Genetic Variance Components Research Articles

Elucidation of Combining Ability and Gene in Bottle Gourd [Lagenaria siceraria (Mol.) Standl.

Aims: To Study combining ability effects and evaluate gene action for fruit yield with associated traits of bottle gourd.
 Study Design: Randomized block design.
 Place and Duration of Study: The seeds of F1 hybrids were produced during summer 2021 at Potato Research Station, S. D. Agricultural University, Deesa.
 Methodology: The experimental material consisted of twelve parents, their 35 Line × Tester crosses and one standard check (ABGH 1).
 Results: The analysis of variance for combining ability revealed that the mean sum of squares due to female (lines) and male (testers) were highly significant for all the traits except fruit girth, average fruit weight, chlorophyll a, chlorophyll b and total chlorophyll. The gca effects indicated that four male parents ABGS 14-25, ABGS 11-17, ABGS 11-24 and PUNJAB LONG and three female parents DBG 5, NDBG 132 and LOCAL were found good general combiners for fruit yield per plant and its some of the contributing traits. Based on estimates of sca effects, the most promising hybrids for fruit yield per plant were DBG 5 × ABGS 14-27, NDBG 132 × PUNJAB LONG and GPBG 108 × ABGS 11-24. The good general combiners for fruit yield and contributing traits can be utilized in intensive crossing programme and select transgressive segregants for desired characters in segregating generations to develop superior lines.
 Conclusion: The ratio of σ2GCA / σ2SCAwas less than unity for all the characters under study, which suggested greater role of non-additive genetic variance in the inheritance of these characters. The genetic components of variance revealed that different type of gene action were involved for fruit yield associated with different traits in bottle gourd.

Selection of inbreds with better combining ability is instrumental in developing CMS-based heterotic hybrids in tropical carrot (Daucus carota L.)

Abstract Carrot is an important vegetable crop worldwide valued for its fleshy edible roots of varied colours. Owing to its highly cross-pollinated nature and small flower size, cytoplasmic male sterility (CMS) is being utilized for hybrid development. Among different types of male sterility, petaloid CMS is widely used for hybrid carrot breeding globally. This study aimed to develop selection criteria for parents in developing heterotic F1 hybrids using CMS lines. A large number of agro-morphological traits and Simple Sequence Repeats (genomic-SSRs) were used to assess the diversity among parental lines. We developed 60 F1 hybrids by crossing four petaloid CMS lines and 15 testers in line × tester mating design and evaluated them in replicated randomized block design trial for four vegetative and 11 economic traits. The mean squares of all the traits in line × tester interactions were significant. The estimates of genetic components of variance indicated predominance of non-additive gene action except for root maturity, root length and core diameter. The hybrids with highest per se performance also had significant positive specific combining ability effects. The root yield and root weight showed highest heterosis percentage (33%). The best performing heterotic hybrids were DCatH-5392, DCatH-700 and DCatH-9892. Correlation between genetic distance and relative heterosis of economic traits indicated no significant association and thus genetic distance could not be used to predict heterosis. As most of the yield-related traits were controlled by non-additive gene action, heterosis breeding could be potentially used along with combining ability analysis to reduce time in selection of best parents and crosses in tropical carrot.

Hybrid Vigour and Combining Ability in Biofortified Maize (Zea mays L.)

The study was conducted during winter season of 2020–2021 and rainy season of 2021 at Maize Research Station, Sardarkrushinagar Dantiwada Agricultural University, Bhiloda, Gujarat, India. The aim of the study was to assess magnitude of heterosis and combining ability of forty-five single cross hybrids developed by half-diallel mating design involving ten parents and two standard checks. The field experiment was laid out in randomized block design with three replications. The heterosis, combining ability and components of genetic variance were studied for diverse thirteen characters. The analysis of variance revealed that mean square values of genotypes were significant for all the characters which indicated the existence of considerable amount of genetic variation in genotypes for all the characters. Among single crosses, IMR-76×IMR-58 exhibited maximum mean and desired SCA effect and standard heterosis for β-carotene and IMR-53×IMR-72 for kernel yield. The general and specific combining ability variances observed highly significant for all traits except days to tasseling (only additive gene action), anthesis-silking interval and shelling percentage (only non-additive gene action). The σ2A/σ2D ratio indicated that preponderance of non-additive gene action for the inheritance of these characters suggesting due weightage should be given to heterosis breeding for genetic improvement of these traits. The crosses namely IMR-52×IMR-72 and IMR-51×IMR-58 presented significant heterosis for days to maturity, grain yield, iron and β-carotene content.

