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Saif-Ur-Rehman M, Hassan FU, Reecy J, Deng T. Whole-genome SNP markers reveal runs of homozygosity in indigenous cattle breeds of Pakistan. Anim Biotechnol 2023; 34:1384-1396. [PMID: 35044288 DOI: 10.1080/10495398.2022.2026369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The runs of homozygosity (ROH) were identified in 14 Pakistani cattle breeds (n = 105) by genotyping with the Illumina 50 K SNP BeadChip. These breeds were categorized into Dairy, Dual, and Draft breeds based on their utility and production performance. We identified a total of 10,936 ROHs which mainly consisted of a high number of shorter segments (1-4 Mb). Dairy group exhibited the highest level of inbreeding (FROH: 0.078 ± 0.028) while the lowest (FROH: 0.002 ± 0.008) was observed in Dual group. In 48 genomic regions identified with a high frequency of ROH, 207 genes were detected in the three breed groups. A substantially higher number of ROH islands detected in dairy breeds indicated the impact of the positive selection pressure over the years. Important candidate genes and QTL were detected in the ROH islands associated with economic traits like milk production, reproduction, meat, carcass, and health traits in dairy cattle.
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Affiliation(s)
| | - Faiz-Ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - James Reecy
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Tingxian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
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Xu J, Ruan Y, Sun J, Shi P, Huang J, Dai L, Xiao M, Xu H. Association Analysis of PRKAA2 and MSMB Polymorphisms and Growth Traits of Xiangsu Hybrid Pigs. Genes (Basel) 2022; 14:genes14010113. [PMID: 36672854 PMCID: PMC9858937 DOI: 10.3390/genes14010113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
In this study, Xiangsu hybrid pig growth traits were evaluated via PRKAA2 and MSMB as candidate genes. Sanger sequencing revealed three mutation sites in PRKAA2, namely, g.42101G>T, g.60146A>T, and g.61455G>A, and all these sites were intronic mutations. Moreover, six mutation sites were identified in MSMB: intronic g.4374G>T, exonic g.4564T>C, exonic g.6378G>A, exonic g.6386C>T, intronic g.8643G>A, and intronic g.8857A>G. Association analysis revealed that g.42101G>T, g.60146A>T, g.61455G>A, g.4374G>T, g.4564T>C, g.6378G>A, g.6386C>T, g.8643G>A, and g.8857A>G showed different relationship patterns among body weight, body length, body height, chest circumference, abdominal circumference, tube circumference, and chest depth. Real-time polymerase chain reaction results revealed that the expression of PRKAA2 was highest in the longissimus dorsi muscle, followed by that in the heart, kidney, liver, lung, and spleen. The expression of MSMB was highest in the spleen, followed by that in the liver, kidney, lung, heart, and longissimus dorsi muscle. These results suggest that PRKAA2 and MSMB can be used in marker-assisted selection to improve growth related traits in Xiangsu hybrid pigs, providing new candidate genes for Pig molecular breeding.
