Articles | Volume 60, issue 4
https://doi.org/10.5194/aab-60-391-2017
© Author(s) 2017. 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-60-391-2017
© Author(s) 2017. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Original study
| 
18 Oct 2017
Original study |
| 18 Oct 2017
| 18 Oct 2017
Copy number variations of five Y chromosome genes in donkeys
Haoyuan Han
College of Animal Science and Technology, Northwest A&F University,
Yangling, Shaanxi 712100, China
Xiaocheng Zhao
College of Animal Science and Technology, Northwest A&F University,
Yangling, Shaanxi 712100, China
Xiaoting Xia
College of Animal Science and Technology, Northwest A&F University,
Yangling, Shaanxi 712100, China
Hong Chen
College of Animal Science and Technology, Northwest A&F University,
Yangling, Shaanxi 712100, China
Chuzhao Lei
CORRESPONDING AUTHOR
College of Animal Science and Technology, Northwest A&F University,
Yangling, Shaanxi 712100, China
Ruihua Dang
College of Animal Science and Technology, Northwest A&F University,
Yangling, Shaanxi 712100, China
Related authors
Haoyuan Han, Xin Zhang, Xiaocheng Zhao, Xiaoting Xia, Chuzhao Lei, and Ruihua Dang
Arch. Anim. Breed., 61, 263–270, https://doi.org/10.5194/aab-61-263-2018, https://doi.org/10.5194/aab-61-263-2018, 2018
Short summary
Short summary
The occurrence of copy number variations (CNVs) has been confirmed on the Y
chromosome in horses. However, the copy numbers (CNs) of Equus caballus Y
chromosome (ECAY) genes are largely unknown. This study aimed to demonstrate the copy number variations of Y chromosome genes in horses. Therefore, the quantitative real-time polymerase chain reaction (qPCR) method was applied to measure the CNVs of eight Y chromosome specific genes from 14 different Chinese horse breeds.
Zhenyu Lai, Fei Wu, Zihui Zhou, Mei Li, Yuan Gao, Guijun Yin, Jie Yu, Chuzhao Lei, and Ruihua Dang
Arch. Anim. Breed., 63, 377–386, https://doi.org/10.5194/aab-63-377-2020, https://doi.org/10.5194/aab-63-377-2020, 2020
Short summary
Short summary
The purpose of this study was to investigate the expression level and genetic variation of the ACSL1 gene of the Dezhou donkey and its effect on growth traits. The results show that the ACSL1 gene is regularly expressed in Dezhou donkey tissue. Through the association analysis of the genotype and haplotype combination and growth traits, it is speculated that the ACSL1 gene can be used as a candidate gene for Dezhou donkey breeding.
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
Xiaogang Wang, Xiukai Cao, Yifan Wen, Yilei Ma, Ibrahim Elsaeid Elnour, Yongzhen Huang, Xianyong Lan, Buren Chaogetu, Linyong Hu, and Hong Chen
Arch. Anim. Breed., 62, 571–578, https://doi.org/10.5194/aab-62-571-2019, https://doi.org/10.5194/aab-62-571-2019, 2019
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
Short summary
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, https://doi.org/10.5194/aab-62-325-2019, https://doi.org/10.5194/aab-62-325-2019, 2019
Short summary
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.
Lulan Zeng, Ruihua Dang, Hong Dong, Fangyu Li, Hong Chen, and Chuzhao Lei
Arch. Anim. Breed., 62, 181–187, https://doi.org/10.5194/aab-62-181-2019, https://doi.org/10.5194/aab-62-181-2019, 2019
Short summary
Short summary
Donkeys are an important livestock in China for their nourishment and medical values. Indigenous donkey populations of China retain relatively abundant genetic diversity and Chinese donkeys were grouped into two lineages, which correspond to their geographic distribution and breeding history.
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
Short summary
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.
