scholarly journals Detection of one large insertion/deletion (indel) and two novel SNPs within the <i>SPEF2</i> gene and their associations with male piglet reproduction traits

2016 ◽  
Vol 59 (2) ◽  
pp. 275-283 ◽  
Author(s):  
Rui Chen ◽  
Shuai Yu ◽  
Fa Ren ◽  
Xiao Yan Lv ◽  
Chuan Ying Pan
Keyword(s):  
Dna Marker ◽  
Male Reproduction ◽  
Nucleotide Polymorphisms ◽  
Chromosome 16 ◽  
Large White ◽  
Single Nucleotide ◽  
Association Testing ◽  
Normal Sperm ◽  
Reproduction Traits ◽  
Large Insertion

Abstract. The sperm flagella 2 (SPEF2) gene is essential for normal sperm tail development and male fertility. To fully characterize the structure of the mutation and to further study the function of the pig SPEF2 gene, we explored the insertion/deletion (indel) and novel single-nucleotide polymorphisms (SNPs) within the pig SPEF2 gene, and tested their associations with the testicular sizes in male Large White (LW) and Landrace (LD) pigs from China. Herein, a large insertion located at the SPEF2 gene in chromosome 16 was found, and two alleles of "I" (insertion) and "D" (deletion) were designated. Allele "D" was dominant in all analyzed pigs. Two novel SNPs (namely (NC_010458) g.19642G > A, resulting in AfaI aCRS PCR–PFLP, and g.19886C > G, resulting in EcoRI aCRS PCR–PFLP) were found in LW and LD pigs. Association testing revealed that g.19886C > G was significantly associated with the testis long circumference (TLC) in LW pigs (P < 0.05), suggesting that this SNP would be the DNA marker for the marker-assisted selection (MAS) in reproduction traits. This preliminary result indicates that the pig SPEF2 gene had significant effects on male reproduction traits. These findings could not only extend the spectrum of genetic variations in the pig SPEF2 gene but also contribute to implementing MAS in genetics and breeding in pigs.

scholarly journals Association of non-synonymous SNPs of <i>OPN</i> gene with litter size traits in pigs

2015 ◽  
Vol 58 (2) ◽  
pp. 317-323 ◽  
Author(s):  
T. Kumchoo ◽  
S. Mekchay
Keyword(s):  
Litter Size ◽  
Reproductive Traits ◽  
Snp Markers ◽  
Strong Linkage Disequilibrium ◽  
Nucleotide Polymorphisms ◽  
Large White ◽  
Single Nucleotide ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Acid Exchange

Abstract. Osteopontin (OPN) gene is a secreted phosphoprotein which appears to play a key function in the conceptus implantation, placentation and maintenance of pregnancy in pigs. The objectives of this study were to verify the non-synonymous single nucleotide polymorphisms (SNPs) and their association with litter size traits in commercial Thai Large White pigs. A total of 320 Thai Large White sows were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Three SNPs at c.425G> A, c.573T> C and c.881C> T revealed amino acid exchange rates of p.110Ala> Thr, p.159Val> Ala and p.262Pro> Ser, respectively, and were then segregated. These three SNPs were significantly associated with total number born (TNB) and number born alive (NBA) traits. No polymorphisms of the two SNP markers (c.278A> G and c.452T> G) were observed in this study. Moreover, the SNPs at c.425G> A and c.573T> C were found to be in strong linkage disequilibrium. The association of OPN with litter size emphasizes the importance of porcine OPN as a candidate gene for reproductive traits in pig breeding.

scholarly journals Genetic Association Study of KCNQ5 Polymorphisms with High Myopia

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Xuan Liao ◽  
Maurice K. H. Yap ◽  
Kim Hung Leung ◽  
Patrick Y. P. Kao ◽  
Long Qian Liu ◽  
...  
Keyword(s):  
Refractive Error ◽  
Odds Ratio ◽  
High Myopia ◽  
Permutation Test ◽  
Minor Allele ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Association Testing ◽  
Hypersensitive Sites

