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Wang T, Ma X, Zheng Q, Ma C, Zhang Z, Pan H, Guo X, Wu X, Chu M, Liang C, Yan P. A comprehensive study on the longissius dorsi muscle of Ashdan yaks under different feeding regimes based on transcriptomic and metabolomic analyses. Anim Biotechnol 2024; 35:2294785. [PMID: 38193799 DOI: 10.1080/10495398.2023.2294785] [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: 01/10/2024]
Abstract
Yak is an important dominant livestock species at high altitude, and the growth performance of yak has obvious differences under different feeding methods. This experiment was conducted to compare the effects of different feeding practices on growth performance and meat quality of yaks through combined transcriptomic and metabolomic analyses. In terms of yak growth performance, compared with traditional grazing, in-house feeding can significantly improve the average daily weight gain, carcass weight and net meat weight of yaks; in terms of yak meat quality, in-house feeding can effectively improve the quality of yak meat. A combined transcriptomic and metabolomic analysis revealed 31 co-enriched pathways, among which arginine metabolism, proline metabolism and glycerophospholipid metabolism may be involved in the development of the longissimus dorsi muscle of yak and the regulation of meat quality-related traits. The experimental results increased our understanding of yak meat quality and provided data materials for subsequent deep excavation of the mechanism of yak meat quality.
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Affiliation(s)
- Tong Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Life science and Engineering College, Northwest Minzu University, Lanzhou, China
| | - Xiaoming Ma
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Qingbo Zheng
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Chaofan Ma
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Life science and Engineering College, Northwest Minzu University, Lanzhou, China
| | - Zhilong Zhang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Heping Pan
- Life science and Engineering College, Northwest Minzu University, Lanzhou, China
| | - Xian Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xiaoyun Wu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Min Chu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Chunnian Liang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
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Yang L, Lin X, Chen Y, Peng P, Lan Q, Zhao H, Wei H, Yin Y, Liu M. Association analysis of the sorting nexin 29 (SNX29) gene copy number variations with growth traits in Diannan small-ear (DSE) pigs. Anim Biotechnol 2024; 35:2309956. [PMID: 38315463 DOI: 10.1080/10495398.2024.2309956] [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: 02/07/2024]
Abstract
SNX29 is a potential functional gene associated with meat production traits. Previous studies have shown that SNX29 copy number variation (CNV) could be implicated with phenotype in goats. However, in Diannan small-ear (DSE) pigs, the genetic impact of SNX29 CNV on growth traits remains unclear. Therefore, this study investigated the associations between SNX29 CNVs (CNV10810 and CNV10811) and growth traits in 415 DSE pigs. The results revealed that the CNV10810 mutation was significantly associated with backfat thickness in DSE pigs at 12 and 15 months old (P < 0.05), while the CNV10811 mutation had significant effects on various growth traits at 6 and 12 months old, particularly for body weight, body height, back height and backfat thickness (P < 0.05 or P < 0.001). In conclusion, our results confirm that SNX29 CNV plays a role in regulating growth and development in pigs, thus suggesting its potential application for pig breeding programmes.
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Affiliation(s)
- Long Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xiaoding Lin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Yuhan Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Peiya Peng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Qun Lan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Heng Zhao
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, China
| | - Hongjiang Wei
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, China
| | - Yulong Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Mei Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
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Zhang Y, Wei Z, Zhang M, Wang S, Gao T, Huang H, Zhang T, Cai H, Liu X, Fu T, Liang D. Population Structure and Selection Signal Analysis of Nanyang Cattle Based on Whole-Genome Sequencing Data. Genes (Basel) 2024; 15:351. [PMID: 38540410 PMCID: PMC10970060 DOI: 10.3390/genes15030351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/07/2024] [Accepted: 03/09/2024] [Indexed: 06/14/2024] Open
Abstract
With a rich breeding history, Nanyang cattle (NY cattle) have undergone extensive natural and artificial selection, resulting in distinctive traits such as high fertility, excellent meat quality, and disease resistance. This makes them an ideal model for studying the mechanisms of environmental adaptability. To assess the population structure and genetic diversity of NY cattle, we performed whole-genome resequencing on 30 individuals. These data were then compared with published whole-genome resequencing data from 432 cattle globally. The results indicate that the genetic structure of NY cattle is significantly different from European commercial breeds and is more similar to North-Central Chinese breeds. Furthermore, among all breeds, NY cattle exhibit the highest genetic diversity and the lowest population inbreeding levels. A genome-wide selection signal analysis of NY cattle and European commercial breeds using Fst, θπ-ratio, and θπ methods revealed significant selection signals in genes associated with reproductive performance and immunity. Our functional annotation analysis suggests that these genes may be responsible for reproduction (MAP2K2, PGR, and GSE1), immune response (NCOA2, HSF1, and PAX5), and olfaction (TAS1R3). We provide a comprehensive overview of sequence variations in the NY cattle genome, revealing insights into the population structure and genetic diversity of NY cattle. Additionally, we identify candidate genes associated with important economic traits, offering valuable references for future conservation and breeding efforts of NY cattle.
