 180 SNPs with XP-EHH values greater than |3|. Four candidate regions with adjacent SNPs identified via two association methods of analysis are located on VPA6, VPA9, VPA29 and one chromosomally unassigned scaffold. This study represents the first analysis of alpaca whole genome association with fiber diameter, using a recently assembled alpaca SNP microarray.
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Affiliation(s)
- Manuel More
- Facultad de Agronomía y Zootecnia, Universidad Nacional de San Antonio Abad del Cusco, Cusco 08006, Peru;
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru; (A.C.); (F.A.P.d.L.)
| | - Eudosio Veli
- Centro Experimental La Molina, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru;
| | - Alan Cruz
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru; (A.C.); (F.A.P.d.L.)
- Estación Científica de Pacomarca, Inca Tops S.A., Arequipa 04007, Peru
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain;
| | - Gustavo Gutiérrez
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru; (A.C.); (F.A.P.d.L.)
- Instituto de Investigación de Bioquímica y Biología Molecular, Universidad Nacional Agraria La Molina, Lima 15024, Peru
| | - F. Abel Ponce de León
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru; (A.C.); (F.A.P.d.L.)
- Department of Animal Science, University of Minnesota, Minneapolis, MN 55108, USA
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Easa AA, Selionova M, Aibazov M, Mamontova T, Sermyagin A, Belous A, Abdelmanova A, Deniskova T, Zinovieva N. Identification of Genomic Regions and Candidate Genes Associated with Body Weight and Body Conformation Traits in Karachai Goats. Genes (Basel) 2022; 13:genes13101773. [PMID: 36292658 PMCID: PMC9601913 DOI: 10.3390/genes13101773] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/23/2022] [Accepted: 09/28/2022] [Indexed: 11/04/2022] Open
Abstract
The objective of this study was to identify the SNPs and candidate genes related to body weight and seven body conformation traits at the age of 8 months in the Russian aboriginal Karachai goats (n = 269) by conducting genome-wide association studies (GWAS), using genotypes generated by Goat SNP BeadChip (Illumina Inc., USA). We identified 241 SNPs, which were significantly associated with the studied traits, including 47 genome-wide SNPs (p < 10−5) and 194 suggestive SNPs (p < 10−4), distributed among all goat autosomes except for autosome 23. Fifty-six SNPs were common for two and more traits (1 SNP for six traits, 2 SNPs for five traits, 12 SNPs for four traits, 20 SNPs for three traits, and 21 SNPs for two traits), while 185 SNPs were associated with single traits. Structural annotation within a window of 0.4 Mb (±0.2 Mb from causal SNPs) revealed 238 candidate genes. The largest number of candidate genes was identified at Chr13 (33 candidate genes for the five traits). The genes identified in our study were previously reported to be associated with growth-related traits in different livestock species. The most significant genes for body weight were CRADD, HMGA2, MSRB3, MAX, HACL1 and RAB15, which regulate growth processes, body sizes, fat deposition, and average daily gains. Among them, the HMGA2 gene is a well-known candidate for prenatal and early postnatal development, and the MSRB3 gene is proposed as a candidate gene affecting the growth performance. APOB, PTPRK, BCAR1, AOAH and ASAH1 genes associated with withers height, rump height and body length, are involved in various metabolic processes, including fatty acid metabolism and lipopolysaccharide catabolism. In addition, WDR70, ZBTB24, ADIPOQ, and SORCS3 genes were linked to chest width. KCNG4 was associated with rump height, body length and chest perimeter. The identified candidate genes can be proposed as molecular markers for growth trait selection for genetic improvement in Karachai goats.
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Affiliation(s)
- Ahmed A. Easa
- Timiryazev Agricultural Academy, Russian State Agrarian University-Moscow, Timiryazevskaya Street, 41, Moscow 127550, Russia
- Department of Animal and Poultry Production, Faculty of Agriculture, Damanhour University, Damanhour 22511, Egypt
- Correspondence: (A.A.E.); (N.Z.)
| | - Marina Selionova
- Timiryazev Agricultural Academy, Russian State Agrarian University-Moscow, Timiryazevskaya Street, 41, Moscow 127550, Russia
| | - Magomet Aibazov
- Timiryazev Agricultural Academy, Russian State Agrarian University-Moscow, Timiryazevskaya Street, 41, Moscow 127550, Russia
| | - Tatiana Mamontova
- Timiryazev Agricultural Academy, Russian State Agrarian University-Moscow, Timiryazevskaya Street, 41, Moscow 127550, Russia
| | - Alexander Sermyagin
- L K Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, Podolsk Municipal District, Moscow 142132, Russia
| | - Anna Belous
- L K Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, Podolsk Municipal District, Moscow 142132, Russia
| | - Alexandra Abdelmanova
- L K Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, Podolsk Municipal District, Moscow 142132, Russia
| | - Tatiana Deniskova
- L K Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, Podolsk Municipal District, Moscow 142132, Russia
| | - Natalia Zinovieva
- L K Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, Podolsk Municipal District, Moscow 142132, Russia
- Correspondence: (A.A.E.); (N.Z.)
