Restricted Maximum Likelihood Analysis Research Articles

Carcass characteristics and meat quality of cull cows from different genetic groups

We aimed to evaluate the quality of the carcass and meat of cull cows from different genetic groups. It was considered 48 cows being 16 of the Nellore breed (NEL), 16 ½Angus ½Nellore (ANGNEL), and 16 ½Caracu ½Nellore (CARNEL), slaughtered at the end of eight pregnancy seasons, with approximately 11 years of age. For carcass analysis, body weight at slaughter (SW), hot carcass weight (HCW), carcass yield (CY), carcass finishing (CF), fat distribution (FDIST), cold storage conformation (CSC), marbling (MAR), subcutaneous fat thickness (SFT), ribeye area (REA), internal depth (INTD), external depth (EXTD), carcass length (CL), physiological maturity (FMAT), muscle color (COLOR) and texture (TEXT). For meat analysis, samples taken from the Longissimus muscle were analyzed after zero and 14 days of maturation for exudation losses (ExuL at 0 and 14 days), cooking losses (CookL), pH (pH at 0 and 14 days), color components of meat (L*, a* and b* 0 and 14 days) and shear force (SF at 0 and 14 days), the ether extract (EE) of the samples was also evaluated according to the genetic group of the cull cows. The Means were compared according to the adjusted Tukey-Kramer test (α = 0.05). The data were evaluated for the presence of outliers, homogeneity of variance, and normality of residuals. The effects of genetic groups on the described characteristics were evaluated by restricted maximum likelihood (REML) analysis, adjusting a mixed model containing the effects of cow age, genetic group, and slaughter date. NEL and ANGNEL cows presented higher SFT results when compared to CARNEL cows. The REA, INTD, and EXTD, ANGNEL and CARNEL cows obtained greater results when compared to NEL cows group. There was no significant effect on the genetic group of cull cows for the variables CY, CF, FDIST, CSC, MARM, FMAT, COLOR and TEXT. A significant difference was observed only for the L* characteristic (0 and 14 days of maturation), in which NEL cows presented darker meat than ANGNEL, with CARNEL cows having intermediate results. The ANGNEL cull cows have higher slaughter weights, and carcass weights, and AOL and EGS with better carcass finish. Cull cows slaughtered at an advanced age, between 10 and 11 years old, have similar meat quality. We recommend the meat maturation process for 14 days to improve the tenderness of the meat from cull cows, since in this 14-day meat maturation process, calpains degrade the myofibrillar proteins at certain internal points of the molecules and improve the tenderness of the meat, regardless of the genetic group.

Genetic parameters for carcass traits of progeny of beef bulls mated to dairy cows.

Beef × dairy crossbred cattle (n = 615) were used to evaluate the effect of preharvest indicator traits and genotypes on the accuracy of estimated breeding values (EBVs) of seedstock candidates for selection. Genotypes for 100,000 single nucleotide polymorphisms were provided by the American Simmental Association of purebred and crossbred seedstock animals (n = 2,632). Five hundred and ninety-five of the 615 beef × dairy cattle had carcass camera and ultrasound data. Phenotypes were not used for any of the seedstock animals even though some may have had performance and ultrasound data. We estimated the genomic relationship matrix among 3,247 animals including both phenotyped and unphenotyped animals. We computed genetic parameters among 37 traits using 666 bivariate restricted maximum likelihood analyses. The accuracy of EBV depends on heritability. For the sake of brevity, we report accuracy for marbling as a proxy for other traits with similar heritability. We focus on accuracy for marbling because marbling is the primary determinant of carcass value. We computed EBV for all 3,247 animals for marbling based on camera data postharvest using best linear unbiased prediction. We report evidence of overlap in causative genes among postharvest carcass traits; marbling, ribeye area, yield grade, fat thickness, and hot carcass weight (HCW) based on genetic correlations. Genetic correlations range from -0.73 to 0.89. Several live animal traits (frame size, body weight and ultrasound fat thickness and ribeye area) were genetically correlated with postharvest traits; including HCW, ribeye area, yield grade, fat thickness, and marbling. Genetic correlations between pre- and postharvest traits ranged from -0.53 to 0.95. Accuracy for marbling ranged from 0.64 to 0.80 for animals with marbling recorded, and from 0.09 to 0.60 for animals without marbling recorded. The accuracy of animals without phenotypes was related to the genomic relationship between animals with phenotype and those without. Live animal traits were useful for predicting economically important carcass traits based on genetic correlations. The accuracy of EBV for seedstock animals that were not phenotyped was low, but this is consistent with theory, and accuracy is expected to increase with the addition of genotypes and carcass data from beef × dairy animals.