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Affiliation(s)
- Yan Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Z.W.); (M.Z.); (S.W.); (T.G.); (H.H.); (T.Z.); (H.C.); (T.F.)
| | - Zhitong Wei
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Z.W.); (M.Z.); (S.W.); (T.G.); (H.H.); (T.Z.); (H.C.); (T.F.)
| | - Man Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Z.W.); (M.Z.); (S.W.); (T.G.); (H.H.); (T.Z.); (H.C.); (T.F.)
| | - Shiwei Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Z.W.); (M.Z.); (S.W.); (T.G.); (H.H.); (T.Z.); (H.C.); (T.F.)
| | - Tengyun Gao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Z.W.); (M.Z.); (S.W.); (T.G.); (H.H.); (T.Z.); (H.C.); (T.F.)
| | - Hetian Huang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Z.W.); (M.Z.); (S.W.); (T.G.); (H.H.); (T.Z.); (H.C.); (T.F.)
| | - Tianliu Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Z.W.); (M.Z.); (S.W.); (T.G.); (H.H.); (T.Z.); (H.C.); (T.F.)
| | - Hanfang Cai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Z.W.); (M.Z.); (S.W.); (T.G.); (H.H.); (T.Z.); (H.C.); (T.F.)
| | - Xian Liu
- Henan Animal Husbandry Station, Zhengzhou 450008, China;
| | - Tong Fu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Z.W.); (M.Z.); (S.W.); (T.G.); (H.H.); (T.Z.); (H.C.); (T.F.)
| | - Dong Liang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Z.W.); (M.Z.); (S.W.); (T.G.); (H.H.); (T.Z.); (H.C.); (T.F.)
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Sood V, Rodas-González A, Valente TS, Virtuoso MCS, Li C, Lam S, López-Campos Ó, Segura J, Basarab J, Juárez M. Genome-wide association study for primal cut lean traits in Canadian beef cattle. Meat Sci 2023; 204:109274. [PMID: 37437385 DOI: 10.1016/j.meatsci.2023.109274] [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: 02/28/2023] [Revised: 06/07/2023] [Accepted: 07/02/2023] [Indexed: 07/14/2023]
Abstract
This study identified genomic variants and underlying candidate genes related to the whole carcass and individual primal cut lean content in Canadian commercial crossbred beef cattle. Genotyping information of 1035 crossbred beef cattle were available alongside estimated and actual carcass lean meat yield and individual primal cut lean content in all carcasses. Significant fixed effects and covariates were identified and included in the animal model. Genome-wide association analysis were implemented using the weighted single-step genomic best linear unbiased prediction (WssGBLUP). A number of candidate genes identified linked to lean tissue production were unrelated to estimated lean meat yield and were specific to the actual lean traits. Among these, 41 genes were common for actual lean traits, on specific regions of BTA4, BTA13 and BTA25 indicating potential involvement in lean mass synthesis. Therefore, the results suggested the inclusion of primal cut lean traits as a selection objective in breeding programs with consideration of further functional studies of the identified genes could help in optimizing lean yield for maximal carcass value.
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Affiliation(s)
- Vipasha Sood
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada; Department of Food and Human Nutritional Science, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Argenis Rodas-González
- Department of Animal Science, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Tiago S Valente
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Marcos Claudio S Virtuoso
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Changxi Li
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada; Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Stephanie Lam
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Óscar López-Campos
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Jose Segura
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - John Basarab
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Manuel Juárez
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada.
