1
|
Li Y, Liu T, Zhang M, Pan C, Liu X, Zhao H, Lan X. A Functional 67-bp Duplication Locating at the Core Promoter Region within the Bovine ADIPOQ Gene Is Associated with Ovarian Traits and mRNA Expression. Animals (Basel) 2024; 14:2362. [PMID: 39199896 PMCID: PMC11350689 DOI: 10.3390/ani14162362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 09/01/2024] Open
Abstract
ADIPOQ plays a crucial role in regulating the reproductive system, but there are few reports on the effects of ADIPOQ on ovarian in dairy cows. Previous studies have verified the presence of a 67-bp mutation in the promoter region of the ADIPOQ gene. Hence, we employed ovarian tissues (n = 2111) and blood samples (n = 108) from Chinese Holstein cows as experimental samples to examine the association between ADIPOQ promoter variants and ovarian traits. We extracted DNA from these samples and conducted genetic typing identification on each sample using advanced techniques like PCR and agarose gel electrophoresis. Consequently, the DD, ID, and II genotypes were discovered. and it has been observed that the mutation frequency of this locus is low in the Chinese Holstein cow. Importantly, the correlational analysis unveiled a significant relationship (p < 0.05) between the weight of ovaries in late estrus and the width of ovaries during the estrus interval with the mutation. Result of the RT-PCR revealed that the ID genotype partially diminished the expression of the ADIPOQ gene. The results of this study suggest that the identified variable duplication could serve as a potential genetic marker for enhancing the ovarian traits of Chinese Holstein cows.
Collapse
Affiliation(s)
- Yufu Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.L.); (T.L.); (M.Z.); (C.P.)
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China;
| | - Tingting Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.L.); (T.L.); (M.Z.); (C.P.)
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221008, China
| | - Mengyang Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.L.); (T.L.); (M.Z.); (C.P.)
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.L.); (T.L.); (M.Z.); (C.P.)
| | - Xu Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China;
| | - Haiyu Zhao
- College of Life Science, Lanzhou University, Lanzhou 730000, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.L.); (T.L.); (M.Z.); (C.P.)
| |
Collapse
|
2
|
Liu LL, Chen B, Chen SL, Liu WJ. A Genome-Wide Association Study of the Chest Circumference Trait in Xinjiang Donkeys Based on Whole-Genome Sequencing Technology. Genes (Basel) 2023; 14:genes14051081. [PMID: 37239441 DOI: 10.3390/genes14051081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Animal genotyping by means of genome-wide association studies is important for connecting phenotypes of interest with their underlying genetics in livestock. However, the use of whole genome sequencing to investigate chest circumference (CC) in donkeys has rarely been reported. We aimed to use the genome-wide association study approach to detect significant single nucleotide polymorphisms (SNPs) and key genes associated with chest circumference traits in Xinjiang donkeys. We assessed 112 Xinjiang donkeys in this study. The chest circumference of each was measured 2 h before milking. We re-sequenced blood samples from the Xinjiang donkeys, and genome-wide association study analyses were performed using a mixed model with the PLINK, GEMMA, and REGENIE programs. We tested 38 donkeys for candidate SNPs for genome-wide association study using three software programs. Additionally, 18 SNP markers reached genome-wide significance (p < 1.61 × 10-9). On the basis of these, 41 genes were identified. Previously proposed candidate genes for CC traits were supported by this study, including NFATC2 (Nuclear Factor of Activated T Cells 2), PROP1 (PROP Paired-Like Homeobox 1), UBB (Ubiquitin B), and HAND2 (Heart and Neural Crest Derivatives Expressed 2). These promising candidates provide a valuable resource for validating potential meat production genes and will facilitate the development of high-yielding Xinjiang donkey breeds through marker-assisted selection or gene editing.
Collapse
Affiliation(s)
- Ling-Ling Liu
- Department of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Bin Chen
- Department of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Sheng-Lei Chen
- Department of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Wu-Jun Liu
- Department of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| |
Collapse
|
3
|
Wang X, Ran X, Niu X, Huang S, Li S, Wang J. Whole-genome sequence analysis reveals selection signatures for important economic traits in Xiang pigs. Sci Rep 2022; 12:11823. [PMID: 35821031 PMCID: PMC9276726 DOI: 10.1038/s41598-022-14686-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/10/2022] [Indexed: 11/30/2022] Open
Abstract
Xiang pig (XP) is one of the best-known indigenous pig breeds in China, which is characterized by its small body size, strong disease resistance, high adaptability, favorite meat quality, small litter sizes, and early sexual maturity. However, the genomic evidence that links these unique traits of XP is still poorly understood. To identify the genomic signatures of selection in XP, we performed whole-genome resequencing on 25 unrelated individual XPs. We obtained 876.70 Gb of raw data from the genomic libraries. The LD analysis showed that the lowest level of linkage disequilibrium was observed in Xiang pig. Comparative genomic analysis between XPs and other breeds including Tibetan, Meishan, Duroc and Landrace revealed 3062, 1228, 907 and 1519 selected regions, respectively. The genes identified in selected regions of XPs were associated with growth and development processes (IGF1R, PROP1, TBX19, STAC3, RLF, SELENOM, MSTN), immunity and disease resistance (ZCCHC2, SERPINB2, ADGRE5, CYP7B1, STAT6, IL2, CD80, RHBDD3, PIK3IP1), environmental adaptation (NR2E1, SERPINB8, SERPINB10, SLC26A7, MYO1A, SDR9C7, UVSSA, EXPH5, VEGFC, PDE1A), reproduction (CCNB2, TRPM6, EYA3, CYP7B1, LIMK2, RSPO1, ADAM32, SPAG16), meat quality traits (DECR1, EWSR1), and early sexual maturity (TAC3). Through the absolute allele frequency difference (ΔAF) analysis, we explored two population-specific missense mutations occurred in NR6A1 and LTBP2 genes, which well explained that the vertebrae numbers of Xiang pigs were less than that of the European pig breeds. Our results indicated that Xiang pigs were less affected by artificial selection than the European and Meishan pig breeds. The selected candidate genes were mainly involved in growth and development, disease resistance, reproduction, meat quality, and early sexual maturity. This study provided a list of functional candidate genes, as well as a number of genetic variants, which would provide insight into the molecular basis for the unique traits of Xiang pig.