Understanding the underlying genetic mechanisms for age at first calving, inter-calving period and scrotal circumference in Bonsmara cattle

BackgroundReproduction is a key feature of the sustainability of a species and thus represents an important component in livestock genetic improvement programs. Most reproductive traits are lowly heritable. In order to gain a better understanding of the underlying genetic basis of these traits, a genome-wide association was conducted for age at first calving (AFC), first inter-calving period (ICP) and scrotal circumference (SC) within the South African Bonsmara breed. Phenotypes and genotypes (120,692 single nucleotide polymorphisms (SNPs) post editing) were available on 7,128 South African Bonsmara cattle; the association analyses were undertaken using linear mixed models.ResultsGenomic restricted maximum likelihood analysis of the 7,128 SA Bonsmara cattle yielded genomic heritability’s of 0.183 (SE = 0.021) for AFC, 0.207 (SE = 0.022) for ICP and 0.209 (SE = 0.019) for SC. A total of 16, 23 and 51 suggestive (P ≤ 4 × 10-6) SNPs were associated with AFC, ICP and SC, while 11, 11 and 44 significant (P ≤ 4 × 10-7) SNPs were associated with AFC, ICP and SC respectively. A total of 11 quantitative trait loci (QTL) and 11 candidate genes were co-located with these associated SNPs for AFC, with 10 QTL harbouring 11 candidate genes for ICP and 41 QTL containing 40 candidate genes for SC. The QTL identified were close to genes previously associated with carcass, fertility, growth and milk-related traits. The biological pathways influenced by these genes include carbohydrate catabolic processes, cellular development, iron homeostasis, lipid metabolism and storage, immune response, ovarian follicle development and the regulation of DNA transcription and RNA translation.ConclusionsThis was the first attempt to study the underlying polymorphisms associated with reproduction in South African beef cattle. Genes previously reported in cattle breeds for numerous traits bar AFC, ICP or SC were detected in this study. Over 20 different genes have not been previously reported in beef cattle populations and may have been associated due to the unique genetic composite background of the SA Bonsmara breed.

Association of gut microbiota, plasma and fecal metabolite profiles with intellectual development in school-age children.

Little is known about how the gut microbiota and metabolic profiles are related to cognitive outcomes in young children until now. It was hypothesized that the gut microbiota, the plasma and fecal metabolites significantly correlated with intelligence quotient (IQ) in school-age children in current study. This cross-sectional study enrolled 452 children aged 6-9 years old. IQ was measured using the Wechsler Intelligence Scale for Children-Fourth Edition. Fecal microbiota, plasma and fecal metabolites were analyzed using 16S rRNA amplicon sequencing and targeted metabolomic technologies, respectively. Restricted maximum likelihood (REML) analyses showed that microbiota composition and fecal metabolites were associated with neither subscale nor full-scale IQ (P: 0.059-0.500). However, plasma metabolites were significantly correlated with the processing speed (P=0.008). In multiple regression analysis after adjusting for confounders and multiple test correction, benzoic acid, azelaic acid, adipic acid, suberic acid and malonic acid selected by the multivariate methods with unbiased variable selection were positively associated with processing speed index (PSI) [Pfalse discovery rate (FDR): 0.006-0.024], whereas pyruvic acid was negatively associated with the PSI and full-scale IQ (PFDR: 0.014-0.030). In normal school-age children, certain plasma metabolites concentrations but not the gut microbiota composition nor fecal metabolites are correlated with intelligence.

Layer myocardial strain is the most heritable echocardiographic trait.

Myocardial deformation assessed by strain analysis represents a significant advancement in our assessment of cardiac mechanics. However, whether this variable is genetically heritable or whether all/most of its variability is related to environmental factors is currently unknown.We sought to determine the heritability of echocardiographically determined cardiac mechanics indices in a population setting. A total of 1357 initially healthy subjects (women 51.6%; 48.2 ± 14.1 years) were included in this study from 20 years follow-up after the 4th visit of the longitudinal familial STANISLAS cohort (Lorraine, France). Data were acquired using state-of-the-art cardiac ultrasound equipment, using acquisition and measurement protocols recommended by the EACVI/ASE/Industry Task Force. Layer-specific global longitudinal strain (GLS) and global circumferential strain (GCS) (full-wall, subendocardial and subepicardial) and conventional structural and functional cardiac parameters and their potential heritability were assessed using restricted maximum likelihood analysis, with genetic relatedness matrix calculated from genome-wide association data. Indices of longitudinal/circumferential myocardial function and left ventricular (LV) ejection fraction had low heritability (ranging from 10 to 20%). Diastolic and standard LV function parameters had moderate heritability (ranging from 20 to 30%) except for end-systolic and end-diastolic volumes (respectively 30 and 45%). In contrast, GLSEndo/GLSEpi ratio had a high level of heritability (65%). Except for GLSendo/GLSepi ratio, a large percentage of variance remained unexplained (greater than 50%). In our population cohort, GLSendo/GLSepi ratio had a high level of heritability whereas other classical and mechanical LV function parameters did not. Given the increasing recognition of GLSendo/GLSepi ratio as an early/sensitive imaging biomarker of systolic dysfunction, our results suggest the possible existence of individual genetic predispositions to myocardial decline.

