Articles | Volume 64, issue 1
https://doi.org/10.5194/aab-64-147-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/aab-64-147-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Original study
| 
30 Apr 2021
Original study |
| 30 Apr 2021
| 30 Apr 2021
Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Xiaohua Yi
College of Animal Science and Technology, Northwest A&F
University, Yangling, Shaanxi, 712100, PR China
Shuai He
College of Animal Science and Technology, Northwest A&F
University, Yangling, Shaanxi, 712100, PR China
Shuhui Wang
College of Animal Science and Technology, Northwest A&F
University, Yangling, Shaanxi, 712100, PR China
Haidong Zhao
College of Animal Science and Technology, Northwest A&F
University, Yangling, Shaanxi, 712100, PR China
Mingli Wu
College of Animal Science and Technology, Northwest A&F
University, Yangling, Shaanxi, 712100, PR China
Shirong Liu
College of Animal Science and Technology, Northwest A&F
University, Yangling, Shaanxi, 712100, PR China
Xiuzhu Sun
CORRESPONDING AUTHOR
College of Grassland Agriculture, Northwest A&F University,
Yangling, Shaanxi 712100, PR China
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Wanxia Zhao, Ziteng Wang, Yichen Lei, Xiaoqin Tang, Xiaohua Yi, Junyi Jiang, Jiapeng Li, Shuhui Wang, and Xiuzhu Sun
Arch. Anim. Breed., 67, 343–351, https://doi.org/10.5194/aab-67-343-2024, https://doi.org/10.5194/aab-67-343-2024, 2024
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In this study, InDels loci of YAP and TAZ genes in two goat breeds were screened and identified, and the association between InDels loci of YAP and TAZ genes and growth traits was analyzed. The results showed that eight InDels loci were identified from goat YAP and TAZ genes. These InDels loci significantly affected growth traits such as chest width, body height, and body weight of goats. These findings can provide new molecular markers for goat molecular breeding.
Wanxia Zhao, Ziteng Wang, Yichen Lei, Xiaoqin Tang, Xiaohua Yi, Junyi Jiang, Jiapeng Li, Shuhui Wang, and Xiuzhu Sun
Arch. Anim. Breed., 67, 343–351, https://doi.org/10.5194/aab-67-343-2024, https://doi.org/10.5194/aab-67-343-2024, 2024
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In this study, InDels loci of YAP and TAZ genes in two goat breeds were screened and identified, and the association between InDels loci of YAP and TAZ genes and growth traits was analyzed. The results showed that eight InDels loci were identified from goat YAP and TAZ genes. These InDels loci significantly affected growth traits such as chest width, body height, and body weight of goats. These findings can provide new molecular markers for goat molecular breeding.
Mingli Wu, Shipeng Li, Guoliang Zhang, Yingzhi Fan, Yuan Gao, Yongzhen Huang, Xianyong Lan, Chuzhao Lei, Yun Ma, and Ruihua Dang
Arch. Anim. Breed., 62, 465–475, https://doi.org/10.5194/aab-62-465-2019, https://doi.org/10.5194/aab-62-465-2019, 2019
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Four indels were identified by sequencing with DNA pool. Association analysis showed that three of them were associated with growth traits (P<0.05). Our results demonstrated that the polymorphisms in bovine MSRB3 gene were significantly associated with growth traits, which could be candidate loci for marker-assisted selection (MAS) in cattle breeding. These molecular markers are expected to accelerate the process of molecular breeding.
Haidong Zhao, Mingli Wu, Shuhui Wang, Xiaohui Yu, Ze Li, Ruihua Dang, and Xiuzhu Sun
Arch. Anim. Breed., 61, 71–78, https://doi.org/10.5194/aab-61-71-2018, https://doi.org/10.5194/aab-61-71-2018, 2018
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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 a novel 24 bp indel within the AR gene. It 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.
Haidong Zhao, Shuai He, Yanjiao Zhu, Xin Cao, Renyun Luo, Yong Cai, Hongwei Xu, and Xiuzhu Sun
Arch. Anim. Breed., 60, 79–85, https://doi.org/10.5194/aab-60-79-2017, https://doi.org/10.5194/aab-60-79-2017, 2017
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The 29 bp indel of sheep LHX3 gene was firstly verified in four Chinese indigenous sheep breeds of various fecundity. Genotypic frequency and allelic frequency distributions were significantly different between the high-fecundity breeds (Hu sheep, HS; small-tail Han sheep, STHS; and Lanzhou fat-tail sheep, LFTS) and the low-fecundity breed (Tong sheep (TS)) based on an χ2 test (P < 0.05). Moreover, four significant differences were found in body length and chest width in TS and STHS (P < 0.05).
