Non-additive Genetic Effects Research Articles

Performance and Phenotypic Stability of Norway Spruce Provenances, Families, and Clones Growing under Diverse Climatic Conditions in Four Nordic Countries

Genetic variation and phenotypic stability in Norway spruce were studied based on provenances, families, and clones planted in trials at 12 sites in four Nordic countries. The families were generated in a factorial cross between 10 parents of Norwegian origin and 10 parents of Eastern European origin, and the clones were propagated from seedlings within 20 of the same families. Traits analyzed were survival, proportion of trees with stem defects, and tree heights. Stability was analyzed by regression analyses with the genetic entries’ annual shoot increment as the dependent variable and the total site mean as an environmental index. Information about growth and phenology traits were available from short-term tests. For tree heights, significant variance components were present both among female and male parents, but not for their interactions, indicating that non-additive genetic effects are small. Genotype × environment interactions were significant at all three genetic levels, but their variance components had considerably lower values than the variance components estimated for the effects of families and clones. For the set of families of Norwegian origin, strong relationships were observed between the timing of annual shot elongation, mortality, and height growth. Large variation was found at all three genetic levels for phenotypic stability measured by regression coefficients. A positive relationship was present between the regression coefficient and the timing of annual shoot growth for families, indicating that later flushing families responded more to a high site index. The regression coefficient can be a useful supplement to the breeding value when selecting for superior and stable genotypes.

Genome-wide scan reveals important additive and non-additive genetic effects associated with resistance to Haemonchus contortus in Florida Native sheep

Florida Native sheep is among the sheep breeds best adapted to humid and hot climatic conditions such as those of Florida, USA, and have shown a superior ability to regulate nematode burdens. This is one of the oldest sheep breeds in North America and is an endangered species. To ensure genetic diversity and long-term survival of the breed, protection of the current genetic stock is critical and conservation efforts are required to promote its breeding and production. The objective of the present study was to investigate the importance of additive and non-additive genetic effects on resistance to natural Haemonchus contortus infections in Florida Native sheep using a whole genome scan. A total of 200 sheep were evaluated in the present study. Phenotypic records included faecal egg count (FEC, eggs/gram), FAMACHA® score, packed cell volume (PCV, %), body condition score and average daily gain (ADG, kg). Sheep were genotyped using the GGP Ovine 50K SNP chip and 45.2 k single nucleotide polymorphism (SNP) markers spanning the entire genome were available for quality control procedures. Mixed models were used to analyse the response variables and included the identity by state matrix to control for population structure. Bonferroni correction was used to control for multiple testing and a second arbitrary threshold (0.1 × 10−3) was used. Fifteen SNPs with additive and non-additive genetic effects and located in Ovis aries chromosome OAR1, 2, 3, 6, 8, 10, 11, 12, 13 and 21 were associated with FEC, FAMACHA® score, PCV and ADG. These SNPs could be potential genetic markers for resistance to natural H. contortus exposure in Florida Native sheep.

Predicting the purebred-crossbred genetic correlation from the genetic variance components in the parental lines

BackgroundThe genetic correlation between purebred and crossbred performance ({r}_{pc}) is an important parameter in pig and poultry breeding, because response to selection in crossbred performance depends on the value of {r}_{pc} when selection is based on purebred (PB) performance. The value of {r}_{pc} can be substantially lower than 1, which is partly due to differences in allele frequencies between parental lines when non-additive genetic effects are present. This relationship between {r}_{pc} and parental allele frequencies suggests that {r}_{pc} can be expressed as a function of genetic parameters for the trait in the parental lines. In this study, we derived expressions for {r}_{pc} based on genetic variances within, and the genetic covariance between parental lines. It is important to note that the variance components used in our expressions are not the components that are typically estimated in empirical data. The expressions were derived for a genetic model with additive and dominance effects (D), and additive and epistatic additive-by-additive effects (EAA). We validated our expressions using simulations of purebred parental lines and their crosses, where the parental lines were either selected or not. Finally, using these simulations, we investigated the value of {r}_{pc} for genetic models with both dominance and epistasis or with other types of epistasis, for which expressions could not be derived.ResultsOur simulations show that when non-additive effects are present, {r}_{pc} decreases with increasing differences in allele frequencies between the parental lines. Genetic models that involve dominance result in lower values of {r}_{pc} than genetic models that involve epistasis only. Using information of parental lines only, our expressions provide exact estimates of {r}_{pc} for models D and EAA, and accurate upper and lower bounds of {r}_{pc} for two other genetic models.ConclusionThis work lays the foundation to enable estimation of {r}_{pc} from information collected in PB parental lines only.