Genomic heritability and correlation between carcass traits in Japanese Black cattle evaluated under different ceilings of relatedness among individuals.

The investigation of carcass traits to produce meat with high efficiency has been in focus on Japanese Black cattle since 1972. To implement a successful breeding program in carcass production, a comprehensive understanding of genetic characteristics and relationships between the traits is of paramount importance. In this study, genomic heritability and genomic correlation between carcass traits, including carcass weight (CW), rib eye area (REA), rib thickness (RT), subcutaneous fat thickness (SFT), yield rate (YI), and beef marbling score (BMS) were estimated using the genomic data of 9,850 Japanese Black cattle (4,142 heifers and 5,708 steers). In addition, we investigated the effect of genetic relatedness degree on the estimation of genetic parameters of carcass traits in sub-populations created based on different GRM-cutoff values. Genome-based restricted maximum likelihood (GREML) analysis was applied to estimate genetic parameters. Using all animal data, the heritability values for carcass traits were estimated as moderate to relatively high magnitude, ranging from 0.338 to 0.509 with standard errors, ranging from 0.014 to 0.015. The genetic correlations were obtained low and negative between SFT and REA [-0.198 (0.034)] and between SFT and BMS [-0.096 (0.033)] traits, and high and negative between SFT and YI [-0.634 (0.022)]. REA trait was genetically highly correlated with YI and BMS [0.811 (0.012) and 0.625 (0.022), respectively]. In sub-populations created based on the genetic-relatedness ceiling, the heritability estimates ranged from 0.212 (0.131) to 0.647 (0.066). At the genetic-relatedness ceiling of 0.15, the correlation values between most traits with low genomic correlation were overestimated while the correlations between the traits with relatively moderate to high correlations, ranging from 0.380 to 0.811, were underestimated. The values were steady at the ceilings of 0.30-0.95 (sample size of 5,443-9,850) for most of the highly correlated traits. The results demonstrated that there is considerable genetic variation and also favorable genomic correlations between carcass traits. Therefore, the genetic improvement for the traits can be simultaneously attained through genomic selection. In addition, we observed that depending on the degree of relationship between individuals and sample size, the genomic heritability and correlation estimates for carcass traits may be different.

Disentangling genetic variation for endurance and resistance to visceral white-nodules disease in large yellow croaker (Larimichthys crocea) using genome information

Visceral white-nodules disease (VWND) caused by Pseudomonas plecoglossicida is a major threat for large yellow croaker (Larimichthys crocea) farming, resulting in considerable economic loss. Selection breeding for enhancing host resistance to infectious disease is an alternative strategy for disease control. The present work is aimed at using genome-wide association studies (GWAS) to identify quantitative trait loci (QTLs) and potential genes associated with VWND endurance and resistance in large yellow croaker. A total of 1408 fish from different populations were exposed to P. plecoglossicida. The first dead fish were labelled as susceptible group, whereas the last dead fish were assigned to endurant group, and the survivals were jugged to resistant group. Genotyping was conducted using whole genome resequencing and 10,586,121 high quality single nucleotide polymorphisms (SNPs) were discovered. Both binary survival (BS) and time to death (DT) traits were used in GWAS for endurant (421) and resistant (479) fish. A total of 6 SNPs were associated with disease endurance, and 7 SNPs were associated with disease resistance, where a major QTL associated with disease endurance was discovered on chromosome 5. Within these QTL regions, 41 candidate genes were mapped with immune response and defense mechanisms, and 4 SNPs were found in intron region of trim21, gtse1, pot1 and cald1. In addition, moderate to high heritability values (0.51–0.72) were estimated using a restricted maximum likelihood (REML) analysis. Finally, the correlation between Estimated Breeding Value (EBV) and the phenotype was calculated in different groups with the values of 0.39–0.55. Based on our investigations, VWND endurance and resistance are two perfectly distinct traits, and they can evolve independently in population. These results will be useful for the future breeding programs for improving the natural resistance of large yellow croaker against VWND. To our knowledge, this is the first study in large yellow croaker disentangling the genetic basis of endurance and resistance to VWND.