Estimation of Combining Ability, Gene Action and Components of Genetic Variation in Forage Sorghum [Sorghum bicolor (L.)

Aims: To Study the combining ability effects and evaluate the genetics of the parents for fodder yield and its component traits in sorghum.
 Study Design: Randomized block design.
 Place and Duration of Study: The seeds of F1 hybrids were produced during summer 2022 at Center for Millets Research, S. D. Agricultural University, Deesa.
 Methodology: Six parental genotypes were used in the experiment, which produced 15 half-diallel crosses in sorghum.
 Results: The analysis of variance for combining-ability (CA) studies revealed that mean sum of squares due to general combining ability (GCA) were important for most of the characters except the leaf length of blade. Based on the gca effect, the parents CSV 46, IS 3338 and Malwan were good general combiners for green and dry fodder yield per plant. The unit slope of regression line and non- significant t2 value asserted the validity of the additive-dominance model for total plant height, number of leaf per plant, stem diameter, leaf length of blade, leaf width of blade, dry fodder yield per plant and crude protein content in dry fodder. The value of H1 was superior to H2 for most of the characters representing that gene distribution frequency in the parent genotypes was asymmetry and that was supported by the ratio of H2/4H1 (i.e., less than 0.25). The KD/KR components value was greater than one among most of the traits except for number of leaf per plant and crude protein content in dry fodder showed that parents had more dominant genes compared to recessive genes frequency.
 Conclusion: The ratio of σ2gca/σ2sca being more than unity, which suggested greater role of additive genetic variance in the inheritance of these traits. The genetic components of variance and graphical analysis revealed that different type of gene action were involved for forage yield and components traits in sorghum.

Behavioral genetics of temporal framing: Heritability of time perspective and its common genetic bases with major personality traits.

The present study aimed to provide a seminal behavioral genetic analysis of time perspectives (TPs). Moreover, we intended to investigate the magnitude of genetic vs. environmental components of the well-established assocations between TPs and personality features. Individual differences in temporal framing processes, referred to as TPs, are vital psychological and behavioral outcomes. Although proponents of TP theory emphasize mainly environmental origins of the tendencies to adopt certain TPs, research provides evidence for marked associations between the temporal dimensions and major personality traits that are known to be heritable. Hence, it was essential to empirically verify these claims. The article reports an analysis of genetic and environmental components of variance in TPs based on a study adopting a twin design, conducted on a sample of 393 pairs of twins (135 monozygotic and 258 dizygotic). Multivariate Cholesky decomposition supported an EA model assuming impacts of both unshared environmental factors (E) and additive genetic factors (A) across all TP dimensions, suggesting that the effects of shared environment on TPs are plausibly negligible. Heritability indices of TPs ranged between 0.51 for Present-Fatalistic and 0.62 for Present-Hedonistic, suggesting that the majority of the variance in TPs stems from genetic influences. Substantial genetic correlations were found between TPs and the Big Five personality traits. The findings provide further evidence for conceptualizing TPs as biologically based personality traits and challenge the claims that TP is mainly a product of culture, education, and personal experiences.

Genetic (co)variance components for slaughter traits in a multi-breed sheep population.

Carcass value is one of the main contributors to revenue in meat sheep enterprises, while age at slaughter is also a major component to the cost of production. Despite the contribution of such traits to overall profit, little is actually known on the extent of exploitable genetic variability in the traits that govern carcass value (i.e. carcass weight, carcass conformation, carcass fat) and age at slaughter, especially independent of each other. The objective of the present study was to estimate genetic (co)variances for and among carcass weight, carcass conformation, carcass fat, kill-out percentage and age at slaughter as well as their genetic (co)variances with traits measured earlier in life. Data consisted of slaughter records from 15714 lambs, with 12630 of these lambs having at least one live weight measure. The heritability (SE) of carcass weight, carcass conformation, carcass fat, kill-out percentage, and age at slaughter was 0.14 (0.02), 0.19 (0.02), 0.08 (0.01), 0.22 (0.03), and 0.16 (0.02), respectively. The maternal heritability for age at slaughter was 0.07 (0.02); no maternal genetic influence was found on any of the other slaughter traits. The coefficient of genetic variation for carcass weight and age at slaughter was 3 and 8%, respectively. The correlations between the direct genetic effects for live weight throughout life, and carcass weight were weak up to weaning but were strong (0.83) thereafter. The correlation between the direct genetic effects of birth weight and age at slaughter was zero, but varied from -0.91 to -0.56 between live weight measured later in life and age at slaughter. Results demonstrate significant exploitable genetic variability in a range of slaughter traits with the prediction of genetic merit for carcass traits and age at slaughter being possible using live weight measures taken on live animals. For example, the accuracy of selection for slaughter traits (comprising of age at slaughter, carcass conformation and carcass fat) from weaning weight records available on 100 progeny was 0.37; when slaughter data were also available for 10 progeny, the accuracy of selection increased to 0.56.

