Category Archives: ORIGINAL ARTICLE

Genome‐wide association studies for epistatic genetic effects on fertility and reproduction traits in Holstein cattle

Posted on by

Abstract

Non-additive genetic effects are well known to play an important role in the phenotypic expression of complex traits, such as fertility and reproduction. In this study, a genome scan was performed using 41,640 single nucleotide polymorphism (SNP) markers to identify genomic regions associated with epistatic (additive-by-additive) effects in fertility and reproduction traits in Holstein cattle. Nine fertility and reproduction traits were analysed on 5825 and 6090 Holstein heifers and cows with phenotypes and genotypes, respectively. The Marginal Epistasis Test (MAPIT) was used to identify SNPs with significant marginal epistatic effects at a chromosome-wise 5% and 10% false discovery rate (FDR) level. The −log10(p) values were adjusted by the genomic inflation factor (λ) to correct for the potential bias on the p-values and minimize the possible effects of population stratification. After adjustments, MAPIT enabled the identification of genomic regions with significant marginal epistatic effects for heifers on BTA5 for age at first insemination, BTA3 and BTA24 for non-return rate (NRR); BTA16 and BTA28 for gestation length (GL); BTA1, BTA4 and BTA17 for stillbirth (SB). For the cow traits, MAPIT enabled the identification of regions on BTA11 for GL, BTA11 and BTA16 for SB and BTA19 for calf size (CZ). An additional approach for mapping epistasis in a genome-wide association study was also proposed, in which the genome scan was performed using estimates of epistatic values as the input pseudo-phenotypes, computed using single-trait animal models. Significant SNPs were identified at the chromosome-wise 5% and 10% FDR levels for all traits. For the heifer traits, significant regions were found on BTA7 for AFS; BTA12 for NRR; BTA14 and BTA19 for GL; BTA19 for calving ease (CE); BTA5, BTA24, BTA25 and in the X chromosome for SB; BTA23 and in the X chromosome for CZ and in the X chromosome for the number of services (NS). For the cow traits, significant regions were found on BTA29 and in the X chromosome for NRR, BTA11, BTA16 and in the X chromosome for SB, BTA2 for GL, BTA28 for CZ, BTA19 for calving to first insemination, and in the X chromosome for NS and first insemination to conception. The results suggest that the epistatic genetic effects are likely due to many loci with a small effect rather than few loci with a large effect and/or a single SNP marker alone do not capture the epistatic effects well. The genomic architecture of fertility and reproduction traits is complex, and these results should be validated in independent dairy cattle populations and using alternative statistical models.

Genomic inbreeding estimation, runs of homozygosity, and heterozygosity‐enriched regions uncover signals of selection in the Quarter Horse racing line

Posted on by

Abstract

With the advent of genomics, significant progress has been made in the genetic improvement of livestock species, particularly through increased accuracy in predicting breeding values for selecting superior animals and the possibility of performing a high-resolution genetic scan throughout the genome of an individual. The main objectives of this study were to estimate the individual genomic inbreeding coefficient based on runs of homozygosity (F ROH), to identify and characterize runs of homozygosity and heterozygosity (ROH and ROHet, respectively; length and distribution) throughout the genome, and to map selection signatures in relevant chromosomal regions in the Quarter Horse racing line. A total of 336 animals registered with the Brazilian Association of Quarter Horse Breeders (ABQM) were genotyped. One hundred and twelve animals were genotyped using the Equine SNP50 BeadChip (Illumina, USA), with 54,602 single nucleotide polymorphisms (SNPs; 54K). The remaining 224 samples were genotyped using the Equine SNP70 BeadChip (Illumina, USA) with 65,157 SNPs (65K). To ensure data quality, we excluded animals with a call rate below 0.9. We also excluded SNPs located on non-autosomal chromosomes, as well as those with a call rate below 0.9 or a p-value below 1 × 10−5 for Hardy–Weinberg equilibrium. The results indicate moderate to high genomic inbreeding, with 46,594 ROH and 16,101 ROHet detected. In total, 30 and 14 candidate genes overlap with ROH and ROHet regions, respectively. The ROH islands showed genes linked to crucial biological processes, such as cell differentiation (CTBP1, WNT5B, and TMEM120B), regulation of glucose metabolic process (MAEA and NKX1-1), heme transport (PGRMC2), and negative regulation of calcium ion import (VDAC1). In ROHet, the islands showed genes related to respiratory capacity (OR7D19, OR7D4G, OR7D4E, and OR7D4J) and muscle repair (EGFR and BCL9). These findings could aid in selecting animals with greater regenerative capacity and developing treatments for muscle disorders in the QH breed. This study serves as a foundation for future research on equine breeds. It can contribute to developing reproductive strategies in animal breeding programs to improve and preserve the Quarter Horse breed.