Recent Consanguinity and Outbred Autozygosity Are Associated With Increased Risk of Late-Onset Alzheimer's Disease.

Prior work in late-onset Alzheimer’s disease (LOAD) has resulted in discrepant findings as to whether recent consanguinity and outbred autozygosity are associated with LOAD risk. In the current study, we tested the association between consanguinity and outbred autozygosity with LOAD in the largest such analysis to date, in which 20 LOAD GWAS datasets were retrieved through public databases. Our analyses were restricted to eight distinct ethnic groups: African–Caribbean, Ashkenazi–Jewish European, European–Caribbean, French–Canadian, Finnish European, North-Western European, South-Eastern European, and Yoruba African for a total of 21,492 unrelated subjects (11,196 LOAD and 10,296 controls). Recent consanguinity determination was performed using FSuite v1.0.3, according to subjects’ ancestral background. The level of autozygosity in the outbred population was assessed by calculating inbreeding estimates based on the proportion (FROH) and the number (NROH) of runs of homozygosity (ROHs). We analyzed all eight ethnic groups using a fixed-effect meta-analysis, which showed a significant association of recent consanguinity with LOAD (N = 21,481; OR = 1.262, P = 3.6 × 10–4), independently of APOE∗4 (N = 21,468, OR = 1.237, P = 0.002), and years of education (N = 9,257; OR = 1.274, P = 0.020). Autozygosity in the outbred population was also associated with an increased risk of LOAD, both for FROH (N = 20,237; OR = 1.204, P = 0.030) and NROH metrics (N = 20,237; OR = 1.019, P = 0.006), independently of APOE∗4 [(FROH, N = 20,225; OR = 1.222, P = 0.029) (NROH, N = 20,225; OR = 1.019, P = 0.007)]. By leveraging the Alzheimer’s Disease Sequencing Project (ADSP) whole-exome sequencing (WES) data, we determined that LOAD subjects do not show an enrichment of rare, risk-enhancing minor homozygote variants compared to the control population. A two-stage recessive GWAS using ADSP data from 201 consanguineous subjects in the discovery phase followed by validation in 10,469 subjects led to the identification of RPH3AL p.A303V (rs117190076) as a rare minor homozygote variant increasing the risk of LOAD [discovery: Genotype Relative Risk (GRR) = 46, P = 2.16 × 10–6; validation: GRR = 1.9, P = 8.0 × 10–4]. These results confirm that recent consanguinity and autozygosity in the outbred population increase risk for LOAD. Subsequent work, with increased samples sizes of consanguineous subjects, should accelerate the discovery of non-additive genetic effects in LOAD.

Evidence that genetic compatibility underpins female mate choice in a monandrous amphibian.

Mate choice for genetic benefits remains controversial, largely because few studies have estimated the relative contributions of additive and non-additive sources of genetic variation to offspring fitness. Moreover, there remains a deficit of these estimates for species where female-mate preferences have been quantified in the wild, especially species characterized by monandry or monogamy. Here, we use artificial fertilization techniques combined with a cross-classified breeding design to simultaneously test for "good genes" and "compatible genes" benefits of mate choice in the monandrous red backed toadlet (Pseudophryne coriacea). In addition, we used a genomic approach to estimate effects of parental-genetic relatedness (assessed using 27, 768 single nucleotide polymorphisms) on offspring fitness. Our results revealed no significant additive genetic effects (sire effects), but highly significant non-additive genetic effects (sire × dam interaction effects), on fertilization success, survival during embryonic development, and hatching success. We also found significant associations between parental genetic similarity and offspring survival (whereby survival was higher when parents were more related), and significant positive relationships between fertilization success and embryo survival through to hatching. These results indicate that offspring viability is significantly influenced by the genetic compatibility of parental genotypes, that more related parents are more genetically compatible, and that gametes with greater compatibility at fertilization produce more viable offspring. More broadly, our findings provide new quantitative genetic evidence that genetic incompatibility underpins female mate preferences. Continued quantitative genetic assessment of the relative importance of good genes versus compatible genes is needed to ascertain the general importance of genetic benefits as a driver of female mate choice.