Genetic diversity in tropical wheat germplasm and selection via multitrait index

AbstractGenetic diversity studies and analysis of the selection gain of wheat (Triticum aestivum L.) genotypes released over the decades allow the planning of strategies and support decision‐making for crossing in wheat breeding. We investigated genetic diversity in tropical wheat germplasm, discussed the main trends in breeding programs and selected potential parents. Therefore, a trial with 90 commercial cultivars released in Brazil between 1800–2000 and 2001–2019 was conducted during the 2020 winter crop in Viçosa, MG, Brazil. The following traits were evaluated: spike height and plant height, heading date, spike weight, grain mass per spike, 100‐grain mass, number of spikelets per spike, number of grains per spike, hectoliter weight, and grain yield. The data were subjected to restricted maximum likelihood or best linear unbiased prediction analysis and used to calculate the standardized average Euclidean distance and then unweighted pair group method with arithmetic mean clusters were generated from the genotypic distance matrix. The selection of the genotypes with the best performance in each phase was accomplished using the multitrait genotype‐ideotype distance index (MGIDI). High genetic diversity was observed between the genotypes evaluated. Multitrait index revealed selection gain in the desired direction in the two phases. The present study will support the efficient use of the genetic variability present in tropical wheat germplasm. Three genotypes were selected by MGIDI in the first phase, while in the second phase 12 were selected. Two groups of dissimilar and potential genotypes were proposed to compose a partial diallel.

Capturing Genetic Variability and Identification of Promising Drought-Tolerant Lines in Exotic Landrace Derived Population Under Reproductive Drought Stress in Rice.

Drought is one of the most predominant abiotic stresses in this century, leading to a drastic reduction in the yield of rainfed rice ecosystems. Breeding of drought-resilient rice varieties is very much in demand for sustainable rice production in drought-prone rainfed ecology. An experiment was designed under irrigated non-stress and drought-stress situations involving an exotic drought-tolerant landrace (Chao Khaw) and a high-yielding aromatic rice cultivar (Kasturi), and an F2:4 derived population of 156 breeding lines was developed at IRRI South Asia Hub, Hyderabad. The objective of the study was to assess the genetic variability, drought tolerance behavior, and identify promising breeding lines for different rice ecologies and drought breeding programs. Restricted maximum likelihood (REML) analysis using the mixed model approach revealed a considerable genetic variation in the population for yield and yield contributing traits in non-stress and drought-stress conditions. We observed very high heritability for all the selected traits under stress 2015 WS (73.8% to 85.3%) and 2016 WS (72.4% to 93.5%) and non-stress 2015 WS (68.2% To 92.9%) and 2016 WS (61.4% to 92.6%) environments, indicating possible selection for grain yield under drought stress and non-stress with the same precision level. None of the secondary traits except harvest index and biomass included in our study showed a positive association with grain yield, indicating indirect selection’s ineffectiveness in improving yield under drought. A total of 48 promising breeding lines were found to have a better yield than donor Chao Khaw (up to 38% advantage) and popular drought-tolerant cultivars Shabhagidhan (up to 48% advantage) in stress conditions and recommended for rainfed upland ecology, 34 breeding lines under the well-watered condition suited for rainfed lowland ecology. Overall, the study found 21 common breeding lines that showed their superiority in non-stress and under drought stress situations, fitting best in rainfed lowland ecology with occasional drought occurrence. The large genetic variation found in this population can be exploited further to develop a few forward breeding high-yielding lines with better drought tolerance ability and used as drought donors in drought breeding programs.

Selection of barley pure lines with high yield and desirable agronomic characteristics in warm areas of Iran