Assessment of body shape variation using Elliptic Fourier descriptors and ellipse fitting estimators and their genetic estimates in the flatfish Senegalese sole

Body shape is an important morphological trait in aquaculture. This study investigates the use of Elliptic Fourier descriptors (EFDs) analysis and ellipse fitting estimators to assess shape variation in Senegalese sole and their genetic variance components. A total of 2271 fish were individually photographed and body contours reconstructed using 20 Elliptic Fourier harmonics. Principal component analysis identified four symmetric components that explained the 68.6% of the total variation. They were mainly related to the adjustment of the body to an ellipse (PC1s and PC3s) and caudal fin morphological features (PC2s, PC3s, PC4s). Moreover, four asymmetric components related to caudal fin (PC1a, PC2a, PC3a) and head orientation (PC4a) that explained 24.5% of the total variation were also found. In addition to EFDs, body perimeter and five ellipse fitting estimators including the maximum body height to caudal peduncle height ratio (MBH/CPH), body aspect ratio (AR), ellipticity (ELL), AR from theoretical ellipse (ARe) and solidity (SOL) were calculated. PC1s was strongly correlated with ARe, AR and ELL (≥0.75), PC2s with SOL (−0.79) and PC3s with AR and ELL (0.48–0.49). Males appeared more elliptic than females as revealed by all ellipse descriptors with a tendency to caudal fins with obtuse angles (PC3a) and heads orientated toward the abdominal cavity (PC4a). Overall, heritabilities for symmetric components were higher than for asymmetric. Heritabilities for body ellipse fitting estimators including PC1s were high or very high with the highest values for AR (0.80) and ARe (0.78) for body and whole-body, respectively. Heritability for MBH/CPH was high (0.51) with low genetic correlation with other morphological traits. Heritabilities for symmetrical and asymmetrical features of caudal fin were moderate or low and indirect selection using other highly correlated traits such as PC2s through SOL and PC3a through PC4a or PC1s would facilitate progress in the selection. Perimeter showed a moderate heritability and it was more genetically correlated with growth than shape-related traits. The data provided represent a valuable tool to assess body shape in sole and in the design of genetic breeding programs in Senegalese sole.

Breeding for Higher Ascorbic Acid and Mineral Nutrients in Snowball Cauliflower (Brassica oleracea var. botrytis L.)