Nasljeđivanje porodne mase kod križanaca Istarske, Awassi, Istočnofrizijske i Travničke pasmine ovaca u Hrvatskoj: studija sa jedne farme

The purpose of the study was to estimate the influence of the additive and non-additive genetic effects on the birth weight, using two different crossbreed models. Data on 1176 birth weights were collected. The animals were crosses, with different ratios of Awassi, East-Friesian, Istrian, and Travnik Pramenka sheep breed. The focal breed in this study was Istrian, which is an autochthonous breed in Croatia. In both models mixed procedure was used with random effect of sire and fixed effects of sex, year and month of birth, litter size, and direct inbreeding. The first model contained the additive breed effects, while the second model additionally included non-additive effects of heterosis and recombination loss. Sex, litter size, year and month of birth significantly affected birth weight in both models. Effect of direct inbreeding was negative and significant only in second model. Significant positive additive breed effect was estimated for Awassi breed in both models. The East-Friesian additive breed effect was positive in both models, but it was significant for the first one only. The positive and significant heterosis effect for the birth weight was estimated for the crosses between East-Friesian and Travnik Pramenka, as well as between Travnik Pramenka and Istrian breed. Same crosses showed significant and positive effect of recombination loss. The negative effect of recombination loss was estimated for the crosses of Awassi breed.

Detection of Non-Additive Gene Action within Elite Maize Populations Evaluated in Contrasting Environments under Rainforest Ecology in Nigeria

Proper understanding of the mode of gene action in open-pollinated varieties (OPVs) maize parents helps breeder in the choice of appropriate breeding method to improve its genetic value. The objectives of the present study were to determine gene action controlling grain yield and other agronomic traits of late maturing elite OPVs and classify the varieties into heterotic groups. Ninety-one hybrids generated from 14 elite OPV parents using diallel mating design were evaluated with their parents plus three commercial checks under marginal rainfall, drought, and optimal environments in Nigeria from 2017 to 2018. The experiment was laid out in a 9 × 12 alpha lattice with three replications in each environment. Results showed that there were significant mean squares for grain yield and most agronomic traits. Significant general combining ability (GCA) and specific combining ability (SCA) mean squares for some of the traits indicated that additive and non-additive genetic gene actions were important in the inheritance of yield and those traits among this set of genotypes. However, non-additive genetic effects were more important than additive for grain yield and other agronomic traits in all research environments. Only TZL Comp-3 C3 DT had significant and positive GCA effects (0.336*) while three hybrids had significant and positive SCA for grain yield across research environments. Because of the preponderance of non-additive gene action over additive gene action, distinct heterotic groups could not be identified but four tester groups were identified by HSGCA (Heterotic grouping based on Specific and General Combining Ability) and three groups by HGCAMT (Heterotic grouping based on the GCA of Multiple Traits). Results of grouping were not related to the endosperm colour but grouping based on HGCAMT was related to the pedigree of the varieties. In conclusion, this study has demonstrated preponderance of non-additive gene action over the additive gene action for all measured traits. The presence of the non-additive gene action present in the studied materials can enhance identification of outstanding varietal hybrids and population testers that can serve as base genetic materials for future maize improvement through reciprocal recurrent selection program in SSA.