Identification of genetic variations related to high myopia may advance our knowledge of the etiopathogenesis of refractive error. This study investigated the role of potassium channel gene (KCNQ5) polymorphisms in high myopia. We performed a case-control study of 1563 unrelated Han Chinese subjects (809 cases of high myopia and 754 emmetropic controls). Five tag single-nucleotide polymorphisms (SNPs) of KCNQ5 were genotyped, and association testing with high myopia was conducted using logistic regression analysis adjusted for sex and age to give Pasym values, and multiple comparisons were corrected by permutation test to give Pemp values. All five noncoding SNPs were associated with high myopia. The SNP rs7744813, previously shown to be associated with refractive error and myopia in two GWAS, showed an odds ratio of 0.75 (95% CI 0.63–0.90; Pemp = 0.0058) for the minor allele. The top SNP rs9342979 showed an odds ratio of 0.75 (95% CI 0.64–0.89; Pemp = 0.0045) for the minor allele. Both SNPs are located within enhancer histone marks and DNase-hypersensitive sites. Our data support the involvement of KCNQ5 gene polymorphisms in the genetic susceptibility to high myopia and further exploration of KCNQ5 as a risk factor for high myopia.

scholarly journals Porcine prolactin receptor genotypes and production and reproduction traits in Hungarian Large White and Landrace sows (Brief Report)

2010 ◽  
Vol 53 (4) ◽  
pp. 497-499
Author(s):  
K. Kovacs ◽  
L. Fesus ◽  
A. Zsolnai ◽  
A. Nyiri ◽  
I. Anton
Keyword(s):  
Litter Size ◽  
Receptor Gene ◽  
Mammalian Species ◽  
Prolactin Receptor ◽  
Reproductive Traits ◽  
Pituitary Hormone ◽  
Chromosome 16 ◽  
Large White ◽  
Anterior Pituitary Hormone ◽  
Reproduction Traits

Abstract. Prolactin is an anterior pituitary hormone involved in many endocrine activities and plays and essential role in reproduction. Its receptor (PRLR) was detected in various tissues including brain, ovary, placenta, an uterus in several mammalian species (BOLE-FEYSOT et al. 1998). Reproductive performance of sows is a crutial point in pig production with significant economic importance and may be estimated with the help of markers. Porcine prolactin receptor gene is said to be a candidate genetic marker for reproductive traits. It has been mapped to porcine chromosome 16 (Vincent et al. 1997). There is a C/G SNP in PRLR gene (KMIEC et al. 2001) at the position of 203 (GAN: U96306) which eliminates an AluI cleavage site. The effect of this polymorphism on litter size in various breeds has been estimated (VINCENT et al. 1998, ROTHSCHILD et al. 1998, VAN RENS et al. 2002, KMIEC and TERMAN, 2004, DRÖGEMÜLLER et al. 2001, KORWIN-KOSSAKOWSKA et al. 2003). The influence of the bovine hormone variant was also estimated (RATNA-KUMARI et al. 2008). The aim of the study was to estimate PRLR AluI polymorphism effects on litter size in Hungarian Large White (HLW) and Hungarian Landrace (HL) breeds.

scholarly journals Polymorphic sites in the 5´-region of the porcine <i>C8A</i> gene

2011 ◽  
Vol 54 (4) ◽  
pp. 430-438 ◽  
Author(s):  
D. V. A. Khoa ◽  
S. Ponsuksili ◽  
E. Muráni ◽  
K. Wimmers
Keyword(s):  
Animal Species ◽  
Membrane Attack Complex ◽  
Nucleotide Polymorphisms ◽  
Large White ◽  
Single Nucleotide ◽  
Binding Motifs ◽  
High Identity ◽  
High Conservation ◽  
The Complement System ◽  
Human And Mouse

