Dataset Information

Diversity of Mitochondrial DNA Haplogroups and Their Association with Bovine Antral Follicle Count.

ABSTRACT: Maternal origins based on the bovine mitochondrial D-loop region are proven to have two main origins: Bos taurus and Bos indicus. To examine the association between the maternal origins of bovine and reproductive traits, the complete mitochondrial D-loop region sequences from 501 Chinese Holstein cows and 94 individuals of other breeds were analyzed. Based on the results obtained from the haplotype analysis, 260 SNPs (single nucleotide polymorphism), 32 indels (insertion/deletion), and 219 haplotypes were identified. Moreover, the nucleotide diversity (π) and haplotype diversity (Hd) were 0.024 ± 0.001 and 0.9794 ± 0.003, respectively, indicating the abundance of genetic resources in Chinese Holstein cows. The results of the median-joining network analysis showed two haplogroups (HG, including HG1 and HG2) that diverged in genetic distance. Furthermore, the two haplogroups were significantly (p < 0.05) correlated with the antral follicle (diameter ≥ 8 mm) count, and HG1 individuals had more antral follicles than HG2 individuals, suggesting that these different genetic variants between HG1 and HG2 correlate with reproductive traits. The construction of a neighbor-joining phylogenetic tree and principal component analysis also revealed two main clades (HG1 and HG2) with different maternal origins: Bos indicus and Bos taurus, respectively. Therefore, HG1 originating from the maternal ancestors of Bos indicus may have a greater reproductive performance, and potential genetic variants discovered may promote the breeding process in the cattle industry.

SUBMITTER: Liu H

PROVIDER: S-EPMC9495067 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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Diversity of Mitochondrial DNA Haplogroups and Their Association with Bovine Antral Follicle Count.

Liu Hongfei H Zhai Junjun J Wu Hui H Wang Jingyi J Zhang Shaowei S Li Jie J Niu Zhihan Z Shen Chenglong C Zhang Kaijuan K Liu Zhengqing Z Jiang Fugui F Song Enliang E Sun Xiuzhu X Wang Yongsheng Y Lan Xianyong X

Animals : an open access journal from MDPI 20220908 18

Maternal origins based on the bovine mitochondrial D-loop region are proven to have two main origins: Bos taurus and Bos indicus. To examine the association between the maternal origins of bovine and reproductive traits, the complete mitochondrial D-loop region sequences from 501 Chinese Holstein cows and 94 individuals of other breeds were analyzed. Based on the results obtained from the haplotype analysis, 260 SNPs (single nucleotide polymorphism), 32 indels (insertion/deletion), and 219 haplo ...[more]

PMID: 36139210

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Project description:BackgroundPhthalates are ubiquitously used in a variety of products and have an adverse effect on folliculogenesis. However, previous epidemiological studies on the associations between phthalate exposure and antral follicle count (AFC) produced conflicting results. The present study aimed to evaluate the associations between urinary phthalate metabolite concentrations and AFC among women undergoing in vitro fertilization (IVF).MethodsWe collected 525 urine samples and measured 8 phthalate metabolites from IVF patients. Poisson regression models were conducted to evaluate the associations between phthalate metabolite concentrations and AFC. In addition, participants were stratified into a younger group (< 35 years) and an older group (≥ 35 years) to explore the potential effect modification by age. We also performed sensitivity analyses by restricting our analyses to only infertile women diagnosed with tubal factor infertility to test the robustness of the results.ResultsSignificant positive associations were observed among urinary MBP, MEOHP and ∑PAEs concentrations and AFC after adjusting for age, BMI, year of study and infertility diagnosis. Compared with women in the first tertile, women in the third tertile of MBP and MEOHP had 7.02% (95% CI: 1.18%, 12.9%) and 8.84% (95% CI: 2.83%, 14.9%) higher AFC, respectively, and women in the second and third tertiles of ∑PAEs had 6.19% (95% CI: 0.37%, 12.0%) and 9.09% (95% CI: 3.22%, 15.0%) higher AFC, respectively. In addition, MBP, MEOHP and ∑PAEs also had significant positive associations with AFC in trend tests for dose-response. In the age-stratified analysis, we found a stronger relationship between phthalate metabolite concentrations and AFC among older women and an inverse association among younger women. We observed similar results in the sensitivity analyses.ConclusionWe found positive associations between phthalate exposure and AFC, which support the idea that phthalate exposure may accelerate primordial follicle recruitment and lead to higher AFC in women undergoing IVF. More studies are needed to better understand their relationships.