Formulation of a decision support tool incorporating both genetic and non-genetic effects to rank young growing cattle on expected market value

While breeding indexes exist globally to identify candidate parents of the next generation, fewer tools exist that provide guidance on the expected monetary value of young animals. The objective of the present study was therefore to develop the framework for a cattle decision-support tool which incorporates both the genetic and non-genetic information of an animal and, in doing so, better predict the potential market value of an animal, whatever the age. Two novel monetary indexes were constructed and their predictive ability of carcass value was compared to that of the Irish national Terminal breeding index, typical of other terminal indexes used globally. A constructed Harvest index was composed of three carcass-related traits [i.e., 1) carcass weight, 2) carcass conformation and 3) carcass fat, each weighted by their respective economic value] and aimed at purchasers of animals close to harvest; the second index, termed the Calf index, also included docility and feed intake (weighted by their respective economic value), thus targeting purchasers of younger calves for growing (and eventually harvesting). Genetic and non-genetic fixed and random effect model solutions from the Irish national genetic evaluations underpinned all indexes. The two novel indexes were formulated using three alternative estimates of an animal's total merit for comparative purposes: 1) an index based solely on the animal's breed solutions, 2) an index which also included within-breed animal differences, and 3) an index which, as well as considering additive and non-additive genetic effects, also included non-genetic effects (referred to as production values [PVs]). As more information (i.e., within breed effects and subsequently non-genetic effects) was included in the total merit estimate, the correlations strengthened between the two proposed indexes and the animal's calculated carcass market value; the correlation coefficients almost doubled in strength when total merit was based on PV-based estimates as compared to the breed solutions alone. Including phenotypic live-weight data, collected during the animal's life, strengthened the predictive ability of the indexes further. Based on the results presented, the proposed indexes may fill the void in decision support when purchasing or selling cattle. In addition, given the dynamic nature of indexes, they have the potential to be updated in real-time as information becomes available.

Estimation of Gene Action and Heterosis in F1 And F2 Diallel Crosses among Seven Genotypes of Field Bean

Heterosis, gene action, combining ability (GCA and SCA) effects and variances were studied in 21 F1 and F2 crosses derived from 7x7 half diallel scheme of field bean. To detect prospective and efficient material for immediate use in breeding programs to enhance field bean productivity. F1 and F2 with parents were arranged in RCBD with 3 replicates to evaluate seed yield and its components traits in 2018/2019 season. Mean squares (MS) for genotype and its partitioning (parent, crosses and parent vs crosses) were significant for all studied traits in both generations. P1xP5 and P3xP6 exhibited significant heterotic effect for seed yield plant-1 in F1 and F2 generations. Significant GCA and SCA MS were found for all studied traits, where proportion of additive was great for most traits in both generations, reveling predominance of additive gene effects. P2 (Sakha 2), P5 (M-13), P7 (M-1017) in F1 and P6 (M-148) in F2 were good combiners for seed yield and at least one of its components. More than 25 % of studied crosses showed positive and significant SCA effects for seed yield in F1 and F2 generations. The cross P1xP5 showed desirable SCA effects in both generation for seed yield and resistance to chocolate spot disease%. Significant and larger values of dominance component (H1) than additive were obtained for all studied traits resulting in more values of (H1/D)0.5 which were exceeded unity in both generations. Low narrow-sense heritability was exhibited in both generations for all traits, indicating that presence of non-additive genetic effects.