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Subject: DNA markers and gene expressions | Animal: Cattle
Mitochondrial DNA diversity of D-loop region in three native Turkish cattle breeds
Assessment of the association of the MOGAT1 and MOGAT3 gene with growth traits in different growth stages in Holstein calves
Genetic polymorphism of Pit-1 and CSN3 genes in Holstein calves and its associations with calf birth weight
The relationships between κ-casein (CSN3) gene polymorphism and some performance traits in Simmental cattle
Allele-specific polymerase chain reaction for the discrimination of elite Korean cattle associated with high beef quality and quantity
Determination of the association of GHR/AluI gene polymorphisms with milk yield traits in Holstein and Jersey cattle raised in Turkey
Regulating glycolysis and heat shock proteins in Gannan yaks (Bos grunniens) in response to hypoxia of the Qinghai–Tibet Plateau
Variation in bovine leptin gene affects milk fatty acid composition in New Zealand Holstein Friesian × Jersey dairy cows
Regulation of microRNA-33, SREBP and ABCA1 genes in a mouse model of high cholesterol
Effects of polymorphism of the GPAM gene on milk quality traits and its relation to triglyceride metabolism in bovine mammary epithelial cells of dairy cattle
Determination of the effect of functional single-nucleotide polymorphisms associated with glycerolipid synthesis on intramuscular fat deposition in Korean cattle steer
DNA analysis of the Russian populations of Aberdeen Angus, Hereford and Belgian Blue cattle
Variation in the stearoyl-CoA desaturase gene (SCD) and its influence on milk fatty acid composition in late-lactation dairy cattle grazed on pasture
Genetic variant of SPARC gene and its association with growth traits in Chinese cattle
Effect of DNA markers on the fertility traits of Japanese Black cattle for improving beef quantity and quality
The effect of polymorphism in the FADS2 gene on the fatty acid composition of bovine milk
Potential of TLR-gene diversity in Czech indigenous cattle for resistance breeding as revealed by hybrid sequencing
Exploring insertions and deletions (indels) of MSRB3 gene and their association with growth traits in four Chinese indigenous cattle breeds
Exploring genetic diversity and phylogenic relationships of Chinese cattle using gene mtDNA 16S rRNA
The effect of acyl-CoA synthetase long-chain family member 5 on triglyceride synthesis in bovine preadipocytes
Copy number variation (CNV) in the IGF1R gene across four cattle breeds and its association with economic traits
Polymorphisms of the ASIP gene and the haplotype are associated with fat deposition traits and fatty acid composition in Chinese Simmental steers
Comprehensive assessment of candidate genes associated with fattening performance in Holstein–Friesian bulls
Assessment of growth hormone gene polymorphism effects on reproductive traits in Holstein dairy cattle in Tunisia
Effects of polymorphisms in CAPN1 and CAST genes on meat tenderness of Chinese Simmental cattle
Effect of leptin genetic polymorphism on lameness prevalence in Tunisian Holstein cows
The microRNA gene bta-mir-2313 in cattle: an atlas of regulatory elements and an association analysis with growth and carcass traits in the Slovenian Simental cattle breed
The effect of short/branched chain acyl-coenzyme A dehydrogenase gene on triglyceride synthesis of bovine mammary epithelial cells
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
A combined genotype of three SNPs in the bovine gene is related to growth performance in Chinese cattle
Evaluation of novel SNPs and haplotypes within the ATBF1 gene and their effects on economically important production traits in cattle
Identification and expression analysis of miR-144-5p and miR-130b-5p in dairy cattle
SIRT1 gene polymorphisms associated with carcass traits in Luxi cattle
The 10 bp duplication insertion/deletion in the promoter region within paired box 7 gene is associated with growth traits in cattle
PSAP gene variants and haplotypes reveal significant effects on carcass and meat quality traits in Chinese Simmental-cross cattle
Exploration of the exonic variations of the iPSC-related Nanog gene and their effects on phenotypic traits in cattle
A novel 17 bp indel in the SMAD3 gene alters transcription level, contributing to phenotypic traits in Chinese cattle
Indels within the bovine visfatin gene affect its mRNA expression in longissimus muscle and subcutaneous fat
Eymen Demir, Nina Moravčíková, Bahar Argun Karsli, Radovan Kasarda, Ibrahim Aytekin, Umit Bilginer, and Taki Karsli
Arch. Anim. Breed., 66, 31–40, https://doi.org/10.5194/aab-66-31-2023, https://doi.org/10.5194/aab-66-31-2023, 2023
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This study confirmed that mtDNA could make a significant contribution to cattle farming in both theory and practice. In theory, even if they were domesticated in different geographical areas, the patterns of crossbreeding between taurine and indicine were detected in Anatolian cattle at a low frequency. In practice, pedigree records could be revised in terms of admixture level and species-specific haplotypes of taurine and indicine by the farmers via molecular studies such as mtDNA.
Gökhan Gökçe and Mervan Bayraktar
Arch. Anim. Breed., 65, 301–308, https://doi.org/10.5194/aab-65-301-2022, https://doi.org/10.5194/aab-65-301-2022, 2022
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The study was conducted on Holstein calves to find the association between MOGAT1, MOGAT3/g.A229G, and MOGAT3/g.G1627A and growth traits. Association analysis showed a statistically significant difference between the MOGAT1 and body weight, body length, and chest circumference, MOGAT3/g.A229G with ADG and withers height, and MOGAT3/g.G1627A with body weight and body length (p < 0.05). The results confirmed that the MOGAT1, MOGAT3/g.A229G, and MOGAT3/g.G1627A locus are strong candidate genes.
Ismail Fındık and Memis Özdemir
Arch. Anim. Breed., 65, 285–292, https://doi.org/10.5194/aab-65-285-2022, https://doi.org/10.5194/aab-65-285-2022, 2022
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HinfI polymorphisms of Pit-1 and CSN3 genes were identified in DNA isolated from blood samples of 100 Holstein calves used in the study, using the PCR-RFLP method. According to the Hardy–Weinberg genetic equilibrium test, it was observed that the distribution of genotype frequencies of HinfI polymorphisms of Pit-1 genes in the studied population was in equilibrium, but not in equilibrium in terms of CSN3 gene location.
Hamiye Ünal and Sinan Kopuzlu
Arch. Anim. Breed., 65, 129–134, https://doi.org/10.5194/aab-65-129-2022, https://doi.org/10.5194/aab-65-129-2022, 2022
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This study's aim is to investigate the polymorphism of Simmental cattle raised on a private farm in terms of the CSN3 gene locus from milk proteins by using the PCR-RFLP method and to reveal the distribution of genotype and allele frequencies of animals in terms of related gene locations. In addition, the relationship between genotypes and some performance characteristics is investigated.