Abstract. The membrane attack complex (MAC) of the complement system is known as a natural immune mechanism of hosts against invading pathogens. This study was undertaken to structurally characterize and computationally analyzed the 5´-region, i.e. the downstream promoter region and the 5´-UTR nucleotide sequence of the porcine C8A, one of the components of the MAC. Sequencing approximately 950 bp of the 5´-region and analyzing in silico revealed the transcription start site, the TATA-box, the CAAAT-box, and the GATAAbox. High identity was found in range of 37–74 % among the sequences of pig, human, cattle, and mouse. Transcription factor binding sites, such as NFκB, Oct-1, HNF1, CDP, and C/EBP, showed high conservation between vertebrate animal species, especially between human and mouse, or pig and cattle. Seven single nucleotide polymorphisms were detected in the breeds Hampshire, Duroc, German Landrace, Large White, Pietrain, Berlin Miniature Pig, and Muong Khuong. Nucleotide exchanges could cause the generation of new binding motifs, which may affect the expression of the porcine C8A, particularly the C/EBP regulation of the porcine C8A gene – as described in the human C6 and C7 promoter.

scholarly journals Identification of 1093-bp intron A, SNPS and indels discovered in the porcine pregnancy-associated glycoprotein 2-like (pPAG2-L) gene subfamily in pigs

Genetika ◽  
2020 ◽  
Vol 52 (3) ◽  
pp. 851-866
Author(s):  
Martyna Bieniek-Kobuszewska ◽  
Grzegorz Panasiewicz ◽  
Bożena Szafranska
Keyword(s):  
Genetic Variation ◽  
Single Nucleotide Polymorphisms ◽  
General Knowledge ◽  
Nucleotide Polymorphisms ◽  
Porcine Genome ◽  
Large White ◽  
Bac Clone ◽  
Single Nucleotide ◽  
Noncoding Regions ◽  
Gene Subfamily

The objective of this study was to identify the intron A sequence (between exons 1 and 2) of pPAG2-L, novel single nucleotide polymorphisms (SNPs) and mutations (InDels) within intron A in the crossbreed (Landrace x Large White), Hirshmann hybrid and Duroc pigs. Genomic templates were isolated from leukocytes, amplified, and the gel-out were purified and then sequenced. Positive amplification control included CH242-60C13 BAC clone (Duroc) containing pPAG1-L and pPAG2-L. This is the first report that describes the 1093-bp intron A sequence from the pPAG2-L (Acc. No. KF471015; GenBank), which increased general knowledge of the porcine genome. Novel SNPs/InDels were identified within the intron A of the pPAG2-L in the crossbreeds (72), Duroc (45) and Hirshmann hybrids (17). This is a pioneer study describing identification of the intron A and SNPs/InDels in crossbreeds that provides a novel major pattern that represents a large portion of the genetic variation within the porcine genome. This information should be valuable when genotyping (coding and noncoding regions) multiparous sows from many breeds, in which reproductive phenotypes are known.

scholarly journals Identification and Monitoring of Amomi Fructus and its Adulterants Based on DNA Barcoding Analysis and Designed DNA Markers

Molecules ◽  
2019 ◽  
Vol 24 (22) ◽  
pp. 4193 ◽  
Author(s):  
Eui Jeong Doh ◽  
Jung-Hoon Kim ◽  
Guemsan Lee
Keyword(s):  
Dna Barcoding ◽  
Dna Markers ◽  
Dna Marker ◽  
Intergenic Spacer ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Traditional Medicines ◽  
Amomum Villosum ◽  
Reliable Methods ◽  
A New Species

Amomi Fructus is one of the traditional medicines derived from the ripe fruits of the Zingiberaceae family of plants, which include Amomum villosum, A. villosum var. xanthioides, and A. longiligulare. Owing to their highly similar morphological traits, several kinds of adulterants of Amomi Fructus have been reported. Therefore, accurate and reliable methods of identification are necessary in order to ensure drug safety and quality. We performed DNA barcoding using five regions (ITS, matK, rbcL, rpoB, and trnL-F intergenic spacer) of 23 Amomi Fructus samples and 22 adulterants. We designed specific DNA markers for Amomi Fructus based on the single nucleotide polymorphisms (SNPs) in the ITS. Amomi Fructus was well separated from the adulterants and was classified with the species of origin based on the detected SNPs from the DNA barcoding results. The AVF1/ISR DNA marker for A. villosum produced a 270 bases amplified product, while the ALF1/ISF DNA marker produced a 350 bases product specific for A. longiligulare. Using these DNA markers, the monitoring of commercially distributed Amomi Fructus was performed, and the monitoring results were confirmed by ITS analysis. This method identified samples that were from incorrect origins, and a new species of adulterant was also identified. These results confirmed the accuracy and efficiency of the designed DNA markers; this method may be used as an efficient tool for the identification and verification of Amomi Fructus.