Haiyu Zhao, Sihuan Zhang, Xianfeng Wu, Chuanying Pan, Xiangchen Li, Chuzhao Lei, Hong Chen, and Xianyong Lan
Arch. Anim. Breed., 62, 59–68, https://doi.org/10.5194/aab-62-59-2019, https://doi.org/10.5194/aab-62-59-2019, 2019
Short summary
Short summary
This study analyzed the DNA methylation profile of the PITX1 gene and its relevance to lactation performance in goats. The methylation rates of the overall CpG island and the 3rd and 12th CpG-dinucleotide loci in blood were significantly associated with average milk yield. The overall methylation rates of the CpG island in mammary gland tissue from dry and lactation periods showed a significant difference. These results could be used as potential epigenetic markers for lactation performance.
Haoyuan Han, Xin Zhang, Xiaocheng Zhao, Xiaoting Xia, Chuzhao Lei, and Ruihua Dang
Arch. Anim. Breed., 61, 263–270, https://doi.org/10.5194/aab-61-263-2018, https://doi.org/10.5194/aab-61-263-2018, 2018
Short summary
Short summary
The occurrence of copy number variations (CNVs) has been confirmed on the Y
chromosome in horses. However, the copy numbers (CNs) of Equus caballus Y
chromosome (ECAY) genes are largely unknown. This study aimed to demonstrate the copy number variations of Y chromosome genes in horses. Therefore, the quantitative real-time polymerase chain reaction (qPCR) method was applied to measure the CNVs of eight Y chromosome specific genes from 14 different Chinese horse breeds.
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
Short summary
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.
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
Short summary
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.
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
Short summary
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, https://doi.org/10.5194/aab-59-151-2016, https://doi.org/10.5194/aab-59-151-2016, 2016
Short summary
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, https://doi.org/10.5194/aab-59-91-2016, https://doi.org/10.5194/aab-59-91-2016, 2016
Short summary
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.
Related subject area
Subject: Biodiversity | Animal: Other
The influence of age and sex on carcass characteristics and chemical composition of the longissimus thoracis et lumborum muscle in wild boars (Sus scrofa)
Possible mathematical definitions of the biological term “breed”
Tomasz Żmijewski and Monika Modzelewska-Kapituła
Arch. Anim. Breed., 64, 199–210, https://doi.org/10.5194/aab-64-199-2021, https://doi.org/10.5194/aab-64-199-2021, 2021
Short summary
Short summary
The effect of wild boars' age and sex on the quality of the carcass composition and meat quality was studied. The highest percentage of lean meat in the carcass and a moderate fat and bone content were found in male boars (1–3 yr). Higher fat content was found in females from all age groups, and a lower bone content was noted in yearlings (1–2 yr) and adult (2–3 yr) females. The chemical composition of the loin was most desirable in adults (2–3 yr) and least desirable in piglets (< 1 yr).
Gregor Langer
Arch. Anim. Breed., 61, 229–243, https://doi.org/10.5194/aab-61-229-2018, https://doi.org/10.5194/aab-61-229-2018, 2018
Short summary
Short summary
For scientific discussions it is necessary to clearly define the terms used; otherwise, scientific statements are open to interpretation which hampers the scientific progress. A clear specification of scientific terms can be reached via mathematical definitions. In this paper, four mathematical definitions of the term "breed" for gonochoric species are proposed. Although all proposed definitions are consistent with common word-based definitions, the result of the whippet test differs.
Cited articles
Cahan, P., Li Y., Izumi, M., and Graubert, T. A.: The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells, Nat. Genet., 41, 430–437, 2009.
Dunn, O. J.: Multiple comparisons among means, J. Am. Stat. Assoc., 56, 52–64, 1961.
Geraldes, A. and Ferrand, N.: A 7-bp insertion in the 39 untranslated region suggests the duplication and concerted evolution of the rabbit SRY gene, Genetics, selection, evolution, Genetics, selection, evolution: GSE, 38, 313–320, 2006.
Graves, J. A.: Evolution of the mammalian Y chromosome and sex-determining genes, J. Exp. Zool., 281, 472–481, 1998.
Hamilton, C. K., Favetta, L. A., Di Meo, G. P., Floriot, S., Perucatti, A., Peippo, J., Kantanen, J., Eggen, A., Iannuzzi, L., and King, W. A.: Copy number variation of testis-specific protein, Y-encoded (TSPY) in 14 different breeds of cattle (Bos taurus), Sex. Dev., 3, 205–213, 2009.