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Affiliation(s)
- Jiali Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Yong Ruan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Jinkui Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Pengfei Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Jiajin Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Lingang Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Meimei Xiao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Houqiang Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
- Correspondence:
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Effects of Genetic Variation of the Sorting Nexin 29 ( SNX29) Gene on Growth Traits of Xiangdong Black Goat. Animals (Basel) 2022; 12:ani12243461. [PMID: 36552381 PMCID: PMC9774745 DOI: 10.3390/ani12243461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/20/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
Previous studies have found that the copy number variation (CNV) and insertion/deletion (indels) located in the sorting nexin 29 (SNX29) gene, which is an important candidate gene related to meat production and quality, are associated with growth traits of African goats and Shaanbei white cashmere goats. However, the genetic effects of SNX29 genetic variation on growth traits of Xiangdong black (XDB) goat (a representative meat goat breed in China) are still unclear. The purpose of this study was to detect the mRNA expression level of SNX29 and to explore the genetic effects of CNV and indel within SNX29 on growth traits and gene expression in XDB goat. The SNX29 mRNA expression profile showed that the SNX29 was highly expressed in adipose tissues, indicating that the SNX29 gene could play a key role in subcutaneous adipose deposition of XDB goat. 17 bp indel (g.10559298-10559314), 21 bp indel (g.10918982-10919002) and CNV were detected in 516 individuals of XDB goat by PCR or qPCR. The association analysis of SNX29 CNV with growth traits in XDB goats showed that SNX29 CNV was significantly correlated with chest circumference and abdominal circumference (p < 0.01), and the normal type of SNX29 CNV goat individuals were more advantageous. For the mRNA expression of SNX29 gene, individuals with SNX29 copy number normal type had a higher trend than that of SNX29 gene with copy number gain type in longissimus dorsi muscle (p = 0.07), whereas individuals with SNX29 copy number gain type had a higher trend in abdominal adipose (p = 0.09). Overall, these results suggested that the SNX29 gene could play an important role in growth and development of XDB goats and could be used for marker-assisted selection (MAS) in XDB goats.
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Wang T, Shi X, Liu Z, Ren W, Wang X, Huang B, Kou X, Liang H, Wang C, Chai W. A Novel A > G Polymorphism in the Intron 1 of LCORL Gene Is Significantly Associated with Hide Weight and Body Size in Dezhou Donkey. Animals (Basel) 2022; 12:ani12192581. [PMID: 36230323 PMCID: PMC9559650 DOI: 10.3390/ani12192581] [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: 08/23/2022] [Revised: 09/12/2022] [Accepted: 09/26/2022] [Indexed: 11/22/2022] Open
Abstract
Several studies have shown the association between the ligand-dependent nuclear receptor compression-like protein (LCORL) gene and body size in horses, pigs and donkeys. Based on previous studies, the LCORL gene was hypothesized to be associated with growth traits and hide weight in Dezhou donkeys. In this study, we aimed to reveal the variation of the LCORL gene in the Dezhou donkey and explore whether the gene is associated with hide weight and body size. In this study, genetic polymorphisms in the LCORL gene of the Dezhou donkey were studied using targeted sequencing technology, and single nucleotide polymorphisms (SNPs) of the LCORL gene were analyzed for association with hide weight and body size in Dezhou donkeys. The results showed that there was an SNP locus situated in intron 1 of the LCORL gene. Association analysis revealed that individuals with the GG genotype had significantly higher body height, body length, chest circumference and hide weight than those with the AA genotype (p < 0.05). Therefore, the g.112558859 A > G locus can be used as a potential candidate marker affecting body size and hide weight. This study provides the foundation for breeding high-quality donkeys with high hide yield.
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KAT2B Gene Polymorphisms Are Associated with Body Measure Traits in Four Chinese Cattle Breeds. Animals (Basel) 2022; 12:ani12151954. [PMID: 35953943 PMCID: PMC9367347 DOI: 10.3390/ani12151954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Genetic improvement is one of the most important keys to overcoming the shortcomings of beef production. Identifying molecular markers related to growth characteristics and meat quality is significant in improving beef cattle breeds. Studies have shown that KAT2B, a transcriptional co-activator regulating the acetylation modification of histones, may be involved in the development and metabolism of muscle and adipose. However, there are no reports on investigating KAT2B genetic variation in Chinese native cattle. Firstly, this manuscript reports the initial bioinformatics