The components of genetic variance and gene action effects for ascorbic acid and mineral nutrient contents in snowball cauliflower lines were estimated through line × tester analysis involving 5 Ogura based CMS lines and 7 male fertile testers. The mean squares due to lines and testers were significant for ascorbic acid and mineral nutrients (Ca, Mg, Na, K, S, Fe, Mn and Zn). Ogu 103 was best performing CMS line for K (182.32 mg/100 g), S (29.48 mg/100 g), Ca (23.19 mg/100 g), Mg (13.22 mg/100 g), Zn (313.33 μg/100 g) and Mn (235.00 μg/100 g) whereas maximum ascorbic acid (81.26), Na (24.37) and Fe content (645.03 μg/100 g) was noted in Ogu 119, Ogu 13-85 and Ogu 13-01, respectively. Among the testers, Kt-18 recorded maximum value (mg/100 g) for Na (98.03), K (277.52), S (42.87), Ca (43.73) and Mg (29.44), respectively, whereas Kt-22 had highest ascorbic acid (70.84 mg/100 g) and Mn content (343.50 μg/100 g) and Sel-26 had maximum Fe (1424.93 μg/100 g) and Zn (458.70 μg/100 g) contents. The best-performing hybrids for different macro-nutrients (mg/100 g) were, Ogu 101 × Sel-26 for ascorbic acid (94.05), Ogu 103 × Sel-26 for Na (98.63), Ogu 13-01 × Sel-26 for K (300.18), Ogu 101 × Lalchowk Maghi for S (49.34), Ogu 119 × Suprimax Late for Ca (54.65), Ogu 13-85 × DB-187 for Mg (35.60). For micronutrients (μg/100 g FW), the best hybrids were Ogu 13-01 × DB-187 for Fe (1775.60), Ogu 101 × Lalchowk Maghi for Zn (642.10) and Ogu 101 × Kt-22 for Mn content (381.60). Predominance of dominance component of variance was observed for vitamin C and mineral nutrients. The traits studied had narrow differences among GCV, PCV and broad sense heritability values, suggesting low effect of environment. The variance due to general (σ2gca) and specific combining abilities (σ2sca) were highly significant indicating the importance of both additive (σ2A) as well as non-additive (σ2D) type of gene actions. However, the ratios of σ2gca/ σ2sca (<1) and σ2A/σ2D (<1) revealed the preponderance of non-additive variance for the inheritance of traits studied. The study’s results suggest the possibility of improving these traits through recurrent selection and hybridization.

Complex traits and candidate genes: estimation of genetic variance components across multiple genetic architectures.

Large-effect loci-those statistically significant loci discovered by genome-wide association studies or linkage mapping-associated with key traits segregate amidst a background of minor, often undetectable, genetic effects in wild and domesticated plants and animals. Accurately attributing mean differences and variance explained to the correct components in the linear mixed model analysis is vital for selecting superior progeny and parents in plant and animal breeding, gene therapy, and medical genetics in humans. Marker-assisted prediction and its successor, genomic prediction, have many advantages for selecting superior individuals and understanding disease risk. However, these two approaches are less often integrated to study complex traits with different genetic architectures. This simulation study demonstrates that the average semivariance can be applied to models incorporating Mendelian, oligogenic, and polygenic terms simultaneously and yields accurate estimates of the variance explained for all relevant variables. Our previous research focused on large-effect loci and polygenic variance separately. This work aims to synthesize and expand the average semivariance framework to various genetic architectures and the corresponding mixed models. This framework independently accounts for the effects of large-effect loci and the polygenic genetic background and is universally applicable to genetics studies in humans, plants, animals, and microbes.

Relationship between Seed Properties and Outcome Components for Selection Criteria of Corn (Zea Mays L.) Products at Various Dosages of Popostium Fertilizer

This research was conducted to determine the relationship between seed developmental characteristics and yield components in a population of maize (Zea mays L.) grown at different potassium fertilizer rates. The information could be utilized as alternative selection criteria for maize genotypes with high-yielding potential. This research was conducted at the Experimental field of the Horticulture Seed Agency, Pekanbaru. Seven maize genotypes with four potassium fertilizer rates were grown in a 350 cm x 200 cm experimental plot with three replications. The genotypes used were Bisi 228. Pertiwi 3. Bisi 2. Decoral, Bisi 18. Betras 4. and Srikandi. Potassium fertilizer rates included 30 kg, 50 kg, 70 kg, and 90 kg per ha, respectively. Traits observed were plant height, tesseling flowering date, silking date, seed dry accumulation rate, effective seed filling period, cob length, cob weight, number of seed rows, number of seeds per cob, seed weight per cob, the weight of 100 seeds and seed yield per m2. Analysis of variance was performed to the data using SAS and further tested by honesty significant difference at 5% level. Variance component, heritability, genetic correlation coefficient, and selection response were calculated for all characters and effective seed filling duration. The results indicated that the genetic variance component was significant for all characters except for the dry matter accumulation rate. All characters' heritability values were quite high except for effective seed-filling duration and the number of seeds per cob. Phenotypic correlation coefficients were positively significant between seed yield per m2 and plant height, seed development rate, cob length, ear weight, number of seeds per ear, seed weight per ear, and weight of 100 seeds. The genetic correlations was significant between seed yield per m2 and plant height, seed development rate, number of seeds per ear, and seed weight per ear. All characters' direct selection response value is higher than the indirect selection response value.

Additive genetic and environmental variation interact to shape the dynamics of seasonal migration in a wild bird population.