Collapse
Affiliation(s)
- Xiying Wang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China.,Tongren University, Tongren, 554300, China
| | - Xueqin Ran
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China.
| | - Xi Niu
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Shihui Huang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Sheng Li
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Jiafu Wang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China.
| |
Collapse
|
4
|
Wang R, Wang Z, Wang X, Li Y, Qu L, Lan X. A novel 4-bp insertion within the goat CFAP43 gene and its association with litter size. Small Rumin Res 2021. [DOI: 10.1016/j.smallrumres.2021.106456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
5
|
Chong Y, Liu G, Girmay S, Jiang X. Novel mutations in the signal transducer and activator of transcription 3 gene are associated with sheep body weight and fatness traits. Mamm Genome 2021; 32:38-49. [PMID: 33492461 DOI: 10.1007/s00335-020-09850-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 09/29/2020] [Indexed: 12/01/2022]
Abstract
The signal transducer and activator of transcription 3 (STAT3) gene plays a crucial role in leptin-mediated energy metabolism, upon which the growth and development of animals depend. Nevertheless, no studies have reported the effects of STAT3 gene polymorphisms on body weight and fatness modulation in sheep. This study aimed to illustrate STAT3 mRNA expression across tissues and various developmental stages of sheep and to highlight the association of STAT3 gene polymorphisms with body weight and fat-related traits in sheep, in order to identify a genetic marker that may conceivably be of value for marker-assisted selection (MAS). This study revealed that STAT3 was differentially expressed across age and sex (p < 0.05), with higher expression in the ram liver. The abundant expression of STAT3 in the liver of male sheep and increased expression in the hypothalamus and longissimus dorsi muscle from birth to six months of age may indicate the vital role of the STAT3 gene in animal growth and development. Moreover, SNP association analysis also revealed that the novel SNPs of the STAT3 gene detected in this study showed a significant association with body weight and fatness traits (p < 0.05). In conclusion, the significant genetic effects of the STAT3 gene polymorphisms on sheep growth and development revealed that STAT3 could be a marker gene for the selection of growth-related traits in sheep.
Collapse
Affiliation(s)
- Yuqing Chong
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, 430070, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guiqiong Liu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, 430070, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shishay Girmay
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xunping Jiang
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, 430070, China. .,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
6
|
Mao C, Ju X, Cheng H, Huang X, Jiang F, Yao Y, Lan X, Song E. Determination of genetic variation within the DYRK2 gene and its associations with milk traits in cattle. Arch Anim Breed 2020; 63:315-323. [PMID: 32964102 PMCID: PMC7500071 DOI: 10.5194/aab-63-315-2020] [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: 02/05/2020] [Accepted: 07/25/2020] [Indexed: 11/11/2022] Open
Abstract
To speed up the progress of marker-assisted selection (MAS) in cattle
breeding, the dual-specificity tyrosine phosphorylation-regulated kinase 2
(DYRK2), cadherin 2 (CDH2), and kinesin family member 1A (KIF1A) genes were chosen based
on our pervious genome-wide association study (GWAS) analysis results.
DYRK2 is a kinase that may participate in cell growth and/or development; it
shows phosphorylation activity toward serine, threonine, and tyrosine
fragments of proteins, and it is different from other protein kinases. The CDH2 gene
encodes a classic cadherin, which is a member of the cadherin superfamily. The
protein encoded by KIF1A is a member of the kinesin family and plays a role in
the transportation of membrane organelles along axon microtubules. We
detected insertion/deletion (InDel) variation in these three candidate genes
in 438 individual cattle (Xinjiang Brown cattle and Wagyu × Luxi
crossbreed cattle). Only DYRK2-P3-11 bp was polymorphic and genotyped. The
polymorphism information content of DYRK2-P3-11 bp was 0.336. Correlation analyses
showed that InDel polymorphism was significantly associated with six
different milk traits. These findings may aid future analyses of InDel
genotypes in cattle breeds, and speed up the progress of MAS in cattle
breeding.
Collapse
Affiliation(s)
- Cui Mao
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250000, China
| | - Xing Ju
- College of Animal Science and Technology, Xinjiang Agricultural University, Urumqi, Xinjiang, 830000, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haijian Cheng
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250000, China
| | - Xixia Huang
- College of Animal Science and Technology, Xinjiang Agricultural University, Urumqi, Xinjiang, 830000, China
| | - Fugui Jiang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250000, China
| | - Yuni Yao
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250000, 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, China
| | - Enliang Song
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250000, China.,College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250000, China
| |
Collapse
|
7
|
Mao C, Akhatayeva Z, Cheng H, Zhang G, Jiang F, Meng X, Yao Y, Elnour IE, Lan X, Song E. A novel 23 bp indel mutation in PRL gene is associated with growth traits in Luxi Blackhead sheep. Anim Biotechnol 2020; 32:740-747. [PMID: 32293991 DOI: 10.1080/10495398.2020.1753757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Prolactin is a highly versatile pituitary hormone with multiple biological functions. PRL expression is regulated by POU1F1 and the prophet of POU1F1 (PROP1). The aim of this study was to investigate the indel variations in ovine PRL and the directly related (PROP1 and POU1F1) genes, and their associations with growth traits in Luxi Blackhead (LXBH) sheep. A monomorphism in PROP1 and POU1F1 genes, and one novel 23-bp insertion mutation in the PRL gene, were identified in LXBH sheep. The 23 bp insertion mutation within PRL gene was significantly associated with several body measurements (e.g., body weight, body height) in sheep of different ages (p < 0.05). Ram lambs (p = 0.036) of genotype insertion/insertion (II) had significantly higher body weights. Weaners (p = 0.018) of genotypes insertion/insertion (II) and insertion/deletion (ID) also had significantly higher body weights compared with male sheep of deletion/deletion (DD) genotype. Moreover, among ewe lambs, individuals of genotype insertion/insertion (II) had a higher paunch girth compared to those with other genotypes (p = 0.044). These findings indicate that a 23 bp indel variant of the ovine PRL gene is correlated with body measurements in LXBH sheep. The findings have potential utility for sheep breeding programs based on marker-assisted selection.