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Qi A, Yan J, Yang Y, Tang J, Ru W, Jiang X, Lei C, Sun X, Chen H. SNP within the bovine ASB-3 gene and their association analysis with stature traits in three Chinese cattle breeds. Gene 2022; 838:146700. [PMID: 35772652 DOI: 10.1016/j.gene.2022.146700] [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: 08/11/2021] [Revised: 06/11/2022] [Accepted: 06/24/2022] [Indexed: 11/18/2022]
Abstract
ASB-3 is one of the 18 members of ASB gene family. As a special negative regulation factor of TNF-R2, ASB-3 inhibits the signal transduction of JNK-TNF-R2 and JNK-STAT signaling pathway by TNF-R2 protein. In this study, the genetic polymorphisms of ASB-3 were detected in total of 637 from Qinchuan, Jinnan and Xianan cattle using the sequence of mixed DNA pool, Tetra-primer ARMS-PCR and PCR-RFLP methods. Four mutation sites were detected including the g.C41255T, g.G74754A, and g.T75438C were synonymous mutation, whereas the g.C115213T was missense mutation (Pro > Ser). The associated analysis of four polymorphic loci of ASB-3 gene respectively with growth traits in the three cattle breeds. The result showed that SNP1 site was significantly related with Qinchuan cattle height and TT was the dominant genotype; SNP2 had a significant relationship with body length of Xianan cattle and cross department height of Qinchuan cattle, AA was the dominant genotype; SNP3 was significantly related to cross height of Xianan cattle, TT was the dominant genotype; SNP4 site was significantly correlated with body height of Xianan cattle and cross height of Jinnan cattle. Genotype combinations were only significantly correlated with the hucklebone width in the adult Qinchuan cattle. The combination genotype CTAGCTCC was outperformed other combination genotypes of Qinchuan cattle. The results showed that ASB-3 could be an important candidate gene and the four SNPs in ASB-3 can be used for molecular marker-assisted selection of four beef cattle breeds.
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Affiliation(s)
- Ao Qi
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Jianyu Yan
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Yu Yang
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Jia Tang
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Wenxiu Ru
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Xiaojun Jiang
- Shaanxi Agricultural and Animal Husbandry Good Seed Farm, Fufeng, Shaanxi 722203, China
| | - Chuzhao Lei
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Xiuzhu Sun
- College of Grassland Agriculrure, Northwest A&F University, Shaanxi 712100, China.
| | - Hong Chen
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China; College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China.
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Brunes LC, Baldi F, Lopes FB, Lôbo RB, Espigolan R, Costa MFO, Stafuzza NB, Magnabosco CU. Weighted single-step genome-wide association study and pathway analyses for feed efficiency traits in Nellore cattle. J Anim Breed Genet 2020; 138:23-44. [PMID: 32654373 DOI: 10.1111/jbg.12496] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/11/2020] [Accepted: 06/13/2020] [Indexed: 02/06/2023]
Abstract
The aim was to conduct a weighted single-step genome-wide association study to detect genomic regions and putative candidate genes related to residual feed intake, dry matter intake, feed efficiency (FE), feed conversion ratio, residual body weight gain, residual intake and weight gain in Nellore cattle. Several protein-coding genes were identified within the genomic regions that explain more than 0.5% of the additive genetic variance for these traits. These genes were associated with insulin, leptin, glucose, protein and lipid metabolisms; energy balance; heat and oxidative stress; bile secretion; satiety; feed behaviour; salivation; digestion; and nutrient absorption. Enrichment analysis revealed functional pathways (p-value < .05) such as neuropeptide signalling (GO:0007218), negative regulation of canonical Wingless/Int-1 (Wnt) signalling (GO:0090090), bitter taste receptor activity (GO:0033038), neuropeptide hormone activity (GO:0005184), bile secretion (bta04976), taste transduction (bta0742) and glucagon signalling pathway (bta04922). The identification of these genes, pathways and their respective functions should contribute to a better understanding of the genetic and physiological mechanisms regulating Nellore FE-related traits.