283 Heterosis and its potential influence on pulmonary arterial pressure in beef cattle

Abstract High altitude disease (HAD) is a hypoxia-influenced pathologic condition experienced by cattle raised at high elevations (> 1,524 m). Pulmonary arterial pressure (PAP) is a common diagnostic tool used as an indicator of susceptibility to develop HAD. Given PAP is moderately heritable, possibilities to genetically reduce the incidence of HAD are feasible. However, an alternative strategy could be given by heterosis, since non-additive genetic effects have been related to survivability and environmental fitness. Therefore, objectives of this study were to determine heterosis and breed percentage effects on PAP measurements. A total of 1,083 cattle with varying percentages of Simmental, Angus, Hereford and Red Angus breeds were used for the study. Such animals’ available information included PAP records, PAP test date, PAP technician, sex, herd of origin and breed percentages of parents. A general linear model was utilized to estimate the effect of heterosis on PAP. Contemporary group (defined as a combination between herd, PAP date, PAP technician and sex) was included as a categorical fixed effect; whereas the age at PAP measurement and the degree of outcross were included as linear covariates. Similarly, breed effects were estimated by including breed percentages of Simmental, Angus, Hereford, Red Angus and “Other” breeds as linear covariates in the model. The general average for PAP measurements in the entire dataset was 41.29 ± 0.22, with range of 26 and 108 mmHg. The estimated regression coefficient for PAP on heterosis was -1.834 ± 1.676 mmHg/percent of outcross (P = 0.276), whereas, the range of breed effects on PAP was 15.08 mmHg. These results suggested that heterosis had no significant effects on PAP measurements. However, further research including other multibreed populations is required in order to better understand if increased levels of heterozygosity could potentially be related to lower PAP scores.

296 Awardee Talk: The Genetics of Sow Longevity

Abstract Sow longevity is a key productivity indicator trait that has real economic and welfare importance for commercial swine farms globally. The average parity at culling is 3.8 parities. Reports indicate that it takes 3 to 4 parities before a sow “pays for herself.” Research groups around the world have reported heritabilities estimates for sow longevity traits ranging from 0.05 to 0.35. Estimate differences result from the animal population under evaluation, the trait being evaluated, and the methodology employed to obtain the genetic parameter estimate. Because sow longevity is measured at the end of the sow’s productive life, indicator traits like age at first farrowing, leg conformation, and other traits are utilized in gilt selection programs. The genetic correlations between sow longevity and lifetime production traits range have been reported to range from 0.64 to 0.94, suggesting that selection will improve sow longevity. Genetic markers have been identified that affect both sow longevity and other indicator traits. Selection to improved sow longevity still requires phenotypes. Future technologies, e.g. CT scans, digital images, and automated disease detection, will provide additional phenotypes. Continued hardware, software, and molecular developments will improve selection accuracy for sow longevity traits and related traits. Research is needed to evaluate the impact that non-additive genetic effects have on sow longevity and other fitness-related traits. Sow longevity seems to be an ideal trait to employ genomic selection in order to make more rapid trait improvements because it is measured late in life, it is sex-limited, and the trait is not directly measured on nucleus animals. In conclusion, sow longevity and related traits have sufficient heritability and variation to improve through traditional and genomic enhanced selection methods. Selection programs employing effective genomic selection programs will be more effective in improving sow longevity trait and related traits and ultimately economical return.

Combining Ability, Heterosis and Gene Action for Grain Yield and Its Related Traits of Some WA-CMS with Tester Lines of Rice (Oryza sativa L.)

An understanding the nature and relative extent of gene actions and combining ability is useful for a breeder to develop superior rice hybrids. In this association, an attempt was made to identify good general and specific combiners for selecting better parents and better cross combinations for developing high yielding and short duration rice hybrids. Four cytoplasmic male sterile lines viz., IR69625A, IR70368A, IR58025A and IR79575A were crossed with ten elite testers, 40 hybrids along with their fourteen parents were evaluated for grain yield and its related traits at the experimental farm of Rice Research and Training Center, Sakha, Kafr El-Sheikh, Egypt, during the rice-growing seasons of 2018 and 2019. The differences among genotypes, parents and crosses were highly significant for all studied traits. The specific combining ability (SCA) played the major role in determining inheritance traits, revealing that the largest part of the total genetic variability associated with most traits was a result of non-additive gene action. The parental line, IR58025A was demonstrated as a great general combiner for grain yield per plant and most of yield components and therefore could be utilized in future breeding programs to improve grain yield. HHZ12-SAL8-Y1-SAL1, HHZ5-Y7-Y2-SUB1 and HUA564 were seen as a good general combiner among testers for grain yield per plant and some studied traits. Four crosses, namely IR58025A / HHZ8-SAL9-DT2-Y2, IR70368A / WEED TOLERANT RICE1, IR70368A / HHZ12-SAL8-Y1-SAL1 and IR70368A / HHZ5-Y7-Y2-SUB1 exhibited significantly good specific combining ability effects for grain yield per plant. Hence, it can be seen that non-additive genetic effects are controlling the inheritance of the studied traits and indicated that selection for the traits inherited with this manner should be performed in the further generations.