Hamilton, C. K., Revay, T., Domander, R., Favetta, L. A., and Allan King, W. A.: large expansion of the HSFY gene family in cattle shows dispersion across Yq and testis-specific expression, PLoS One, 6, e17790, https://doi.org/10.1371/journal.pone.0017790, 2011.
Henrichsen, C. N., Chaignat, E., and Reymond, A.: Copy number variants, diseases and gene expression, Hum. Mol. Genet., 18, R1–8, 2009.
Hughes, J. F., Skaletsky, H., Pyntikova, T., Graves, T. A., van Daalen, S. K., Minx, P. J., Fulton, R. S., McGrath, S. D., Locke, D. P., Friedman, C., Trask, B. J., Mardis, E. R., Warren, W. C., Repping, S., Rozen, S., Wilson, R. K., and Page, D. C.: Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content, Nature, 463, 536–539, 2010.
Jakubiczka, S., Schnieders, F., and Schmidtke, J.: A bovine homologue of the human TSPY gene, Genomics, 17, 732–735, 1993.
Jobling, M. A.: Copy number variation on the human Y chromosome, Cytogenet. Genome Res., 123, 253–262, 2008.
Justel Peña, A. D. and Zamar, R.: A multivariate Kolmogorov-Smirnov test of goodness of fit, Stat. Probab. Lett., 35, 251–259, 1997.
Lahn, B. T., Pearson, N. M., and Jegalian, K.: The human Y chromosome, in the light of evolution, Nat. Rev. Genet., 2, 207–216. 2001.
Mann, H. B. and Whitney, D. R.: On a test of whether one of two random variables is stochastically larger than the other, Ann. Math. Stat., 18, 50–60, 1947.
Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., Abyzov, A., Yoon, S. C., Ye, K., Cheetham, R. K., Chinwalla, A., Conrad, D. F., Fu, Y., Grubert, F., Hajirasouliha, I., Hormozdiari, F., Iakoucheva, L. M., Iqbal, Z., Kang, S., Kidd, J. M., Konkel, M. K., Korn, J., Khurana, E., Kural, D., Lam, H. Y., Leng, J., Li, R., Li, Y., Lin, C., Luo, R., Mu, X. J., Nemesh, J., Peckham, H. E., Rausch, T., Scally, A., Shi, X., Stromberg, M. P., Stutz, A. M., Urban, A. E., Walker, J. A., Wu, J., Zhang, Y., Zhang, Z. D., Batzer, M. A., Ding, L., Marth, G. T., McVean, G., Sebat, J., Snyder, M., Wang, J., Ye, K., Eichler, E. E., Gerstein, M. B., Hurles, M. E., Lee, C., McCarroll, S. A., Korbel, J. O., and 1000 Genomes Project: Mapping copy number variation by population-scale genome sequencing, Nature, 470, 59–65, 2011.
Murphy, W. J., Pearks Wilkerson, A. J., Raudsepp, T., Agarwala, R., Schaffer, A. A., Stanyon, R., and Chowdhary, B. P.: Novel gene acquisitionon carnivore Y chromosomes, PLoS genet., 2, e43, https://doi.org/10.1371/journal.pgen.0020043, 2006.
Nickkholgh, B., Noordam, M. J., Hovingh, S. E., van Pelt, A. M., van der Veen, F., and Repping, S.: Y chromosome TSPY copy numbers and semen quality, Fertil. Steril., 94, 1744–1747, 2010.
Paria, N., Raudsepp, T., Wilkerson, A. J. P., O'Brien, P. C. M., Ferguson-Smith, M. A., Love, C. C., Arnold, C., Rakestraw, P., Murphy, W. J., and Chowdhary, B. P.: A gene catalogue of the euchromatic male-specific region of the horse Y chromosome: comparison with human and other mammals, PLoS One, 6, e21374, https://doi.org/10.1371/journal.pone.0021374, 2011.
Pearks Wilkerson, A. J, Raudsepp, T., Graves, T., Albracht, D., Warren, W., Chowdharya, B. P., Skowa, L. C., and Murphy, W. J.: Gene discovery and comparative analysis of X-degenerate genes from the domestic cat Y chromosome, Genomics, 92, 329–338, 2008.