analysis of KAT2B, finding that KAT2B protein is highly conserved among ruminants. The KAT2B gene expression profile in Qinchuan cattle was characterized, showing the spatiotemporal specificity of KAT2B gene expression in tissues such as adipose and liver during fetal and adult periods. Then, the investigation of KAT2B gene polymorphisms was carried out. Three SNPs of the KAT2B gene were identified and were found to be correlated with multiple body measurements in Fu, Qinchuan, Yak, and Chaidam cattle. These findings suggest that these three SNPs of KAT2B can serve as the molecular markers to select individuals for beef cattle breed improvement. Abstract Identifying molecular markers related to growth characteristics or meat quality is significant for improving beef cattle breeds. K(lysine) acetyltransferase 2B (KAT2B) is a transcriptional co-activator regulating the acetylation modification of histones, which may be involved in the development and metabolism of muscle and adipose. However, investigations of KAT2B genetic variations in Chinese native cattle are still limited. This study aimed to identify crucial single nucleotide polymorphisms (SNPs) influencing the body measurements of Chinese native cattle. Biological evolution and conservation analysis showed that KAT2B was highly conserved among the ruminants. By qPCR assay, KAT2B gene expression was found to be spatiotemporally specific in bovine tissues such as adipose and liver. By the RFLP-PCR method, three SNPs of KAT2B (g.T61908C, g.T62131C, and g.C73406T) were identified in 827 individuals of four Chinese cattle breeds, including Qinchuan (n = 658), Fu (n = 52), Yak (n = 48), and Chaidam (n = 69) cattle. Association analysis between these KAT2B polymorphisms and the body measurements of Chinese native cattle revealed significant observations. The genetic effects of g.T61908C, g.T62131C, and g.C73406T on the associated phenotypes were illustrated in each breed. In Qinchuan cattle, g.T62131C was significantly associated with better body height, chest width, hip width, and withers height, for which TC and/or TT were the advantageous genotype. In Fu cattle, TT genotype of g.T61908C was associated to better body length, while individuals with TT or CC of g.T62131C showed higher circumference of cannon bone than those with TC genotype. In Yak, individuals with TT genotype of g.C73406T had heavier body weight. In Chaidam cattle, TC genotype of g.C73406T was associated to superior body weight, while CC genotype of g.C73406T was associated to superior chest girth and circumference of cannon bone. These findings suggest that KAT2B gene polymorphisms can be used as the molecular markers for the early molecular marker-assisted selection in beef cattle breeding programs.
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Seo D, Lee DH, Jin S, Won JI, Lim D, Park M, Kim TH, Lee HK, Kim S, Choi I, Lee JH, Gondro C, Lee SH. Long-term artificial selection of Hanwoo (Korean) cattle left genetic signatures for the breeding traits and has altered the genomic structure. Sci Rep 2022; 12:6438. [PMID: 35440706 PMCID: PMC9018707 DOI: 10.1038/s41598-022-09425-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/01/2022] [Indexed: 11/09/2022] Open
Abstract
Indigenous Korean breeds such as Hanwoo (Korean) cattle have adapted to their local environment during the past 5000 years. In the 1980s, the National Genetic Improvement Program was established to develop a modern economic breed for beef production in Korea through artificial selection. This process is thought to have altered the genomic structure of breeding traits over time. The detection of genetic variants under selection could help to elucidate the genetic mechanism of artificial selection in modern cattle breeds. Indigenous Hanwoo cattle have adapted in response to local natural and artificial selection during a 40-year breeding program. We analyzed genomic changes in the selection signatures of an unselected population (USP; n = 362) and a selected population (KPN; n = 667) of Hanwoo cattle. Genomic changes due to long-term artificial selection were identified using a genome-wide integrated haplotype score (iHS) and a genome-wide association study (GWAS). Signatures of recent selection were detected as positive (piHS > 6) or negative (piHS < –6) iHS scores spanning more than 46 related genes in KPN cattle, but none in USP cattle. A region adjacent to the PLAG1 gene was found to be under strong selection for carcass weight. The GWAS results also showed a selection signature on BTA14, but none on BTA13. Pathway and quantitative trait locus analysis results identified candidate genes related to energy metabolism, feed efficiency, and reproductive traits in Hanwoo cattle. Strong selection significantly altered Hanwoo cattle genome structural properties such as linkage disequilibrium (LD) and haplotypes through causal mutation for target traits. Haplotype changes of genome structure which are changes of ancestral allele to derived alleles due to selection were clearly identified on BTA13 and BTA14; however, the structure of the LD block was not clearly observed except BTA14. Thus, selection based on EBVs would be working very well in Hanwoo cattle breeding program appears to have been highly successful.