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Affiliation(s)
- Ludmilla C Brunes
- Department of Animal Science, Federal University of Goiás (UFG), Goiânia, Brazil.,Embrapa Rice and Beans, Santo Antônio de Goiás, Brazil
| | - Fernando Baldi
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, Brazil
| | | | - Raysildo B Lôbo
- National Association of Breeders and Researchers (ANCP), Ribeirão Preto, Brazil
| | - Rafael Espigolan
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Brazil
| | | | - Nedenia B Stafuzza
- Beef Cattle Research Center, Animal Science Institute, Sertãozinho, Brazil
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Association of single nucleotide polymorphism in NLRC3, NLRC5, HIP1, and LRP8 genes with fecal egg counts in goats naturally infected with Haemonchus contortus. Trop Anim Health Prod 2019; 52:1583-1598. [PMID: 31828571 DOI: 10.1007/s11250-019-02154-z] [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] [Received: 03/12/2019] [Accepted: 11/18/2019] [Indexed: 10/25/2022]
Abstract
Haemonchus contortus is a common, intractably pathogenic and economically important gastrointestinal nematode for goat producers worldwide, especially in tropical and subtropical regions. The objective of this study is to identify single nucleotide polymorphisms (SNPs) of 12 candidate goat genes mainly related to the innate immune response associated with fecal egg counts (FECs) of Haemonchus contortus in goat as an indicator of the level of parasite infection. Phenotypic data including FEC and blood traits were recorded in 189 native goats from China and 191 ones from Bangladesh, respectively. Bangladeshi goats had significantly (P < 0.01) lower FEC compared to that of Chinese goats, suggesting higher susceptible and infection rates in Chinese goat populations. FEC was significantly positive correlated with body weight (r = 0.64, P < 0.01) and hemoglobin (r = 0.49, P < 0.01) value, but negative with pack cell volume (r = - 0.63, P < 0.05) in goats. Genotyping of SNPs was performed using a matrix-assisted laser desorption ionization time of flight mass spectrometry assay and a generalized linear model was used to evaluate the association between each SNP and goat FEC trait. Eleven novel SNPs in the NLRC3, NLRC5, HIP1, and LRP8, out of 46 variants from these 12 genes, were significantly associated with FEC of goats with a nominal significance level of P < 0.05. Of these 11 SNPs, linkage disequilibrium were revealed among SNPs in LRP8 (r2 = 0.87 to 1), between SNPs in NLRC3, NLRC5, and HIP1 (r2 = 0.96 to 0.99), respectively. Further, haplotypes within NLRC3, NLRC5, and HIP1 were significantly associated (P < 0.001) with FEC. In artificial challenge trail, quantitative real-time PCR exposed that the relative expression of mRNA was higher in the resistant group for NLRC3 (P < 0.01), LRP8 and HIP1 (P < 0.001) but lower in the resistant group for NLRC5 (P < 0.0001), compared to the susceptible group. The possible SNP markers and genes identified in this study could be potentially used in marker-assisted selection for breeding local goats breeds resistant to gastrointestinal nematode parasite particularly for Haemonchus contortus, and then for improving health and productivity of goat.
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Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak. Animals (Basel) 2019; 9:ani9121008. [PMID: 31766342 PMCID: PMC6940794 DOI: 10.3390/ani9121008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/16/2019] [Accepted: 11/18/2019] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Cell adhesion molecule 2 (CADM2), also known as synaptic cell adhesion molecule 2 (SYNCAM2), is the mediator of synaptic signals enriched in the brain. Overlaps between copy number variation (CNV) regions in CADM2 and quantitative trait loci (QTL) related to body weight have been clarified in a previous study. In this study, two loci were amplified in the CADM2 gene (CNV1: 235,915 bp, exon 1 and partial intron 1; CNV2: 60,430 bp, intron 9) to explore the relationship between CNV types in the CADM2 gene and growth traits in 350 Ashidan yaks. Association analysis illustrated that no significant effect was found on growth traits in CNV1. However, the CNV2 mutation had a significant effect on body weight at the sixth month (p < 0.05). Individuals with the gain-type copy number variation CNV2 were significantly superior to those with loss- or normal-type in terms of body weight (p < 0.05). In summary, this study confirmed that CADM2-CNVs affect growth traits in yaks, and may be candidate genes for successful yak breeding and genetics projects. Abstract Copy number variation (CNV) is currently accepted as a common source of genetic variation. It is reported that CNVs may influence the resistance to disease and complex economic traits, such as residual feed intake, muscle formation, and fat deposition in livestock. Cell adhesion molecule 2 (CADM2) is expressed widely in the brain and adipose tissue and can regulate body weight through the central nervous system. Growth traits are important economic traits for animal selection. In this study, we aimed to explore the effect of CADM2 gene copy number variants on yak growth traits. Here, two CNVs in the CADM2 gene were investigated using the quantitative polymerase chain reaction (qPCR), and the association of the CNVs with growth traits in yak was analyzed using statistical methods by SPSS software. Differences were considered significant if the p value was < 0.05. Statistical analysis indicated significant association of CADM2-CNV2 with the body weight of the Chinese Ashidan yak. A significant effect of CNV2 (p < 0.05) was found on body weight at 6 months. In CNV2, the gain-type copy number variation exhibited greater performance than the other variants, with greater body weight observed at 6 months (p < 0.05). To the best of our knowledge, this is the first attempt to investigate the function of CADM2-CNVs and their association with growth traits in animals. This may be a useful candidate marker in marker-assisted selection of yaks.