Dissecting joint micro-evolutionary and plastic responses to environmental perturbations requires quantifying interacting components of genetic and environmental variation underlying expression of key traits. This ambition is particularly challenging for phenotypically discrete traits where multiscale decompositions are required to reveal non-linear transformations of underlying genetic and environmental variation into phenotypic variation, and when effects must be estimated from incomplete field observations. We devised a joint multistate capture-recapture and quantitative genetic animal model, and fitted this model to full-annual-cycle resighting data from partially-migratory European shags (Gulosus aristotelis) to estimate key components of genetic, environmental and phenotypic variance in the ecologically critical discrete trait of seasonal migration versus residence. We demonstrate non-negligible additive genetic variance in latent liability for migration, resulting in detectable micro-evolutionary responses following two episodes of strong survival selection. Further, liability-scale additive genetic effects interacted with substantial permanent individual and temporary environmental effects to generate complex non-additive effects on expressed phenotypes, causing substantial intrinsic gene-by-environment interaction variance on the phenotypic scale. Our analyses therefore reveal how temporal dynamics of partial seasonal migration arise from combinations of instantaneous micro-evolution and within-individual phenotypic consistency, and highlight how intrinsic phenotypic plasticity could expose genetic variation underlying discrete traits to complex forms of selection.

Tests for associations between sexual dimorphism and patterns of quantitative genetic variation in the water strider, Aquarius remigis

The evolution of sexual dimorphisms requires divergence between sexes in the evolutionary trajectories of the traits involved. Discerning how genetic architecture could facilitate such divergence has proven challenging because of the difficulty in estimating non-additive and sex-linked genetic variances using traditional quantitative genetic designs. Here we use a three-generation, double-first-cousin pedigree design to estimate additive, sex-linked and dominance (co)variances for 12 traits in the water strider, Aquarius remigis. Comparisons among these traits, which have size ratios ranging from 1 to 5 (larger/smaller), allow us to ask if sexual dimorphisms are associated with characteristic patterns of quantitative genetic variation. We frame our analysis around three main questions, derived from existing theory and empirical evidence: Are sexual dimorphisms associated with (1) lower additive inter-sex genetic correlations, (2) higher proportions of sex-linked variance, or (3) differences between sexes in autosomal additive and dominance genetic variances? For questions (1) and (2), we find weak and non-significant trends in the expected directions, which preclude definitive conclusions. However, in answer to question (3), we find strong evidence for a positive relationship between sexual dimorphism and differences between sexes in proportions of autosomal dominance variance. We also find strong interactions among the three genetic components indicating that their relative influence differs among traits and between sexes. These results highlight the need to include all three components of genetic (co)variance in both theoretical evolutionary models and empirical estimations of the genetic architecture of dimorphic traits.

Phenotype differentiation of Capsicum annuum var. glabriusculum of three regions in Mexico and its relation to climate

Background: Populations of Capsicum annuum var. glabriusculum are found in a wide portion of the Mexican territory, and it is ancestor of many cultivated forms relevant for the Mexican diet.
 Questions: What are the proportions of phenotypic and genetic variation distributed among its sampled regions, populations and within populations. How does the climate correlates to the population’s phenotypic variation.
 Species: Capsicum annuum var. glabriusculum.
 Study sites and years: 24 populations form three regions were sampled: Northwest, states of Sonora and Sinaloa; South: Oaxaca and Southeast Tabasco and Yucatán, in Mexico. The experiment was performed between years 2016 to 2018.
 Methods: Fruits from single plants were collected in wild populations. Plants were grown in a greenhouse. Nested ANOVAS were performed to estimate phenotypic and genetic variance components for different spatial scales. Climate correlation was estimated through univariate and multivariate methods.
 Results: 49.8 % of phenotypic variation was detected within families, 11.1 % among families (within populations), 21.3 % among populations and 17.6 % among regions. The genetic basis of phenotypic variation was 50.1% on average, for this genetic variation 34.2 % was found among regions, 39.4% among populations and 26.3 % within populations. Climate factors generated different patterns of correlations for vegetative, foliar and reproductive traits.
 Conclusions: Northwest plants were shorth, with small leaves and large fruits, Southeast plants were tall, with large leaves and small fruits, South plants developed intermediate phenotypic traits. Climate explained a large proportion of phenotypic differentiation.