scholarly journals Reduced Representation Libraries from DNA Pools Analysed with Next Generation Semiconductor Based-Sequencing to Identify SNPs in Extreme and Divergent Pigs for Back Fat Thickness

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Samuele Bovo ◽  
Francesca Bertolini ◽  
Giuseppina Schiavo ◽  
Gianluca Mazzoni ◽  
Stefania Dall’Olio ◽  
...  
Keyword(s):  
Frequency Estimation ◽  
Breeding Value ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Large White ◽  
Single Nucleotide ◽  
Reduced Representation ◽  
Novel Variants ◽  
Dna Pools ◽  
Fat Thickness

The aim of this study was to identify single nucleotide polymorphisms (SNPs) that could be associated with back fat thickness (BFT) in pigs. To achieve this goal, we evaluated the potential and limits of an experimental design that combined several methodologies. DNA samples from two groups of Italian Large White pigs with divergent estimating breeding value (EBV) for BFT were separately pooled and sequenced, after preparation of reduced representation libraries (RRLs), on the Ion Torrent technology. Taking advantage from SNAPE for SNPs calling in sequenced DNA pools, 39,165 SNPs were identified; 1/4 of them were novel variants not reported in dbSNP. Combining sequencing data with Illumina PorcineSNP60 BeadChip genotyping results on the same animals, 661 genomic positions overlapped with a good approximation of minor allele frequency estimation. A total of 54 SNPs showing enriched alleles in one or in the other RRLs might be potential markers associated with BFT. Some of these SNPs were close to genes involved in obesity related phenotypes.

scholarly journals Effect of leukemia inhibitory factor polymorphism on litter size traits in Thai commercial pig breeds

2020 ◽  
Vol 19 (2) ◽  
pp. 185-196
Author(s):  
Worrarak Norseeda ◽  
◽  
Guisheng Liu ◽  
Tawatchai Teltathum ◽  
Korawan Sringarm ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Litter Size ◽  
Leukemia Inhibitory Factor ◽  
Inhibitory Factor ◽  
Untranslated Regions ◽  
Nucleotide Polymorphisms ◽  
Large White ◽  
Single Nucleotide ◽  
Synonymous Snps ◽  
Implantation Process

Leukemia inhibitory factor (LIF) is a crucial candidate gene that impacts on implantation process. In this study, the effects of the porcine LIF polymorphism on litter size traits were elucidated in Thai commercial pig populations. Genotyping of three single nucleotide polymorphisms (SNPs) of the porcine LIF gene was detected in coding and 3ˊ-untranslated regions. The porcine LIF c.*24C>T was segregating in Large White, Landrace, and Large White × Landrace (LW × LR) crossbred sows. No polymorphisms at two non-synonymous SNPs loci (LIF c.28C>A and LIF c.161A>G) were found in this study. The porcine LIF c.*24C>T was significantly associated with the total number born (TNB), the number born alive (NBA), and the number of piglets weaned alive (NWA) traits in Large White and Landrace sows. Moreover, the porcine LIF c.*24C>T was associated with the NBA and NWA traits in LW × LR crossbred sows. The favorable LIF c.*24C allele was positively correlated with the litter size traits. These findings indicated that the polymorphism of the porcine LIF gene was associated with litter size traits and confirms the significance of porcine LIF as a candidate gene for litter size traits in pig breeding. Thus, the porcine LIF gene could be used for improving prolific traits in these Thai commercial pig populations.

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