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Alam MBB, Omar AI, Faruque MO, Notter DR, Periasamy K, Mondal MMH, Sarder MJU, Shamsuddin M, Cao J, Du X, Wu Z, Zhao S. Single nucleotide polymorphisms in candidate genes are significantly associated with resistance to Haemonchus contortus infection in goats. J Anim Sci Biotechnol 2019; 10:30. [PMID: 30918657 PMCID: PMC6419443 DOI: 10.1186/s40104-019-0327-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/24/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Haemonchosis is a major economic problem in goat production in humid, tropical and subtropical regions. The disease is caused by an abomasal nematode, Haemonchus contortus, which is highly pathogenic in small ruminants. The aim of this study was to identifying single-nucleotide polymorphisms (SNP) that were associated with fecal egg counts (FEC) and could be used as markers to identify resistance to H. contortus in goats. RESULTS Ten novel variants in the CIITA, ATP2A3, HSPA8, STAT5B, ESYT1, and SERPING1 genes were associated with FEC in goats with a nominal significance level of P < 0.05. Two missense mutation in the exon region of the caprine CIITA gene resulted in replacement of arginine with cysteine at position 9473550 (R9473550C) and aspartic acid with glutamic acid at position 9473870 (D9473870E). Chinese goat breeds had significantly higher FEC than Bangladeshi goat breeds within their respective genotypes. Polymorphism information content (PIC), effective allele number (Ne), and heterozygosity (He) were greatest for the STAT5B_197_A > G SNP locus in all goat breeds. Pairwise coefficients of linkage disequilibrium (D´, r 2) revealed complete LD (r 2 = 1) between significant SNP polymorphisms in CIITA and SERPING1 and strong LD (r 2 = 0.93 and 0.98) between polymorphisms in HSPA8 and ATP2A3, respectively. Correlation coefficient (r) between FEC and body weight (BW) was significantly positive (r = 0.56***, P < 0.001) but that between FEC and packed cell volume (PCV) was negatively significant (r = - 0.47**, P < 0.01) in the total population of goats. On the other hand, correlation coefficient (r) between BW and PCV was not significant in total population of goats. Association analysis revealed that haplotypes within ATP2A3, HSPA8, and SERPING1 were significantly associated with FEC. Quantitative real-time PCR revealed that the relative expression of mRNA was higher (P < 0.001) for resistant, compared to susceptible, groups of goats for all candidate genes except CIITA. CONCLUSIONS This study identified SNP markers that can potentially be used in marker-assisted selection programs to develop goat breeds that are resistant to H. contortus.