Petroski, M. D. and Deshaies, R. J.: Function and regulation of cullin-RING ubiquitin ligases, Nat. Rev. Mol. Cell Biol., 6, 9–20, 2005.
Quintana-Murci, L. and Fellous, M.: The human Y chromosome: The biological role of a “functional wasteland”, J. Biomed. Biotechnol., 1, 18–24, 2001.
Redon, R., Ishikawa, S., Fitch, K. R., Feuk, L., Perry, G. H., Daniel Andrews, T., Fiegler, H., Shapero, M. H., Carson, A. R., Chen, W., Kyung Cho, E., Dallaire, S., Freeman, J. L., González, J. R., Gratacòs, M., Huang, J., Kalaitzopoulos, D., Komura, D., MacDonald, J. R., Marshall, C. R., Mei, R., Montgomery, L., Nishimura, K., Okamura, K., Shen, F., Somerville, M. J., Tchinda, J., Valsesia, A., Woodwark, C., Yang, F., Zhang, J., Zerjal, T., Zhang, J., Armengol, L., Conrad, D. F., Estivill, X., Tyler-Smith, C., Carter, N. P., Aburatani, H., Lee, C., Jones, K. W., Scherer, S. W., and Hurles, M. E.: Global variation in copy number in the human genome, Nature, 444, 444–454, 2006.
Sambrook, J. and Russell, D. W.: Molecular cloning: A laboratory manual, translated by: Huang, P. T., Beijing: Science Press; Beijing, China, 2002.
Shapiro, S. S. and Wilk, M. B.: An analysis of variance test for normality (complete samples), Biometrika, 52, 591–611, 1965.
Skaletsky, H., Kuroda-Kawaguchi, T., Minx, P. J., Cordum, H. S., Hillier, L., Brown, L. G., Repping, S., Pyntikova, T., Ali, J., Bieri, T., Chinwalla, A., Delehaunty, A., Delehaunty, K., Du, H., Fewell, G., Fulton, L., Fulton, R., Graves, T., Hou, S. F., Latrielle, P., Leonard, S., Mardis, E., Maupin, R., McPherson, J., Miner, T., Nash, W., Nguyen, C., Ozersky, P., Pepin, K., Rock, S., Rohlfing, T., Scott, K., Schultz, B., Strong, C., Tin-Wollam, A., Yang, S. P., Waterston, R. H., Wilson, R. K., Rozen, S., and Page, D. C.: The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes, Nature, 423, 825–837, 2003.
Toft, M. and Ross, O. A.: Copy number variation in Parkinson's disease, Genome Medicine, 2, p. 62, 2010.
Toure, A., Szot, M., Mahadevaiah, S. K., Rattigan, A., Ojarikre, O. A., and Burgoyne, P. S.: A new deletion of the mouse Y chromosome long arm associated with the loss of Ssty expression, abnormal sperm development and sterility, Genetics, 166, 901–912, 2004
Turner, M. E., Martin, C., Martins, A. S., Dunmire, J., Farkas, J., Ely, D. L., and Milsted, A.: Genomic and expression analysis of multiple Sry loci from a single Rattus norvegicus Y chromosome, BMC Genet., 8, p. 11, 2007.
Vodicka, R., Vrtel, R., Dusek, L., Singh, A.R., Krizova, K., Svacinova, V., Horinova, V., Dostal, J., Oborna, I., Brezinova, J., Sobek, A., and Santavy, J.: TSPY gene copy number as a potential new risk factor for male infertility, Reprod. Biomed. Online, 14, 579–587, 2007.
Wilhelm, D., Palmer, S., and Koopman, P.: Sex determination and gonadal development in mammals, Physiol. Rev., 87, 1–28, 2007.
Yue, X. P., Chang, T. C., DeJarnette, J. M., Marshall, C. E., Lei, C. Z., and Liu, W. S.: Copy number variation of PRAMEY across breeds and its association with male fertility in Holstein sires, J. Dairy Sci., 96, 8024–8034, 2013.
Zhang, F., Gu, W., Hurles, M. E., and Lupski, J. R.: Copy number variation in human health, disease, and evolution, Annu. Rev. Genomics Hum. Genet., 10, 451–481, 2009.
