Articles | Volume 61, issue 3
Original study 11 Jul 2018
Original study | 11 Jul 2018
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
Špela Malovrh et al.
No articles found.
Božidarka Marković, Peter Dovč, Milan Marković, Dušica Radonjić, Mirjana Adakalić, and Mojca Simčič
Arch. Anim. Breed., 62, 393–402,Short summary
The characterization of local sheep breeds, two Slovenian (Bela Krajina and Istrian Pramenka) and four Montenegrin (Bardoka, Sjenička, Pivska Pramenka, and Zeta Žuja), was done on the basis of morphometric measures and indices. The PCA of morphometric parameters extracted three components explaining 96.6 % of cumulative variance. A cluster analysis grouped Pivska Pramenka with Sjenička and Istrian with Bela Krajina Pramenka in two clusters, while Bardoka and Zeta Žuja were clustered separately.
Related subject area
Subject: DNA markers and gene expressions | Animal: CattleDetermination of the association of GHR/AluI gene polymorphisms with milk yield traits in Holstein and Jersey cattle raised in TurkeyRegulating glycolysis and heat shock proteins in Gannan yaks (Bos grunniens) in response to hypoxia of the Qinghai–Tibet PlateauVariation in bovine leptin gene affects milk fatty acid composition in New Zealand Holstein Friesian × Jersey dairy cowsDetection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1Regulation of microRNA-33, SREBP and ABCA1 genes in a mouse model of high cholesterolEffects of polymorphism of the GPAM gene on milk quality traits and its relation to triglyceride metabolism in bovine mammary epithelial cells of dairy cattleDetermination of the effect of functional single-nucleotide polymorphisms associated with glycerolipid synthesis on intramuscular fat deposition in Korean cattle steerDNA analysis of the Russian populations of Aberdeen Angus, Hereford and Belgian Blue cattleVariation in the stearoyl-CoA desaturase gene (SCD) and its influence on milk fatty acid composition in late-lactation dairy cattle grazed on pastureGenetic variant of SPARC gene and its association with growth traits in Chinese cattleEffect of DNA markers on the fertility traits of Japanese Black cattle for improving beef quantity and qualityThe effect of polymorphism in the FADS2 gene on the fatty acid composition of bovine milkPotential of TLR-gene diversity in Czech indigenous cattle for resistance breeding as revealed by hybrid sequencingExploring insertions and deletions (indels) of MSRB3 gene and their association with growth traits in four Chinese indigenous cattle breedsExploring genetic diversity and phylogenic relationships of Chinese cattle using gene mtDNA 16S rRNAThe effect of acyl-CoA synthetase long-chain family member 5 on triglyceride synthesis in bovine preadipocytesCopy number variation (CNV) in the IGF1R gene across four cattle breeds and its association with economic traitsPolymorphisms of the ASIP gene and the haplotype are associated with fat deposition traits and fatty acid composition in Chinese Simmental steersComprehensive assessment of candidate genes associated with fattening performance in Holstein–Friesian bullsAssessment of growth hormone gene polymorphism effects on reproductive traits in Holstein dairy cattle in TunisiaEffects of polymorphisms in CAPN1 and CAST genes on meat tenderness of Chinese Simmental cattleEffect of leptin genetic polymorphism on lameness prevalence in Tunisian Holstein cowsThe effect of short/branched chain acyl-coenzyme A dehydrogenase gene on triglyceride synthesis of bovine mammary epithelial cellsIdentification of a novel 24 bp insertion–deletion (indel) of the androgen receptor gene and its association with growth traits in four indigenous cattle breedsA combined genotype of three SNPs in the bovine gene is related to growth performance in Chinese cattleEvaluation of novel SNPs and haplotypes within the ATBF1 gene and their effects on economically important production traits in cattleIdentification and expression analysis of miR-144-5p and miR-130b-5p in dairy cattleSIRT1 gene polymorphisms associated with carcass traits in Luxi cattleThe 10 bp duplication insertion/deletion in the promoter region within paired box 7 gene is associated with growth traits in cattlePSAP gene variants and haplotypes reveal significant effects on carcass and meat quality traits in Chinese Simmental-cross cattleExploration of the exonic variations of the iPSC-related Nanog gene and their effects on phenotypic traits in cattleA novel 17 bp indel in the SMAD3 gene alters transcription level, contributing to phenotypic traits in Chinese cattleIndels within the bovine visfatin gene affect its mRNA expression in longissimus muscle and subcutaneous fat
Ozden Cobanoglu, Ertugrul Kul, Eser K. Gurcan, Samet H. Abaci, and Soner Cankaya
Arch. Anim. Breed., 64, 417–424,Short summary
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,Short summary
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,Short summary
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.