Inbreeding depression and its effect on sperm quality traits in Pietrain pigs

Posted on by

Abstract

In most cases, inbreeding is expected to have unfavourable effects on traits in livestock. The consequences of inbreeding depression could be substantial, primarily in reproductive and sperm quality traits, and thus lead to decreased fertility. Therefore, the objectives of this study were (i) to compute inbreeding coefficients using pedigree (F PED) and genomic data based on runs of homozygosity (ROH) in the genome (F ROH) of Austrian Pietrain pigs, and (ii) to assess inbreeding depression on four sperm quality traits. In total, 74,734 ejaculate records from 1034 Pietrain boars were used for inbreeding depression analyses. Traits were regressed on inbreeding coefficients using repeatability animal models. Pedigree-based inbreeding coefficients were lower than ROH-based inbreeding values. The correlations between pedigree and ROH-based inbreeding coefficients ranged from 0.186 to 0.357. Pedigree-based inbreeding affected only sperm motility while ROH-based inbreeding affected semen volume, number of spermatozoa, and motility. For example, a 1% increase in pedigree inbreeding considering 10 ancestor generations (F PED10) was significantly (p < 0.05) associated with a 0.231% decrease in sperm motility. Almost all estimated effects of inbreeding on the traits studied were unfavourable. It is advisable to properly manage the level of inbreeding to avoid high inbreeding depression in the future. Further, analysis of effects of inbreeding depression for other traits, including growth and litter size for the Austrian Pietrain population is strongly advised.

Quantitative analysis of parent‐of‐origin effect in reproductive and morphological selection criteria in the Pura Raza Española horse

Posted on by

Abstract

It is generally assumed that parents make a genetically equal contribution to their offspring, but this assumption might not always hold. This is because the expression of a gene can be blocked by methylation during gametogenesis, and the degree of methylation can depend on the origin of the parental gene (imprinting) or by preferential management associated with genetic merit. The first consequences of this for quantitative genetics is that the mean phenotypes of reciprocal heterozygotes need no longer be the same, as would be expected according to Mendelian heritage. We analysed three mare reproductive traits (reproductive efficiency, age at first foaling and foaling number) and three morphological traits (height at withers, thoracic circumference, and scapula-ischial length) in the Pura Raza Española (PRE) horse population, which possesses a deep and reliable pedigree, making it a perfect breed for analysing the quantitative effect of parent-of-origin. The number of animals analysed ranged from 44,038 to 144,191, all of them with both parents known. The model comparison between a model without parent-of-origin effects and three different models with parent-of-origin effects revealed that both maternal and paternal gametic effects influence all the analysed traits. The maternal gametic effect had a higher influence on most traits, accounting for between 3% and 11% of the total phenotypic variance, while the paternal gametic effect accounted for a higher proportion of variance in one trait, age at first foaling (4%). As expected, the Pearson's correlations between additive breeding values of models that consider parent-of-origin and that do not consider parent-of-origin were very high; however, the percentage of coincident animals slightly decreases when comparing animals with the highest estimated breeding values. Ultimately, this work demonstrates that parent-of-origin effects exist in horse gene transmission from a quantitative point of view. Additionally, including an estimate of the parent-of-origin effect within the PRE horse breeding program could be a great tool for a better parent's selection and that could be of interest for breeders, as this value will determine whether the animals acquire genetic categories and are much more highly valued.

Validating genomic prediction for nitrogen efficiency index and its composition traits of Holstein cows in early lactation

Posted on by

Abstract

Nitrogen (N) use efficiency (NUE) is an economically important trait for dairy cows. Recently, we proposed a new N efficiency index (NEI), that simultaneously considers both NUE and N pollution. This study aimed to validate the genomic prediction for NEI and its composition traits and investigate the relationship between SNP effects estimated directly from NEI and indirectly from its composition traits. The NEI composition included genomic estimated breeding value of N intake (NINT), milk true protein N (MTPN) and milk urea N yield. The edited data were 132,899 records on 52,064 cows distributed in 773 herds. The pedigree contained 122,368 animals. Genotypic data of 566,294 SNP was available for 4514 individuals. A total of 4413 cows (including 181 genotyped) and 56 bulls (including 32 genotyped) were selected as the validation populations. The linear regression method was used to validate the genomic prediction of NEI and its composition traits using best linear unbiased prediction (BLUP) and single-step genomic BLUP (ssGBLUP). The mean theoretical accuracies of validation populations obtained from ssGBLUP were higher than those obtained from BLUP for both NEI and its composition traits, ranging from 0.57 (MTPN) to 0.72 (NINT). The highest mean prediction accuracies for NEI and its composition traits were observed for the genotyped cows estimated under ssGBLUP, ranging from 0.48 (MTPN) to 0.66 (NINT). Furthermore, the SNP effects estimated from NEI composition traits, multiplied by the relative weight were the same as those estimated directly from NEI. This study preliminary showed that genomic prediction can be used for NEI, however, we acknowledge the need for further validation of this result in a larger dataset. Moreover, the SNP effects of NEI can be indirectly calculated using the SNP effects estimated from its composition traits. This study provided a basis for adding genomic information to establish NEI as part of future routine genomic evaluation programs.

