Exploring the Genetic Signature of Body Size in Yucatan Miniature Pig

Kim, Hyeongmin; Song, Ki Duk; Kim, Yang Soo; Park, WonCheoul; Kim, Jaemin; Lee, Taeheon; Shin, Donghyun; Kwak, Woori; Kwon, Young-Jun; Sung, Samsun; Moon, Seok-Jae; Lee, Kyung-Tai; Kim, Namshin; Hong, Joon Ki; Eo, Kyung-Yeon; Seo, Kang Seok; Kim, Girak; Park, Sung-Moo; Yun, Cheol-Heui; Kim, Hyunil; Choi, Kihwan; Kim, Jiho; Lee, Woon Kyu; Kim, Duk Kyung; Oh, Jae-Don; Kim, Eui-Soo; Cho, Seoae; Lee, Hak-Kyo; Kim, Tae-Hun; Kim, Heebal

doi:10.1371/journal.pone.0121732

Cited by 37 publications

(44 citation statements)

References 55 publications

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“…Abundance of MiRNAs from Yorkshire and Landrace sperm were individually compared to Duroc sperm; thereafter, Yorkshire and Landrace were compared. On a genome analysis of cumulative average of nucleotide diversity, Duroc differed significantly from both Yorkshire and Landrace, whereas the latter two breeds had a very close relationship for nucleotide diversity, consistent with being the two closest breeds of pigs based on phylogenetic analyses20. In that regard, Yorkshire and Landrace shared components with each other20 and based on principal component analyses, could not be clearly distinguished20.…”

Section: Resultsmentioning

confidence: 90%

MicroRNA in sperm from Duroc, Landrace and Yorkshire boars

Kasimanickam

Kastelic

2016

Sci Rep

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Sperm contain microRNAs (miRNAs), which may have roles in epigenetic control. Regarding phylogenetic relationships among various swine breeds, Yorkshire and Landrace, are considered phenotypically and genetically very similar, but distinctly different from Duroc. The objective of the present study was to compare abundance of boar sperm miRNAs in these three breeds. Overall, 252 prioritized miRNAs were investigated using real-time PCR; relative expression of miRNAs in sperm was similar in Yorkshire and Landrace boars, but significantly different compared to Duroc. Seventeen miRNAs (hsa-miR-196a-5p, hsa-miR-514a-3p, hsa-miR-938, hsa-miR-372-3p, hsa-miR-558, hsa-miR-579-3p, hsa-miR-595, hsa-miR-648, hsa-miR-524-3p, hsa-miR-512-3p, hsa-miR-429, hsa-miR-639, hsa-miR-551a, hsa-miR-624-5p, hsa-miR-585-3p, hsa-miR-508-3p and hsa-miR-626) were down-regulated (P < 0.05; fold regulation ≤−2) in Yorkshire and Landrace sperm, compared to Duroc sperm. Furthermore, three miRNAs (hsa-miR-9-5p, hsa-miR-150-5p, and hsa-miR-99a-5p) were significantly up-regulated in Yorkshire and Landrace sperm compared to Duroc sperm, However, 240 miRNAs were not significantly different (within + 2 fold) between Yorkshire and Landrace sperm. We concluded that miRNAs in sperm were not significantly different between Yorkshire and Landrace boars, but there were significant differences between those two breeds and Duroc boars. Furthermore, integrated target genes for selected down-regulated miRNAs (identified via an in-silico method) appeared to participate in spermatogenesis and sperm functions.

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Section: Resultsmentioning

confidence: 90%

MicroRNA in sperm from Duroc, Landrace and Yorkshire boars

Kasimanickam

Kastelic

2016

Sci Rep

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“…Importantly, the average adult human body mass in United States is 82 kg, 23 while adult FP body mass is 150-300 kg at skeletal maturity. 24 The Yucatan minipig's body mass is 82 kg. 24 Despite humans and minipigs having large differences in body mass when compared to FPs, their TMJ discs did not scale proportionately.…”

Section: Discussionmentioning

confidence: 99%

“…24 The Yucatan minipig's body mass is 82 kg. 24 Despite humans and minipigs having large differences in body mass when compared to FPs, their TMJ discs did not scale proportionately. The width-to-length ratios of the human, FP, and minipig TMJ disc were 1.69, 1.94, and 1.95, respectively.…”