Background and objectives: Barley (Hordeum vulgare L.) is one of the most important plants in the cereal family after wheat, rice and corn. Barley is the second most important crop in Iran after wheat in terms of agricultural value and nutrition. The purpose of this study was to evaluate and select superior lines with high yield, early maturity and dormancy resistance in warm regions of the south and north of the country using the selection index of ideal genotype (SIIG). Materials and methods: In order to selection of pure barley lines with high yield and desirable agronomic characteristics in the warm regions of the south and north of the country, 108 pure lines in the non-repeating Augment design with four controls (Norooz /Sahra, Auxin, Nobahar and WB-96-19) in three blocks, in the Centers for Agricultural Research and Education and Natural Resources Fars (Darab), Ahvaz, Sistan (Zabol) and Golestan (Gonbad) were evaluated during 2019-20 cropping year. Results: The results of restricted maximum likelihood (REML) analysis showed that the heritability of grain yield in Gonbad, Ahvaz, Darab and Zabol were 0.993, 0.258, 0.498 and 0.063, respectively. The results of correlation analysis showed that there is a positive and significant correlation between SIIG index and plant height, 1000-kernal weight and grain yield in all regions. SIIG index showed that 21, 28, 16 and 5 lines in Darab, Ahvaz, Zabol and Gonbad, respectively, with high SIIG index value (0.6-0.9) were the best lines. Based on the results of the average SIIG index of lines 68, 102, 44, 66, 13, 47, 16, 34, 46, 99, 25, 65 and 35, respectively, with SIIG value higher than 0.500 were the best lines in most regions, so they are recommended for cultivation in later years and for advanced testing and compatibility. In order to evaluate the efficiency of SIIG index in selecting the best lines in terms of grain yield, 1000 kernel weight, plant height and early maturity, the studied lines were grouped based on SIIG index in different regions. The studied lines were classified into 6, 7, 8 and 7 groups in Darab, Ahvaz, Gonbad and Zabol, respectively. Conclusion: Based on the results of the average SIIG index in all regions, 16 lines with the highest average value of the SIIG index were top lines in most regions. Selected lines in each region can be recommended for experiments in that region, and lines with the highest SIIG values in most regions for additional testing in all introduced regions in later years.

Evaporation rates and pollutants emission from heated cooking oils and influencing factors

The heating of edible oils during cooking activities promotes the emissions of pollutants that have adverse impacts on the health of humans. This study investigated the evaporative emissions of fifteen (15) commonly used cooking oils. Split-plot experimental design under the response surface methodology framework was used to study singular and interaction effects of influencing parameters (temperature, volume of cooking oil and time) on cooking oil evaporation rate and pollutants emissions (i.e. Particulate matter of aerodynamic diameter ≤1 μm (PM1.0); ≤2.5 μm (PM2.5); ≤10 μm (PM10); Total Suspended Particulate (TSP); Total Volatile Organic Compounds -TVOCs, and Carbon Monoxide- CO) on a groundnut oil sample that served as a case study. Obtained values of density, viscosity, kinematic viscosity, smoke, flash and fire points were; 873–917 kg/m3; 1.12–9.7 kg/ms; 2.4–3.4 m2/s; 96 -100 °C; 124–179 °C and 142–186 °C, respectively. The role of temperature as the most significant parameter influencing the rate of evaporative emissions was established. Evaporation rate and pollutants emission from unrefined samples were the highest. The restricted maximum likelihood (REML) analysis results suggested a strong relationship between the actual values and the predicted values as R-squared values obtained were greater than 0.8 for all the responses. These results suggest that minimal rates of evaporation and pollutants emission from heating cooking oils can be achieved with a high volume of the cooking oil at moderate temperature levels.

Statistical driver genes as a means to uncover missing heritability for age-related macular degeneration

BackgroundAge-related macular degeneration (AMD) is a progressive retinal disease contributing to blindness worldwide. Multiple estimates for AMD heritability (h2) exist; however, a substantial proportion of h2 is not attributable to known genomic loci. The International AMD Genomics Consortium (IAMDGC) gathered the largest dataset of advanced AMD (ADV) cases and controls available and identified 34 loci containing 52 independent risk variants defining known AMD h2. To better define AMD heterogeneity, we used Pathway Analysis by Randomization Incorporating Structure (PARIS) on the IAMDGC data and identified 8 statistical driver genes (SDGs), including 2 novel SDGs not discovered by the IAMDGC. We chose to further investigate these pathway-based risk genes and determine their contribution to ADV h2, as well as the differential ADV subtype h2.MethodsWe performed genomic-relatedness-based restricted maximum-likelihood (GREML) analyses on ADV, geographic atrophy (GA), and choroidal neovascularization (CNV) subtypes to investigate the h2 of genotyped variants on the full DNA array chip, 34 risk loci (n = 2758 common variants), 52 variants from the IAMDGC 2016 GWAS, and the 8 SDGs, specifically the novel 2 SDGs, PPARA and PLCG2.ResultsVia GREML, full chip h2 was 44.05% for ADV, 46.37% for GA, and 62.03% for CNV. The lead 52 variants’ h2 (ADV: 14.52%, GA: 8.02%, CNV: 13.62%) and 34 loci h2 (ADV: 13.73%, GA: 8.81%, CNV: 12.89%) indicate that known variants contribute ~ 14% to ADV h2. SDG variants account for a small percentage of ADV, GA, and CNV heritability, but estimates based on the combination of SDGs and the 34 known loci are similar to those calculated for known loci alone. We identified modest epistatic interactions among variants in the 2 SDGs and the 52 IAMDGC variants, including modest interactions between variants in PPARA and PLCG2.ConclusionsPathway analyses, which leverage biological relationships among genes in a pathway, may be useful in identifying additional loci that contribute to the heritability of complex disorders in a non-additive manner. Heritability analyses of these loci, especially amongst disease subtypes, may provide clues to the importance of specific genes to the genetic architecture of AMD.