Collapse
Affiliation(s)
- Cui Mao
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Zhanerke Akhatayeva
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Haijian Cheng
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Guoping Zhang
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Fugui Jiang
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Xianfeng Meng
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Yuni Yao
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Ibrahim Elsaeid Elnour
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Enliang Song
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China.,College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| |
Collapse
|
8
|
Functional impact of cytochrome P450 3A (CYP3A) missense variants in cattle. Sci Rep 2019; 9:19672. [PMID: 31873175 PMCID: PMC6927969 DOI: 10.1038/s41598-019-56271-8] [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: 08/22/2019] [Accepted: 12/09/2019] [Indexed: 12/26/2022] Open
Abstract
Cytochrome P450 3A is the most important CYP subfamily in humans, and CYP3A4/CYP3A5 genetic variants contribute to inter-individual variability in drug metabolism. However, no information is available for bovine CYP3A (bCYP3A). Here we described bCYP3A missense single nucleotide variants (SNVs) and evaluated their functional effects. CYP3A28, CYP3A38 and CYP3A48 missense SNVs were identified in 300 bulls of Piedmontese breed through targeted sequencing. Wild-type and mutant bCYP3A cDNAs were cloned and expressed in V79 cells. CYP3A-dependent oxidative metabolism of testosterone (TST) and nifedipine (NIF) was assessed by LC-MS/MS. Finally, SNVs functional impact on TST hydroxylation was measured ex vivo in liver microsomes from individually genotyped animals. Thirteen missense SNVs were identified and validated. Five variants showed differences in CYP3A catalytic activity: three CYP3A28 SNVs reduced TST 6β-hydroxylation; one CYP3A38 variant increased TST 16β-hydroxylation, while a CYP3A48 SNV showed enhanced NIF oxidation. Individuals homozygous for rs384467435 SNV showed a reduced TST 6β-hydroxylation. Molecular modelling showed that most of SNVs were distal to CYP3A active site, suggesting indirect effects on the catalytic activity. Collectively, these findings demonstrate the importance of pharmacogenetics studies in veterinary species and suggest bCYP3A genotype variation might affect the fate of xenobiotics in food-producing species such as cattle.
Collapse
|
9
|
Chen M, Yan H, Wang K, Cui Y, Chen R, Liu J, Zhu H, Qu L, Pan C. Goat SPEF2: Expression profile, indel variants identification and association analysis with litter size. Theriogenology 2019; 139:147-155. [DOI: 10.1016/j.theriogenology.2019.08.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/04/2019] [Accepted: 08/04/2019] [Indexed: 01/04/2023]
|
10
|
TP53 Polymorphism Contributes to the Susceptibility to Bipolar Disorder but Not to Schizophrenia in the Chinese Han Population. J Mol Neurosci 2019; 68:679-687. [DOI: 10.1007/s12031-019-01330-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/25/2019] [Indexed: 12/15/2022]
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Zhang S, Zhao H, Lei C, Pan C, Chen H, Lin Q, Lan X. Effects of genetic variations within goat PITX2 gene on growth traits and mRNA expression. Anim Biotechnol 2019; 31:107-114. [PMID: 30652937 DOI: 10.1080/10495398.2018.1551229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Paired-like homeodomain 2 (PITX2), a key gene in hypothalamic-pituitary-adrena axis, influences animal growth and development. The objective of this study was to identify the association of the functional genetic variations within goat PITX2 gene with growth traits and mRNA expression levels. According to the reported single nucleotide polymorphisms (SNPs) information in Guanzhong dairy goat (GZDG), we identified genotypes of the known SNPs in Hainan black goat (HNBG). Association analysis uncovered that the SNPs of AC_000163: g.18117T > C, g.18161C > G and g.18353T > C loci were significantly associated with several growth traits (e.g., body height and body length) in HNBG and GZDG breeds. According to the quantitative real-time PCR assay, β-Actin and ribosomal protein L19 (RPL19) were the most stable expressed housekeeping genes in heart and skeletal muscle, respectively; meanwhile, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was the most stable expressed housekeeping gene in the other tissues. Based on the best housekeeping gene of varied tissues, we found the different genotypes of above loci were significantly associated with PITX2 mRNA expression in heart, muscle and small intestine. Briefly, the genetic variants of goat PITX2 associating with mRNA expression affected growth traits significantly, which would benefit for goat breeding in the future.
Collapse
Affiliation(s)
- Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Haiyu Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Qing Lin
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China.,State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai 810016, P. R. China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| |
Collapse
|
13
|
Gene polymorphisms in PROP1 associated with growth traits in sheep. Gene 2018; 683:41-46. [PMID: 30316920 DOI: 10.1016/j.gene.2018.10.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/03/2018] [Accepted: 10/09/2018] [Indexed: 01/13/2023]
Abstract
The PROP paired-like homeobox 1 (PROP1) gene encodes a protein that regulates growth and development in mammals. Possessing DNA-binding and transcriptional activation abilities, PROP1 is able to control the expression of crucial anterior pituitary hormones including growth hormone, thyroid-stimulating hormone, and prolactin. The objective of this study was to identify genetic variation in ovine PROP1 in 670 New Zealand Romney sheep. Three single nucleotide polymorphisms (SNPs) were detected, two of which located in intron 1 were novel (c.109+40 T>C and c.109+207C>T), whilst the one located in exon 1 (c.45A>G) had been previously reported. These SNPs were arranged into three haplotypic variants - A1, B1 and C1. At each locus, all three genotypes were observed with frequencies in accordance with the Hardy-Weinberg Equilibrium. Association analysis revealed that the variant GG, CC and CC genotypes for c.45A>G, c.109+40 T>C and c.109+207C>T respectively were significantly associated with higher lamb tailing and weaning weights, and growth rate-to-weaning. The A1 haplotype had a positive effect on tailing weight, weaning weight and growth rate, while the B1 haplotype impacted growth traits negatively. These findings suggest that variations in ovine PROP1 could serve as potential genetic markers for use in marker-assisted selection and the breeding for animals with superior growth traits.
Collapse
|
14
|
Genome-wide analyses of the Jeju, Thoroughbred, and Jeju crossbred horse populations using the high density SNP array. Genes Genomics 2018; 40:1249-1258. [PMID: 30099720 DOI: 10.1007/s13258-018-0722-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 07/24/2018] [Indexed: 12/23/2022]
Abstract
The Jeju horse is an indigenous Korean horse breed that is currently registered with the Food and Agriculture Organization of the United Nations. However, there is severe lack of genomic studies on Jeju horse. This study was conducted to investigate genetic characteristics of horses including Jeju horse, Thoroughbred and Jeju crossbred (Jeju × Thoroughbred) populations. We compared the genomes of three horse populations using the Equine SNP70 Beadchip array. Short-range Linkage disequilibrium was the highest in Thoroughbred, whereas r2 values were lowest in Jeju horse. Expected heterozygosity was the highest in Jeju crossbred (0.351), followed by the Thoroughbred (0.337) and Jeju horse (0.311). The level of inbreeding was slightly higher in Thoroughbred (- 0.009) than in Jeju crossbred (- 0.035) and Jeju horse (- 0.038). FST value was the highest between Jeju horse and Thoroughbred (0.113), whereas Jeju crossbred and Thoroughbred showed the lowest value (0.031). The genetic relationship was further assessed by principal component analysis, suggesting that Jeju crossbred is more genetically similar to Thoroughbred than Jeju horse population. Additionally, we detected potential selection signatures, for example, in loci located on LCORL/NCAPG and PROP1 genes that are known to influence body. Genome-wide analyses of the three horse populations showed that all the breeds had somewhat a low level of inbreeding within each population. In the population structure analysis, we found that Jeju crossbred was genetically closer to Thoroughbred than Jeju horse. Furthermore, we identified several signatures of selection which might be associated with traits of interest. To our current knowledge, this study is the first genomic research, analyzing genetic relationships of Jeju horse, Thoroughbred and Jeju crossbred.
