Single nucleotide markers of D-loop for identification of Indian wild pig (Sus scrofa cristatus)

Srivastava, Gaurav; Rajput, Nidhi; Jadav, Kajal Kumar; Shrivastav, Avadh Bihari; Joshi, Himanshu R.

doi:10.14202/vetworld.2015.532-536

Cited by 10 publications

(6 citation statements)

References 10 publications

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“…Literatures review and in silico analysis were performed to determine the primers used in this study: universal primer pair for PCR-RFLP [15] and two sets of primer pairs for duplex PCR [16,17]. Analysis of primer characteristics was summarized in table 1.…”

Section: Resultsmentioning

confidence: 99%

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Rapid Pcr–based Detection Optimization of Porcine Dna in Gelatin Capsule Shell

2018

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Objective: This study was conducted to optimize the genomic deoxyribonucleic acid (DNA) based molecular detection of gelatin derived from porcine by performing polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and duplex PCR method employing cyt B gene.Methods: Optimization was carried out for DNA extraction, PCR conditions, and the sensitivity of the PCR-RFLP method. Due to the very low DNA trace in gelatin after the various manufacturing process, the extraction was optimized to obtain sufficient DNA which was visible on the agarose gel. PCR-RFLP was carried out using universal primers and BsaJI restriction enzyme, and duplex PCR was carried out using two sets of porcine-specific primers. Porcine and bovine DNA were mixed in various concentration to confirm sensitivity of both methods, i.e. 100%, 50%, 10%, 1%, 0.5%, 0.1%, 0.05%, and 0.01%Results: Both methods, PCR-RFLP, and Duplex PCR, were able to detect as low as 0.01% porcine DNA, indicated by the presence of porcine DNA amplicon bands (131 bp and 228 bp for PCR-RFLP, 212 bp and 398 bp for duplex PCR). Although DNA bands presented in low intensity, identification of porcine and bovine species and estimation of DNA quantities were possible.Conclusion: Both conventional PCR methods, i.e. PCR-RFLP and Duplex PCR, were sensitive, specific, and suitable as a rapid initial detection method for molecular detection of porcine in gelatin capsule shells.

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Section: Resultsmentioning

confidence: 99%

“…Duplex PCR was carried out using two porcine-specific primers [16,17] simultaneously. Annealing temperature was optimized to obtain the most effective amplification result.…”

Section: Primer Characterization Analysismentioning

confidence: 99%

Rapid Pcr–based Detection Optimization of Porcine Dna in Gelatin Capsule Shell

2018

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“…The mtDNA contains a non-coding (D-loop) sequence comprising regulatory sequences regulating both replication and transcription of the mtDNA [ 8 ]. Many studies of farm animals, including pigs, have shown the effectiveness of applying the D-loop as a diversity marker when studying the mitochondrial genome [ 9 , 10 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial DNA Diversity in Large White Pigs in Russia

Getmantseva

Bakoev

et al. 2020

Animals

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The Large White pig is the most commonly raised commercial pig breed in the world. The aim of this work was to investigate D-loop mtDNA in Large White pigs (n = 402) of various selections bred in the Russian Federation from 2000 to 2019. The general sample consisted of three groups: Old (n = 78) (Russian selection, 2000–2010); Imp (n = 123) (imported to Russia in 2008–2014); New (n = 201) (2015–2019). The synthesized score (Fz) was calculated by analyzing the main PCA (principal component analysis components). An affiliation to Asian or European haplogroups was determined according to the NCBI (National Center for Biotechnology Information). In the study, we defined 46 polymorphic sites and 42 haplotypes. Significant distinctions between groups Old, Imp and New in frequencies of haplotypes and haplogroups were established. The distribution of Asian and European haplotypes in the groups was Old: 50%/50%, Imp: 43%/57%, New: 75%/25%, respectively. The variety of haplotypes and haplogroups in the pigs of the group New is related to the farms in which they breed. Haplotype frequencies significantly differ between the clusters Old_Center, Old_Siberia and Old_South. This study will provide information on the genetic diversity of Large White breed pigs. The results will be useful for the conservation and sustainable use of these resources.

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“…The introgression of exotic genome under state sponsored programs to upgrade the local population using semen or live animals of exotic breeds has diluted the gene pool of local breeds, thus breed specification of the local domestic pig remains questionable. Most studies on Indian domestic pig mitochondrial DNA (MtDNA) are restricted to capillary electrophoresis (CE)-derived short sequence fragments analysis of cytocgrome b, 12S rRNA (Jadav et al 2014a,b), D-loop region of mitogenome (Srivastava et al 2014). There are no reports on characterization of the complete mitogenome of any of the domestic pigs of India.…”

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confidence: 99%

“…2014a , b ), D-loop region of mitogenome (Srivastava et al. 2014 ). There are no reports on characterization of the complete mitogenome of any of the domestic pigs of India.…”

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confidence: 99%

Complete mitochondrial genome sequencing of central Indian domestic pig

Singh

Jadav

Kumar

et al. 2016

Mitochondrial DNA Part B

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2016) Complete mitochondrial genome sequencing of central Indian domestic pig, Mitochondrial DNA Part B, 1:1, 949-950, ABSTRACT Domestic pig (Sus scrofa domesticus) is one of the important farm animal contributing 7% of the country's total animal protein sources in India. In the present study, random hexamer primer was used to amplify the complete mitochondrial genome of Central Indian domestic pig and resolved the complete mitochondrial sequence by shotgun sequencing followed by de novo assembly in MIRA version 4.0.5. The sequence assembly revealed to be 15,827 bp mitogenome of pig (accession no. KT965278). The mitogenome in the present study has 99% homology with previously reported mitogenome of pigs from different parts of the world. The present study is the first report of complete sequence of mitogenome of pig from Indian subcontinent. Mitogenome analysis by MITOS web server revealed similarity of gene order, organization with the other pig breeds and vertebrates, comprising of 13 proteincoding genes, 22 tRNAs, 2 rRNAs and a control region. It was concluded that modified random hexamer can be successfully used for whole mitogenome sequencing using NGS without designing mitogenome-specific primer, thereby reducing cost and labor. ARTICLE HISTORY

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Single nucleotide markers of D-loop for identification of Indian wild pig (Sus scrofa cristatus)

Cited by 10 publications

References 10 publications

Rapid Pcr–based Detection Optimization of Porcine Dna in Gelatin Capsule Shell

Rapid Pcr–based Detection Optimization of Porcine Dna in Gelatin Capsule Shell

Mitochondrial DNA Diversity in Large White Pigs in Russia

Complete mitochondrial genome sequencing of central Indian domestic pig

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