Non-additive Genetic Variance Research Articles

Genetic dissection of complex traits in citrus: additive and non-additive genetic variances, inbreeding depression, and single-chromosome heritability

Genetic evaluation in breeding programs generally considers only additive genetic effects; however, non-additive genetic effects may also contribute to phenotypic and genotypic values. Furthermore, the distributions of causal variants in target traits are associated with the efficiency of accumulation of favorable alleles and are therefore important for plant breeding. Despite this, non-additive effects remain to be fully investigated in citrus. Moreover, although quantitative trait loci in citrus have been previously identified, they cannot adequately explain the genetic variance. Therefore, we attempted to estimate non-additive effects, such as dominance and additive-by-additive effects, together with directional dominance as an indicator of inbreeding depression and with chromosome heritability, which reflects the distributions of causal variants for fruit-quality traits in citrus. Phenotypic records of the fruit weight, sugar content, and acid content of 455 cultivars and their progeny were analyzed. Genomic relationship matrices for non-additive effects and single-chromosome genetic effects were constructed using 2319 genome-wide single nucleotide polymorphism loci, which were also used to evaluate directional dominance. These phenotype and genotype records were analyzed using genomic best linear unbiased prediction models. Through this analysis, we showed (1) overestimation of narrow-sense heritability due to substantial contributions of non-additive effects in the tested traits, (2) evidence of inbreeding depression in fruit weight, and (3) highly polygenic architectures in the tested traits. These findings could contribute to precise evaluation of genotypic values and the development of efficient breeding strategies.

Increasing genomic prediction accuracy for unphenotyped full-sib families by modeling additive and dominance effects with large datasets in white spruce.

Genomic selection is becoming a standard technique in plant breeding and is now being introduced into forest tree breeding. Despite promising results to predict the genetic merit of superior material based on their additive breeding values, many studies and operational programs still neglect non-additive effects and their potential for enhancing genetic gains. Using two large comprehensive datasets totaling 4,066 trees from 146 full-sib families of white spruce (Picea glauca (Moench) Voss), we evaluated the effect of the inclusion of dominance on the precision of genetic parameter estimates and on the accuracy of conventional pedigree-based (ABLUP-AD) and genomic-based (GBLUP-AD) models. While wood quality traits were mostly additively inherited, considerable non-additive effects and lower heritabilities were detected for growth traits. For growth, GBLUP-AD better partitioned the additive and dominance effects into roughly equal variances, while ABLUP-AD strongly overestimated dominance. The predictive abilities of breeding and total genetic value estimates were similar between ABLUP-AD and GBLUP-AD when predicting individuals from the same families as those included in the training dataset. However, GBLUP-AD outperformed ABLUP-AD when predicting for new unphenotyped families that were not represented in the training dataset, with, on average, 22% and 53% higher predictive ability of breeding and genetic values, respectively. Resampling simulations showed that GBLUP-AD required smaller sample sizes than ABLUP-AD to produce precise estimates of genetic variances and accurate predictions of genetic values. Still, regardless of the method used, large training datasets were needed to estimate additive and non-additive genetic variances precisely. This study highlights the different quantitative genetic architectures between growth and wood traits. Furthermore, the usefulness of genomic additive-dominance models for predicting new families should allow practicing mating allocation to maximize the total genetic values for the propagation of elite material.

Diallel crosses in Picea abies IV. Genetic variation and inheritance patterns in short-term trials

Abstract The complete diallel cross is the only mating design that provides estimates of variance components of general combining (GCA), specific combining ability (SCA), maternal and reciprocal effects, in addition to heritabilities and genetic correlations. To obtain such estimates, complete diallels were made among 10 trees in each of three natural Norway spruce populations from altitude 300 and 500 m in southern Norway. Seedlings from families from the diallels and open pollinations were tested in short-term tests on agricultural soil at one site at altitude 85 m until age 10 years from seed. Tree height at ages 7 and 10 years and diameter at age 10 had strongly significant GCA variance components within each population. The components for SCA and maternal effects were small and not significant, indicating low levels of non-additive genetic variation. For the days of initiation and cessation of the shoot elongation period the GCA components were dominating and had the highest heritability estimates in two of the diallels. Estimates of genetic correlations between traits measured in earlier nursery trials and height and diameter in the short-term trials had low and not consistent values in the three diallels. The duration of the shoot growth period and rate of growth showed positive relationships with height and diameter. Strong relationships were present between half-sib family means from the diallels and open-pollinated families for height, diameter and phenology traits. Progeny trials testing open-pollinated half-sib families from natural populations can be used for selection of candidates for the initial breeding populations.

Genetic Variability Parameters and Character Associations among Yield Attributing Traits in Advanced Backcross Lines of Groundnut

Groundnut is currently a major industrial oilseed crop with good commercial significance. It is highly variable in phenotypic characters and thus it is important to investigate the variations and associations of these morphological features. 20 advanced Groundnut lines were planted in Randomized Complete Block Design along with parental lines and two checks and they were evaluated for 13 traits. Significant variations were revealed in analysis of variance. High GCV (20.21) coupled with high heritability (91.2) and GAM (39.77) were observed is plant height suggested that environment had lesser influence on the expression of this trait, as this character is governed by an additive gene action, making them effective for selection. High heritability combined with low GCV and GAM were recorded in oil content, days to 50 percent flowering, shelling outturn and number of secondary branches per plant revealed that non-additive genetic variation played a significant role in the expression of this trait thus, selection for this character would be inefficient. Pod yield per plant showed a positive and significant association with seed yield per plant, plant height, number of secondary branches per plant, pod length, pod width and number of pods per plant. Path coefficient analysis have revealed that positive direct effects towards pod yield per plant were reported for seed yield per plant, plant height, number of secondary branches per plant, pod length, pod width, and number of pods per plant. Thus the characters seed yield per plant, number of pods per plant, pod length and number of secondary branches per plant which are the most essential characters contributed significantly towards higher pod yield per plant.