Ascertaining the genetic background of the Celtic‐Iberian pig strain: A signatures of selection approach

Posted on by

Abstract

Celtic-Iberian pig breeds were majority in Spain and Portugal until the first half of the 20th century. In the 1990s, they were nearly extinct as a result of the introduction of foreign improved pig breeds. Despite its historical importance, the genetic background of the Celtic-Iberian pig strain is poorly documented. In this study, we have identified genomic regions that might contain signatures of selection peculiar of the Celtic-Iberian genetic lineage. A total of 153 DNA samples of Celtic-Iberian pigs (Spanish Gochu Asturcelta and Portuguese Bísara breeds), Iberian pigs (Spanish Iberian and Portuguese Alentejano breeds), Cinta Senese pig, Korean local pig and Cosmopolitan pig (Hampshire, Landrace and Large White individuals) were analysed. A pairwise-comparison approach was applied: the Gochu Asturcelta and the Bísara samples as test populations and the five other pig populations as reference populations. Three different statistics (XP-EHH, F ST and ΔDAF) were computed on each comparison. Strict criteria were used to identify selection sweeps in order to reduce the noise brought on by the Gochu Asturcelta and Bísara breeds' severe population bottlenecks. Within test population, SNPs used to construct potential candidate genomic areas under selection were only considered if they were identified in four of ten two-by-two pairwise comparisons and in at least two of three statistics. Genomic regions under selection constructed within test population were subsequently overlapped to construct candidate regions under selection putatively unique to the Celtic-Iberian pig strain. These genomic regions were finally used for enrichment analyses. A total of 39 candidate regions, mainly located on SSC5 and SSC9 and covering 3130.5 kb, were identified and could be considered representative of the ancient genomic background of the Celtic-Iberian strain. Enrichment analysis allowed to identify a total of seven candidate genes (NOL12, LGALS1, PDXP, SH3BP1, GGA1, WIF1, and LYPD6). Other studies reported that the WIF1 gene is associated with ear size, one of the characteristic traits of the Celtic-Iberian pig strain. The function of the other candidate genes could be related to reproduction, adaptation and immunity traits, indirectly fitting with the rusticity of a non-improved pig strain traditionally exploited under semi-extensive conditions.

Phenological description and thermal time requirements for the seedling phase of three Brazilian native forest species

Posted on by
Phenological description and thermal time requirements for the seedling phase of three Brazilian native forest species

Morphology of the germination process (epigeal) and seedlings development stages of Libidibia ferrea (co: cotyledon; e1-e2: first pair of eophylls; in: embryo; ep: epicotyl; fr: fruit; hp: hypocotyl; me: metaphyll; pr: primary root; se: seed). Drawings made by Bruna Oliveira Borges.


Abstract

Understanding the phenological stages and thermal requirements of the seedling phase of forest species is crucial for sustainable nursery management. This study proposed an adaptation of a phenological scale based on the basic Biologische Bundesanstalt, Bundessortenamt, and Chemical industry, associated with the thermal requirement to describe the phenological stages during the seedling phase of three forest species: Cybistax antisyphilitica, Libidibia ferrea, and Platycyamus regnellii. The phenological scale of C. antisyphilitica and L. ferrea was defined and described through 22 seedling development stages ranging from dry seed to 20th visible leaf emitted on the main stem (from 00 to 120) and P. regnellii for 12 leaf development stages, from dry seed to 10th visible leaf emitted on the main stem (from 00 to 110). In addition, the duration (days) and thermal time (°C day) were determined for each seedling development stage. C. antisyphilitica needs to accumulate more energy (and days) to finish the seedling phase (1551.9°C day or 261 days) compared to L. ferrea (1127°C day or 175 days) and P. regnellii (1109.7°C day or 193 days). However, the three forest species exhibit similar energy demands throughout most stages of seedling development, except code 09–12 for C. antisyphilitica. This study provides important information for optimizing silvicultural techniques, evaluating the response of temperature on phenological stages, and assessing the impacts of global warming on forest seedling development.