Wonhee Lee, Insik Nam, Daehyun Kim, Kukdong Kim, and Yoonseok Lee
Arch. Anim. Breed., 65, 47–53, https://doi.org/10.5194/aab-65-47-2022, https://doi.org/10.5194/aab-65-47-2022, 2022
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The AS-PCR analyzes genotypes using two pairs of primer in basic equipment: a thermal cycler and an electrophoresis system. This research team analyzed three SNPs in 10 Korean cattle using the AS-PCR method. The result can be easily confirmed visually through the appearance of different amplification sizes depending on allele. Therefore, the use of the AS-PCR method will enable researchers to carry out genotyping analysis for SNPs without the use of sophisticated instrumentation and at low cost.
Ozden Cobanoglu, Ertugrul Kul, Eser K. Gurcan, Samet H. Abaci, and Soner Cankaya
Arch. Anim. Breed., 64, 417–424, https://doi.org/10.5194/aab-64-417-2021, https://doi.org/10.5194/aab-64-417-2021, 2021
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This study aimed to detect a potential association between GHR/AluI polymorphism and milk yield and milk composition traits in dairy cows raised in commercial herds using the PCR-RFLP assay. In conclusion, the GHR gene should be regarded as potential candidate genes in marker-assisted selection programs to improve the performance of milk and related traits in Turkey dairy cattle populations.
Yuliang Wen, Jiqing Wang, Xiu Liu, Shaobin Li, Jiang Hu, and Yuzhu Luo
Arch. Anim. Breed., 64, 345–353, https://doi.org/10.5194/aab-64-345-2021, https://doi.org/10.5194/aab-64-345-2021, 2021
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The regulation of glycolysis and heat shock proteins (HSPs) in Gannan yaks at different altitudes were determined. We found that HIF1A and PDK4 expression and glycolysis-related enzyme level were significantly increased, but CA level was significantly decreased with altitude. HSP27 and HSP60 were highly expressed with altitude. These results are useful to better understand the unique adaptability of Gannan yaks, allowing them to survive in hypoxia conditions.
Ishaku Lemu Haruna, Huitong Zhou, and Jon G. H. Hickford
Arch. Anim. Breed., 64, 245–256, https://doi.org/10.5194/aab-64-245-2021, https://doi.org/10.5194/aab-64-245-2021, 2021
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The polymerase chain reaction (PCR) coupled with single-strand conformational polymorphism (SSCP) analysis was used to reveal variation in bovine leptin gene (LEP) in New Zealand (NZ) Holstein Friesian × Jersey (HF × J) dairy cows. This is the first report of findings of this kind in NZ HF × J cows, and they suggest that variation in exon 3 of bovine leptin gene could be explored as a means of decreasing the concentration of saturated fatty acids in milk.
Xianglun Zhang, Hongbo Zhao, Qingkai Sheng, Xiaomu Liu, Wei You, Haichao Lin, and Guifen Liu
Arch. Anim. Breed., 64, 103–108, https://doi.org/10.5194/aab-64-103-2021, https://doi.org/10.5194/aab-64-103-2021, 2021
Haibin Yu, Yaolu Zhao, Ambreen Iqbal, Lixin Xia, Zitong Bai, Hao Sun, Xibi Fang, Runjun Yang, and Zhihui Zhao
Arch. Anim. Breed., 64, 35–44, https://doi.org/10.5194/aab-64-35-2021, https://doi.org/10.5194/aab-64-35-2021, 2021
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In this study, we examine the correlation between the expression of GPAM and adipogenesis in bovine mammary epithelial cells (bMECs). Additionally, three novel polymorphisms are identified within the bovine key functional domain of GPAM. GPAM plays a pivotal role in the regulation of phospholipid levels and cellular triacylglycerol, and its mutations could serve as a competent molecular marker that could be utilized for marker-assisted selection.
Hyeongrok Kim, Dong-Yep Oh, and Yoonseok Lee
Arch. Anim. Breed., 64, 27–33, https://doi.org/10.5194/aab-64-27-2021, https://doi.org/10.5194/aab-64-27-2021, 2021
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Intramuscular fat deposition in the longissimus dorsi muscle of Hanwoo is regulated by several genes related to lipid metabolism. One of these genes encodes the enzyme bovine glycerol-3-phosphate acyltransferase, mitochondrial (GPAM). This gene regulates triacylglycerol by gene expression. Thus, our research group has identified SNPs related to the regulation of glycerolipid synthesis in the 3′-UTR of GPAM and verified the function of SNPs affecting intramuscular fat deposition in Hanwoo.
Elena N. Konovalova, Olga S. Romanenkova, Valeria V. Volkova, and Olga V. Kostyunina
Arch. Anim. Breed., 63, 409–416, https://doi.org/10.5194/aab-63-409-2020, https://doi.org/10.5194/aab-63-409-2020, 2020
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This F94L MSTN polymorphism study demonstrates the high genetic potential of Aberdeen Angus and Belgian Blue cattle. The Aberdeen Angus populations have animal carriers of the AM, OS, DD and M1 genetic defects points. Animal carriers of HY and MSUD genetic defects were absent in the Hereford herds. These facts allow us to conclude that the breeding of the above breeds has great potential for improving meat cattle industry profitability under genetic defect control.
