Association Analysis of Endogenous retrovirus (ERV) Transposon Insertion Polymorphism and Growth Traits in Intron 1 of Pig (Sus scrofa domesticus) SLC26A7 Gene
CHEN Zi-Xuan, CHI Cheng-Lin, AN Ya-Long, CHEN Cai, SONG Cheng-Yi, WANG Xiao-Yan*
College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China
Abstract The SLC26A7 (solute carrier family 26 member 7) gene in the members of the sulfate/anion transporter gene family (SLC26) can be used as a selective chloride ion channel to regulate renal electrolyte balance and mediate thyroid hormone biosynthesis. Its mutation causes thyroid insufficiency and affects individual growth and development. In this study, comparative genomics and bioinformatics methods were used to analyze the transposon insertion of the pig (Sus scrofa domesticus) SLC26A7 gene, and the polymorphisms in different breeds and their effects on the growth characteristics of Yorkshire were detected. The results showed that SLC26A7 gene had a 280 bp ERV insertion in intron 1, and the frequency of introduction of ERV+ is higher than that of Chinese native pig breeds. The age of 100 kg body weight of ERV+/+ individuals in the Yorkshire were significantly higher than that of ERV-/- individuals (P<0.05), and the ERV+/+ individuals is significantly lower than the ERV-/-(P<0.05). Insertion of ERV in the first intron of SLC26A7 gene inhibited its promoter activity. This study confirmed that the ERV insertion in pig SLC26A7 intron 1 had a significant effect on the age of 100 kg body weight and pre-slaughter weight (P<0.05). The results provided a reference for the application of this molecular marker in pig molecular breeding.
[1] Alper S L, Sharma A K.2013. The SLC26 gene family of anion transporters and channels[J]. Molecular Aspects of Medicine, 34(2-3): 494-515. [2] Bannert N, Kurth R.2006. The evolutionary dynamics of human endogenous retroviral families[J]. Annual Review of Genomics and Human Genetics, 7(1): 149-173. [3] Batzer M A, Stoneking M, Alegria-Hartman M, et al.1994. African origin of human-specific polymorphic Alu insertions[J]. Proceeding of the National Academy of Science of USA, 91(25): 12288-12292. [4] Beyer U, Moll-Rocek J, Moll U M, et al.2011. Endogenous retrovirus drives hitherto unknown proapoptotic p63 isoforms in the male germ line of humans and great apes[J]. Proceedings of the National Academy of Sciences of the USA, 108: 3624-3629. [5] Biemont C, Vieira C.2006. Genetics-Junk DNA as an evolutionary force[J]. Nature, 443(7111): 521-524. [6] Bogdanik L P, Chapman H D, Miers K E, et al.2012. A MusD retrotransposon insertion in the mouse SLC26A7 gene causes alterations in neuromuscular junction maturation and behavioral phenotypes[J]. PLOS ONE, 7(1): e30217. [7] Burgess D J.2013. Population genetics: Mobile elements across human populations[J]. Nature Reviews Genetics. 14(6): 370-370. [8] Cangul H, Liao X H, Schoenmakers E.2018. Homozygous loss-of-function mutations in SLC26A7 cause goitrous congenital hypothyroidism[J]. JCI Insight, 3(20): e99631. [9] David W, Joram M M, José A A, et al.2013. Endogenous retrovirus EAV-HP Linked to blue egg phenotype in Mapuche Fowl[J]. PLOS ONE, 8(8): e71393. [10] Feuchter A E, Freeman D J, Mager D L.1993. Splicing of a human endogenous retrovirus to phospholipase A2 related gene[J]. Nucleic Acids Research, 21: 135-143. [11] Galindo-González L, Mhiri C, Deyholos M K, et al.2017. LTR-retrotransposons in plants: Engines of evolution[J]. Gene, S0378111917303220. [12] Henikoff S, Greene E A, Pietrokovski S, et al.1997. Gene families: The taxonomy of protein paralogs and chimeras[J]. Science, 278: 609-614. [13] Huang X, Lu G, Zhao Q, et al.2008. Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice[J]. Plant Physiology, 148(1): 25-40. [14] Jacques P É, Jeyakani J, Bourque G.2013. The majority of primate-specific regulatory sequences are derived from transposable elements[J]. PLOS Genetics 9(5): e1003504. [15] Jern P, Coffin J M.2008. Host-Retrovirus arms race: Trimming the budget[J]. Cell Host & Microbe, 4(3): 0-197. [16] Kalendar R, Grob T, Regina M, et al.1999. IRAP and REMAP: Two new retrotransposon-based DNA fingerprinting techniques[J]. Theoretical and Applied Genetics, 98(5): 704-711. [17] Kawasaki J, Nishigaki K.2018. Tracking the continuous evolutionary processes of an endogenous retrovirus of the domestic cat: ERV-DC[J]. Viruses, 10(4): e179. [18] Lee J, Mun S, Kim D H, et al.2017. Chicken (Gallus gallus) endogenous retrovirus generates genomic variations in the chicken genome[J]. Mobile DNA, 8(1): 2. [19] Mount D, Romero M.2004. The SLC26 gene family of multifunctional anion exchangers[J]. Pfluegers Archiv European Journal of Physiology, 447(5): 710-721. [20] Pauline L K, Daniel E, Lee B, et al.2014. The population history of endogenous retroviruses in Mule Deer (Odocoileus hemionus)[J]. Journal of Heredity, 105(2): 173-187. [21] Pettersson M E, Jern P.2019. Whole-genome analysis of domestic chicken selection lines suggests segregating variation in ERV makeups[J]. Genes, 10(2): e162. [22] Rebollo R, Romanish M T, Mager D L.2012. Transposable elements: An abundant and natural source of regulatory sequences for host genes[J]. Annual Review of Genetics, 46(1): 21. [23] Rivas-Carrillo S D, Pettersson M E, Rubin C J, et al.2018. Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations[J]. Proceeding of the National Academy of Science of the USA, 115(43): 11012-11017. [24] Schulte A M, Lai S, Kurtz A, et al.1996. Human trophoblast and choriocarcinoma expression of the growth factor pleiotrophin attributable to germ-line insertion of an endogenous retrovirus[J]. Proceedings of the National Academy of Sciences of the USA, 93: 14759-14764. [25] Sun C, Skaletsky H, Rozen S, et al.2000. Deletion of azoospermia factor a (AZFa) region of human Y chromosome caused by recombination between HERV15 proviruses[J]. Human Molecular Genetics, 9(15): 2291-2296.