Combining Ability and Genetic Components of Yield Characteristics, Dry Matter Content, and Total Carotenoids in Provitamin A Cassava F1 Cross-Progeny

Cassava is an important root crop in sub-Saharan Africa, largely cultivated for its starchy edible roots. Biofortified cassava varieties with enhanced provitamin A carotenoid content (PVAC) developed through conventional breeding provide a solution for vitamin A deficiency among vulnerable communities. The aim of this study was to use diallel analysis of six provitamin A cassava genotypes to determine the combining ability, genetic components, heritability, and heterosis of the most important yield characteristics and total carotenoids. Genetic variability for measured characteristics were evident. Fresh root yield was mainly determined by non-additive genetic effects, while dry matter content and total carotenoids were determined by additive effects. Total carotenoids were negatively correlated with fresh root yield, indicating that selection for higher provitamin A content could reduce yield. Mid and higher parent heterosis was seen in some of the crosses for fresh root yield, dry matter content, and total carotenoids. Narrow sense heritability was moderate for fresh root yield and dry matter content, and was high for total carotenoids. This study indicated that yield and dry matter content can be improved in provitamin A cassava but that increased provitamin A content may carry a yield penalty.

Habilidad combinatoria general y específica relacionada con los componentes del rendimiento en cinco líneas endogámicas de maíz (Zea mays L.)

Con el fin de obtener información teórica de los efectos genéticos que gobiernan los componentes del rendimiento y poder tener mayor información que permitiera elegir los mejores progenitores para la formación de híbridos con interés comercial, se estimaron los efectos y la capacidad combinatoria general (H.C.G) y específica (H.C.E) en cinco líneas endocríadas de maíz tropical de endospermo amarillo pertenecientes al programa de mejoramiento genético de maíz tropical de la empresa Sem Latam S.A. Se encontró que los efectos de habilidad combinatoria específica para los caracteres relacionados con el componente rendimiento presentaron valores positivos, no obstante, estos no fueron significativamente distintos de cero, lo que se traduce en la no existencia de un patrón heterótico en las líneas evaluadas. De igual modo, las líneas evaluadas presentaron una escasa capitalización de los efectos genéticos no aditivos o dominantes en el proceso de selección genealógica, permitiendo interpretar la baja manifestación de la heterosis como expresión del vigor hibrido de los cruzamientos F1 comparados con los genotipos parentales.

Genomic Prediction of Additive and Dominant Effects on Wool and Blood Traits in Alpine Merino Sheep.

Dominant genetic effects may provide a critical contribution to the total genetic variation of quantitative and complex traits. However, investigations of genome-wide markers to study the genomic prediction (GP) and genetic mechanisms of complex traits generally ignore dominant genetic effects. The increasing availability of genomic datasets and the potential benefits of the inclusion of non-additive genetic effects in GP have recently renewed attention to incorporation of these effects in genomic prediction models. In the present study, data from 498 genotyped Alpine Merino sheep were adopted to estimate the additive and dominant genetic effects of 9 wool and blood traits via two linear models: (1) an additive effect model (MAG) and (2) a model that included both additive and dominant genetic effects (MADG). Moreover, a method of 5-fold cross validation was used to evaluate the capability of GP in the two different models. The results of variance component estimates for each trait suggested that for fleece extension rate (73%), red blood cell count (28%), and hematocrit (25%), a large component of phenotypic variation was explained by dominant genetic effects. The results of cross validation demonstrated that the MADG model, comprising additive and dominant genetic effects, did not display an apparent advantage over the MAG model that included only additive genetic effects, i.e., the model that included dominant genetic effects did not improve the capability for prediction of the genomic model. Consequently, inclusion of dominant effects in the GP model may not be beneficial for wool and blood traits in the population of Alpine Merino sheep.