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Affiliation(s)
- Dongwon Seo
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Doo Ho Lee
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Shil Jin
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang, South Korea
| | - Jung Il Won
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang, South Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Jeonju, Korea
| | - Mina Park
- Animal Breeding and Genetics Division, National Institute of Animal Science, RDA, Seonghwan, South Korea
| | - Tae Hun Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Jeonju, Korea
| | - Hak Kyo Lee
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, South Korea
| | - Sidong Kim
- Poultry Institute, National Institute of Animal Science, RDA, Pyeongchang, South Korea
| | - Inchul Choi
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Cedric Gondro
- Beacon Center for the Study of Evolution in Action and Department of Animal Science, Michigan State University, East Lansing, USA
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea.
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Chang T, Li M, An X, Bai F, Wang F, Yu J, Lei C, Dang R. Association analysis of IGF2 gene polymorphisms with growth traits of Dezhou donkey. Anim Biotechnol 2021:1-11. [PMID: 34935579 DOI: 10.1080/10495398.2021.2013860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
IGF2 is an insulin-like growth factor that plays an important role in the development of animal embryos. In order to determine whether IGF2 gene is associated with important economic characteristics of donkeys, we investigated the association between single nucleotide polymorphisms (SNPs) of IGF2 gene and body size traits of Chinese Dezhou donkeys and analyzed the expression level of IGF2 gene in different tissues of juvenile and adult Dezhou donkeys. In this study, two SNPs (g.281766 G > A and g.291322 C > T) were detected in IGF2 gene, both of which were in Hardy-Weinberg equilibrium (P > 0.05) and were moderately polymorphic (0.25 < PIC < 0.50). Association analysis showed that the two SNP loci were significantly correlated with body length and rump height (p < 0.05) of female Dezhou donkeys. Quantitative results showed that the expression of IGF2 gene was higher in heart, liver, spleen, lung, kidney, stomach and muscle tissues of juvenile donkeys than that of adult donkeys. Together, IGF2 can be considered as a candidate gene for growth and development of female Dezhou donkey, and its polymorphism can be used as a molecular marker for the Dezhou donkey breeding.
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Affiliation(s)
- Tingjin Chang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Mei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoya An
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Fuxia Bai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jie Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,National Engineering Research Center for Gelatin-Based Traditional Chinese Medicine, Dong-EE-Jiao Co. Ltd, Dong-E, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Wang G, Li M, Zhou J, An X, Bai F, Gao Y, Yu J, Li H, Lei C, Dang R. A novel A > G polymorphism in the intron 2 of TBX3 gene is significantly associated with body size in donkeys. Gene 2021; 785:145602. [PMID: 33766712 DOI: 10.1016/j.gene.2021.145602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 03/03/2021] [Accepted: 03/17/2021] [Indexed: 10/21/2022]
Abstract
T-box transcription factor 3 (TBX3) gene encodes a transcriptional suppressor and plays an important role in embryonic development, which belongs to the T-box family. TBX3 also has been found to be associated with body size traits in horse that is a relative of donkey. Therefore, TBX3 is considered as a promising candidate gene for economic traits of donkey. This study aimed to reveal the significant variation of TBX3 gene in Dezhou donkey and explores the relationship between genotypes and body sizes. In this study, an A > G mutation was found in the intron 2 of TBX3 gene by sequencing, and three genotypes (AA, GG and AG) were identified in 380 Dezhou donkey individuals with Tm-shift method. Association analysis illustrated that there were significant differences between AA and GG genotype in body length, body height, chest depth, chest circumference, body weight, hucklebone width and rump length. Our results demonstrated that the polymorphism of TBX3 is significantly associated with body size traits, which can serve as a marker to improve donkey production performance.