Yunhai Li, Huitong Zhou, Long Cheng, Jenny Zhao, and Jonathan Hickford
Arch. Anim. Breed., 63, 355–366, https://doi.org/10.5194/aab-63-355-2020, https://doi.org/10.5194/aab-63-355-2020, 2020
Danyang Zhang, Jiawei Xu, Peng Yang, Yifan Wen, Hua He, Jiaxiao Li, Juntong Liang, Yining Zheng, Zijing Zhang, Xianwei Wang, Xiang Yu, Eryao Wang, Chuzhao Lei, Hong Chen, and Yongzhen Huang
Arch. Anim. Breed., 63, 31–37, https://doi.org/10.5194/aab-63-31-2020, https://doi.org/10.5194/aab-63-31-2020, 2020
Fuki Kawaguchi, Miyako Tsuchimura, Kenji Oyama, Tamako Matsuhashi, Shin Maruyama, Hideyuki Mannen, and Shinji Sasazaki
Arch. Anim. Breed., 63, 9–17, https://doi.org/10.5194/aab-63-9-2020, https://doi.org/10.5194/aab-63-9-2020, 2020
Witold Stanisław Proskura, Michał Liput, Daniel Zaborski, Zbigniew Sobek, Yu-Hsiang Yu, Yeong-Hsiang Cheng, and Andrzej Dybus
Arch. Anim. Breed., 62, 547–555, https://doi.org/10.5194/aab-62-547-2019, https://doi.org/10.5194/aab-62-547-2019, 2019
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Polyunsaturated fatty acids play an important role in a wide variety of physiological processes. They are produced by a series of chemical reactions. One of the enzymes converting such acids is a delta 6 desaturase encoded by the FADS2 gene. Therefore, we aimed to determine possible associations between the polymorphism in this gene and milk fatty acid composition in dairy cattle. An identified substitution could be used as a potential genetic marker for fatty acid composition in bovine milk.
Karel Novák, Marek Bjelka, Kalifa Samake, and Terezie Valčíková
Arch. Anim. Breed., 62, 477–490, https://doi.org/10.5194/aab-62-477-2019, https://doi.org/10.5194/aab-62-477-2019, 2019
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Resequencing of diversity hidden in the innate-immunity genes of the TLR series in Czech Simmental, its conserved subpopulation, and the ancestral Czech Red cattle showed sufficient potential for infection resistance breeding regardless of the prevailing breeding for production traits on the one hand and a limited potential of diversity preserved in the historical populations on the other. The importance of the characterization of genetic resources to counteract changing infections is implied.
Mingli Wu, Shipeng Li, Guoliang Zhang, Yingzhi Fan, Yuan Gao, Yongzhen Huang, Xianyong Lan, Chuzhao Lei, Yun Ma, and Ruihua Dang
Arch. Anim. Breed., 62, 465–475, https://doi.org/10.5194/aab-62-465-2019, https://doi.org/10.5194/aab-62-465-2019, 2019
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Four indels were identified by sequencing with DNA pool. Association analysis showed that three of them were associated with growth traits (P<0.05). Our results demonstrated that the polymorphisms in bovine MSRB3 gene were significantly associated with growth traits, which could be candidate loci for marker-assisted selection (MAS) in cattle breeding. These molecular markers are expected to accelerate the process of molecular breeding.
Linjun Yan, Yifan She, Mauricio A. Elzo, Chunlei Zhang, Xingtang Fang, and Hong Chen
Arch. Anim. Breed., 62, 325–333, https://doi.org/10.5194/aab-62-325-2019, https://doi.org/10.5194/aab-62-325-2019, 2019
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Most gene mtDNA 16S rRNA studies were with aquatic organisms, insects, and a few mammalian species; no reports involved cattle. The objective of this research was to characterize the genetic and phylogenetic diversity among 12 cattle breeds utilizing gene mtDNA 16S rRNA. The base percentages of this gene had a strong bias towards A + T. Only transitions or transversions were detected. The phylogenetic analysis indicated the existence of Bos taurus and Bos indicus ancestry in Chinese cattle.
Xiang Yu, Xibi Fang, Hang Xiao, Zhihui Zhao, Steffen Maak, Mengyan Wang, and Runjun Yang
Arch. Anim. Breed., 62, 257–264, https://doi.org/10.5194/aab-62-257-2019, https://doi.org/10.5194/aab-62-257-2019, 2019
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The study was to clarify the roles of ACSL5 in regulating synthesis of triglycerides and lipid droplet formation in bovine preadipocytes through vectors constructing and electransfection. Research results confirmed that the ACSL5 gene could promote the synthesis of triglycerides in bovine adipocytes by participating in the fatty acid metabolism pathway. The interaction of ACSL5 with related fatty acid synthase in the fatty acid biosynthesis pathway needs further analysis.
Yi-Lei Ma, Yi-Fan Wen, Xiu-Kai Cao, Jie Cheng, Yong-Zhen Huang, Yun Ma, Lin-Yong Hu, Chu-Zhao Lei, Xing-Lei Qi, Hui Cao, and Hong Chen
Arch. Anim. Breed., 62, 171–179, https://doi.org/10.5194/aab-62-171-2019, https://doi.org/10.5194/aab-62-171-2019, 2019
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We used lots of Chinese cattle to detect the specific regional variation in the IGF1R genome. It was found that this variation in the Chinese cattle population is related to the weight and height of the cattle. There is a lot of genetic information in this mutated region, which may be the cause affecting the traits. Our study provided a preliminary result for the functional role of the IGF1R variation in larger populations and for an important marker in cattle breeding programs.
Yinuo Liu, Xibi Fang, Zhihui Zhao, Junya Li, Elke Albrecht, Lisa Schering, Steffen Maak, and Runjun Yang
Arch. Anim. Breed., 62, 135–142, https://doi.org/10.5194/aab-62-135-2019, https://doi.org/10.5194/aab-62-135-2019, 2019
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ASIP can regulate the obesity of mice but studies of ASIP effects on bovine fat deposition and meat quality are rare. The L1-BT element inserted upstream of bovine ASIP can cause ASIP mRNA overexpression. In this study, L1-BT element indel, two single nucleide polymorphisms (SNPs) in ASIP, and its haplotypes showed significant correlations with fat deposition traits and fatty acid composition in Chinese Simmental steers, suggesting that ASIP may be a biomarker for beef cattle breeding selection.