Collapse
|
15
|
Zhang S, Xu H, Kang Z, Cai H, Dang R, Lei C, Chen H, Guo X, Lan X. Bovine pituitary homeobox 2 (PITX2): mRNA expression profiles of different alternatively spliced variants and association analyses with growth traits. Gene 2018; 669:1-7. [DOI: 10.1016/j.gene.2018.05.083] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/12/2018] [Accepted: 05/21/2018] [Indexed: 12/19/2022]
|
16
|
Jin Y, Yang Q, Zhang M, Zhang S, Cai H, Dang R, Lei C, Chen H, Lan X. Identification of a Novel Polymorphism in Bovine lncRNA ADNCR Gene and Its Association with Growth Traits. Anim Biotechnol 2018; 30:159-165. [DOI: 10.1080/10495398.2018.1456446] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yunyun Jin
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Qing Yang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Meng Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Hanfang Cai
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Ruihua Dang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| |
Collapse
|
17
|
Wu S, Wang Y, Ning Y, Guo H, Wang X, Zhang L, Khan R, Cheng G, Wang H, Zan L. Genetic Variants in STAT3 Promoter Regions and Their Application in Molecular Breeding for Body Size Traits in Qinchuan Cattle. Int J Mol Sci 2018; 19:ijms19041035. [PMID: 29596388 PMCID: PMC5979584 DOI: 10.3390/ijms19041035] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/22/2018] [Accepted: 03/26/2018] [Indexed: 11/16/2022] Open
Abstract
Signal transducer and activator of transcription 3 (STAT3) plays a critical role in leptin-mediated regulation of energy metabolism. This study investigated genetic variation in STAT3 promoter regions and verified their contribution to bovine body size traits. We first estimated the degree of conservation in STAT3, followed by measurements of its mRNA expression during fetal and adult stages of Qinchuan cattle. We then sequenced the STAT3 promoter region to determine genetic variants and evaluate their association with body size traits. From fetus to adult, STAT3 expression increased significantly in muscle, fat, heart, liver, and spleen tissues (p < 0.01), but decreased in the intestine, lung, and rumen (p < 0.01). We identified and named five single nucleotide polymorphisms (SNPs): SNP1-304A>C, SNP2-285G>A, SNP3-209A>C, SNP4-203A>G, and SNP5-188T>C. These five mutations fell significantly outside the Hardy-Weinberg equilibrium (HWE) (Chi-squared test, p < 0.05) and significantly associated with body size traits (p < 0.05). Individuals with haplotype H3H3 (CC-GG-CC-GG-CC) were larger in body size than other haplotypes. Therefore, variations in the STAT3 gene promoter regions, most notably haplotype H3H3, may benefit marker-assisted breeding of Qinchuan cattle.
Collapse
Affiliation(s)
- Sen Wu
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Yaning Wang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Yue Ning
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Hongfang Guo
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Xiaoyu Wang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Le Zhang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
- National Beef Cattle Improvement Center of Northwest A & F University, Yangling 712100, China.
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
- National Beef Cattle Improvement Center of Northwest A & F University, Yangling 712100, China.
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
- National Beef Cattle Improvement Center of Northwest A & F University, Yangling 712100, China.
| |
Collapse
|
18
|
Zhao H, Wu M, Wang S, Yu X, Li Z, Dang R, Sun X. Identification of a novel 24 bp insertion–deletion (indel) of the androgen receptor gene and its association with growth traits in four indigenous cattle breeds. Arch Anim Breed 2018. [DOI: 10.5194/aab-61-71-2018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. During the past decades, insertions and deletions (indels) have become
increasingly popular in animal breeding for understanding the relationship
between genotypes and phenotypes. The androgen receptor (AR) plays the
vital role of a bridge on the function of the androgen and has sexual size
dimorphism. For this reason, the objective of this study was to explore the
novel indel variants within the cattle AR gene and to detect their
effects on growth traits in four breeds of Chinese yellow cattle. Herein, we
first confirmed a novel 24 bp indel (AC_000187.1g.4187270-4187293delAATTTATTGGGAGATTATTGAATT) within the intron of
the cattle AR gene. This is consistent with the results predicted
from the NCBI SNP database. The distribution of the indel genotypes of four
Chinese yellow cattle were significantly different from each other
(P < 0.01). After significant correlation analysis, many remarkable
phenotypic differences among the three genotypes were found (P < 0.05).
In conclusion, a novel 24 bp indel within the AR gene
significantly affected growth traits, suggesting that this indel may be a
useful DNA marker for the elimination or selection of excellent individuals for
cattle breeding.
Collapse
|
19
|
Li J, Erdenee S, Zhang S, Wei Z, Zhang M, Jin Y, Wu H, Chen H, Sun X, Xu H, Cai Y, Lan X. Genetic effects of PRNP gene insertion/deletion (indel) on phenotypic traits in sheep. Prion 2018; 12:42-53. [PMID: 29394137 DOI: 10.1080/19336896.2017.1405886] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Prion protein (PRNP) gene is well known for affecting mammal transmissible spongiform encephalopathies (TSE), and is also reported to regulate phenotypic traits (e.g. growth traits) in healthy ruminants. To identify the insertion/deletion (indel) variations of the PRNP gene and evaluate their effects on growth traits, 768 healthy individuals from five sheep breeds located in China and Mongolia were identified and analyzed. Herein, four novel indel polymorphisms, namely, Intron-1-insertion-7bp (I1-7bp), Intron-2-insertion-15bp (I2-15bp), Intron-2-insertion-19bp (I2-19bp), and 3' UTR-insertion-7bp (3' UTR-7bp), were found in the sheep PRNP gene. In five analyzed breeds, the minor allelic frequencies (MAF) of the above indels were in the range of 0.008 to 0.986 (I1-7bp), 0.113 to 0.336 (I2-15bp), 0.281 to 0.510 (I2-19bp), and 0.040 to 0.238 (3' UTR-7bp). Additionally, there were 15 haplotypes and the haplotype 'II2-15bp-D3'UTR-7bp-DI2-19bp-DI1-7bp' had the highest frequency, which varied from 0.464 to 0.629 in five breeds. Moreover, association analysis revealed that all novel indel polymorphisms were significantly associated with 13 different growth traits (P < 0.05). Particularly, the influences of I2-15bp on chest width (P = 0.001) in Small Tail Han sheep (ewe), 3' UTR-7bp on chest circumference (P = 0.003) in Hu sheep, and I2-19bp on tail length (P = 0.001) in Tong sheep, were highly significant (P < 0.01). These findings may be a further step toward the detection of indel-based typing within and across sheep breeds, and of promising target loci for accelerating the progress of marker-assisted selection in sheep breeding.