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Affiliation(s)
- Gang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Mei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Jun Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Xiaoya An
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Fuxia Bai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Yuan Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Jie Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China; National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co. Ltd., No. 78, E-jiao Street, Done-E Country, Shandong Province 252201, China.
| | - Haijing Li
- National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co. Ltd., No. 78, E-jiao Street, Done-E Country, Shandong Province 252201, China.
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
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Ghoreishifar SM, Eriksson S, Johansson AM, Khansefid M, Moghaddaszadeh-Ahrabi S, Parna N, Davoudi P, Javanmard A. Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds. Genet Sel Evol 2020; 52:52. [PMID: 32887549 PMCID: PMC7487911 DOI: 10.1186/s12711-020-00571-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/21/2020] [Indexed: 02/01/2023] Open
Abstract
Background Thousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation processes can help us design effective breeding objectives to preserve local breeds and improve commercial cattle. To identify regions under putative selection, GGP HD 150 K single nucleotide polymorphism (SNP) arrays were used to genotype 106 individuals representing five Swedish breeds i.e. native to different regions and covering areas with a subarctic cold climate in the north and mountainous west, to those with a continental climate in the more densely populated south regions. Results Five statistics were incorporated within a framework, known as de-correlated composite of multiple signals (DCMS) to detect signatures of selection. The obtained p-values were adjusted for multiple testing (FDR < 5%), and significant genomic regions were identified. Annotation of genes in these regions revealed various verified and novel candidate genes that are associated with a diverse range of traits, including e.g. high altitude adaptation and response to hypoxia (DCAF8, PPP1R12A, SLC16A3, UCP2, UCP3, TIGAR), cold acclimation (AQP3, AQP7, HSPB8), body size and stature (PLAG1, KCNA6, NDUFA9, AKAP3, C5H12orf4, RAD51AP1, FGF6, TIGAR, CCND2, CSMD3), resistance to disease and bacterial infection (CHI3L2, GBP6, PPFIBP1, REP15, CYP4F2, TIGD2, PYURF, SLC10A2, FCHSD2, ARHGEF17, RELT, PRDM2, KDM5B), reproduction (PPP1R12A, ZFP36L2, CSPP1), milk yield and components (NPC1L1, NUDCD3, ACSS1, FCHSD2), growth and feed efficiency (TMEM68, TGS1, LYN, XKR4, FOXA2, GBP2, GBP5, FGD6), and polled phenotype (URB1, EVA1C). Conclusions We identified genomic regions that may provide background knowledge to understand the mechanisms that are involved in economic traits and adaptation to cold climate in cattle. Incorporating p-values of different statistics in a single DCMS framework may help select and prioritize candidate genes for further analyses.
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Affiliation(s)
- Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden.
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Majid Khansefid
- AgriBio Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, 3083, Australia
| | - Sima Moghaddaszadeh-Ahrabi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Islamic Azad University, Tabriz Branch, Tabriz, Iran
| | - Nahid Parna
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, B2N5E3, Canada
| | - Arash Javanmard
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
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10
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Wu M, Li S, Zhang G, Fan Y, Gao Y, Huang Y, Lan X, Lei C, Ma Y, Dang R. Exploring insertions and deletions (indels) of MSRB3 gene and their association with growth traits in four Chinese indigenous cattle breeds. Arch Anim Breed 2019; 62:465-475. [PMID: 31807658 PMCID: PMC6852864 DOI: 10.5194/aab-62-465-2019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 06/21/2019] [Indexed: 12/16/2022] Open
Abstract
Methionine sulfoxide reductase B3 (MSRB3) is instrumental in ossification and fat deposition, which regulate the
growth and development of cattle directly. The purpose of this study was
aimed to explore insertions and deletions (indels) in MSRB3 gene and investigate
their association with growth traits in four indigenous cattle breeds (Luxi
cattle, Qinchuan cattle, Nanyang cattle, and Jiaxian Red cattle). Four indels
were identified by sequencing with DNA pool. Association analysis showed
that three of them were associated with growth traits (P<0.05). For
P1, the DD (deletion and deletion) genotype was significantly associated with body length of Nanyang
cattle; for P6, II (insertion and insertion) and/or DD genotypes were significantly associated with
enhanced growth traits of Qinchuan cattle; for P7, II genotype was
significantly associated with hucklebone width of Luxi cattle. Our results
demonstrated that the polymorphisms in bovine MSRB3 gene were significantly
associated with growth traits, which could be candidate loci for
marker-assisted selection (MAS) in cattle breeding.
