Insertion of 275-bp SINE into first intron of PDIA4 gene is associated with litter size in Xiang pigs

Liu, Chang; Ran, Xueqin; Niu, Xi; Sheng, Li; Wang, Jiafu; Zhang, Qin

doi:10.1016/j.anireprosci.2018.04.079

Cited by 16 publications

(9 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Another candidate gene, PDIA4 (protein disulfide isomerase family A, member 4), one of the redox genes whose expression patterns are related to oocyte quality [41]. Also, PDIA4 gene was reported expressed in ovaries and associated with litter size in pigs [42]. According to our findings, OXTR (oxytocin receptor) and CYP19A1, which were identified by both Fst and XPEHH test could be the most potential genes affecting sheep litter size.…”

Section: Discussionsupporting

confidence: 51%

Using High-Density SNP Array to Reveal Selection Signatures Related to Prolificacy in Chinese and Kazakhstan Sheep Breeds

Wang

Niu

Zeng

et al. 2020

Animals

View full text Add to dashboard Cite

Selection signature provides an efficient tool to explore genes related to traits of interest. In this study, 176 ewes from one Chinese uniparous breed and three Kazakhstan multiparous breeds are genotyped using Affymetrix 600K HD single nucleotide polymorphism (SNP) arrays, F-statistics (Fst), and a Cross Population Extend Haplotype Homozygosity Test (XPEHH). These are conducted to identify genomic regions that might be under selection in three population pairs comprised the one multiparous breed and the uniparous breed. A total of 177 and 3072 common selective signatures were identified by Fst and XPEHH test, respectively. Nearly half of the common signatures detected by Fst were also captured by XPEHH test. In addition, 1337 positive and 1735 common negative signatures were observed by XPEHH in three Kazakhstan multiparous breeds. In total, 242 and 798 genes were identified in selective regions and positive selective regions identified by Fst and XPEHH, respectively. These genes were further clustered in 50 gene ontology (GO) functional terms and 66 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in enrichment analysis. The GO terms and pathways were relevant with reproductive processes, e.g., oxytocin signaling pathway, thyroid hormone synthesis and GnRH signaling pathway, vascular smooth muscle contraction and lipid metabolism (alpha-Linolenic acid metabolism and Linoleic acid metabolism), etc. Based on the findings, six potential candidate genes ESR1, OXTR, MAPK1, RYR1, PDIA4, and CYP19A1, under positive selection related to characteristics of multiparous sheep breeds were revealed. Our results improve our understanding of the mechanisms of selection that underlies the prolificacy trait in sheep, and provide essential references for future sheep breeding.

show abstract

Section: Discussionsupporting

confidence: 51%

Using High-Density SNP Array to Reveal Selection Signatures Related to Prolificacy in Chinese and Kazakhstan Sheep Breeds

Wang

Niu

Zeng

et al. 2020

Animals

View full text Add to dashboard Cite

show abstract

“…More than 100 cases of retrotransposon-mediated insertions causing human genetic diseases have been confirmed [24]. Also, in farm animals, there are numerous examples, such as an association of a 275-bp SINE insertion into the first intron of PDIA4 gene with litter size in pigs [25]. Three SINE insertion polymorphisms in the VRTN gene have been identified [26]; one of them has been suggested as a potential causative mutation contributing to vertebral number variation in domestic pigs [27,28].…”

Section: Introductionmentioning

confidence: 99%

SINE Insertion in the Intron of Pig GHR May Decrease Its Expression by Acting as a Repressor