Combining ability and genetic parameters of some white maize (Zea mays L.) inbred lines using diallel analysis

Nine inbred lines (S5) of white maize derived from Giza -2 and IW- 469 were crossed using of half diallel cross mating design, during spring season of 2019 at the Farm of Faculty of Agriculture, Al-Azhar University at Assiut Branch, to produce thirty six F1 crosses. The parents, crosses and tow checks i.e. SC-163 and SC-10 were evaluated during spring season of 2020 in R.C.B.D with three replications to determine combining ability, heterotic and gene action effects. Significant differences were found among parental and their crosses as well as for general combining ability (GCA) and specific combing ability (SCA) for all studied traits. The previous results indicating the importance of both additive and non-additive genetic effects for studied traits. The ratio of Σg2i/ΣS2ij was less one for all studied traits, indicate that the non-additive gene action in the inheritance of all the studied traits. Parents P1 and P4 showed best GCA effects for grain yield/plant, while the parents P2 and P6 appeared to be the best general combiners for most of the studied traits. The crosses P1 x P8, P2 × P6 and P2 × P5 appeared to be the best mean performance, SCA and superiority percentage for most studied traits. The values of the broad sense heritability were high (>80%) for all studied traits. While, the narrow sense heritability was low for grain yield/plant (13.00%). Results indicated that some inbred lines could be used in breeding program to develop single crosses which have higher grain yield.

Combining ability analysis of yield and resistance to late blight disease caused by Phytophthora infestans in Uganda

Breeding for resistance to late blight disease caused by Phytophthora infestans (Mont.) de Bary in potato is the most economically, effective and ecologically sustainable method to control the disease and boost productivity. The study estimated combining ability effects of yield, yield related traits, late blight resistance and gene action controlling resistance to Phytophthora infestans. Eighteen F1 families generated from two sets of 12 parents, using a North Carolina Design II, were evaluated for relative area under disease progress curve (rAUDPC), yield and yield related traits in two late blight hotspot locations of Kachwekano and Kalengyere research stations. Trials were established using an alpha lattice design (6 x 5) with two replications. Both additive and non-additive genetic effects were important in controlling yield and late blight resistance. However, additive gene action was dominant. The general combining ability (GCA) to specific combining ability ratio (SCA); (GCA/SCA) for total tuber weight and late blight resistance was 0.53 and 0.62 respectively. Broad-sense heritability estimates were 0.78 for total tuber weight and 0.68 for relative area under disease progress curve (rAUDPC). This study showed some evidence of maternal effects for rAUDPC (1.45) and average tuber weight (ATW) (1.56), although these were not significant at P<0.05. Parents Kinigi, 392657.8, 396034.103, 396038.107, 395011.2, NKRK19.17, NKRN59.58 and 395017.14 had good GCA effects for both late blight resistance and yield related traits. Crosses of 392657.8 x 395017.14 and 396038.107 x NKRN59.58 had the highest SCA effects for yield related traits, while families Kinigi x NKRK19.17and 392657.8 x NKRN59.41 had the lowest SCA effects for rAUDPC. The relatively high heritability estimates and predominant additive genetic effects imply that genetic advances in resistance to Phytophthora infestans and tuber yield among these genotypes can be realized by selecting superior clones.

The Heritability of Type D Personality by an Extended Twin-Pedigree Analysis in the Netherlands Twin Register

Type D (Distressed) personality combines negative affectivity (NA) and social inhibition (SI) and is associated with an increased risk of cardiovascular disease. We aimed to (1) validate a new proxy based on the Achenbach System of Empirically Based Assessment (ASEBA) for Type D personality and its NA and SI subcomponents and (2) estimate the heritability of the Type D proxy in an extended twin-pedigree design in the Netherlands Twin Register (NTR). Proxies for the dichotomous Type D classification, and continuous NA, SI, and NAxSI (the continuous measure of Type D) scales were created based on 12 ASEBA items for 30,433 NTR participants (16,449 twins and 13,984 relatives from 11,106 pedigrees) and sources of variation were analyzed in the ‘Mendel’ software package. We estimated additive and non-additive genetic variance components, shared household and unique environmental variance components and ran bivariate models to estimate the genetic and non-genetic covariance between NA and SI. The Type D proxy showed good reliability and construct validity. The best fitting genetic model included additive and non-additive genetic effects with broad-sense heritabilities for NA, SI and NAxSI estimated at 49%, 50% and 49%, respectively. Household effects showed small contributions (4–9%) to the total phenotypic variation. The genetic correlation between NA and SI was .66 (reflecting both additive and non-additive genetic components). Thus, Type D personality and its NA and SI subcomponents are heritable, with a shared genetic basis for the two subcomponents.