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Mohammadi H, Farahani AHK, Moradi MH, Mastrangelo S, Di Gerlando R, Sardina MT, Scatassa ML, Portolano B, Tolone M. Weighted Single-Step Genome-Wide Association Study Uncovers Known and Novel Candidate Genomic Regions for Milk Production Traits and Somatic Cell Score in Valle del Belice Dairy Sheep. Animals (Basel) 2022; 12:ani12091155. [PMID: 35565582 PMCID: PMC9104502 DOI: 10.3390/ani12091155] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/05/2022] [Accepted: 04/25/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Milk production is the most economically crucial dairy sheep trait and constitutes the major genetic enhancement purpose via selective breeding. Also, mastitis is one of the most frequently encountered diseases, having a significant impact on animal welfare, milk yield, and quality. The aim of this study was to identify genomic region(s) associated with the milk production traits and somatic cell score (SCS) in Valle del Belice sheep using single-step genome-wide association (ssGWA) and genotyping data from medium density SNP panels. We identified several genomic regions (OAR1, OAR2, OAR3, OAR4, OAR6, OAR9, and OAR25) and candidate genes implicated in milk production traits and SCS. Our findings offer new insights into the genetic basis of milk production traits and SCS in dairy sheep. Abstract The objective of this study was to uncover genomic regions explaining a substantial proportion of the genetic variance in milk production traits and somatic cell score in a Valle del Belice dairy sheep. Weighted single-step genome-wide association studies (WssGWAS) were conducted for milk yield (MY), fat yield (FY), fat percentage (FAT%), protein yield (PY), protein percentage (PROT%), and somatic cell score (SCS). In addition, our aim was also to identify candidate genes within genomic regions that explained the highest proportions of genetic variance. Overall, the full pedigree consists of 5534 animals, of which 1813 ewes had milk data (15,008 records), and 481 ewes were genotyped with a 50 K single nucleotide polymorphism (SNP) array. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. We considered the top 10 genomic regions in terms of their explained genomic variants as candidate window regions for each trait. The results showed that top ranked genomic windows (1 Mb windows) explained 3.49, 4.04, 5.37, 4.09, 3.80, and 5.24% of the genetic variances for MY, FY, FAT%, PY, PROT%, and total SCS, respectively. Among the candidate genes found, some known associations were confirmed, while several novel candidate genes were also revealed, including PPARGC1A, LYPLA1, LEP, and MYH9 for MY; CACNA1C, PTPN1, ROBO2, CHRM3, and ERCC6 for FY and FAT%; PCSK5 and ANGPT1 for PY and PROT%; and IL26, IFNG, PEX26, NEGR1, LAP3, and MED28 for SCS. These findings increase our understanding of the genetic architecture of six examined traits and provide guidance for subsequent genetic improvement through genome selection.
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Affiliation(s)
- Hossein Mohammadi
- Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak 38156-8-8349, Iran; (A.H.K.F.); (M.H.M.)
- Correspondence: ; Tel.: +98-9127584572
| | - Amir Hossein Khaltabadi Farahani
- Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak 38156-8-8349, Iran; (A.H.K.F.); (M.H.M.)
| | - Mohammad Hossein Moradi
- Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak 38156-8-8349, Iran; (A.H.K.F.); (M.H.M.)
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy; (S.M.); (R.D.G.); (M.T.S.); (B.P.); (M.T.)
| | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy; (S.M.); (R.D.G.); (M.T.S.); (B.P.); (M.T.)
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy; (S.M.); (R.D.G.); (M.T.S.); (B.P.); (M.T.)
| | - Maria Luisa Scatassa
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, 90129 Palermo, Italy;
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy; (S.M.); (R.D.G.); (M.T.S.); (B.P.); (M.T.)
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy; (S.M.); (R.D.G.); (M.T.S.); (B.P.); (M.T.)
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The variation in promoter sequences of the Akt3 gene between cow and buffalo revealed different responses against mastitis. J Genet Eng Biotechnol 2021; 19:164. [PMID: 34677734 PMCID: PMC8536807 DOI: 10.1186/s43141-021-00258-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 09/28/2021] [Indexed: 11/23/2022]
Abstract
Background Serine/threonine kinase 3 (AKT3) is a protein-coding gene that is associated with several cattle immune diseases including different tumors and cancers. The objective of this study was to investigate the differences in structures and functions of AKT3 of cow and buffalo cattle. Methods The sequence differences of gene-coding sequence (CDS) and core promoter region of AKT3 in cow and buffalo were analyzed by using bioinformatics tools and PCR sequencing. Also, the functional analysis of promoter regulating gene expression by RT-PCR was performed using 500 Holstein cows and buffalos. And, evaluation of AKT3 inflammatory response to the lipopolysaccharide (LPS)-induced mastitis was performed between both species. Results The results revealed the variation in 6 exons out of 13 exons of the two species of CDS. Also, 4 different regions in 3-kb promoters of the AKT3 gene were significantly different between cow and buffalo species, in which cow’s AKT3 promoter sequence region was started from − 371 to − 1247, while in buffalo, the sequence was started from − 371 to − 969 of the promoter crucial region. Thus, the promoter was overexpressed in cows compared to buffaloes. As a result, significant differences (P < 0.05) between the two species in the AKT3 gene expression level related to the LPS stimulation in their mammary epithelial cell line. Conclusions This study emphasized the great importance of the structural differences of AKT3 between the animal species on their different responses against immune diseases like mastitis.
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