Project description:BACKGROUND: From the beginning of domestication, the transportation of domestic animals resulted in genetic and demographic processes that explain their present distribution and genetic structure. Thus studying the present genetic diversity helps to better understand the history of domestic species. METHODOLOGY/PRINCIPAL FINDINGS: The genetic diversity of domestic goats has been characterized with 2430 individuals from all over the old world, including 946 new individuals from regions poorly studied until now (mainly the Fertile Crescent). These individuals represented 1540 haplotypes for the HVI segment of the mitochondrial DNA (mtDNA) control region. This large-scale study allowed the establishment of a clear nomenclature of the goat maternal haplogroups. Only five of the six previously defined groups of haplotypes were divergent enough to be considered as different haplogroups. Moreover a new mitochondrial group has been localized around the Fertile Crescent. All groups showed very high haplotype diversity. Most of this diversity was distributed among groups and within geographic regions. The weak geographic structure may result from the worldwide distribution of the dominant A haplogroup (more than 90% of the individuals). The large-scale distribution of other haplogroups (except one), may be related to human migration. The recent fragmentation of local goat populations into discrete breeds is not detectable with mitochondrial markers. The estimation of demographic parameters from mismatch analyses showed that all groups had a recent demographic expansion corresponding roughly to the period when domestication took place. But even with a large data set it remains difficult to give relative dates of expansion for different haplogroups because of large confidence intervals. CONCLUSIONS/SIGNIFICANCE: We propose standard criteria for the definition of the different haplogroups based on the result of mismatch analysis and on the use of sequences of reference. Such a method could be also applied for clarifying the nomenclature of mitochondrial haplogroups in other domestic species.

Project description:BackgroundNeurocognitive impairment (NCI) remains an important complication in persons infected with human immunodeficiency virus (HIV). Ancestry-related mitochondrial DNA (mtDNA) haplogroups have been associated with outcomes of HIV infection and combination antiretroviral therapy (CART), and with neurodegenerative diseases. We hypothesize that mtDNA haplogroups are associated with NCI in HIV-infected adults and performed a genetic association study in the CNS HIV Antiretroviral Therapy Effects Research (CHARTER) cohort.MethodsCHARTER is an observational study of ambulatory HIV-infected adults. Haplogroups were assigned using mtDNA sequence, and principal components were derived from ancestry-informative nuclear DNA variants. Outcomes were cross-sectional global deficit score (GDS) as a continuous measure, GDS impairment (GDS ≥ 0.50), and HIV-associated neurocognitive disorder (HAND) using international criteria. Multivariable models were adjusted for comorbidity status (incidental vs contributing), current CART, plasma HIV RNA, reading ability, and CD4 cell nadir.ResultsHaplogroups were available from 1027 persons; median age 43 years, median CD4 nadir 178 cells/mm(3), 72% on CART, and 46% with HAND. The 102 (9.9%) persons of genetically determined admixed Hispanic ancestry had more impairment by GDS or HAND than persons of European or African ancestry (P < .001 for all). In multivariate models including persons of admixed Hispanic ancestry, those with haplogroup B had lower GDS (β = -0.34; P = .008) and less GDS impairment (odds ratio = 0.16; 95% confidence interval, .04, .63; P = .009) than other haplogroups. There were no significant haplogroup associations among persons of European or African ancestry.ConclusionsIn these mostly CART-treated persons, mtDNA haplogroup B was associated with less NCI among persons of genetically determined Hispanic ancestry. mtDNA variation may represent an ancestry-specific factor influencing NCI in HIV-infected persons.

Dataset Information

Diversity of Mitochondrial DNA Haplogroups and Their Association with Bovine Antral Follicle Count.

Publications

Diversity of Mitochondrial DNA Haplogroups and Their Association with Bovine Antral Follicle Count.

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