Sena Ardicli, Hale Samli, Buse Vatansever, Bahadir Soyudal, Deniz Dincel, and Faruk Balci
Arch. Anim. Breed., 62, 9–32, https://doi.org/10.5194/aab-62-9-2019, https://doi.org/10.5194/aab-62-9-2019, 2019
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An extensive genetic evaluation of cattle fattening performance was performed in this study. Fifteen SNPs in the LEP, FABP4, DGAT1, TG, IGF1, IGF1R, MYF5, LGB, CAPN1, CAST, GHR, and OLR1 genes were evaluated in 296 purebred Holstein–Friesian bulls using PCR-RFLP. This study clearly demonstrated that individual or combined effects of the genotypes at the selected genes may be effective on performance traits at different periods of animal growth and fattening.
Sihem Amiri, Bayrem Jemmali, Mohamed Amine Ferchichi, Hajer Jeljeli, Rekik Boulbaba, and Abderrahmane Ben Gara
Arch. Anim. Breed., 61, 481–489, https://doi.org/10.5194/aab-61-481-2018, https://doi.org/10.5194/aab-61-481-2018, 2018
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Genetic polymorphims in the growth hormone (GH) gene were studied in 410 Holstein dairy cows. Genotyping was carried out using PCR-RFLP. Data were analyzed by the MIXED procedure to reveal the effect of GH genotypes on reproductive traits. GH-AluI had a favorable effect on exanimate traits except for the age at the first calving. The homozygous LL genotype seemed to be advantageous for calving interval and days open. A significant effect of different GH-AluI–MspI combined genotypes was found.
Xiaomei Sun, Xiuxiang Wu, Yongliang Fan, Yongjiang Mao, Dejun Ji, Bizhi Huang, and Zhangping Yang
Arch. Anim. Breed., 61, 433–439, https://doi.org/10.5194/aab-61-433-2018, https://doi.org/10.5194/aab-61-433-2018, 2018
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Genetic markers are important tools for beef cattle breeding. Our work suggests that CAPN1 genetic markers have a positive effect on meat tenderness and marbling traits, the most important meat quality traits for consumers. The associations between the genotyped SNPs in this research and meat quality traits are of potential interest to the beef industry and could lay an important foundation for the expanding panel of functional variation relevant to meat quality.
Mohamed Amine Ferchichi, Bayrem Jemmali, Sihem Amiri, Abderrahmane Ben Gara, and Boulbaba Rekik
Arch. Anim. Breed., 61, 305–310, https://doi.org/10.5194/aab-61-305-2018, https://doi.org/10.5194/aab-61-305-2018, 2018
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This study aims to investigate the screening of leptin genetic polymorphism and its effect on lameness prevalence. Prevalence of lameness was evaluated and results showed that genotypes and other factors included in the logistic regression model significantly affect the prevalence of lameness in Holstein cows (P < 0.01). The probability of lameness incidence varied between 37 % and 99 % with parity. This recorded incidence is greater in winter and autumn than in the summer and spring.
Špela Malovrh, Tanja Kunej, Milena Kovač, and Peter Dovč
Arch. Anim. Breed., 61, 271–278, https://doi.org/10.5194/aab-61-271-2018, https://doi.org/10.5194/aab-61-271-2018, 2018
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Effects of miRNA polymorphisms on phenotypic traits have been studied in several species but much less in cattle. We tested the association between polymorphisms of bta-miR-2313 and growth and carcass traits in the Slovenian Simmental cattle breed and developed an atlas of miRNA regulatory elements. Bta-miR-2313 warrants further functional analysis since it overlaps with several QTL, has over 3100 predicted targets, and is located within GRAMD1B, associated with production traits in cattle.
Ping Jiang, Xibi Fang, Zhihui Zhao, Xianzhong Yu, Boxing Sun, Haibin Yu, and Runjun Yang
Arch. Anim. Breed., 61, 115–122, https://doi.org/10.5194/aab-61-115-2018, https://doi.org/10.5194/aab-61-115-2018, 2018
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ACADSB is a member of the acyl-CoA dehydrogenase family, which can catalyze the dehydrogenation of acyl-CoA derivatives in lipometabolism. Our previous transcriptome analysis results identified it as a differentially expressed gene in mammary tissue between low and high milk fat cattle. Current results showed that ACADSB expression level was positively correlated with cellular triglycerides content, and it was actively involved in fatty acid metabolism pathway in BME cell of dairy cattle.
Haidong Zhao, Mingli Wu, Shuhui Wang, Xiaohui Yu, Ze Li, Ruihua Dang, and Xiuzhu Sun
Arch. Anim. Breed., 61, 71–78, https://doi.org/10.5194/aab-61-71-2018, https://doi.org/10.5194/aab-61-71-2018, 2018
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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 a novel 24 bp indel within the AR gene. It 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.
Jieping Huang, Qiuzhi Zheng, Shuzhe Wang, Qiongqiong Zhang, Lijun Jiang, Ruijie Hao, Fen Li, and Yun Ma
Arch. Anim. Breed., 60, 357–362, https://doi.org/10.5194/aab-60-357-2017, https://doi.org/10.5194/aab-60-357-2017, 2017
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We investigated the expression profile and polymorphism of bovine PPARD as well as their association with growth traits in Chinese cattle. Association analysis suggested that individuals with the GAAGTT combined genotype of three SNPs detected showed optimal values in all the growth traits analyzed. These results revealed that the GAAGTT combined genotype of three SNPs detected in the bovine PPARD gene was a significant potential genetic marker for marker-assisted selection in Chinese cattle.
