Nuclear Genome-Encoded Mitochondrial OXPHOS Complex I Genes in Female Buffalo Show Tissue-Specific Differences

Buffalo physiology intricately balances energy, profoundly influencing health, productivity, and reproduction. This study explores nuclear-mitochondrial crosstalk, revealing OXPHOS Complex I gene expression variations in buffalo tissues through high-throughput RNA sequencing. Unveiling tissue-specific disparities, the research elucidates the genomic landscape of crucial energy production genes, with broader implications for veterinary and agricultural progress. Post-slaughter, tissues from post-pubertal female buffaloes underwent meticulous processing and RNA extraction using the TRIzol method. RNA-Seq library preparation and IlluminaHiSeq 2500 sequencing were performed on QC-passed samples. Data underwent stringent filtration, mapping to the Bubalus bubalis genome using HISAT2. DESeq2 facilitated differential expression gene (DEG) analysis focusing on 57 Mitocarta 3-derived genes associated with OXPHOS complex I. Nuclear-encoded mitochondrial protein transcripts of OXPHOS complex 1 exhibited tissue-specific variations, with 51 genes expressing significantly across tissues. DEG analysis emphasized tissue-specific expression patterns, highlighting a balanced OXPHOS complex I subunit expression in the kidney vs. brain. Gene Ontology (GO) enrichment showcased mitochondria-centric terms, revealing distinct proton motive force-driven mitochondrial ATP synthesis regulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses emphasized Thermogenesis and OXPHOS pathways, enriching our understanding of tissue-specific energy metabolism. Noteworthy up-regulation of NDUFB10 in the heart and kidney aligned with heightened metabolic activity. Brain-specific up-regulation of NDUFAF6 indicated a focus on mitochondrial function, while variations in NDUFA11 and ACAD9 underscored pivotal roles in the heart and kidney. GO and KEGG analyses highlighted tissue-specific mitochondrial ATP synthesis and NADH dehydrogenase processes, providing molecular insights into organ-specific metabolic demands and regulatory mechanisms. Our study unveils conserved and tissue-specific nuances in nuclear-encoded mitochondrial OXPHOS complex I genes, laying a foundation for understanding diverse energy demands and potential health implications.

The relationship between mitochondrial DNA haplotype and its copy number on body weight and morphological traits of Wuliangshan black-bone chickens

Mitochondria play a pivotal role as carriers of genetic information through their circular DNA molecules. The rapid evolution of the D-loop region in mitochondria makes it an ideal molecular marker for exploring genetic differentiation among individuals within species and populations with close kinship. However, the influence of mtDNA D-loop region haplotypes and mtDNA copy numbers on phenotypic traits, particularly production traits in chickens, remains poorly understood. In this comprehensive study, we conducted D-loop region amplification and sequencing in the blood mitochondria of 232 female Wuliangshan black-bone chickens. Our investigation identified a total of 38 haplotypes, with a focus on 10 haplotypes that included more than five individuals. We meticulously analyzed the correlations between these haplotypes and a range of traits, encompassing body weight, tibial length, tibial circumference, body oblique length, chest width, and chest depth. The results unveiled significant disparities in specific tested traits across different haplotypes, indicating a tangible association between mtDNA haplotypes and traits in chickens. These findings underscore the potential impact of mitochondrial DNA variations on energy metabolism, ultimately leading to divergent chicken phenotypes. Furthermore, our examination revealed positive correlations between mtDNA copy numbers and tested traits for select haplotypes, while other haplotypes exhibited non-uniform relationships between traits and mtDNA copy numbers. In addition, phylogenetic analysis disclosed the involvement of two subspecies of red jungle chicken in the origin of Wuliangshan black-bone chickens. Consequently, our research contributes novel insights into mitochondrial genomic selection, augments comprehension of the roles played by haplotypes and mtDNA copy numbers in chicken population genetics and phylogenetic analysis, and furnishes fundamental data crucial for the preservation and provenance determination of black-bone chickens.