Collapse
Affiliation(s)
- Jie Li
- a College of Animal Science and Technology, Innovation Experimental College, Northwest A&F University , Xi'an, Shaanxi , China
| | - Sarantsetseg Erdenee
- b College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Shaoli Zhang
- a College of Animal Science and Technology, Innovation Experimental College, Northwest A&F University , Xi'an, Shaanxi , China
| | - Zhenyu Wei
- b College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Meng Zhang
- b College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Yunyun Jin
- b College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Hui Wu
- b College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Hong Chen
- c Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University , Yangling , Shaanxi , China
| | - Xiuzhu Sun
- b College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Hongwei Xu
- d Science Experimental Center, College of Life Science and Engineering, Northwest University for Nationalities , Chengguan District, Lanzhou City in northwest, Lanzhou , Gansu , China
| | - Yong Cai
- d Science Experimental Center, College of Life Science and Engineering, Northwest University for Nationalities , Chengguan District, Lanzhou City in northwest, Lanzhou , Gansu , China
| | - Xianyong Lan
- b College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| |
Collapse
|
20
|
Yang Q, Zhang S, Liu L, Cao X, Lei C, Qi X, Lin F, Qu W, Qi X, Liu J, Wang R, Chen H, Lan X. Application of mathematical expectation (ME) strategy for detecting low frequency mutations: An example for evaluating 14-bp insertion/deletion (indel) within the bovine PRNP gene. Prion 2017; 10:409-419. [PMID: 27580010 DOI: 10.1080/19336896.2016.1211593] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The detection method based on the mathematical expectation (ME) strategy is fast and accuracy for low frequency mutation screening in large samples. Previous studies have found that the 14-bp insertion/deletion (indel) variants of the 3' untranslated region (3' UTR) within bovine PRNP gene have been characterized with low frequency (≤5%) in global breeds outside China, which has not been determined in Chinese cattle breeds yet. Therefore, this study aimed to identify the 14-bp indel within PRNP gene in 5 major Chinese indigenous cattle breeds and to evaluate its associations with phenotypic traits. It was the first time to use ME strategy to detect low frequency indel polymorphisms and found that minor allele frequency was 0.038 (Qinchuan), 0.033 (Xianan), 0.013 (Nanyang), 0.003 (Jiaxian), and zero (Ji'an), respectively. Compared to the traditional detection method by which the sample was screened one by one, the reaction time by using the ME method was decreased 62.5%, 64.9%, 77.6%, 88.9% and 66.4%, respectively. In addition, the 14-bp indel was significantly associated with the growth traits in 2 cattle breeds, with the body length of Qinchuan cattle as well as the body weight and waistline of Xianan cattle. Our results have uncovered that the method based on ME strategy is rapid, reliable, and cost-effective for detecting the low frequency mutation as well as our findings provide a potential valuable theoretical basis for the marker-assisted selection (MAS) in beef cattle.
Collapse
Affiliation(s)
- Qing Yang
- a Innovation Experimental College , Northwest A&F University , Yangling , Shaanxi , P. R. China.,b College of Animal Science and Technology , Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture , Yangling , Shaanxi , P. R. China
| | - Sihuan Zhang
- b College of Animal Science and Technology , Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture , Yangling , Shaanxi , P. R. China
| | - Liangliang Liu
- c School of Statistics and Information , ShangHai University of International Business and Economics , Shanghai , P. R. China
| | - Xiukai Cao
- b College of Animal Science and Technology , Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture , Yangling , Shaanxi , P. R. China
| | - Chuzhao Lei
- b College of Animal Science and Technology , Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture , Yangling , Shaanxi , P. R. China
| | - Xinglei Qi
- d Xianan Cattle Technology Development Company , Biyang , Henan , P. R. China.,e Bureau of Animal Husbandry , Biyang , Henan , P. R. China
| | - Fengpeng Lin
- d Xianan Cattle Technology Development Company , Biyang , Henan , P. R. China.,e Bureau of Animal Husbandry , Biyang , Henan , P. R. China
| | - Weidong Qu
- e Bureau of Animal Husbandry , Biyang , Henan , P. R. China
| | - Xingshan Qi
- e Bureau of Animal Husbandry , Biyang , Henan , P. R. China
| | - Jiming Liu
- f Animal Husbandry Technology Promotion Station of Jiangxi , Nanchang , Jiangxi , P. R. China
| | - Rongmin Wang
- f Animal Husbandry Technology Promotion Station of Jiangxi , Nanchang , Jiangxi , P. R. China
| | - Hong Chen
- b College of Animal Science and Technology , Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture , Yangling , Shaanxi , P. R. China
| | - Xianyong Lan
- b College of Animal Science and Technology , Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture , Yangling , Shaanxi , P. R. China
| |
Collapse
|
21
|
Xu H, Zhang S, Zhang X, Dang R, Lei C, Chen H, Lan X. Evaluation of novel SNPs and haplotypes within the <i>ATBF1</i> gene and their effects on economically important production traits in cattle. Arch Anim Breed 2017. [DOI: 10.5194/aab-60-285-2017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. AT motif binding factor 1 (ATBF1) gene can promote the expression level of the growth hormone 1 (GH1) gene by binding to the enhancers of the POU1F1 and PROP1 genes; thus, it affects the growth and development of livestock. Considering that the ATBF1 gene also has a close relationship with the Janus kinase–signal transductor and activator of transcription (JAK–STAT) pathway, the objective of this work was to identify novel single-nucleotide polymorphism (SNP) variations and their association with growth traits in native Chinese cattle breeds. Five novel SNPs within the ATBF1 gene were found in 644 Qinchuan and Jinnan cattle for first time using 25 pairs of screening and genotyping primers. The five novel SNPs were named as AC_000175:g.140344C>G (SNP1), g.146573T>C (SNP2), g.205468C>T (SNP3), g.205575A>G (SNP4) and g.297690C<T (SNP5). Among them, SNP1 and SNP2 were synonymous coding SNPs, while SNP5 was a missense coding SNP, and the other SNPs were intronic. Haplotype analysis found 18 haplotypes in the two breeds, and three and five closely linked loci were revealed in Qinchuan and Jinnan breeds, respectively. Association analysis revealed that SNP1 was significantly associated with the height across the hip in Qinchuan cattle. SNP2 was found to be significantly related to chest circumference and body side length traits in Jinnan cattle. SNP3 was found to have significant associations with four growth traits in Qinchuan cattle. Moreover, the different combined genotypes, SNP1–SNP3, SNP1–SNP4 and SNP2–SNP5 were significantly associated with the growth traits in cattle. These findings indicated that the bovine ATBF1 gene had marked effects on growth traits, and the growth-trait-related loci can be used as DNA markers for maker-assisted selection (MAS) breeding programs in cattle.