Han Xu, Sihuan Zhang, Xiaoyan Zhang, Ruihua Dang, Chuzhao Lei, Hong Chen, and Xianyong Lan
Arch. Anim. Breed., 60, 285–296, https://doi.org/10.5194/aab-60-285-2017, https://doi.org/10.5194/aab-60-285-2017, 2017
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This work identified SNPs in the growth- and development-related ATBF1 gene in cattle. Five novel SNPs were found in 644 cattle. The results found that SNP1, SNP2, and SNP3 and the combined genotypes SNP1–SNP3, SNP1–SNP4 and SNP2–SNP5 were significantly associated with growth traits in Qinchuan and Jinnan cattle. These findings indicate that the bovine ATBF1 gene has marked effects on growth traits, and the growth-trait-related loci can be used as DNA markers for MAS breeding programs in cattle.
Zhixiong Li, Hongliang Wang, Ling Chen, Mengxing Zhai, Si Chen, Na Li, and Xiaolin Liu
Arch. Anim. Breed., 60, 199–204, https://doi.org/10.5194/aab-60-199-2017, https://doi.org/10.5194/aab-60-199-2017, 2017
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Bovine mastitis, a prevalent and complex infectious disease, can result in significant dairy cattle losses. MicroRNAs (miRNAs) play important roles in regulating innate and adaptive immune responses. The results in this paper show that the expression of miR-144-5p and miR-130b-5p in mastitis-infected mammary tissue was significantly downregulated and upregulated, respectively, compared to healthy tissue. Our findings may provide a method for the treatment of mastitis.
Guifen Liu, Hongbo Zhao, Xiuwen Tan, Haijian Cheng, Wei You, Fachun Wan, Yifan Liu, Enliang Song, and Xiaomu Liu
Arch. Anim. Breed., 60, 27–32, https://doi.org/10.5194/aab-60-27-2017, https://doi.org/10.5194/aab-60-27-2017, 2017
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The main contribution of our paper is the identification of several SNPs of the SIRT1 gene in beef cattle and their relationships to carcass traits such as weight and meat percentage. We believe that this contribution is theoretically and practically relevant because beef cattle are bred to maximize carcass quality, but traits that lead to carcass quality are difficult to assess in vivo. We provide a method to select individuals for breeding based on genetic propensity for meat production.
Yunyun Jin, Hanfang Cai, Jiming Liu, Fengpeng Lin, Xinglei Qi, Yueyu Bai, Chuzhao Lei, Hong Chen, and Xianyong Lan
Arch. Anim. Breed., 59, 469–476, https://doi.org/10.5194/aab-59-469-2016, https://doi.org/10.5194/aab-59-469-2016, 2016
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Paired box 7 (Pax7) gene, a member of the paired box gene family, plays a critical role in animal growth and muscle development, especially in cell proliferation and self-renewal. In our study, the 10 bp duplication indel was detected in the promoter region within bovine Pax7 gene as well as its association with growth traits. This indel was significantly associated with the body weight in Xianan cattle, the body height in Jinjiang cattle, and the hip width in Pi'nan cattle.
Pengcheng Guo, Zhihui Zhao, Shouqing Yan, Junya Li, Hang Xiao, Dongxue Yang, Yaolu Zhao, Ping Jiang, and Runjun Yang
Arch. Anim. Breed., 59, 461–468, https://doi.org/10.5194/aab-59-461-2016, https://doi.org/10.5194/aab-59-461-2016, 2016
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Prosaposin (PSAP) is involved in muscle development and as a candidate gene in economic traits of cattle. Six novel SNPs of PSAP were identified and 47 traits in beef cattle measured. Association analysis revealed I10-65G > A, I10-162C > T, and E11-93C > G were significantly associated with carcass composition traits. Individuals with GCCCGC and ACCTCC haplotypes showed higher dressed weight, backfat thickness, and rib eye area, thus suggesting a genetic influence on cattle carcass composition.
Meng Zhang, Chuanying Pan, Qin Lin, Shenrong Hu, Ruihua Dang, Chuzhao Lei, Hong Chen, and Xianyong Lan
Arch. Anim. Breed., 59, 351–361, https://doi.org/10.5194/aab-59-351-2016, https://doi.org/10.5194/aab-59-351-2016, 2016
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Nanog is an important pluripotent transcription regulator, and its overexpression leads to a high expression of the growth and differentiation factor 3, affecting animal growth traits. 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 were found in six cattle breeds and indicated that Nanog could be a candidate gene for marker-assisted selection in cattle breeding.
Tao Shi, Wenwen Peng, Jianyu Yan, Hanfang Cai, Xianyong Lan, Chuzhao Lei, Yueyu Bai, and Hong Chen
Arch. Anim. Breed., 59, 151–157, https://doi.org/10.5194/aab-59-151-2016, https://doi.org/10.5194/aab-59-151-2016, 2016
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SMAD3 plays essential roles in myogenesis and osteogenesis and may relate to the regulation of body weight. In this study, a 17 bp indel in intron3 of the SMAD3 gene was detected in four Chinese cattle breeds (Qinchuan, Jiaxian, Nanyang and Caoyuan) by using DNA pool sequencing, and it was significantly associated with gene expression and growth traits of Qinchuan and Caoyuan cattle. This indel could be could be a promising marker for beef cattle breeding.
H. Cai, Z. Wang, X. Lan, Y. Xu, H. Chen, and C. Lei
Arch. Anim. Breed., 59, 91–95, https://doi.org/10.5194/aab-59-91-2016, https://doi.org/10.5194/aab-59-91-2016, 2016
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In this research, the effects of two indel loci of the visfatin gene on mRNA expression levels were studied. The results imply that the expression levels of bovine visfatin vary with age and its indels might be putative variants mediating the expression of the bovine visfatin gene. This study provides useful information for further functional studies of bovine visfatin.
Cited articles
Alexandrov, A., Chernyakov, I., Gu, W., Hiley, S. L., Hughes, T. R.,
Grayhack, E. J., and Phizicky, E. M.: Rapid tRNA decay can result from lack of
nonessential modifications, Mol. Cell, 21, 87–96,
https://doi.org/10.1016/j.molcel.2005.10.036, 2006.