Xiaohua Yi, Shuai He, Shuhui Wang, Haidong Zhao, Mingli Wu, Shirong Liu, and Xiuzhu Sun
Arch. Anim. Breed., 64, 147–155,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.
Xianglun Zhang, Hongbo Zhao, Qingkai Sheng, Xiaomu Liu, Wei You, Haichao Lin, and Guifen Liu
Arch. Anim. Breed., 64, 103–108,
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,Short summary
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,Short summary
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,Short summary
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,
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,
Fuki Kawaguchi, Miyako Tsuchimura, Kenji Oyama, Tamako Matsuhashi, Shin Maruyama, Hideyuki Mannen, and Shinji Sasazaki
Arch. Anim. Breed., 63, 9–17,
Witold Stanisław Proskura, Michał Liput, Daniel Zaborski, Zbigniew Sobek, Yu-Hsiang Yu, Yeong-Hsiang Cheng, and Andrzej Dybus
Arch. Anim. Breed., 62, 547–555,Short summary
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,Short summary
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,Short summary
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,Short summary
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,Short summary
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,Short summary
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,Short summary
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,Short summary
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,Short summary
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,Short summary
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,Short summary
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.
Ping Jiang, Xibi Fang, Zhihui Zhao, Xianzhong Yu, Boxing Sun, Haibin Yu, and Runjun Yang
Arch. Anim. Breed., 61, 115–122,Short summary
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,Short summary
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,Short summary
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,Short summary
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,Short summary
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,Short summary
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,Short summary
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,Short summary
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,Short summary
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,Short summary
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,Short summary
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.
Agarwal, V., Bell, G. W., Nam, J. W., and Bartel, D. P.: Predicting effective microRNA target sites in mammalian mRNAs, Elife, 4, e05005, https://doi.org/10.7554/eLife.05005, 2015.
Bartel, D. P.: MicroRNAs: genomics, biogenesis, mechanism, and function, Cell, 116, 281–297, 2004.
Chou, C. H., Chang, N. W., Shrestha, S., Hsu, S. D., Lin, Y. L., Lee, W. H., Yang, C. D., Hong, H. C., Wei, T. Y., Tu, S. J., Tsai, T. R., Ho, S. Y., Jian, T. Y., Wu, H. Y., Chen, P. R., Lin, N. C., Huang, H. T., Yang, T. L., Pai, C. Y., Tai, C. S., Chen, W. L., Huang, C. Y., Liu, C. C., Weng, S. L., Liao, K. W., Hsu, W. L., and Huang, H. D.: miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database, Nucleic Acids Res., 44, D239–D247, https://doi.org/10.1093/nar/gkv1258, 2016.
Gao, Q., Ju, Z., Zhang, Y., Huang, J., Zhang, X., Qi, C., Li, J., Zhong, J., Li, G., and Wang, C.: Association of TNP2 gene polymorphisms of the bta-miR-154 target site with the semen quality traits of Chinese Holstein bulls, PLoS One, 9, e84355, https://doi.org/10.1371/journal.pone.0084355, 2014.
Georges, M., Coppieters, W., and Charlier, C.: Polymorphic miRNA-mediated gene regulation: contribution to phenotypic variation and disease, Curr. Opin. Genet. Dev., 17, 166–176, https://doi.org/10.1016/j.gde.2007.04.005, 2007.
