Abstract To gain a better understanding for the relationship between the genome structure and the reproduction mechanism of Xiang pig, the genome sequence of Xiang pig (Sus scrofa) was detected using next-generation sequencing method. Plenty of structural variations (SVs) were detected from chromosome X (chrX) of two Xiang pig groups with high (XH) or low (XL) litter size using several bioinformatics programs. There were 3 246 SVs being screened out from chrX of Xiang pig, in which 311 SVs were unique in XH group and 138 SVs in XL group with 449 SVs in total. It was notified that a SV hotspot locating at 61~109 Mb of chrX group was found out from samples of group XH. There were 138 SVs in the SV hotspot region, with 65 of them in deletion genotype. In addition, about 47 proteins might be disturbed by 80 of specific SVs in genes of Xiang pig. Out of 31 in the 47 genes contained QTL which was related with reproduction traits such as genes of NLGN4X, GPR143, ZDHHC15, ATRX, NXF2, AMOT, GRIA3, THOC2. These genes were significantly enriched in the adrenal gland development, regulation of intracellular steroid hormone receptor signaling pathway, RIG-I-like receptor signaling pathway and lipoprotein metabolic process base on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. 10/47 SVs in populations of Xiang pig were genotyped by PCR methods. The frequency of SV_GPR143 genotypes was significantly different between XH and XL groups (P＜0.05). And the SV_GPR143 locus showed a correlation ship with the litter sizes (ρ=0.217) of Xiang pig with 1.96 piglets in DD genotype lower than that in NN genotype (P＜0.05). It indicated that much more amount of SVs presented in group XH and might contribute to the high reproduction trait of Xiang pig.
LIU Chang,YU Jia-Fu,HUANG Shi-Hui, et al. Comparative Analysis of Structural Variations on Chromosome X in Two Xiang Pig (Sus scrofa) Groups with High and Low Litter Size[J]. , 2017, 25(7): 1045-1058.
[1] 申学林，杨秀江．从江香猪生长发育繁殖性能测定[J]．种业研究，2007（11）：39-41（Shen XL，Yang XJ．Performance Test on the Reproductive and Growth Traits of Congjiang Xiang Pig [J]．Zhongye Yanjiu，2007（11）：39-41） [2] 杨广礼，张淑红，韩进诚，等．猪X染色体QTL定位和候选基因的研究进展[J]．黑龙江畜牧兽医，2010，6(11)：38–40（Yang GL，Zhang SH，Han JC，et al．QTL mapping on Porcine chromosome X and progress of candidate genes [J]．Heilongjiang Animal Science and Veterinary Medicine，2010，6(11)：38–40） [3] 杨廷模，刘畅，赵恒鑫，等．高产从江香猪资源调查及其FSH 基因型分析[J]．畜牧与兽医，2014，46(8)：5-8（Yang TM，Liu C，Zhao HX，et al．Investigation on xiang pigs of high fecundity in Congjiang county of Guizhou province [J]．Animal Husbandry and VeterinaryMedicine，2014，46(8)：5-8） [4] 姚娇娇，田亮，胡健，等．妊娠母猪膘情对其繁殖性能的影响[J]．动物营养学报，2014，26（6）：1638-1643（YAO jiaojiao，TIAN Liang，HU Jian et al. Fat Mass：Effects on Reproductive Performance of Pregnant Sows [J]．Chinese Journal of Animal Nutrition，2014，26（6）：1638-1643 [5] Agoulnik IU，Krause WC，Bingman WE 3rd，et al．Repressors of androgen and progesterone receptor action [J]．J Biol Chem，2003，278(33)：31136-48 [6] Anguera MC，Ma W，Clift D，et al．Tsx produces a long noncoding RNA and has general functions in the germline,stem cells, and brain [J]．PLoS Genet，2011，7(9)：e1002248 [7] Bartenhagen C，Dugas M．Robust and exact structural variation detection with paired-end and soft-clipped alignments: SoftSV compared with eight algorithms [J]．Brief Bioinform，2016，17：51-62 [8] Boerboom D，Pil on N，Behdjani R，et al．Expression and regulat ion of transcripts encoding two members of the NR5A nuclear receptor subfamily of orphan nuclear receptors ， steroidogenicfactor-1 and NR5A2, in equine ovarian cells during the ovulatory process[J]．Endocrinology， 2000， 141(12)：4647-4656 [9] Bopp D，Horabin JI，Lersch RA，et al．Expression of the Sex-lethal gene is controlled at multiple levels during Drosophila oogenesis [J]．Development，1993，118(3)：797-812 [10] Bridges CB．The Bar "Gene" a Duplication[J]．Science，1936，83：210-211 [11] Chen K，Wallis JW，McLellan MD，et al．BreakDancer: an algorithm for high-resolution mapping of genomic structural variation [J]．Nat Methods，2009，6：677-681 [12] Chen Z，Gao X，Lei T，et al．Molecular characterization,expression and chromosomal localization of porcine PNPLA3 and PNPLA4 [J]．Biotechnol Lett，2011，33(7)：1327-37 [13] Durruthy-Durruthy J，Sebastiano V，Wossidlo M，et al． The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming [J]．Nat Genet， 2016，48(1)：44-52 [14] Feuk L，Carson AR，Scherer SW．Structural variation in the human genome [J]．Nat Rev Genet， 2006，7(2)：85-97 [15] Holter E，Kotaja N，M?kela S，et al．Inhibition of androgen receptor (AR) function by the reproductive orphan nuclear receptor DAX-1 [J]．MolEndocrinol，2002，16(3)：515-28 [16] Iyer AK，McCabe ER．Molecular mechanisms of DAX1 action [J]．