Barrett, J. C., Hansoul, S., Nicolae, D. L., Cho, J. H., Duerr, R. H., Rioux, J. D., Brant, S. R., Silverberg, M. S., Taylor, K. D., Barmada, M. M., Bitton, A., Dassopoulos, T., Datta, L. W., Green, T., Griffiths, A. M., Kistner, E. O., Murtha, M. T., Regueiro, M. D., Rotter, J. I., Schumm, L. P., Steinhart, A. H., Targan, S. R., Xavier, R. J., Consortium, N. I. G., Libioulle, C., Sandor, C., Lathrop, M., Belaiche, J., Dewit, O., Gut, I., Heath, S., Laukens, D., Mni, M., Rutgeerts, P., Gossum, A, V., Zelenika, D., Franchimont, D., Hugot, J. P., Vos, M. D., Vermeire, S., Louis, E., Consortium, B. F. I., Consortium, W. T. C. C., Cardon, L. R., Anderson, C. A., Drummond, H., Nimmo, E., Ahmad, T., Prescott, N. J., Onnie, C. M., Fisher, S. A., Marchini, J., Ghori, J., Bumpstead, S., Gwilliam, R., Tremelling, M., Deloukas, P., Mansfield, J., Jewell, D., Satsangi, J., Mathew, C, G., Parkes, M., Georges, M., and Daly, M. J: Genome-wide association defines
more than 30 distinct susceptibility loci for Crohn's disease, Nat.
Genet., 40, 955–962, https://doi.org/10.1038/ng.175, 2008.
Bohnsack, K. E., Höbartner, C., and Bohnsack, M. T.: Eukaryotic
5-methylcytosine (m5C) RNA Methyltransferases: Mechanisms, Cellular
Functions, and Links to Disease, Genes, 10, 102, https://doi.org/10.3390/genes10020102, 2019.
Cătoi, A. F., Pârvu, A., Mureşan, A., and Busetto, L.: Metabolic
Mechanisms in Obesity and Type 2 Diabetes: Insights from Bariatric/Metabolic
Surgery, Obesity Facts, 8, 350–363, https://doi.org/10.1159/000441259,
2015.
Chen, H., Yang, H., Zhu, X., Yadav, T., Ouyang, J., Truesdell, S. S., Tan,
J., Wang, Y., Duan, M., Wei, L., Zou, L., Levine, A. S., Vasudevan, S., and Lan,
L.: m5C modification of mRNA serves a DNA damage code to promote homologous
recombination, Nat. Commun., 11, 2834,
https://doi.org/10.1038/s41467-020-16722-7, 2020.
Derikx, M. H., Geisz, A., Kereszturi, É., and Sahin-Tóth, M.: Functional
significance of SPINK1 promoter variants in chronic pancreatitis, American
journal of physiology, Gastrointestinal and Liver Physiology, 308,
G779–G784, https://doi.org/10.1152/ajpgi.00022.2015, 2015.
Franke, B., Vermeulen, S. H., Steegers-Theunissen, R. P., Coenen, M. J.,
Schijvenaars, M. M., Scheffer, H., den Heijer, M., and Blom, H. J.: An
association study of 45 folate-related genes in spina bifida: Involvement of
cubilin (CUBN) and tRNA aspartic acid methyltransferase 1 (TRDMT1), Birth Defects Res. A, 85,
216–226, https://doi.org/10.1002/bdra.20556, 2009.
Goll, M. G., Kirpekar, F., Maggert, K. A., Yoder, J. A., Hsieh, C. L.,
Zhang, X., Golic, K. G., Jacobsen, S. E., and Bestor, T. H.: Methylation of
tRNAAsp by the DNA methyltransferase homolog Dnmt2, Science, 311, 395–398, https://doi.org/10.1126/science.1120976, 2006.
Grosjean, H., Breton, M., Sirand-Pugnet, P., Tardy, F., Thiaucourt, F.,
Citti, C., Barré, A., Yoshizawa, S., Fourmy, D., de Crécy-Lagard,
V., and Blanchard, A.: Predicting the minimal translation apparatus: lessons
from the reductive evolution of mollicutes, PLoS Genet., 10, e1004363,
https://doi.org/10.1371/journal.pgen.1004363, 2014.
Hopper, A. K. and Phizicky, E. M.: tRNA transfers to the limelight, Gene.
Dev., 17, 162–180, https://doi.org/10.1101/gad.1049103, 2003.
Jurkowski, T. P., Meusburger, M., Phalke, S., Helm, M., Nellen, W., Reuter,
G., and Jeltsch, A.: Human DNMT2 methylates tRNA(Asp) molecules using a DNA
methyltransferase-like catalytic mechanism, RNA, 14,
1663–1670, https://doi.org/10.1261/rna.970408, 2008.
Kadonaga, J. T., Jones, K. A., and Tjian, R.: Promoter-specific activation of
rna polymerase ii transcription by sp1, Trends in Biochemical ences, 11,
20–23, https://doi.org/10.1016/0968-0004(86)90226-4, 1986.
Kunert, N., Marhold, J., Stanke, J., Stach, D., and Lyko, F.: A Dnmt2-like
protein mediates DNA methylation in Drosophila, Development, 130, 5083–5090, https://doi.org/10.1242/dev.00716, 2003.
Letovsky, J. and Dynan, W. S.: Measurement of the binding of transcription
factor Sp1 to a single GC box recognition sequence, Nucleic Acids Res.,
17, 2639–2653, https://doi.org/10.1093/nar/17.7.2639, 1989.
Li, L. C. and Dahiya, R.: MethPrimer: designing primers for methylation PCRs,
Bioinformatics, 18, 1427–1431,
https://doi.org/10.1093/bioinformatics/18.11.1427, 2002.
