Mitochondrial DNA Sequence and Phylogenetic Evaluation of Geographically Disparate<i>Sus scrofa</i>Breeds

Mitochondrial DNA (mtDNA) is widely used in various genetic studies of domesticated animals. Many applications require comprehensive knowledge about the phylogeny of mtDNA variants. Herein, we provide the most up-to-date mtDNA phylogeny (i.e. haplogroup tree or matrilineal genealogy) and a standardized hierarchical haplogroup nomenclature system for domesticated cattle, dogs, goats, horses, pigs, sheep, yaks and chickens. These high-resolution mtDNA haplogroup trees based on 1240 complete or near-complete mtDNA genome sequences are available in open resource DomeTree (http://www.dometree.org). In addition, we offer the software MitoToolPy (http://www.mitotool.org/mp.html) to facilitate the mtDNA data analyses. We will continuously and regularly update DomeTree and MitoToolPy.

show abstract

“…; Cannon et al . ). The generated confusion and chaos complicates the comparison of different studies.…”

Section: Introductionmentioning

confidence: 97%

DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals

Peng

Fan

Shi

et al. 2015

Molecular Ecology Resources

View full text Add to dashboard Cite

show abstract

“…, Large White breed) are used in such cross-breeding efforts with Meishan females or other prolific Chinese native breeds, to generate F1 hybrid offspring. Therefore, it was not surprising to find Large White genetics within mitochondrial populations within Chinese indigenous pig breed as was noted with other European breed sequences 21 22 .…”

Section: Discussionmentioning

confidence: 65%

Mitochondrial Haplotypes Influence Metabolic Traits in Porcine Transmitochondrial Cybrids

Xiang

Tian

et al. 2015

Sci Rep

View full text Add to dashboard Cite

In farm animals, mitochondrial DNA mutations exist widely across breeds and individuals. In order to identify differences among mtDNA haplotypes, two porcine transmitochondrial cybrids were generated by fusion of a Lantang pig cell line devoid of mitochondrial DNA with enucleated cytoplasm from either a Large White pig or a Xiang pig harboring potentially divergent mitochondrial haplotypes. These cybrid cells were subjected to mitochondrial genome sequencing, copy number detecting and analysis of biochemical traits including succinate dehydrogenase (SDH) activity, ATP content and susceptibility to reactive oxygen species (ROS). The Lantang and Xiang mitochondrial genomes were highly homologous with only 18 polymorphic sites, and differed radically from the Large White with 201 and 198 mutations respectively. The Large White and Xiang cybrids exhibited similar mtDNA copy numbers and different values among biochemical traits, generated greater ROS production (P < 0.05) and less SDH activity (P < 0.05) and a lesser ATP content (P < 0.05). The results show that functional differences exist between cybrid cells which differ in mitochondrial genomic background. In conclusion, transmitochondrial cybrids provide the first direct evidence on pig biochemical traits linking different mitochondrial genome haplotypes.

show abstract

“…Using neither 18S nor GAPDH mRNA to normalize target gene expression altered the results compared to using S15 as the control gene. Data are expressed as a fold change relative to baseline and calculated according to REST-MCS v2.0 [ 19 , 20 , 21 ]. Pre-scald and post-scald group means are reported as the average value of adipose or muscle tissue sampled across 8 individual animals per group, with each animal value representing the mean of three replicates from the animal.…”

Section: Methodsmentioning

confidence: 99%

Sampling Adipose and Muscle Tissue following Post-Harvest Scalding Does Not Affect RNA Integrity or Real-Time PCR Results in Market Weight Yorkshire Pigs

Bohan

Purvis²,

Sawyer³

et al. 2022

Foods

View full text Add to dashboard Cite

Improving production efficiency while enhancing pork quality is pivotal for strengthening sustainable pork production. Being able to study both gene expression and indices of pork quality from the same anatomical location of an individual animal would better enable research conducted to study relationships between animal growth and carcass merit. To facilitate gene expression studies, adipose and muscle tissue samples are often collected immediately following exsanguination to maximize RNA integrity, which is a primary determinant of the sensitivity of RNA-based assays, such as real-time PCR. However, collecting soft tissue samples requires cutting through the hide or skin. This leaves the underlying tissue exposed during scalding, poses possible food safety issues, and potentially confounds pork quality measures. To overcome these limitations, the effect of tissue sample timing post-harvest on RNA integrity, real-time PCR results, and pork quality measurements was investigated by sampling subcutaneous adipose tissue and longissimus thoracis et lumborum muscle immediately following either exsanguination, scalding, or chilling. Sampling time did not affect RNA quality, as determined by the RNA integrity number of RNA samples purified from either adipose (RIN; p > 0.54) or muscle tissue (p > 0.43). Likewise, the sampling time did not influence the results of real-time PCR analysis of gene expression when comparing RNA samples prepared from adipose or muscle tissue immediately following either exsanguination or scalding (p > 0.92). However, sampling tissue prior to scalding resulted in a greater visual color score (p < 0.001) and lesser L* (p < 0.001) and b* (p < 0.001) values without impacting the 24 h pH (p < 0.41). These results suggested that if both RNA-based assays and meat quality endpoints are to be performed at the same anatomical location on an animal, tissue sampling to facilitate RNA-based assays should occur at a time point immediately following scalding. These findings demonstrated that sampling of adipose and muscle tissue can be delayed until after scalding/dehairing without decreasing the RNA integrity or altering the results of real-time PCR assays, while doing so was associated with little impact on measures of pork quality.

show abstract

Mitochondrial DNA Sequence and Phylogenetic Evaluation of Geographically DisparateSus scrofaBreeds

Cited by 13 publications

References 31 publications

DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals

DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals

Mitochondrial Haplotypes Influence Metabolic Traits in Porcine Transmitochondrial Cybrids

Sampling Adipose and Muscle Tissue following Post-Harvest Scalding Does Not Affect RNA Integrity or Real-Time PCR Results in Market Weight Yorkshire Pigs

Contact Info

Product

Resources

About