Effect of in ovo feeding of folic acid on Disabled‐1 and gga‐miR‐182‐5p expression in the cerebral cortex of chick embryo

Posted on by

Abstract

Folate (vitamin B9) has been shown to reduce the prevalence of neural tube defects (NTDs). Many genes comprising Disabled-1 (DAB1) and miRNAs have been shown to play important role in normal brain development. Reelin-signalling has been shown to play key role in regulating of neuronal migration during brain development. The aim of this study was to evaluate the effects of in ovo administration of folic acid (FA) on DAB1 and gga-miR-182-5p expression in the cerebral cortex of chick embryo. A total number of 30 hatching eggs were used in this study. The number of 10 eggs were injected into the yolk sac with FA (150 µg/egg), 10 eggs by normal saline (sham group) on embryonic day 11 and 10 eggs were left without injection as control. Then the cerebral cortices were collected on E19 and the expression of DAB1 and gga-miR-182-5p was studied by Real-Time PCR. The results showed that DAB1 expression in the cerebral cortex of FA-treated, sham and control were 2.51 ± 0.13, 1.01 ± 0.04 and 1.03 ± 0.04 fold changes, respectively, and this amount for gga-miR-182-5p were 0.54 ± 0.03, 1.09 ± 0.07 and 1.00 ± 0.06-fold change respectively. Statistical analysis showed that there is a significant increase in DAB1 and a decrease in gga-miR-182-5p expression in FA injected cerebral cortex as compared either with either SHAM or control (p < 0.0001). But, no significant change in DAB1 and gga-miR-182-5p expression was observed between sham and the control group (p = 0.99 and p = 0.57 respectively). It is concluded that in ovo feeding of FA increases DAB1 and decreases gga-miR-182-5p expression in the developing chick cerebral cortex.

Mother’s education and infant survival in Ethiopia

Posted on by

Abstract

Objective

Few studies in Ethiopia have explored the impact of the mothers' education on infant survival. Therefore, this study aimed to identify and analyze the proximate factors in the relationship between maternal education and infant survival in Ethiopia.

Methods

This study used the nationally representative 2016 Ethiopian Demographic and Health Survey dataset. It analyzed a sample of 3831 newborn children using Cox regression models.

Results

The findings revealed that infants born to educated mothers had lower odds of infant mortality than those born to mothers without formal education. Specifically, infants whose mothers had completed secondary school and had a better antenatal care attendance rate had 49.9% lower odds of infant mortality than those born to mothers with no formal education and a poor antenatal care attendance rate. Furthermore, infants whose mothers had at least some postsecondary education and who used delivery by health-care professionals, clean drinking water, and improved toilet facilities had 65.3%, 56.3%, and 68.6% lower odds of infant mortality, respectively, than those born to mothers with no formal education and who did not use those facilities.

Conclusions

This study concluded that the mothers' educational disparity is intimately tied to infant mortality, and that access to formal education, mainly for women, increases infant survival in Ethiopia. Future research should focus on mothers without formal education who do not have access to antenatal care visits for safe pregnancy, delivery by health-care professionals, clean drinking water, and improved toilet facilities in Ethiopia and elsewhere in Sub-Saharan Africa.

Human adaptation to cold and warm climatic conditions: A comparison between two geographically diverse Indigenous populations

Posted on by

Abstract

Objectives

The present study aims to compare body adiposity and blood pressure (BP) in two climatically and ethnically diverse populations, examining whether thermoregulatory adaptive mechanism may protect Indigenous populations from exhibiting adverse consequences of increased adiposity.

Methods

A cross sectional sample of 404 subjects, of which 200 were Monpa and 204 were Santhal, from two ethnically and geographically distinct populations of India were studied. Body mass index (BMI; kg/m2), fat mass (FM; kg), fat free mass (kg), and percent body fat (%BF) were calculated for evaluation of body adiposity. Multivariate multiple regression analysis was adopted to examine the influence of age and sex of populations under study, on body adiposity and BP variables.

Results

BMI, %BF, and FM were found to be significantly higher (p ˂ .001) among the Monpa males and females compared with their Santhal counterparts. In contrast, the prevalence of hypertension among Monpa and Santhal is comparable (3.5%Monpa vs. 3.9%Santhal for systolic BP; 8.5%Monpa vs. 8.3%Santhal for diastolic BP). Adiposity, as quantitated by the fat mass index and %BF was significantly (p ˂ .001) correlated to age and sex of study population, explaining ~75.3% and ~75.4% of total variations of these variables, respectively.

Conclusions

Overall the present study suggests that modern human populations follow thermoregulatory mechanism for adaptation to different climatic conditions. Consequently, greater adiposity was evident among the Monpa who adapt to the cold climate, in comparison to their Santhal counterparts who dwell in warm climate.