Godnic, I., Zorc, M., Jevsinek Skok, D., Calin, G. A., Horvat, S., Dovc, P., Kovac, M., and Kunej, T.: Genome-wide and species-wide in silico screening for intragenic MicroRNAs in human, mouse and chicken, PLoS One, 8, e65165, https://doi.org/10.1371/journal.pone.0065165, 2013.
Hrovatin, K. and Kunej, T.: Classification of miRNA-related sequence variations, Epigenomics, 10, 463–481, https://doi.org/10.2217/epi-2017-0126, 2018.
Höglund, J. K., Buitenhuis, B., Guldbrandtsen, B., Lund, M. S., and Sahana, G.: Genome-wide association study for female fertility in Nordic Red cattle, BMC Genet., 16, 110, https://doi.org/10.1186/s12863-015-0269-x, 2015.
Hu, Z. L., Park, C. A., and Reecy, J. M.: Developmental progress and current status of the Animal QTLdb, Nucleic Acids Res., 44, D827–D833, https://doi.org/10.1093/nar/gkv1233, 2016.
Jevsinek Skok, D., Godnic, I., Zorc, M., Horvat, S., Dovc, P., Kovac, M., and Kunej, T.: Genome-wide in silico screening for microRNA genetic variability in livestock species, Anim. Genet., 44, 669–677, https://doi.org/10.1111/age.12072, 2013.
Jin, Y., Cai, H., Liu, J., Lin, F., Qi, X., Bai, Y., Lei, C., Chen, H., and Lan, X.: The 10 bp duplication insertion/deletion in the promoter region within paired box 7 gene is associated with growth traits in cattle, Arch. Anim. Breed., 59, 469–476, https://doi.org/10.5194/aab-59-469-2016, 2016.
Kozomara, A. and Griffiths-Jones, S.: miRBase: integrating microRNA annotation and deep-sequencing data, Nucleic Acids Res., 39, D152–D157, https://doi.org/10.1093/nar/gkq1027, 2011.
Krek, A., Grün, D., Poy, M. N., Wolf, R., Rosenberg, L., Epstein, E. J., MacMenamin, P., da Piedade, I., Gunsalus, K. C., Stoffel, M., and Rajewsky, N.: Combinatorial microRNA target predictions, Nat. Genet., 37, 495–500, https://doi.org/10.1038/ng1536, 2005.
Kunej, T., Godnic, I., Horvat, S., Zorc, M., and Calin, G. A.: Cross talk between microRNA and coding cancer genes, Cancer J., 18, 223–231, https://doi.org/10.1097/PPO.0b013e318258b771, 2012.
Lee, Y., Jeon, K., Lee, J. T., Kim, S., and Kim, V. N.: MicroRNA maturation: stepwise processing and subcellular localization, EMBO J., 21, 4663–4670, 2002.
Lewis, B. P., Burge, C. B., and Bartel, D. P.: Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets, Cell, 120, 15–20, https://doi.org/10.1016/j.cell.2004.12.035, 2005.
Li, L. C. and Dahiya, R.: MethPrimer: designing primers for methylation PCRs, Bioinformatics, 18, 1427–1431, 2002.
Li, R., Zhang, C. L., Liao, X. X., Chen, D., Wang, W. Q., Zhu, Y. H., Geng, X. H., Ji, D. J., Mao, Y. J., Gong, Y. C., and Yang, Z. P.: Transcriptome microRNA profiling of bovine mammary glands infected with Staphylococcus aureus, Int. J. Mol. Sci., 16, 4997–5013, https://doi.org/10.3390/ijms16034997, 2015.
Nicolazzi, E. L., Caprera, A., Nazzicari, N., Cozzi, P., Strozzi, F., Lawley, C., Pirani, A., Soans, C., Brew, F., Jorjani, H., Evans, G., Simpson, B., Tosser-Klopp, G., Brauning, R., Williams, J. L., and Stella, A.: SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species, BMC Genomics, 16, 283, https://doi.org/10.1186/s12864-015-1497-1, 2015.
Obsteter, J., Dovc, P., and Kunej, T.: Genetic variability of microRNA regulome in human, Mol. Genet. Genomic. Med., 3, 30–39, https://doi.org/10.1002/mgg3.110, 2015.