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Affiliation(s)
- Mingli Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Shipeng Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Guoliang Zhang
- Branch of Animal Husbandry, Jilin Academy of Agricultural Science, Gongzhuling, Jilin, 136100, P. R. China
| | - Yingzhi Fan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Yuan Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, 464000, P. R. China.,School of Agriculture, Ningxia University, Yinchuan, Ningxia, 750021, P. R. China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
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11
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Gao Y, Huang B, Bai F, Wu F, Zhou Z, Lai Z, Li S, Qu K, Jia Y, Lei C, Dang R. Two Novel SNPs in RET Gene Are Associated with Cattle Body Measurement Traits. Animals (Basel) 2019; 9:E836. [PMID: 31640119 PMCID: PMC6826558 DOI: 10.3390/ani9100836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 12/19/2022] Open
Abstract
The rearrangement of the transfection (RET) gene, which mediates the functions of the ganglion in the gastrointestinal tract, plays an important role in the development of the gastrointestinal nervous system. Therefore, the RET gene is a potential factor influencing animal body measurement. The aim of this study was to reveal the significant genetic variations in the bovine RET gene and investigate the relationship between genotypes and body measurement in two Chinese cattle breeds (Qinchuan and Nanyang cattle). In this study, two SNPs (c.1407A>G and c.1425C>G) were detected in the exon 7 of RET gene by sequencing. For the SNP1 and SNP2, the GG genotype was significantly associated with body height, hip height, and chest circumference in Qinchuan cattle (p < 0.05). Individuals with an AG-CC genotype showed the lowest value of all body measurement in both breeds. Our results demonstrate that the polymorphisms in the bovine RET gene were significantly associated with body measurement, which could be used as DNA marker on the marker-assisted selection (MAS) and improve the performance of beef cattle.
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Affiliation(s)
- Yuan Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming 650212, China.
| | - Fuxia Bai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Fei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Zihui Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Zhenyu Lai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Shipeng Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Kaixing Qu
- Yunnan Academy of Grassland and Animal Science, Kunming 650212, China.
| | - Yutang Jia
- Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agriculture Science, Hefei 230001, China.
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
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12
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Ma YL, Wen YF, Cao XK, Cheng J, Huang YZ, Ma Y, Hu LY, Lei CZ, Qi XL, Cao H, Chen H. Copy number variation (CNV) in the IGF1R gene across four cattle breeds and its association with economic traits. Arch Anim Breed 2019; 62:171-179. [PMID: 31807627 PMCID: PMC6852844 DOI: 10.5194/aab-62-171-2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 03/27/2019] [Indexed: 01/21/2023] Open
Abstract
The insulin-like growth factor 1 receptor (IGF1R) plays a vital role in
immunomodulation and muscle and bone growth. The copy number variation (CNV) is
believed to the reason for many complex phenotypic variations. In
this paper, we statistically analyzed the copy number and the expression
profiling in different tissue types of the IGF1R gene using the
422 samples from four Chinese beef cattle breeds, and the mRNA of
IGF1R was widely expressed in nine tissue types of adult cattle (heart,
liver, kidney, muscle, fat, stomach, spleen, lung and testis). Results of CNV and growth traits indicated that the IGF1R CNV
was significantly associated with body weight and body height of Jinnan (JN)
cattle and was significantly associated with body height and hucklebone width
of Qinchuan (QC) cattle, making IGF1R CNV a promising molecular
marker to improve meat production in beef cattle breeding. Bioinformatics
predictions show that the CNV region is highly similar to the human genome,
and there are a large number of transcription factors, DNase I hypersensitive
sites, and high levels of histone acetylation, suggesting that this region may
play a role in transcriptional regulation, providing directions for further
study of the role of bovine CNV and economic traits.