Collapse
|
22
|
Yang Q, Zhang S, Liu L, Lei C, Qi X, Lin F, Qu W, Qi X, Liu J, Wang R, Chen H, Lan X. The evaluation of 23-bp and 12-bp insertion/deletion within the PRNP gene and their effects on growth traits in healthy Chinese native cattle breeds. JOURNAL OF APPLIED ANIMAL RESEARCH 2017. [DOI: 10.1080/09712119.2017.1348950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Qing Yang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, People’s Republic of China
| | - Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, People’s Republic of China
| | - Liangliang Liu
- School of Business Information, Shanghai University of International Business and Economics, Shanghai, People’s Republic of China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, People’s Republic of China
| | - Xinglei Qi
- Xia'nan cattle Technology Development Company, Biyang, People’s Republic of China
- Bureau of Animal Husbandry, Biyang, People’s Republic of China
| | - Fengpeng Lin
- Xia'nan cattle Technology Development Company, Biyang, People’s Republic of China
- Bureau of Animal Husbandry, Biyang, People’s Republic of China
| | - Weidong Qu
- Bureau of Animal Husbandry, Biyang, People’s Republic of China
| | - Xingshan Qi
- Bureau of Animal Husbandry, Biyang, People’s Republic of China
| | - Jiming Liu
- Animal Husbandry Technology Promotion Station of Jiangxi, Nanchang, People’s Republic of China
| | - Rongmin Wang
- Animal Husbandry Technology Promotion Station of Jiangxi, Nanchang, People’s Republic of China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, People’s Republic of China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, People’s Republic of China
| |
Collapse
|
23
|
Li J, Zhu X, Ma L, Xu H, Cao X, Luo R, Chen H, Sun X, Cai Y, Lan X. Detection of a new 20-bp insertion/deletion (indel) within sheep PRND gene using mathematical expectation (ME) method. Prion 2017; 11:143-150. [PMID: 28362554 DOI: 10.1080/19336896.2017.1300740] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Prion-related protein doppel gene (PRND), as an essential member of the mammalian prion gene family, is associated with the scrapie susceptibility as well as phenotype traits, so the genetic variation of the PRND has been highly concerned recently, including the single nucleiotide polymorphism (SNP) and insertion/deletion (indel). Therefore, the objective of present study was to examine the possible indel variants by mathematical expectation (ME) detection method as well as explore its associations with phenotype traits. A novel 20-bp indel was verified in 623 tested individuals representing 4 diversity sheep breeds. The results showed that 3 genotypes were detected and the minor allelic frequency were 0.008 (Lanzhou Fat-Tail sheep, LFTS), 0.084 (Small Tail Han sheep, STHS), 0.021(Tong sheep, TS) and 0.083 (Hu sheep, HS), respectively. Comparing with the traditional method of detecting samples one by one, the reaction times with ME method was decreased by 36.22% (STHS), 37.00% (HS), 68.67% (TS) and 83.33% (LFTS), respectively. Besides, this locus was significantly associated to cannon circumference index (P = 0.012) and trunk index (P = 0.037) in the Hu sheep breed. Notably, it was not concordance with the present result of DNA sequencing (GCTGTCCCTGCAGGGCTTCT) and dbSNPase of NCBI (NC_443194: g.46184887- 46184906delCTGCTGTCCCTGCAGGGCTT). Consequently, it was the first time to detect the new 20-bp indel of sheep PRND gene by ME strategy, which might provide a valuable theoretical basis for marker-assisted selection in sheep genetics and breeding.
Collapse
Affiliation(s)
- Jie Li
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China.,b Innovation Experimental College , Northwest A&F University , Yangling , China
| | - Xichun Zhu
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Lin Ma
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Hongwei Xu
- c Science Experimental Center , Northwest University for Nationalities , Lanzhou , China.,d College of Life Science and Engineering , Northwest University for Nationalities , Lanzhou , China
| | - Xin Cao
- c Science Experimental Center , Northwest University for Nationalities , Lanzhou , China.,d College of Life Science and Engineering , Northwest University for Nationalities , Lanzhou , China
| | - Renyun Luo
- e Ruilin Sci-Tech Cluture and Breeding Limit Company , Yongjing , China
| | - Hong Chen
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Xiuzhu Sun
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Yong Cai
- c Science Experimental Center , Northwest University for Nationalities , Lanzhou , China.,d College of Life Science and Engineering , Northwest University for Nationalities , Lanzhou , China
| | - Xianyong Lan
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| |
Collapse
|
24
|
Zhao H, He S, Zhu Y, Cao X, Luo R, Cai Y, Xu H, Sun X. A novel 29 bp insertion/deletion (indel) variant of the <i>LHX3</i> gene and its influence on growth traits in four sheep breeds of various fecundity. Arch Anim Breed 2017. [DOI: 10.5194/aab-60-79-2017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Abstract. Belonging to the same LIM homeobox (LHX) family, LHX3 and LHX4 are key transcription factors in animal growth and reproduction. Insertion/deletion (indel) is a relatively simple and effective DNA marker. Therefore, four sheep breeds of various fecundity were used to explore the novel indel variants within the sheep LHX3 and LHX4 gene, as well as to evaluate their effects on growth traits. Herein, only one novel 29 bp indel (NC_019460.2:g.3107494-3107522delGGCCTGGACTGTGATGGGCACCCTCCGGG) within the sheep LHX3 gene was found, and three genotypes were detected. Interestingly, the increasing trends of II (insertion/insertion) genotype frequency and I allelic frequency were the same as the growth of the fertility character. Genotypic frequency and allelic frequency distributions were significantly different between the high-fecundity breeds (HS, STHS and LFTS) and low-fecundity breed (TS) based on a χ2 test (P < 0.05). Association analyses showed that body length was significantly different in female TS and STHS and that chest width was significantly different for the female TS and male STHS (P < 0.05). These findings suggested that the 29 bp indel could extend the spectrum of genetic variations of the LHX3 gene in sheep and provide a valuable theoretical basis for the marker-assisted selection (MAS) in sheep breeding and genetics.