Ancient mitogenomes from Pre-Pottery Neolithic Central Anatolia and the effects of a Late Neolithic bottleneck in sheep (Ovis aries)

Occupied between ~10,300 and 9300 years ago, the Pre-Pottery Neolithic site of Aşıklı Höyük in Central Anatolia went through early phases of sheep domestication. Analysis of 629 mitochondrial genomes from this and numerous sites in Anatolia, southwest Asia, Europe, and Africa produced a phylogenetic tree with excessive coalescences (nodes) around the Neolithic, a potential signature of a domestication bottleneck. This is consistent with archeological evidence of sheep management at Aşıklı Höyük which transitioned from residential stabling to open pasturing over a millennium of site occupation. However, unexpectedly, we detected high genetic diversity throughout Aşıklı Höyük's occupation rather than a bottleneck. Instead, we detected a tenfold demographic bottleneck later in the Neolithic, which caused the fixation of mitochondrial haplogroup B in southwestern Anatolia. The mitochondrial genetic makeup that emerged was carried from the core region of early Neolithic sheep management into Europe and dominates the matrilineal diversity of both its ancient and the billion-strong modern sheep populations.

Association analysis of mitochondrial genome polymorphisms with backfat thickness in pigs

Mitochondrial DNA (mtDNA) variations and associated effects on economic traits have been widely reported in farm animals, as these genetic polymorphisms can affect the efficiency of energy production and cell metabolism. In studies related to metabolism, the deposition of fat was highly correlated with mitochondria. However, the effect of mtDNA polymorphisms on porcine backfat thickness (BFT) remained unclear. In this study, 243 pigs were collected to analyse the relationship between BFT and mtDNA polymorphisms. There were considerable differences in BFT, ranging from 5 mm to 18 mm. MtDNA D-loop sequencing discovered 48 polymorphic sites. Association analysis revealed that 30 variations were associated with BFT (P < 0.05). The polymorphism m.794A > G showed the maximum difference in BFT between A and G carriers, which differed at ∼2.5 mm (P < 0.001). The 48 polymorphic sites generated 22 haplotypes (H1-H22), which clustered into 4 haplogroups (HG1-HG4). HG1 had a lower BFT value than other three haplogroups (P < 0.01), whereas H4 in HG1 exhibited the lowest BFT of all haplotypes analyzed (P < 0.01). The results of this study highlight an association between mtDNA polymorphisms and BFT, and suggest the potential application of mtDNA in pig molecular breeding practices.

The ND1 and CYTB genes polymorphisms associated with in vitro early embryo development of Sanjabi sheep

This study aimed to investigate the association between polymorphisms of ND1 and CYTB genes and in vitro early embryo development of Sanjabi sheep. Blood and ovarian samples were collected from a local slaughterhouse. The cumulus-oocyte complexes with a diameter greater than 3 mm were aspirated from follicles, and in vitro maturation (IVM) and in vitro culture (IVC) rates of them were recorded. A respective 1200 bp and 980 bp fragments of ND1 and CYTB genes were genotyped using a modified single strand conformation polymorphism (SSCP) method. The results of this study revealed that four different patterns, named as A, B, C, and D were observed for both ND1 and CYTB genes. The ND1 gene polymorphisms had significant effects on the IVM and IVC rate (p < 0.05). The pattern C of the ND1 gene significantly increased the IVM rate compared to the patterns A, B and D. For the IVC, the highest and lowest means were related to the C and B patterns, respectively. The CYTB gene polymorphisms also had significant effects on IVC (p < 0.01), but the IVM did not affected (p = 0.07). Here, the pattern D had the highest and the pattern C had the lowest means for both IVM and IVC rates.

The relationship between mitochondrial ND5 gene polymorphisms and in vitro embryo production in Sanjabi sheep

The aim of this study was to investigate mitochondrial ND5 gene polymorphisms and their relationship with in vitro maturation (IVM) and in vitro culture (IVC) of Sanjabi sheep. Blood and ovarian samples of adult ewes were obtained from a local slaughterhouse. For each ovarian sample, cumulus-oocyte complexes larger than 3 mm in diameter were aspirated from follicles, and their IVM and IVC rates were recorded. A 666-bp fragment of the ND5 gene was amplified using the polymerase chain reaction. The samples were genotyped using a modified single-stranded conformation polymorphism (SSCP) method, and an association study was conducted with IVM and IVC rates. Six different SSCP patterns, designated A, B, C, D, E and F with respective frequencies of 8, 47, 4, 4, 32 and 5%, respectively, were observed. According to the results of association analysis, there was no significant association between the ND1 gene polymorphisms and the IVM and IVC rates (P > 0.05).