Section: Discussionmentioning

confidence: 99%

The Yucatan Minipig Temporomandibular Joint Disc Structure–Function Relationships Support Its Suitability for Human Comparative Studies

Vapniarsky

Aryaei

Arzi

et al. 2017

Tissue Engineering Part C: Methods

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Frequent involvement of the disc in temporomandibular joint (TMJ) disorders warrants attempts to tissue engineer TMJ disc replacements. Physiologically, a great degree of similarity is seen between humans and farm pigs (FPs), but the pig's rapid growth confers a significant challenge for in vivo experiments. Minipigs have a slower growth rate and are smaller than FPs, but minipig TMJ discs have yet to be fully characterized. The objective of this study was to determine the suitability of the minipig for TMJ studies by extensive structural and functional characterization. The properties of minipig TMJ discs closely reproduced previously reported morphological, biochemical, and biomechanical values of human and FP discs. The width/length dimension ratio of the minipig TMJ disc was 1.95 (1.69 for human and 1.94 for FP). The biochemical evaluation revealed, on average per wet weight, 24.3% collagen (22.8% for human and 24.9% for FP); 0.8% glycosaminoglycan (GAG; 0.5% for human and 0.4% for FP); and 0.03% DNA (0.008% for human and 0.02% for FP). Biomechanical testing revealed, on average, compressive relaxation modulus of 50 kPa (37 kPa for human and 32 kPa for FP), compressive instantaneous modulus of 1121 kPa (1315 kPa for human and 1134 kPa for FP), and coefficient of viscosity of 13 MPa$s (9 MPa$s for human and 3 MPa$s for FP) at 20% strain. These properties also varied topographically in accordance to those of human and FP TMJ discs. Anisotropy, quantified by bidirectional tensile testing and histology, again was analogous among minipig, human, and FP TMJ discs. The minipig TMJ's ginglymoarthrodial nature was verified through cone beam computer tomography. Collectively, the similarities between minipig and human TMJ discs support the use of minipig as a relevant model for TMJ research; considering the practical advantages conferred by its growth rate and size, the minipig may be a preferred model over FP.

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“…We collected SNPs from 287 pigs, and 6 related species, published in several studies (8, 13, 14, 20, 21) or generated by our laboratory. These samples originated mainly from Eurasia and represent both domestication locations of the pig (22).…”

Section: Introductionmentioning

confidence: 99%

PigVar: a database of pig variations and positive selection signatures

Zhou

Otecko

et al. 2017

Database

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Pigs are excellent large-animal models for medical research and a promising organ donor source for transplant patients. Next-generation sequencing technology has yielded a dramatic increase in the volume of genomic data for pigs. However, the limited amount of variation data provided by dbSNP, and non-congruent criteria used for calling variation, present considerable hindrances to the utility of this data. We used a uniform pipeline, based on GATK, to identify non-redundant, high-quality, whole-genome SNPs from 280 pigs and 6 outgroup species. A total of 64.6 million SNPs were identified in 280 pigs and 36.8 million in the outgroups. We then used LUMPY to identify a total of 7 236 813 structural variations (SVs) in 211 pigs. Positively selected loci were identified through five statistical tests of different evolutionary attributes of the SNPs. Combining the non-redundant variations and the evolutionary selective scores, we built the first pig-specific variation database, PigVar (http://www.ibiomedical.net/pigvar/), which is a web-based open-access resource. PigVar collects parameters of the variations including summary lists of the locations of the variations within protein-coding and long intergenic non-coding RNA (lincRNA) genes, whether the SNPs are synonymous or non-synonymous, their ancestral and derived states, geographic sampling locations, as well as breed information. The PigVar database will be kept operational and updated to facilitate medical research using the pig as model and agricultural research including pig breeding. Database URL: http://www.ibiomedical.net/pigvar/

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Exploring the Genetic Signature of Body Size in Yucatan Miniature Pig

Cited by 37 publications

References 55 publications

MicroRNA in sperm from Duroc, Landrace and Yorkshire boars

MicroRNA in sperm from Duroc, Landrace and Yorkshire boars

The Yucatan Minipig Temporomandibular Joint Disc Structure–Function Relationships Support Its Suitability for Human Comparative Studies

PigVar: a database of pig variations and positive selection signatures

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