The effects of host quantitative genetic architecture on the gut microbiota composition of Chinook salmon (Oncorhynchus tshawytscha).

The microbiota consists of microbes living in or on an organism and has been implicated in host health and function. Environmental and host-related factors were shown to shape host microbiota composition and diversity in many fish species, but the role of host quantitative architecture across populations and among families within a population is not fully characterized. Here, Chinook salmon were used to determine if inter-population differences and additive genetic variation within populations influenced the gut microbiota diversity and composition. Specifically, hybrid stocks of Chinook salmon were created by crossing males from eight populations with eggs from an inbred line created from self-fertilized hermaphrodite salmon. Based on high-throughput sequencing of the 16S rRNA gene, significant gut microbial community diversity and composition differences were found among the hybrid stocks. Furthermore, additive genetic variance components varied among hybrid stocks, indicative of population-specific heritability patterns, suggesting the potential to select for specific gut microbiota composition for aquaculture purposes. Determining the role of host genetics in shaping their gut microbiota has important implications for predicting population responses to environmental changes and will thus impact conservation efforts for declining populations of Chinook salmon.

Rapid evolution during climate change: demographic and genetic constraints on adaptation to severe drought.

Populations often vary in their evolutionary responses to a shared environmental perturbation. A key hurdle in building more predictive models of rapid evolution is understanding this variation-why do some populations and traits evolve while others do not? We combined long-term demographic and environmental data, estimates of quantitative genetic variance components, a resurrection experiment and individual-based evolutionary simulations to gain mechanistic insights into contrasting evolutionary responses to a severe multi-year drought. We examined five traits in two populations of a native California plant, Clarkia xantiana, at three time points over 7 years. Earlier flowering phenology evolved in only one of the two populations, though both populations experienced similar drought severity and demographic declines and were estimated to have considerable additive genetic variance for flowering phenology. Pairing demographic and experimental data with evolutionary simulations suggested that while seed banks in both populations probably constrained evolutionary responses, a stronger seed bank in the non-evolving population resulted in evolutionary stasis. Gene flow through time via germ banks may be an important, underappreciated control on rapid evolution in response to extreme environmental perturbations.

Genomic evaluation for two-way crossbred performance in cattle

BackgroundDairy cattle production systems are mostly based on purebreds, but recently the use of crossbreeding has received increased interest. For genetic evaluations including crossbreds, several methods based on single-step genomic best linear unbiased prediction (ssGBLUP) have been proposed, including metafounder ssGBLUP (MF-ssGBLUP) and breed-specific ssGBLUP (BS-ssGBLUP). Ideally, models that account for breed effects should perform better than simple models, but knowledge on the performance of these methods is lacking for two-way crossbred cattle. In addition, the differences in the estimates of genetic parameters (such as the genetic variance component and heritability) between these methods have rarely been investigated. Therefore, the aims of this study were to (1) compare the estimates of genetic parameters for average daily gain (ADG) and feed conversion ratio (FCR) between these methods; and (2) evaluate the impact of these methods on the predictive ability for crossbred performance.MethodsBivariate models using standard ssGBLUP, MF-ssGBLUP and BS-ssGBLUP for the genetic evaluation of ADG and FCR were investigated. To measure the predictive ability of these three methods, we estimated four estimators, bias, dispersion, population accuracy and ratio of population accuracies, using the linear regression (LR) method.ResultsThe results show that, for both ADG and FCR, the heritabilities were low with the three methods. For FCR, the differences in the estimated genetic parameters were small between the three methods, while for ADG, those estimated with BS-ssGBLUP deviated largely from those estimated with the other two methods. Bias and dispersion were similar across the three methods. Population accuracies for both ADG and FCR were always higher with MF-ssGBLUP than with ssGBLUP, while with BS-ssGBLUP the population accuracy was highest for FCR and lowest for ADG.ConclusionsOur results indicate that in the genetic evaluation for crossbred performance in a two-way crossbred cattle production system, the predictive ability of MF-ssGBLUP and BS-ssGBLUP is greater than that of ssGBLUP, when the estimated variance components are consistent across the three methods. Compared with BS-ssGBLUP, MF-ssGBLUP is more robust in its superiority over ssGBLUP.

Genetic parameters for early piglet weight, litter traits and number of functional teats in organic pigs.