Cybrid Model Supports Mitochondrial Genetic Effect on Pig Litter Size

In pigs, mitochondrial DNA (mtDNA) polymorphism and the correlation to reproductive performance across breeds and individuals have been largely reported, however, experimental proof has never been provided. In this study, we analyzed 807 sows for correlation of total number born (TNB) and mitotype, which presented the maximum of 1.73 piglets for mtDNA contribution. Cybrid models representing different mitotypes were generated for identification of the mtDNA effect. Results indicated significant differences on cellular and molecular characteristics among cybrids, including energy metabolic traits, mtDNA copy numbers and transcriptions, mRNA and protein expressions on mitochondrial biogenesis genes and reproduction-related genes. Referring to mitotypes, the cybrids with prolific mitotypes presented significantly higher oxygen consumption rate (OCR) productions, mtDNA transcriptions and copy numbers than those with common mitotypes, while both mRNA and protein expressions of PPARA, TFAM, ER1, ER2, and ESRRG in prolific cybrids were significantly higher than those with common mitotypes. Cybrid models reflected the mtDNA effect on pig litter size, suggesting the potential application of mtDNA polymorphism in pig selection and breeding practices.

Relationship between mitochondrial DNA haplogroup and litter size in the pig

Mitochondrial DNA (mtDNA) has been widely associated with complex traits in farm animals. The present study evaluated the effects of mtDNA on litter size in pigs. Mitogenome sequencing of 1017 sows distinguished 232 variations, including 229 single nucleotide polymorphisms and three indels, which constituted 11 haplotypes and further clustered into two haplogroups that differed significantly (P&lt;0.05) in litter size. In order to explain the associations between the effect of haplogroup on litter size and different maternal origins, extant mitogenome sequences were used for phylogenetic or principal component analyses. The results of these analyses led to the identification of two groups, representing Chinese and European origins. The haplotypes corresponding to high litter size were all in the Chinese cluster, whereas haplotypes corresponding to low litter size were all in the European cluster. The results of this study suggest that the effect of haplogroup on litter size in the pig could be caused by diverse maternal origins, and that mtDNA haplogroup may be a marker for genetic selection for pig litter size.

Polymorphism of mitochondrial tRNA genes associated with the number of pigs born alive

Background

Mutations in mitochondrial tRNA genes have been widely reported association with human reproductions. It is also important to explore the effect on the number of piglets born alive (NBA). Here, 1017 sows were used to investigate the association between polymorphisms in mitochondrial tRNA genes and NBA.

Results

In total, 16 mutations were found in mitochondrial tRNA genes, of which 13 mutations were significantly associated with NBA (P < 0.05). The reproductions of mutant carriers were significantly greater than that of wild carriers by 0.989 piglets born alive/sow farrowing. To test whether the mutations altered the structure of mitochondrial tRNAs, the secondary and tertiary structures were predicted. In result, C2255T changed the secondary structure of tRNA-Val by elongating the T stem and shrinking the T loop, and C2255T and G2259A in the tRNA-Val gene, C6217T and T6219C in the tRNA-Ala gene, and T15283C in the tRNA-Glu gene altered the tertiary structure of their tRNAs, respectively by changing the folding form of the T arm, and C16487T in the tRNA-Thr gene changed the tertiary structure of mitochondrial tRNA-Thr by influencing the folding form of the acceptor arm.

Conclusions

Results highlight the effect of mitochondrial tRNA genes on the number of piglets born alive, and suggest that polymorphic sites of the tRNA genes be genetic markers for selection of pig reproduction.

Electronic supplementary material

The online version of this article (10.1186/s40104-018-0299-0) contains supplementary material, which is available to authorized users.