Genetic Heritability of Pigmentary Glaucoma and Associations With Other Eye Phenotypes

Mechanisms behind pigmentary glaucoma, a form of early-onset glaucoma that may potentially lead to severe visual impairment or blindness, are poorly understood. To calculate the single-nucleotide polymorphism (SNP) heritability of pigmentary glaucoma and identify genetic associations with the disease. This genome-wide association study included affected individuals from Germany and control participants from the United Kingdom. Genome-wide information was obtained for patients with pigmentary glaucoma and control participants free of glaucoma by using the Illumina Human Omni Express Exome 8v1-2 chip and genomic imputation. The SNP heritability of pigmentary glaucoma was estimated through a restricted maximum likelihood analysis. Associations between the genetic variants and pigmentary glaucoma obtained from age, sex, and principal component-adjusted logistic regression models were compared with those of SNPs previously associated with other eye phenotypes using Pearson product-moment correlations. Data were collected from November 2008 to January 2018, and analysis was completed between April 2018 and August 2019. An estimate of SNP-explained heritability for pigmentary glaucoma; correlations of effect sizes between pigmentary glaucoma and iris pigmentation and myopia; and correlations of effect sizes between pigmentary glaucoma and other eye phenotypes. A total of 227 affected individuals (mean [SD] age, 58.7 [13.3] years) and 291 control participants (mean [SD] age, 80.2 [4.9] years) were included; all were of European ancestry. The SNP heritability of pigmentary glaucoma was 0.45 (SE, 0.22; P = 6.15 × 10-10). Twelve SNPs previously reported with genome-wide significant associations with eye pigmentation were associated with pigmentary glaucoma's SNP heritability (4.9% SNP heritability; 0.022; P = 6.0 × 10-4). Pigmentary glaucoma SNP effect sizes were correlated moderately for myopia (r, 0.42 [95% CI, 0.14-0.63]; P = 4.3 × 10-3) and more strongly with those for iris pigmentation (r = -0.69 [95% CI, -0.91 to -0.20]; P = .01), although this was nonsignificant per a strict adjusted significance threshold (P < .01). These findings support the conclusion that pigmentary glaucoma may have a genetic basis and be highly heritable. Variants associated with lighter eye color and myopia appear to be associated with increased risk of pigmentary glaucoma, but no shared genetic basis with primary open-angle glaucoma (or its quantitative endophenotype of cup-disc ratio) was observed.

Sources of variation in pre-sale weights of osmanabadi goat kids in villages of Maharashtra, India

This study pertains to pre-sale weights (about 3 months of age) of Osmanabadi kids recorded under the Osmanabadi Goat Field Unit of ICAR-All India Coordinated Research Project on Goat Improvement. Pre-sale weight records of 4394 kids born to 1604 does over nine years (2009 to 2018) in 10 villages from six districts of Maharashtra state were analyzed using mixed model restricted maximum likelihood analysis. The fixed effect of strain of kid was not significant, indicating that variation in colour and appearance among kids did not influence their weights. The influence of other fixed effects such as sex, birth type and dam parity on 3-month weight was as expected (females being lighter than males, triplets and quadruplets being lighter than twins and twins being lighter than singles, kids of dams from parity 2 to 4 weighing the highest, followed by kids of dams from parity 5 to 7, parity >7 and lastly parity 1). The effect of whether the birth date of the kids was accurate or estimated was significant, indicating an under-estimation of the age of kids by the owners. A direct genetic effect and a maternal permanent environmental effect (and not the maternal genetic effect) could be fitted in the absence of pedigrees. It was found that the variation in management among owners could best be accounted by fitting owner as a random effect. However, fitting the contemporary group (village-year-season) effect as a fixed effect was a better option than fitting it as a random effect. In village smallholder situations with inherent data recording limitations, as maternal effects cannot be accounted appropriately, it may be a better option to use traits of the dam such as body size and milk yield for selection of kids rather than kids’ pre-sale weight as a selection criterion.