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Affiliation(s)
- Mahmuda Bilkis Bintee Alam
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Abdullah Ibne Omar
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- National Engineering Laboratory for Animal Breeding, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Md. Omar Faruque
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh, 2202 Bangladesh
| | - David Russell Notter
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061 USA
| | - Kathiravan Periasamy
- Animal Production and Health Laboratory, Join FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | | | - Md. Jalal Uddin Sarder
- Department of Veterinary and Animal Science, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Md. Shamsuddin
- Animal Production and Health Laboratory, Join FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | - Jianhua Cao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Xiaoyong Du
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Zhenyang Wu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- College of Agroforestry Engineering and Planning, Tongren Univesity, Tongren, Guizhou 554300 People’s Republic of China
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
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Wang X, Yang Q, Wang K, Yan H, Pan C, Chen H, Liu J, Zhu H, Qu L, Lan X. Two strongly linked single nucleotide polymorphisms (Q320P and V397I) in GDF9 gene are associated with litter size in cashmere goats. Theriogenology 2018; 125:115-121. [PMID: 30414564 DOI: 10.1016/j.theriogenology.2018.10.013] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 10/10/2018] [Accepted: 10/14/2018] [Indexed: 10/28/2022]
Abstract
Growth differentiation factor 9 (GDF9) gene is an effective intra-ovarian regulator; it plays a crucial role in early folliculogenesis in female mammals. The non synonymous mutations: g.3905A > C (also known as p.Gln320Pro/Q320P) and g.4135G > A (also know as p.Val397Ile/V397I), are two well-known and controversial single nucleotide polymorphisms (SNPs) within GDF9 gene in goats with different prolificacy, and so far, there were no studies on linkage between Q320P and V397I. Therefore, the aim of this work was to study whether Q320P and V397I mutations have a significant effect on litter size, in Shaanbei white cashmere goats (SBWC, n = 1511), and to explore the specific relationship between these two SNPs. The results showed that both of Q320P and V397I mutations exhibited three genotypes; the minor allele frequencies (MAF) of the SNPs were 0.286 and 0.477, respectively; and these two SNPs were in strong linkage disequilibrium (D' = 0.976, r2 = 0.348) in the studied goats. Moreover, association analyses revealed that Q320P was significantly associated with the first-born litter size in goats irrespective of the sample size (n = 1511; P = 0.008), while V397I significantly affected litter size until the sample size crossed 1300 (P = 0.015). Meanwhile, the diplotypes PP-II and QP-VI were observed to have a superior effect on litter size (P = 3.78 × 10-5) to that of the haplotypes (P = 1.12 × 10-7). Thus, the findings led us to assume that Q320P mutation was the major SNP affecting goat litter size. These findings can provide useful DNA markers for selecting superior individuals in marker-assisted selection (MAS) for breeding in relation to fecundity in goats.
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Affiliation(s)
- Xinyu Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, PR China
| | - Qing Yang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, PR China
| | - Ke Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, PR China
| | - Hailong Yan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, PR China; Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, 719000, PR China; Life Science Research Center, Yulin University, Yulin, Shaanxi, 719000, PR China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, PR China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, PR China
| | - Jinwang Liu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, 719000, PR China; Life Science Research Center, Yulin University, Yulin, Shaanxi, 719000, PR China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, 719000, PR China; Life Science Research Center, Yulin University, Yulin, Shaanxi, 719000, PR China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, 719000, PR China; Life Science Research Center, Yulin University, Yulin, Shaanxi, 719000, PR China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, PR China.
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11
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Chen R, Yu S, Ren F, Lv XY, Pan CY. Detection of one large insertion/deletion (indel) and two novel SNPs within the <i>SPEF2</i> gene and their associations with male piglet reproduction traits. Arch Anim Breed 2016. [DOI: 10.5194/aab-59-275-2016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract. The sperm flagella 2 (SPEF2) gene is essential for normal sperm tail development and male fertility. To fully characterize the structure of the mutation and to further study the function of the pig SPEF2 gene, we explored the insertion/deletion (indel) and novel single-nucleotide polymorphisms (SNPs) within the pig SPEF2 gene, and tested their associations with the testicular sizes in male Large White (LW) and Landrace (LD) pigs from China. Herein, a large insertion located at the SPEF2 gene in chromosome 16 was found, and two alleles of "I" (insertion) and "D" (deletion) were designated. Allele "D" was dominant in all analyzed pigs. Two novel SNPs (namely (NC_010458) g.19642G > A, resulting in AfaI aCRS PCR–PFLP, and g.19886C > G, resulting in EcoRI aCRS PCR–PFLP) were found in LW and LD pigs. Association testing revealed that g.19886C > G was significantly associated with the testis long circumference (TLC) in LW pigs (P < 0.05), suggesting that this SNP would be the DNA marker for the marker-assisted selection (MAS) in reproduction traits. This preliminary result indicates that the pig SPEF2 gene had significant effects on male reproduction traits. These findings could not only extend the spectrum of genetic variations in the pig SPEF2 gene but also contribute to implementing MAS in genetics and breeding in pigs.