Collapse
|
25
|
Wang Y, Yang W, Gui L, Wang H, Zan L. Association and expression analyses of the Ucp2 and Ucp3 gene polymorphisms with body measurement and meat quality traits in Qinchuan cattle. J Genet 2017; 95:939-946. [PMID: 27994193 DOI: 10.1007/s12041-016-0720-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The uncoupling proteins (UCPs) belong to the mitochondrial inner membrane anion carrier superfamily and play an important role in energy homeostasis. Genetic studies have demonstrated that Ucp2 and Ucp3 gene variants are involved in obesity and metabolic syndrome. The aim of this study was to identify associations between polymorphisms of Ucp2 and Ucp3 genes and economically-important traits in Qinchuan cattle. In the present study, one single-nucleotide polymorphism (SNP) in the 5'UTR region (SNP1:g.C-754G) of the Ucp2 gene was identified by direct sequencing of 441 Qinchuan cattle. Two SNPs in exon 3 (SNP2: g.G4877A: SNP3: g.C4902T) of the Ucp3 gene were identified by sequencing and polymerase chain reactionrestriction fragment length polymorphism (PCR-RFLP) among 441 Qinchuan cattle. Association analysis showed that SNP1 and SNP2 were associated with the meat quality traits (MQTs) including back fat thickness, loin muscle area and intramuscular fat content. SNP3 was found to be associated with part of the body measurement traits (BMTs) which referred to withers height and chest depth. In addition, QTL pyramiding analysis showed that individuals with diplotype P3P3 (GG-GG-CC) exhibited the best performance in terms of back fat thickness, loin muscle area, intramuscular fat content, rump length, hip width, chest depth and chest circumference. With regard to the G4877A mutation, real time PCR analysis revealed that individuals with AA genotype of the Ucp3 gene expressed higher mRNA levels than those with GG genotype. These results suggest that the diplotype P3P3 (GG-GG-CC) could be used as a molecular marker of the combined genotypes for future selection of body measurement traits and meat quality traits in Qinchuan cattle.
Collapse
Affiliation(s)
- Yaning Wang
- College of Animal Science and Technology, Northwest A and F University, Yangling, Shaanxi 712100, People's Republic of China.
| | | | | | | | | |
Collapse
|
26
|
Ren F, Yu S, Chen R, Lv X, Pan C. Identification of a novel 12-bp insertion/deletion (indel) of iPS-related Oct4 gene and its association with reproductive traits in male piglets. Anim Reprod Sci 2017; 178:55-60. [PMID: 28139300 DOI: 10.1016/j.anireprosci.2017.01.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 01/20/2017] [Accepted: 01/22/2017] [Indexed: 01/01/2023]
Abstract
As a key factor of cellular reprogramming, Oct4 is one of vital transcription factors for induced pluripotent stem cells (iPSCs). Loss of its function or deletion causes apoptosis in primordial germ cells (PGCs), which affect reproductive traits in mammals. In this study, a novel 12-bp insertion/deletion (indel) polymorphism (NC_010449:g.2759-2760insGGTTTTTGTCTA) within the Oct4 gene was identified in 442 pigs of Large White (LW) and Landrace (LD) breeds, showing three genotypes designated as II, ID, and DD. The frequencies of allele "I" in LW and LD pigs were 0.587 and 0.648, respectively. The male piglets with homozygous II or DD genotypes of Oct4 gene exhibited better reproductive traits than those with heterozygous ID genotype. Moreover, there were two significant associations between this 12-bp indel polymorphism and testis long circumference (TLC) (P=0.005) and testis short girth (TSG) (P=0.003) as well as 15-day testis weight (TW) (P=0.013) in the LW male piglets. These findings suggest that the 12-bp indel polymorphism of the Oct4 gene might be a potential DNA marker for selecting preferred individuals in relation to reproductive traits in pig marker-assisted selection (MAS) breeding, which could contribute to the breeding and genetics in male piglets.
Collapse
Affiliation(s)
- Fa Ren
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China.
| | - Shuai Yu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China.
| | - Rui Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China.
| | - Xiaoyan Lv
- National Swine Foundation Seed Farm of Ankang Yangchen Modern Agriculture Group Co. Ltd, Ankang, 725000 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.
| |
Collapse
|
27
|
Zhang W, Li J, Guo Y, Zhang L, Xu L, Gao X, Zhu B, Gao H, Ni H, Chen Y. Multi-strategy genome-wide association studies identify the DCAF16-NCAPG region as a susceptibility locus for average daily gain in cattle. Sci Rep 2016; 6:38073. [PMID: 27892541 PMCID: PMC5125095 DOI: 10.1038/srep38073] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 11/04/2016] [Indexed: 01/16/2023] Open
Abstract
Average daily gain (ADG) is the most economically important trait in beef cattle industry. Using genome-wide association study (GWAS) approaches, previous studies have identified several causal variants within the PLAG1, NCAPG and LCORL genes for ADG in cattle. Multi-strategy GWASs were implemented in this study to improve detection and to explore the causal genes and regions. In this study, we conducted GWASs based on the genotypes of 1,173 Simmental cattle. In the SNP-based GWAS, the most significant SNPs (rs109303784 and rs110058857, P = 1.78 × 10−7) were identified in the NCAPG intron on BTA6 and explained 4.01% of the phenotypic variance, and the independent and significant SNP (rs110406669, P = 5.18 × 10−6) explained 3.32% of the phenotypic variance. Similarly, in the haplotype-based GWAS, the most significant haplotype block, Hap-6-N1416 (P = 2.56 × 10−8), spanned 12.7 kb on BTA6 and explained 4.85% of the phenotypic variance. Also, in the gene-based GWAS, seven significant genes were obtained which included DCAF16 and NCAPG. Moreover, analysis of the transcript levels confirmed that transcripts abundance of NCAPG (P = 0.046) and DCAF16 (P = 0.046) were significantly correlated with the ADG trait. Overall, our results from the multi-strategy GWASs revealed the DCAF16-NCAPG region to be a susceptibility locus for ADG in cattle.