Updating maintenance energy requirement for the current sheep flocks and the associated effect of nutritional and animal factors

There is evidence indicating that using the current UK energy feeding system to ration the present sheep flocks may underestimate their nutrient requirements. The objective of the present study was to address this issue by developing updated maintenance energy requirements for the current sheep flocks and evaluating if these requirements were influenced by a range of dietary and animal factors. Data (n = 131) used were collated from five experiments with sheep (5 to 18 months old and 29.0 to 69.8 kg BW) undertaken at the Agri-Food and Biosciences Institute of the UK from 2013 to 2017. The trials were designed to evaluate the effects of dietary type, genotype, physiological stage and sex on nutrient utilization and energetic efficiencies. Energy intake and output data were measured in individual calorimeter chambers. Energy balance (Eg) was calculated as the difference between gross energy intake and a sum of fecal energy, urine energy, methane energy and heat production. Data were analysed using the restricted maximum likelihood analysis to develop the linear relationship between Eg or heat production and metabolizable energy (ME) intake, with the effects of a range of dietary and animal factors removed. The net energy (NEm) and ME (MEm) requirements for maintenance derived from the linear relationship between Eg and ME intake were 0.358 and 0.486 MJ/kg BW0.75, respectively, which are 40% to 53% higher than those recommended in energy feeding systems currently used to ration sheep in the USA and the UK. Further analysis of the current dataset revealed that concentrate supplement, sire type or physiological stage had no significant effect on the derived NEm values. However, female lambs had a significantly higher NEm (0.352 v. 0.306 or 0.288 MJ/kg BW0.75) or MEm (0.507 v. 0.441 or 0.415 MJ/kg BW0.75) than those for male or castrated lambs. The present results indicate that using present energy feeding systems in the UK developed over 40 years ago to ration the current sheep flocks could underestimate maintenance energy requirements. There is an urgent need to update these systems to reflect the higher metabolic rates of the current sheep flocks.

Brazilian Sport Horse: genetic parameters for approval of Brasileiro de Hipismo stallions.

The aim of this study was to evaluate genetic parameters for subjective scores given at the Brazilian Sport Horse (BSH) Stallion Approval by estimating heritability (h2) for morphological, gait, and jumping traits and genetic correlations (γg) among the functional ones and by verifying selection feasibility. The analysis included 1179 complete evaluations from 294 horses, by 4.26 ± 0.96 judges. Each trait was evaluated using mixed models in SAS® v9.2, considering the individual as a random effect. Variance components and genetic parameters were obtained by single and two-trait animal models in a derivative-free restricted maximum likelihood analysis. Since many jumping traits were not described in Breed Regulation, mixed model results were used to enlighten the criteria adopted in the assignment of scores. Balanced bodies and conformations that favor collection were preferred by judges and presented moderate heritabilities. Additive variation was found for most jumping traits, with heritability equal to 0.74 (se = 0.04) for overall jump, and estimates for the separate aspects of the jump movement ranging from near null to 0.43 (se = 0.07) for temperament. Morphological scores had little effect over gait and jump scores while trot may be indicative of some additive value for jump distance and canter for hind limb mechanics. Conformation evaluations of separate body regions presented heritability estimates similar to previous studies and may provide more informative breeding values.

Heritability of a resting heart rate in a 20-year follow-up family cohort with GWAS data: Insights from the STANISLAS cohort.

The association between resting heart rate (HR) and cardiovascular outcomes, especially heart failure, is now well established. However, whether HR is mainly an integrated marker of risk associated with other features, or rather a genetic origin risk marker, is still a matter for debate. Previous studies reported a heritability ranging from 14% to 65%. We assessed HR heritability in the STANISLAS family-study, based on the data of four visits performed over a 20-year period, and adjusted for most known confounding effects. These analyses were conducted using a linear mixed model, adjusted on age, sex, tea or coffee consumption, beta-blocker use, physical activity, tobacco use, and alcohol consumption to estimate the variance captured by additive genetic effects, via average information restricted maximum likelihood analysis, with both self-reported pedigree and genetic relatedness matrix (GRM) calculated from genome-wide association study data. Based on the data of all visits, the HR heritability (h2) estimate was 23.2% with GRM and 24.5% with pedigree. However, we found a large heterogeneity of HR heritability estimations when restricting the analysis to each of the four visits (h2 from 19% to 39% using pedigree, and from 14% to 32% using GRM). Moreover, only a little part of variance was explained by the common household effect (<5%), and half of the variance remained unexplained. Using a comprehensive analysis based on a family cohort, including the data of multiple visits and GRM, we found that HR variability is about 25% from genetic origin, 25% from repeated measures and 50% remains unexplained.

Evaluation and Identification of Promising Introgression Lines Derived From Wild Cajanus Species for Broadening the Genetic Base of Cultivated Pigeonpea [Cajanus cajan (L.) Millsp.