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Zhang X, Wu X, Jia W, Pan C, Li X, Lei C, Chen H, Lan X. Novel Nucleotide Variations, Haplotypes Structure and Associations with Growth Related Traits of Goat AT Motif-Binding Factor (ATBF1) Gene. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1394-406. [PMID: 26323396 PMCID: PMC4554846 DOI: 10.5713/ajas.14.0860] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 03/11/2015] [Accepted: 04/01/2015] [Indexed: 01/05/2023]
Abstract
The AT motif-binding factor (ATBF1) not only interacts with protein inhibitor of activated signal transducer and activator of transcription 3 (STAT3) (PIAS3) to suppress STAT3 signaling regulating embryo early development and cell differentiation, but is required for early activation of the pituitary specific transcription factor 1 (Pit1) gene (also known as POU1F1) critically affecting mammalian growth and development. The goal of this study was to detect novel nucleotide variations and haplotypes structure of the ATBF1 gene, as well as to test their associations with growth-related traits in goats. Herein, a total of seven novel single nucleotide polymorphisms (SNPs) (SNP 1-7) within this gene were found in two well-known Chinese native goat breeds. Haplotypes structure analysis demonstrated that there were four haplotypes in Hainan black goat while seventeen haplotypes in Xinong Saanen dairy goat, and both breeds only shared one haplotype (hap1). Association testing revealed that the SNP2, SNP5, SNP6, and SNP7 loci were also found to significantly associate with growth-related traits in goats, respectively. Moreover, one diplotype in Xinong Saanen dairy goats significantly linked to growth related traits. These preliminary findings not only would extend the spectrum of genetic variations of the goat ATBF1 gene, but also would contribute to implementing marker-assisted selection in genetics and breeding in goats.
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Affiliation(s)
- Xiaoyan Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianfeng Wu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenchao Jia
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuanying Pan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiangcheng Li
- Institute of Beijing Animal Science and Veterinary, Chinese Academy of Agricultural Science, Beijing 100194, China
| | - Chuzhao Lei
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hong Chen
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianyong Lan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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13
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Novel genetic variants associated with mRNA expression of signal transducer and activator of transcription 3(STAT3) gene significantly affected goat growth traits. Small Rumin Res 2015. [DOI: 10.1016/j.smallrumres.2015.05.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Wang A, Fu M, Jiang X, Mao Y, Li X, Tao S. Evolution of the F-box gene family in Euarchontoglires: gene number variation and selection patterns. PLoS One 2014; 9:e94899. [PMID: 24727786 PMCID: PMC3984280 DOI: 10.1371/journal.pone.0094899] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 03/21/2014] [Indexed: 02/06/2023] Open
Abstract
F-box proteins are substrate adaptors used by the SKP1–CUL1–F-box protein (SCF) complex, a type of E3 ubiquitin ligase complex in the ubiquitin proteasome system (UPS). SCF-mediated ubiquitylation regulates proteolysis of hundreds of cellular proteins involved in key signaling and disease systems. However, our knowledge of the evolution of the F-box gene family in Euarchontoglires is limited. In the present study, 559 F-box genes and nine related pseudogenes were identified in eight genomes. Lineage-specific gene gain and loss events occurred during the evolution of Euarchontoglires, resulting in varying F-box gene numbers ranging from 66 to 81 among the eight species. Both tandem duplication and retrotransposition were found to have contributed to the increase of F-box gene number, whereas mutation in the F-box domain was the main mechanism responsible for reduction in the number of F-box genes, resulting in a balance of expansion and contraction in the F-box gene family. Thus, the Euarchontoglire F-box gene family evolved under a birth-and-death model. Signatures of positive selection were detected in substrate-recognizing domains of multiple F-box proteins, and adaptive changes played a role in evolution of the Euarchontoglire F-box gene family. In addition, single nucleotide polymorphism (SNP) distributions were found to be highly non-random among different regions of F-box genes in 1092 human individuals, with domain regions having a significantly lower number of non-synonymous SNPs.
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Affiliation(s)
- Ailan Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Mingchuan Fu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoqian Jiang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuanhui Mao
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiangchen Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Shiheng Tao
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail:
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15
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Zhao H, Wu X, Cai H, Pan C, Lei C, Chen H, Lan X. Genetic variants and effects on milk traits of the caprine paired-like homeodomain transcription factor 2 (PITX2) gene in dairy goats. Gene 2013; 532:203-10. [DOI: 10.1016/j.gene.2013.09.062] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/01/2013] [Accepted: 09/17/2013] [Indexed: 12/20/2022]
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16
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Pan C, Wu C, Jia W, Xu Y, Lei C, Hu S, Lan X, Chen H. A critical functional missense mutation (H173R) in the bovine PROP1 gene significantly affects growth traits in cattle. Gene 2013; 531:398-402. [DOI: 10.1016/j.gene.2013.09.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 08/30/2013] [Accepted: 09/03/2013] [Indexed: 12/20/2022]
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