An assessment of genomic connectedness measures in Nellore cattle.

An important criterion to consider in genetic evaluations is the extent of genetic connectedness across management units (MU), especially if they differ in their genetic mean. Reliable comparisons of genetic values across MU depend on the degree of connectedness: the higher the connectedness, the more reliable the comparison. Traditionally, genetic connectedness was calculated through pedigree-based methods; however, in the era of genomic selection, this can be better estimated utilizing new approaches based on genomics. Most procedures consider only additive genetic effects, which may not accurately reflect the underlying gene action of the evaluated trait, and little is known about the impact of non-additive gene action on connectedness measures. The objective of this study was to investigate the extent of genomic connectedness measures, for the first time, in Brazilian field data by applying additive and non-additive relationship matrices using a fatty acid profile data set from seven farms located in the three regions of Brazil, which are part of the three breeding programs. Myristic acid (C14:0) was used due to its importance for human health and reported presence of non-additive gene action. The pedigree included 427,740 animals and 925 of them were genotyped using the Bovine high-density genotyping chip. Six relationship matrices were constructed, parametrically and non-parametrically capturing additive and non-additive genetic effects from both pedigree and genomic data. We assessed genome-based connectedness across MU using the prediction error variance of difference (PEVD) and the coefficient of determination (CD). PEVD values ranged from 0.540 to 1.707, and CD from 0.146 to 0.456. Genomic information consistently enhanced the measures of connectedness compared to the numerator relationship matrix by at least 63%. Combining additive and non-additive genomic kernel relationship matrices or a non-parametric relationship matrix increased the capture of connectedness. Overall, the Gaussian kernel yielded the largest measure of connectedness. Our findings showed that connectedness metrics can be extended to incorporate genomic information and non-additive genetic variation using field data. We propose that different genomic relationship matrices can be designed to capture additive and non-additive genetic effects, increase the measures of connectedness, and to more accurately estimate the true state of connectedness in herds.

Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops

Key messagePolypoid crop breeders can balance resources between density and sequencing depth, dosage information and fewer highly informative SNPs recommended, non-additive models and QTL advantages on prediction dependent on trait architecture.The autopolyploid nature of potato and sweetpotato ensures a wide range of meiotic configurations and linkage phases leading to complex gene-action and pose problems in genotype data quality and genomic selection analyses. We used a 315-progeny biparental F1 population of hexaploid sweetpotato and a diversity panel of 380 tetraploid potato, genotyped using different platforms to answer the following questions: (i) do polyploid crop breeders need to invest more for additional sequencing depth? (ii) how many markers are required to make selection decisions? (iii) does considering non-additive genetic effects improve predictive ability (PA)? (iv) does considering dosage or quantitative trait loci (QTL) offer significant improvement to PA? Our results show that only a small number of highly informative single nucleotide polymorphisms (SNPs; ≤ 1000) are adequate for prediction in the type of populations we analyzed. We also show that considering dosage information and models considering only additive effects had the best PA for most traits, while the comparative advantage of considering non-additive genetic effects and including known QTL in the predictive model depended on trait architecture. We conclude that genomic selection can help accelerate the rate of genetic gains in potato and sweetpotato. However, application of genomic selection should be considered as part of optimizing the entire breeding program. Additionally, since the predictions in the current study are based on single populations, further studies on the effects of haplotype structure and inheritance on PA should be studied in actual multi-generation breeding populations.