Pigeonpea [Cajanus cajan (L.) Millsp.], a multipurpose and nutritious grain legume crop, is cultivated for its protein-rich seeds mainly in South Asia and Eastern and Southern Africa. In spite of large breeding efforts for pigeonpea improvement in India and elsewhere, genetic enhancement is inadequate largely due to its narrow genetic base and crop susceptibility to stresses. Wild Cajanus species are novel source of genetic variations for the genetic upgradation of pigeonpea cultivars. In the present study, 75 introgression lines (ILs), derived from crosses involving cultivated pigeonpea variety ICPL 87119 and wild Cajanus cajanifolius and Cajanus acutifolius from the secondary gene pool, were evaluated for yield and yield-attributing traits in diverse environments across locations and years. Restricted maximum likelihood (REML) analysis revealed large genetic variations for days to 50% flower, days to maturity, plant height, primary branches per plant, pods per plant, pod weight per plant, 100-seed weight, and grain yield per plant. Superior ILs with mid-early to medium maturity duration identified in this study are useful genetic resources for use in pigeonpea breeding. Additive main effects and multiplicative interaction (AMMI) analysis unfolded large influence of environment and genotype × environment interaction for variations in yield. A few lines such as ICPL 15023 and ICPL 15072 with yield stability were identified, while a number of lines were completely resistant (0%) to sterility mosaic diseases and/or Fusarium wilt. These lines are novel genetic resources for broadening the genetic base of pigeonpea and bring yield stability and stress tolerance. High-yielding lines ICPL 15010, ICPL 15062, and ICPL 15072 have been included in the initial varietal trials (IVTs) of the All India Coordinated Research Project (AICRP) on pigeonpea for wider evaluation across different agro-ecological zones in India for possible release as variety(ies).

Genome-wide association studies identify polygenic effects for completed suicide in the Japanese population

Suicide is a significant public health problem worldwide, and several Asian countries including Japan have relatively high suicide rates on a world scale. Twin, family, and adoption studies have suggested high heritability for suicide, but genetics lags behind due to difficulty in obtaining samples from individuals who died by suicide, especially in non-European populations. In this study, we carried out genome-wide association studies combining two independent datasets totaling 746 suicides and 14,049 non-suicide controls in the Japanese population. Although we identified no genome-wide significant single-nucleotide polymorphisms (SNPs), we demonstrated significant SNP-based heritability (35–48%; P < 0.001) for completed suicide by genomic restricted maximum-likelihood analysis and a shared genetic risk between two datasets (Pbest = 2.7 × 10−13) by polygenic risk score analysis. This study is the first genome-wide association study for suicidal behavior in an East Asian population, and our results provided the evidence of polygenic architecture underlying completed suicide.

Phenotypic and genetic parameter estimates of cheese-making traits and their relationships with milk production, composition and functional traits in Spanish Assaf sheep

Sheep milk is mostly used for the production of cheese. In this study, a commercial population of Spanish Assaf sheep was analyzed for six cheese-making traits: four related to milk-coagulation properties (MCPs) [rennet coagulation time (RCT), curd-firming time (K20), and curd firmness at minutes 30 and 60 (A30, A60)] and two related to cheese yield [individual laboratory cheese yield (ILCY) individual laboratory dried curd yield (ILDCY)]. Records for milk production traits were also available for this study. Restricted maximum likelihood (REML) analysis was used to estimate the genetic parameters and variance components, whereas bivariate models were used to calculate the phenotypic and genetic correlations among the traits considered in this work. Of the 1,143 milk samples included in the study, 147 (13%) did not coagulate, whereas 425 samples (approximately 37%) showed slow coagulation (samples with a record for A60 and a missing record for A30). Also, large mean values were observed for RCT (29.54 min) and logK20 (1.35 min). The heritabilities estimated for the cheese-making traits were moderate, ranging between 0.15 (for ILDCY) and 0.30 (A30 and ILCY). In general, within the pairs of related cheese-making traits, we found moderate-high phenotypic and genetic correlations. The RCT and logK20 traits showed high negative correlations with A30 and A60 at both the genetic and phenotypic levels. From the estimation of genetic parameters among these and several milk traits, the high and positive genetic correlations observed between PP and the two cheese yield traits should be highlighted. Based on the estimated phenotypic correlations, our study supports that subclinical mastitis is related to a delayed gelification of milk and lower curd firmness. Overall, this study provides the first report about the phenotypic and genetic parameters of cheese-making traits in a commercial population of Assaf sheep, offering preliminary information that might help to identify the cheese-making or related milk production traits that could be considered to improve Assaf population toward enhanced cheese performance features.