Li, M. J., Liu, M., Liu, D., Lan, X. Y., Lei, C. Z., Yang, D. Y., and Chen, H.:
Polymorphisms in the Promoter Region of the Chinese Bovine PPARGC1A Gene,
Asian-Austral. J. Anim., 26, 483–487,
https://doi.org/10.5713/ajas.2012.12554, 2013.
Liu, X., Usman, T., Wang, Y., Wang, Z., Xu, X., Wu, M., Zhang, Y., Zhang,
X., Li, Q., Liu, L., Shi, W., Qin, C., Geng, F., Wang, C., Tan, R., Huang,
X., Liu, A., Wu, H., Tan, S., and Yu, Y.: Polymorphisms in epigenetic and
meat quality related genes in fourteen cattle breeds and association with
beef quality and carcass traits, Asian-Austral. J. Anim., 28, 467–475, https://doi.org/10.5713/ajas.13.0837, 2015.
Oh, J. E., Han, J. A., and Hwang, E. S.: Downregulation of transcription factor,
Sp1, during cellular senescence, Biochem. Bioph. Res.
Co., 353, 86–91, https://doi.org/10.1016/j.bbrc.2006.11.118,
2007.
Pang, Y., Wang, J., Zhang, C., Lei, C., Lan, X., Yue, W., Gu, C., Chen, D., and
Chen, H.: The polymorphisms of bovine VEGF gene and their associations with
growth traits in Chinese cattle, Mol. Biol. Rep., 38, 755–759,
https://doi.org/10.1007/s11033-010-0163-6, 2011.
Pütz, J., Florentz, C., Benseler, F., and Giegé, R.: A single methyl
group prevents the mischarging of a tRNA, Nat. Struct. Biol., 1,
580–582, https://doi.org/10.1038/nsb0994-580, 1994.
Rai, K., Chidester, S., Zavala, C. V., Manos, E. J., James, S. R., Karpf, A.
R., Jones, D. A., and Cairns, B. R.: Dnmt2 functions in the cytoplasm to promote
liver, brain, and retina development in zebrafish, Gene. Dev.,
21, 261–266, https://doi.org/10.1101/gad.1472907, 2007.
Safe, S. and Abdelrahim, M.: Sp transcription factor family and its role in
cancer, Eur. J. Cancer, 41, 2438–2448,
https://doi.org/10.1016/j.ejca.2005.08.006, 2005.
Sarin, L. P. and Leidel, S. A.: Modify or die? – RNA modification defects in
metazoans, RNA Biol., 11, 1555–1567,
https://doi.org/10.4161/15476286.2014.992279, 2014.
Schaefer, M., Pollex, T., Hanna, K., Tuorto, F., Meusburger, M., Helm, M., and
Lyko, F.: RNA methylation by Dnmt2 protects transfer RNAs against
stress-induced cleavage, Gene. Dev., 24, 1590–1595,
https://doi.org/10.1101/gad.586710, 2010.
Sibbritt, T., Patel, H. R., and Preiss, T.: Mapping and significance of the mRNA
methylome. Wiley interdisciplinary reviews, RNA, 4, 397–422, https://doi.org/10.1002/wrna.1166, 2013.
Schumann, U., Zhang, H. N., Sibbritt, T., Pan, A., Horvath, A., Gross, S.,
Clark, S. J., Yang, L., and Preiss, T.: Multiple links between 5-methylcytosine
content of mRNA and translation, BMC Biol., 18, 40, https://doi.org/10.1186/s12915-020-00769-5, 2020.
Takami, Y., Russell, M. B., Gao, C., Mi, Z., Guo, H., Mantyh, C. R., and Kuo, P.
C.: Sp1 regulates osteopontin expression in SW480 human colon adenocarcinoma
cells, Surgery, 142, 163–169,
https://doi.org/10.1016/j.surg.2007.02.015, 2007.
Tang, Q., Wu, W., Xu, X., Huang, L., Gao, Q., Chen, H., Sun, H., Xia, Y.,
Sha, J., Wang, X., Chen, D., and Xu, Q.: miR-141 contributes to fetal growth
restriction by regulating PLAG1 expression, PloS one, 8, e58737,
https://doi.org/10.1371/journal.pone.0058737, 2013.
Tuorto, F., Liebers, R., Musch, T., Schaefer, M., Hofmann, S., Kellner, S.,
Frye, M., Helm, M., Stoecklin, G., and Lyko, F.: RNA cytosine methylation by
Dnmt2 and NSun2 promotes tRNA stability and protein synthesis, Nat.
Struct. Mol. Biol., 19, 900–905,
https://doi.org/10.1038/nsmb.2357, 2012.
Vojta, A., Dobrinić, P., Tadić, V., Bočkor, L., Korać, P.,
Julg, B., Klasić, M., and Zoldoš, V.: Repurposing the CRISPR-Cas9 system
for targeted DNA methylation, Nucleic Acids Res., 44, 5615–5628,
https://doi.org/10.1093/nar/gkw159, 2016.
Xue, S., Xu, H., Sun, Z., Shen, H., Chen, S., Ouyang, J., Zhou, Q., Hu, X., and
Cui, H.: Depletion of TRDMT1 affects 5-methylcytosine modification of mRNA
and inhibits HEK293 cell proliferation and migration, Biochem.
Bioph. Res. Co., 520, 60–66,
https://doi.org/10.1016/j.bbrc.2019.09.098, 2019.
Short summary
In this experiment, by detecting the mutation in the promoter region of the bovine TRDMT1 gene, fluorescent recombinant plasmids of different genotypes were constructed at this site, and the relative fluorescence intensity was analyzed by detecting the transfected 293T cells. Our experiment detected a natural genetic variation of a tRNA modification gene TRDMT1, which may provide potential natural molecular materials for the study of tRNA modification.
In this experiment, by detecting the mutation in the promoter region of the bovine TRDMT1 gene,...