Collapse
Affiliation(s)
- Wengang Zhang
- Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Junya Li
- Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yong Guo
- Animal Science and Technology College, Beijing University of Agriculture (BUA), Beijing 102206, China
| | - Lupei Zhang
- Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Lingyang Xu
- Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Xue Gao
- Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Bo Zhu
- Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Huijiang Gao
- Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Hemin Ni
- Animal Science and Technology College, Beijing University of Agriculture (BUA), Beijing 102206, China
| | - Yan Chen
- Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| |
Collapse
|
28
|
Zhang M, Pan C, Lin Q, Hu S, Dang R, Lei C, Chen H, Lan X. Exploration of the exonic variations of the iPSC-related <i>Nanog</i> gene and their effects on phenotypic traits in cattle. Arch Anim Breed 2016. [DOI: 10.5194/aab-59-351-2016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Abstract. Nanog is an important pluripotent transcription regulator transforming somatic cells to induced pluripotent stem cells (iPSCs), and its overexpression leads to a high expression of the growth and differentiation factor 3 (GDF3), which affects animal growth traits. Therefore, the aim of this study was to explore the genetic variations within the Nanog gene and their effects on phenotypic traits in cattle. Six novel exonic single nucleotide polymorphisms (SNPs) were found in six cattle breeds. Seven haplotypes were analyzed: TCAACC (0.260), TCAATA (0.039), TCATCC (0.019), TCGACC (0.506), TCGATA (0.137), TCGTCC (0.036), and CTGATA (0.003). There were strong linkage disequilibriums of SNP1 and SNP2 in Jiaxian cattle as well as of SNP5 and SNP6 in both Jiaxian cattle and Nanyang cattle. Moreover, SNP3, SNP4, and SNP5 were associated with phenotypes. The individuals with GG genotype at the SNP3 locus or AA genotype at the SNP4 locus showed better body slanting length and chest circumference or body height and hucklebone width in Nanyang cattle. The superiority of the SNP5-C allele regarding body height and cannon circumference was observed in Jiaxian cattle. The combination of SNP3 and SNP4 (GG–AA) had positive effects on body height, body slanting length, and chest circumference. These findings may indicate that Nanog, as a regulator of bovine growth traits, could be a candidate gene for marker-assisted selection (MAS) in breeding and genetics in cattle.
Collapse
|
29
|
Zhou F, Yang Q, Lei C, Chen H, Lan X. Relationship between genetic variants of POU1F1 , PROP1 , IGFBP3 genes and milk performance in Guanzhong dairy goats. Small Rumin Res 2016. [DOI: 10.1016/j.smallrumres.2016.05.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
30
|
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]
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
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]
|
33
|
Pausch H, Wurmser C, Reinhardt F, Emmerling R, Fries R. Short communication: Validation of 4 candidate causative trait variants in 2 cattle breeds using targeted sequence imputation. J Dairy Sci 2015; 98:4162-7. [PMID: 25892690 DOI: 10.3168/jds.2015-9402] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/13/2015] [Indexed: 12/15/2022]
Abstract
Most association studies for pinpointing trait-associated variants are performed within breed. The availability of sequence data from key ancestors of several cattle breeds now enables immediate assessment of the frequency of trait-associated variants in populations different from the mapping population and their imputation into large validation populations. The objective of this study was to validate the effects of 4 putatively causative variants on milk production traits, male fertility, and stature in German Fleckvieh and Holstein-Friesian animals using targeted sequence imputation. We used whole-genome sequence data of 456 animals to impute 4 missense mutations in DGAT1, GHR, PRLR, and PROP1 into 10,363 Fleckvieh and 8,812 Holstein animals. The accuracy of the imputed genotypes exceeded 95% for all variants. Association testing with imputed variants revealed consistent antagonistic effects of the DGAT1 p.A232K and GHR p.F279Y variants on milk yield and protein and fat contents, respectively, in both breeds. The allele frequency of both polymorphisms has changed considerably in the past 20 yr, indicating that they were targets of recent selection for milk production traits. The PRLR p.S18N variant was associated with yield traits in Fleckvieh but not in Holstein, suggesting that it may be in linkage disequilibrium with a mutation affecting yield traits rather than being causal. The reported effects of the PROP1 p.H173R variant on milk production, male fertility, and stature could not be confirmed. Our results demonstrate that population-wide imputation of candidate causal variants from sequence data is feasible, enabling their rapid validation in large independent populations.
Collapse
Affiliation(s)
- Hubert Pausch
- Chair of Animal Breeding, Technische Universität München, 85354 Freising, Germany.
| | - Christine Wurmser
- Chair of Animal Breeding, Technische Universität München, 85354 Freising, Germany
| | - Friedrich Reinhardt
- Vereinigte Informationssysteme Tierhaltung w.V. (VIT), 27283 Verden, Germany
| | - Reiner Emmerling
- Institute of Animal Breeding, Bavarian State Research Centre for Agriculture, 85586 Poing, Germany
| | - Ruedi Fries
- Chair of Animal Breeding, Technische Universität München, 85354 Freising, Germany
| |
Collapse
|
34
|
Zhang S, Dang Y, Zhang Q, Qin Q, Lei C, Chen H, Lan X. Tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) rapidly identified a critical missense mutation (P236T) of bovine ACADVL gene affecting growth traits. Gene 2015; 559:184-8. [PMID: 25620159 DOI: 10.1016/j.gene.2015.01.043] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 01/15/2015] [Accepted: 01/20/2015] [Indexed: 10/24/2022]
Abstract
Acyl-CoA dehydrogenase, very long chain (ACADVL), encoding ACADVL protein, targets the inner mitochondrial membrane where it catalyzes the first step of the mitochondrial fatty acid beta-oxidation pathway and plays an important role in body metabolism and oxidation of long chain fatty acid releasing energy. Tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) is an easy-to-operate, rapid, inexpensive, and exact method for SNP genotyping. Herein, T-ARMS-PCR was carried out to detect a critical missense mutation (AC_000176:g.2885C>A; Pro236Thr) within the ACADVL gene in 644 individuals from two cattle breeds. In order to evaluate the accuracy of the T-ARMS-PCR at this locus, the genotype of the sampled individuals was also identified by PCR-RFLP. The concordance between these two methods was 98.76%. Statistical analysis showed that the bovine ACADVL gene had a significant effect on chest width (P<0.05), chest depth (P<0.05), and hip width (P<0.05) in the Qinchuan breed. The cattle with AA genotype had superior growth traits compared to cattle with AC and/or CC genotypes. The "A" allele had positive effects on growth traits. Therefore, T-ARMS-PCR can replace PCR-RFLP for rapid genotyping of this mutation, which could be used as a DNA marker for selecting individuals with superior growth traits in the Qinchuan breed. These findings contribute to breeding and genetics in beef cattle industry.
Collapse
Affiliation(s)
- Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China.
| | - Yonglong Dang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Qingfeng Zhang
- College of Life Sciences, Heze University, Heze, Shangdong 274015, China
| | - Qiaomei Qin
- College of Life Sciences, Heze University, Heze, Shangdong 274015, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China.
| |
Collapse
|
35
|
Wu X, Jia W, Zhang J, Li X, Pan C, Lei C, Chen H, Dang R, Lan X. Determination of the novel genetic variants of goat STAT5A gene and their effects on body measurement traits in two Chinese native breeds. Small Rumin Res 2014. [DOI: 10.1016/j.smallrumres.2014.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|