Knowledge remains limited on genetic variation and genetic correlations for traits in sows and piglets that are reared in an organic or outdoor setting. Here, we estimated genetic variance components for individual piglet weight, litter weight, litter size traits, and number of functional teats in a pig population raised under outdoor organic conditions. Data were collected from the largest organic multiplier farm in Denmark. Individual piglet weight was recorded at birth and on day 10. Number of live and dead piglets were recorded at birth, day 4, and day 11. Mean and total litter weight were calculated based on the individual weight of living piglets at birth and on day 10. The estimated heritability was highest for the number of functional teats (0.49), mean weight of a litter at birth (0.33) and on day 10 (0.25). In contrast, heritability was lowest for litter size traits (0.04-0.08) and piglet weight (0.06-0.07). Maternal heritability was much higher for individual piglet weight than direct heritability. The results showed that selection for higher mean weight results in smaller litters. Also, selection for individual birth weight of piglets results in heavier piglets at 10days. In conclusion, this study confirmed that there is genetic variation in individual piglet weight, litter traits, and number of functional teats in organically and outdoor-reared pigs.

The control of genetic parameters on grain yield and its components in hexaploid wheat

Controlling of genetical parameters on grain yield and its components were study in six generation (P1,P2,F1,F2,B1 and B2) for two crosses of hexaploid wheat, Triticum aestivum L. (Iba-99 x Reyna-27) and (Abochareeb-3 x Jawaher-20) to estimate: gene action parameters, components of genetic variance, environmental variance, average degree of dominance, broad sense heritability, narrow sense heritability and expected genetic advance from selection in F2. Two models were applied in analyzing the component of generation means and the total phenotypic variance for studied traits in six generations for each cross were analyzed. The results showed that: The three parameter genetics models were adequate for the inheritance of spike number and grain yield in tow crosses and there were significant additive, dominance and epistatic effects on the other traits. Over dominance for studied traits, but partial for 100 grain weight in the first cross, plant height and spike length in the second cross. Narrow sense heritability and expected genetic advance were high for most traits.

Estimation of the Genetic Components of (Co)variance and Preliminary Genome-Wide Association Study for Reproductive Efficiency in Retinta Beef Cattle.

In this study, we analyzed the variation of reproductive efficiency, estimated as the deviation between the optimal and real parity number of females at each stage of the cow's life, in 12,554 cows belonging to the Retinta Spanish cattle breed, using classical repeatability and random regression models. The results of the analyses using repeatability model and the random regression model suggest that reproductive efficiency is not homogeneous throughout the cow's life. The h2 estimate for this model was 0.30, while for the random regression model it increased across the parities, from 0.24 at the first calving to 0.51 at calving number 9. Additionally, we performed a preliminary genome-wide association study for this trait in a population of 252 Retinta cows genotyped using the Axiom Bovine Genotyping v3 Array. The results showed 5 SNPs significantly associated with reproductive efficiency, located in two genomic regions (BTA4 and BTA28). The functional analysis revealed the presence of 5 candidate genes located within these regions, which were previously involved in different aspects related to fertility in cattle and mice models. This new information could give us a better understanding of the genetic architecture of reproductive traits in this species, as well as allow us to accurately select more fertile cows.

Fast and accurate joint inference of coancestry parameters for populations and/or individuals.

We introduce a fast, new algorithm for inferring from allele count data the FST parameters describing genetic distances among a set of populations and/or unrelated diploid individuals, and a tree with branch lengths corresponding to FST values. The tree can reflect historical processes of splitting and divergence, but seeks to represent the actual genetic variance as accurately as possible with a tree structure. We generalise two major approaches to defining FST, via correlations and mismatch probabilities of sampled allele pairs, which measure shared and non-shared components of genetic variance. A diploid individual can be treated as a population of two gametes, which allows inference of coancestry coefficients for individuals as well as for populations, or a combination of the two. A simulation study illustrates that our fast method-of-moments estimation of FST values, simultaneously for multiple populations/individuals, gains statistical efficiency over pairwise approaches when the population structure is close to tree-like. We apply our approach to genome-wide genotypes from the 26 worldwide human populations of the 1000 Genomes Project. We first analyse at the population level, then a subset of individuals and in a final analysis we pool individuals from the more homogeneous populations. This flexible analysis approach gives advantages over traditional approaches to population structure/coancestry, including visual and quantitative assessments of long-standing questions about the relative magnitudes of within- and between-population genetic differences.