Zheng

Muráni

D’Alessandro

et al. 2021

Animals

View full text Add to dashboard Cite

The genetic diversity of the GH/IGF axis genes and their association with the variation of gene expression and phenotypic traits, principally represented by SNPs, have been extensively reported. Nevertheless, the impact of retrotransposon insertion polymorphisms (RIPs) on the GH/IGF axis gene activity has not been reported. In the present study, bioinformatic prediction and PCR verification were performed to screen RIPs in four GH/IGF axis genes (GH, GHR, IGF1 and IGF1R). In total, five RIPs, including one SINE RIP in intron 3 of IGF1, one L1 RIP in intron 7 of GHR, and three SINE RIPs in intron 1, intron 5 and intron 9 of GHR, were confirmed by PCR, displaying polymorphisms in diverse breeds. Dual luciferase reporter assay revealed that the SINE insertion in intron 1 of GHR significantly repressed the GHR promoter activity in PK15, Hela, C2C12 and 3T3-L1 cells. Furthermore, qPCR results confirmed that this SINE insertion was associated with a decreased expression of GHR in the leg muscle and longissimus dorsi, indicating that it may act as a repressor involved in the regulation of GHR expression. In summary, our data revealed that RIPs contribute to the genetic variation of GH/IGF axis genes, whereby one SINE RIP in the intron 1 of GHR may decrease the expression of GHR by acting as a repressor.

show abstract

“…These data indicate that SINE RIP markers may be important tools for studying biodiversity and genetics, and even for molecular breeding in domestic animals. In particular, several SINE insertions causing phenotype changes have been reported in pigs, horses, and dogs [35][36][37][38][39][40]. SINEA1-3 represents the youngest subfamily of pig-speci c SINEs and re ects the most recent expansion activity during the last 10 million years [10].…”

Section: Introductionmentioning

confidence: 99%

SINE jumping contributes to large-scale polymorphisms in the pig genomes

D’Alessandro

Muráni

Zheng

et al. 2021

Preprint

View full text Add to dashboard Cite

Background: Molecular markers based on retrotransposon insertion polymorphisms (RIPs) have been developed and are widely used in plants and animals. Short interspersed nuclear elements (SINEs) exert wide impacts on gene activity and even on phenotypes. However, SINE RIP profiles in livestock remain largely unknown, and not be revealed in pigs. Results: Our data revealed that SINEA1 displayed the most polymorphic insertions (22.5% intragenic and 26.5% intergenic), followed by SINEA2 (10.5% intragenic and 9% intergenic) and SINEA3 (12.5% intragenic and 5.0% intergenic). We developed a genome-wide SINE RIP mining protocol and obtained a large number of SINE RIPs (36,284), with over 80% accuracy and an even distribution in chromosomes (14.5/Mb), and 74.34% of SINE RIPs generated by SINEA1 element. Over 65% of pig SINE RIPs overlap with genes, with significant enrichment in the first and second introns of protein-coding and long non-coding RNA genes. Nearly half of the RIPs are common in these pig breeds. Sixteen SINE RIPs were applied for population genetic analysis in 23 pig breeds, the phylogeny tree and cluster analysis were generally consistent with the geographical distributions of native pig breeds in China. Conclusions: Our analysis revealed that SINEA1–3 elements, particularly SINEA1, are high polymorphic across different pig breeds, and generate large-scale structural variations in the pig genomes. And over 35, 000 SINE RIP markers were obtained. These data indicate that young SINE elements play important roles in creating new genetic variations and shaping the evolution of pig genome, and also provide strong evidences to support the great potential of SINE RIPs as genetic markers, which can be used for population genetic analysis and quantitative trait locus (QTL) mapping in pig.

show abstract

Insertion of 275-bp SINE into first intron of PDIA4 gene is associated with litter size in Xiang pigs

Cited by 16 publications

References 30 publications

Using High-Density SNP Array to Reveal Selection Signatures Related to Prolificacy in Chinese and Kazakhstan Sheep Breeds

Using High-Density SNP Array to Reveal Selection Signatures Related to Prolificacy in Chinese and Kazakhstan Sheep Breeds

SINE Insertion in the Intron of Pig GHR May Decrease Its Expression by Acting as a Repressor

SINE jumping contributes to large-scale polymorphisms in the pig genomes

Contact Info

Product

Resources

About