Paraskevopoulou, M. D., Vlachos, I. S., and Hatzigeorgiou, A. G.: DIANA-TarBase and DIANA Suite Tools: Studying Experimentally Supported microRNA Targets, Curr. Protoc. Bioinformatics, 55, 12.14.11–12.14.18, https://doi.org/10.1002/cpbi.12, 2016.
Piletič, K. and Kunej, T.: MicroRNA epigenetic signatures in human disease, Arch. Toxicol., 90, 2405–2419, https://doi.org/10.1007/s00204-016-1815-7, 2016.
Piletič, K. and Kunej, T.: Minimal Standards for Reporting microRNA:Target Interactions, OMICS, 21, 197–206, https://doi.org/10.1089/omi.2017.0023, 2017.
SAS Institute Inc.: Version 9.4 of the SAS System for Unix and Linux, Cary, NC, SAS, Institute Inc., 2013.
Serão, N. V., González-Peña, D., Beever, J. E., Faulkner, D. B., Southey, B. R., and Rodriguez-Zas, S. L.: Single nucleotide polymorphisms and haplotypes associated with feed efficiency in beef cattle, BMC Genet., 14, 94, https://doi.org/10.1186/1471-2156-14-94, 2013.
Strmsek, Z. and Kunej, T.: Data integration of 104 studies related with microRNA epigenetics revealed that miR-34 gene family is silenced by DNA methylation in the highest number of cancer types, Discoveries, 2, e18, https://doi.org/10.15190/d.2014.10, 2014.
Sun, G., Yan, J., Noltner, K., Feng, J., Li, H., Sarkis, D. A., Sommer, S. S., and Rossi, J. J.: SNPs in human miRNA genes affect biogenesis and function, RNA, 15, 1640–1651, https://doi.org/10.1261/rna.1560209, 2009.
Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B. C., Remm, M., and Rozen, S. G.: Primer3–new capabilities and interfaces, Nucleic Acids Res., 40, e115, https://doi.org/10.1093/nar/gks596, 2012.
Xiao, F., Zuo, Z., Cai, G., Kang, S., Gao, X., and Li, T.: miRecords: an integrated resource for microRNA-target interactions, Nucleic Acids Res., 37, D105–D110, https://doi.org/10.1093/nar/gkn851, 2009.
Zerbino, D. R., Achuthan, P., Akanni, W., Amode, M. R., Barrell, D., Bhai, J., Billis, K., Cummins, C., Gall, A., Girón, C. G., Gil, L., Gordon, L., Haggerty, L., Haskell, E., Hourlier, T., Izuogu, O. G., Janacek, S. H., Juettemann, T., To, J. K., Laird, M. R., Lavidas, I., Liu, Z., Loveland, J. E., Maurel, T., McLaren, W., Moore, B., Mudge, J., Murphy, D. N., Newman, V., Nuhn, M., Ogeh, D., Ong, C. K., Parker, A., Patricio, M., Riat, H. S., Schuilenburg, H., Sheppard, D., Sparrow, H., Taylor, K., Thormann, A., Vullo, A., Walts, B., Zadissa, A., Frankish, A., Hunt, S. E., Kostadima, M., Langridge, N., Martin, F. J., Muffato, M., Perry, E., Ruffier, M., Staines, D. M., Trevanion, S. J., Aken, B. L., Cunningham, F., Yates, A., and Flicek, P.: Ensembl 2018, Nucleic Acids Res., 46, D754–D761, https://doi.org/10.1093/nar/gkx1098, 2018.
Zorc, M. and Kunej, T.: Development of Integrative Map of MicroRNA Gene Regulatory Elements, Microrna, 2015.
Zorc, M., Obsteter, J., Dovc, P., and Kunej, T.: Genetic variability of microRNA genes in 15 animal species, Journal of Genomics, 3, 51–56, https://doi.org/10.7150/jgen.11246, 2015.
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.
Effects of miRNA polymorphisms on phenotypic traits have been studied in several species but...