Mol Genet Metab，2004，83(1-2)：60-73 [17] Jalali S，Bhartiya D，Lalwani MK，et al．Systematic transcriptome wide analysis of lncRNA-miRNA interactions [J]．PLoS One, 2013，8(2)：e53823 [18] Kaneko S，Son J，Shen SS，et al．PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells[J]．Nat StructMol Biol， 2013，20(11)：1258-64 [19] Li H，Durbin R．Fast and accurate short read alignment with Burrows-Wheeler transform [J]．Bioinformatics，2009，25：1754-1760 [20] Li H，Handsaker B，Wysoker A，et al．The sequence alignment/map format and SAMtools [J]．Bioinformatics，2009，25：2078-2079 [21] Li W，Chen S， Li H，et al．A New Insertion/Deletion Fragment Polymorphism of Inhibin-α Gene Associated with Follicular Cysts in Large White Sows [J]．J Vet Med Sci，2016，78：473-476 [22] Liu CF，Liu C，Yao HH．Building pathways for ovary organogenesis in the mouse embryo[J]．Curr Top Dev Biol，2010，90：263-90 [23] Loo YM, Gale M., Jr Immune signaling by RIG-I-like receptors. Immunity. 2011;34:680–92. [24] Lu H，Zhang J，Liu KB，et al．Earliest domestication of common millet (Panicummiliaceum) in East Asia extended to 10,000 years ago [J]．ProcNatlAcadSci U S A，2009，106(18)：7367-72 [25] Lubahn DB，Moyer JS，Golding TS，et al．Alteration of reproductive function but not prenatal sexual development after insertional disruption of the mouse estrogen receptor gene [J]．ProcNatlAcadSci U S A，1993，90(23)：11162-6 [26] Lydon JP，DeMayo FJ，Funk CR，et al．Mice lacking progesterone receptor exhibit pleiotropic reproductive abnormalities [J]．Genes Dev，1995，9(18)：2266-78 [27] McKernan KJ，Peckham HE，Costa GL，et al．Sequence and structural variation in a human genome uncovered by short-read，massively parallel ligation sequencing using two-base encoding [J]．Genome Res，2009，19：1527-1541 [28] Martins RS，Power DM，Fuentes J，et al．DAX1 regulatory networks unveil conserved and potentially new functions．Gene， 2013 ，530(1)：66-74 [29] Muller HJ．Bar Duplication [J]．Science，1936，83：528-530 [30] Mulac-Jericevic B，Mullinax RA，DeMayo FJ，et al．Subgroup of reproductive functions of progesterone mediated by progesterone receptor-B isoform [J]．Science，2000，289(5485)：1751-4 [31] Ohba Y，Kitagawa H，Kitoh K，et al．A deletion of the paracellin-1 gene is responsible for renal tubular dysplasia in cattle [J]．Genomics，2000，68(3)：229-36 [32] Pailhoux E，Vigier B，Chaffaux S，et al．A 11.7-kb deletion triggers intersexuality and polledness in goats [J]．Nat Genet，2001，29(4)：453-8 [33] Patel RK，Jain M．NGS QC toolkit: a toolkit for quality control of next generation sequencing data [J]．PLOS ONE，2012，7：e30619 [34] Peng N，Kim JW，Rainey WE，et al．The role of the orphan nuclear receptor, liver receptor homologue-1, in the regulation of human corpus luteum 3beta-hydroxysteroid dehydrogenase type II [J]．J ClinEndocrinolMetab， 2003，88(12)：6020-8 [35] Petrov DA．Mutational equilibrium model of genome size evolution [J]．Theoretical Population Biology，2002，61：531-544 [36] Rothschild M，Jacobson C，Vaske D，et al．The estrogen receptor locus is associated with a major gene influencing litter size in pigs [J]．ProcNatlAcadSci U S A， 1996，93(1)：201-5 [37] Ryu YH，Macdonald PM．RNA sequences required for the noncoding function of oskar RNA also mediate regulation of Oskar protein expression by Bicoid Stability Factor [J]．Dev Biol，2015，407(2)：211-23 [38] Seamark R.F., Hadjisavas M., Robertson S.A. Influence of the immune system on reproductive function. Animal Reproduction Science, 1992, 28, 171-178 [39] Szreder T，Zelazowska B，Zwierzchowski L，et al．A novel nucleotide sequence polymorphism in the 5'-noncoding region of bovine estrogen receptor alpha gene, the RFLP-SnaBI [J]．Biochem Genet，2007，45(3-4)：255-62 [40]Wang C, Wang H, Zhang Y, et al. Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs [J]. Mol Ecol Resour. 2015;15(2):414-24. [41] Yang S, Li X, Li K, et al. A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds[J]. BMC Genet. 2014 Jan 15;15:7. [42] Wilson PA，Gardner SD，Lambie NM，et al．Characterization of the human patatin-like phospholipase family [J]． J Lipid Res，2006，47(9)：1940-9 [43] Ye K，Schulz MH，Long Q，et al．Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads [J]．Bioinformatics，2009，25：2865-2871 [44] Yu CE，Dawson G，Munson J，D'Souza I，et al．Presence of large deletions in kindreds with autism [J]．American Journal of Human Genetics，2002，71：100-115 [45] Zhao P，Li J，Kang H，et al．Structural variant detection by large-scale sequencing reveals new evolutionary evidence on breed divergence between Chinese and European pigs [J]．Sci Rep，2016，6：18501 [46] Zhang H，Thomsen JS，Johansson L，et al．DAX-1 functions as an LXXLL-containing corepressor for activated estrogen receptors [J]．J Biol Chem，2000，275(51)：39855-9