Mitochondrial DNA T7719G in tRNA-Lys gene affects litter size in Small-tailed Han sheep

Background

In farm animals, mitochondrial DNA (mtDNA) effect on economic performance remains hot-topic for breeding and genetic selection. Here, 53 maternal lineages of Small-tailed Han sheep were used to investigate the association of mitochondrial DNA variations and the lambing litter size.

Results

Sequence sweeping of the mitochondrial coding regions discovered 31 non-synonymous mutations, and the association study revealed that T7719G in mtDNA tRNA-Lys gene was associated with litter size (P < 0.05), manifesting 0.29 lambs per litter between the G and T carriers. Furthermore, using the mixed linear model, we assayed the potential association of the ovine litter size and haplogroups and multiple-level mtDNA haplotypes, including general haplotypes, assembled haplotypes of electron transport chain contained sequences (H-ETC), mitochondrial respiratory complex contained sequences (H-MRC) and mitochondrial genes (H-gene, including polypeptide-coding genes, rRNA genes and tRNA genes). The strategy for assembled mitochondrial haplotypes was proposed for the first time in mtDNA association analyses on economic traits, although none of the significant relations could be concluded (P > 0.05). In addition, the nuclear major gene BMPR1B was significantly correlated with litter size in the flock (P < 0.05), however, did not interact with mtDNA T7719G mutation (P > 0.05).

Conclusions

Our results highlight mutations of ovine mitochondrial coding genes, suggesting T7719G in tRNA-Lys gene be a potentially useful marker for selection of sheep litter size.

Electronic supplementary material

The online version of this article (doi:10.1186/s40104-017-0160-x) contains supplementary material, which is available to authorized users.

The role of mitochondrial DNA copy number, variants, and haplotypes in farm animal developmental outcome

The vast majority of cellular energy is generated through the process of oxidative phosphorylation, which takes place in the electron transport chain in the mitochondria. The electron transport chain is encoded by 2 genomes, the chromosomal and the mitochondrial genomes. Mitochondrial DNA is associated with a number of traits, which include tolerance to heat, growth and physical performance, meat and milk quality, and fertility. Mitochondrial genomes can be clustered into groups known as mtDNA haplotypes. Mitochondrial DNA haplotypes are a potential genetic source for manipulating phenotypes in farm animals. The use of assisted reproductive technologies, such as nuclear transfer, allows favorable chromosomal genetic traits to be mixed and matched with sought after mtDNA haplotype traits. As a result super breeds can be generated.

Maternal Lineage of Warmblood Mares Contributes to Variation of Gestation Length and Bias of Foal Sex Ratio

Maternal lineage influences performance traits in horses. This is probably caused by differences in mitochondrial DNA (mtDNA) transferred to the offspring via the oocyte. In the present study, we investigated if reproductive traits with high variability—gestation length and fetal sex ratio—are influenced by maternal lineage. Data from 142 Warmblood mares from the Brandenburg State Stud at Neustadt (Dosse), Germany, were available for the study. Mares were grouped according to their maternal lineage. Influences on the reproduction parameters gestation length and sex ratio of offspring were analyzed by simple and multiple analyses of variance. A total of 786 cases were included. From the 142 mares, 119 were assigned to six maternal lineages with n≥10 mares per lineage, and 23 mares belonged to smaller maternal lineages. The mean number of live foals produced per mare was 4.6±3.6 (±SD). Live foal rate was 83.5%. Mean gestation length was 338.5±8.9 days (±SD) with a range of 313 to 370 days. Gestation length was affected by maternal lineage (p<0.001). Gestation length was also significantly influenced by the individual mare, age of the mare, year of breeding, month of breeding and sex of the foal (p<0.05). Of the 640 foals born alive at term, 48% were male and 52% female. Mare age group and maternal lineage significantly influenced the sex ratio of the foals (p<0.05). It is concluded that maternal lineage influences reproductive parameters with high variation such as gestation length and foal sex ratio in horses. In young primiparous and aged mares, the percentage of female offspring is higher than the expected 1:1 ratio.