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Affiliation(s)
- Yi-Lei Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, 712100, P. R. China
| | - Yi-Fan Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, 712100, P. R. China
| | - Xiu-Kai Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, 712100, P. R. China
| | - Jie Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, 712100, P. R. China
| | - Yong-Zhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, 712100, P. R. China
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan, 464000, P. R. China
| | - Lin-Yong Hu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810001, P. R. China
| | - Chu-Zhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, 712100, P. R. China
| | - Xing-Lei Qi
- Bureau of Animal Husbandry of Biyang County, Biyang, Henan, 463700, P. R. China
| | - Hui Cao
- Shaanxi Kingbull Animal Husbandry Co. Ltd., Yangling, Shaanxi, 712100, P. R. China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, 712100, P. R. China
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13
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Wen YF, Zheng L, Niu H, Zhang GL, Zhang GM, Ma YL, Tian YR, Liu YR, Yang P, Yang DY, Lei CZ, Dang RH, Qi XL, Chen H, Huang BZ, Huang YZ. Exploring genotype-phenotype relationships of the CRABP2 gene on growth traits in beef cattle. Anim Biotechnol 2018; 31:42-51. [PMID: 30570383 DOI: 10.1080/10495398.2018.1531015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Cellular retinoic acid binding protein 2 (CRABP2) is essential to myoblast differentiation. However, there was no report about the function of CRABP2 gene in cattle. This study explored the association of CRABP2 gene polymorphisms with growth traits in cattle breeds by several methods, such as DNA sequencing, PCR, PCR-RFLP and forced PCR-RFLP. Two sequence variants were determined. There were 621 individuals in six cattle breeds from China for the experiment, and three breeds were used to test validation of polymorphisms and extent of linkage disequilibrium (LD). The results showed that both SNPs (SNP1, g.2458 G > T, SNP2, g.3878 G > A) were in intron1. Two SNPs were in low linkage disequilibrium. Association analysis suggested that SNP1 had the significant difference on growth traits with body height, height at hip cross and body slanting length (P < .05), while SNP2 showed a significant difference in growth traits with body height, height at hip cross and body slanting length(P < .05). The results of this investigation displayed that the CRABP2 gene is an available candidate gene and may be used for breed selection and conservation.
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Affiliation(s)
- Yi-Fan Wen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Li Zheng
- Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, People's Republic of China
| | - Hui Niu
- Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, People's Republic of China
| | - Guo-Liang Zhang
- Branch of Animal Science, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin, People's Republic of China
| | - Gui-Min Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Yi-Lei Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Yi-Ran Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Yan-Rong Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Peng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Di-Yi Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Chu-Zhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Rui-Hua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Xing-Lei Qi
- Bureau of Animal Husbandry of Biyang County, Biyang, Henan, People's Republic of China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Bi-Zhi Huang
- Yunnan Academy of grassland animal science, Kunming, People's Republic of China
| | - Yong-Zhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
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14
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Copy number variation of bovine MAPK10 modulates the transcriptional activity and affects growth traits. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.09.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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15
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Liu M, Liu M, Li B, Zhou Y, Huang Y, Lan X, Qu W, Qi X, Bai Y, Chen H. Polymorphisms of FLII implicate gene expressions and growth traits in Chinese cattle. Mol Cell Probes 2016; 30:266-272. [DOI: 10.1016/j.mcp.2016.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/30/2016] [Accepted: 07/20/2016] [Indexed: 01/23/2023]
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16
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Association study and expression analysis of MTNR1A as a candidate gene for body measurement and meat quality traits in Qinchuan cattle. Gene 2015; 570:199-204. [DOI: 10.1016/j.gene.2015.06.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/29/2015] [Accepted: 06/05/2015] [Indexed: 11/23/2022]
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