An exploration into the conversion of dominance to additive genetic variance in contrasting environments.

The evolutionary response of a trait to environmental change depends upon the level of additive genetic variance. It has been long argued that sustained selection will tend to deplete additive genetic variance as favored alleles approach fixation. Non-additive genetic variance, due to interactions among alleles within and between loci, does not immediately contribute to an evolutionary response. However, shifts in the allele frequencies within and between interacting loci may convert non-additive variance into additive variance. Here we consider the possibility that an environmental shift may alter allelic interactions in ways that convert dominance into additive genetic variance. We grew a pedigreed population of Brassica rapa in greenhouse and field conditions. The field conditions mimicked agricultural conditions from which the base population was drawn, while the greenhouse featured benign conditions. We used Bayesian models to estimate the additive, dominance, and maternal components of quantitative genetic variance. We also estimated genetic correlations across environments using parental breeding values. Although the additive genetic variance was elevated in the greenhouse condition, no consistent pattens emerged that would indicate a conversion of dominance variance. The unusually low genetic variance and broad confidence intervals for the variance estimates obtained through this analysis preclude definitive interpretations. Further studies are needed to determine whether between-environment changes in additive genetic variance can be traced to conversion of dominance variance.

Genotype × environment interaction obscures genetic sources of variation in seed size in Dithyrea californica but provides the opportunity for selection on phenotypic plasticity.

In many species, seed size influences individual fitness, but its heritability is low, impeding its evolution. In heterogeneous environments, even if heritability of seed size is low, genetic variation in phenotypic plasticity for seed size may provide the opportunity for selection, but this possibility has rarely been investigated in wild species. The evolutionary trajectory of seed size depends on whether additive, maternal, or non-additive genetic variance dominates; moreover, the expression of any of these sources of variance may be environment-dependent, reflecting genetic variation in plasticity. In this study, we examined these sources of variation in seed size and their response to drought in Dithyrea californica. We used a diallel design to estimate variance components for seed size in three greenhouse-raised populations sampled from California and northern Mexico. We replicated diallels in two watering treatments to examine genetic parameters and genotype × environment interactions affecting seed size. We estimated general (GCA) and specific (SCA) combining ability, reciprocal effects (RGCA and RSCA), and their interactions with water availability, and we sought evidence that sexual conflict influences seed size. Norms of reaction revealed genetic variation in plasticity for seed size in each population. Seed size in D. californica is determined by the combination of watering treatment, GCA and RGCA; parental identity and water availability do not consistently affect seed size, and we detected no evidence for sexual conflict. Multiple sources of genetic variation in phenotypic plasticity for seed size have the potential to influence its evolutionary trajectory in heterogenous environments.

Combining ability studies through Line × Tester design in sweet sorghum (Sorghum bicolor L.) for bioethanol production

In developing of sweet sorghum hybrids, non-additive genetic effects are important in phenotypic expression of the traits of interest. The present experiment was undertaken to assess the combining ability in sweet sorghum genotypes using 16 hybrids developed by crossing four CMS lines with four elite testers in a Line × Tester mating design. The hybrids were evaluated at three locations in  Andhra Pradesh in a Randomized Block Design with two replications during Rabi, 2018. Among the 13 quantitative characters studied the non-additive genetic variance was higher than the additive variance for all the traits except for days to 50 % flowering, days to maturity, plant height and ethanol yield. Among parents, ICSA 14029, ICSA 14030 (females) ICSV 15006 and GGUB-28 (males) were found to be  good general combiners for ethanol yield and its related traits with consistent performance across locations. ICSA 14029 × ICSV-15006 and ICSA 14033 × SEVS-08 were identified as superior crosses for the specific combining ability for high ethanol yield. Keywords: Sweet sorghum, Brix %, Bioethanol, gca, sca components

Combining abilities and genetic parameters for grain yield and some agronomic traits in maize (Zea mays L.)

BackgroundThe improvement of maize hybrids relies on significant genetic variability among the inbred lines used and the degree to which it is transferred to progeny. Understanding the genetic parameters and heritability of traits in every population is an essential precondition for selection program. This study was designed to estimate the magnitude of genetic parameters and heritability of traits in line × tester mating design. Fifteen yellow maize inbred lines derived from different sources were crossed with two lines as tester i.e., Gm-1001 and Gm-1002 in 2019 summer season. During 2020 season, the resulted 30 crosses along with check hybrid SC-168 were evaluated in a yield trial at two locations: Gemmeiza and Sids Agric. Res. Station.ResultsThe mean squares among two locations were highly significant for all studied traits except KR−1. The L1 and L3 had the best general combiners for GY ard fed−1. In addition, the T1 as a tester was a GCA effects good combiner for earliness, shorter plants and lower ear placement traits. While T2 was good combiner for grain yield and some of attributes. Crosses L5 × T1 and L7 × T2 had positive and significant SCA effects for grain yield. The GCA variances were higher than SCA variances for all studied traits except for ED trait, indicating that additive genetic variance played the major role than non-additive genetic variance in the inheritance of these traits. Generally, phenotypic coefficient of variability was higher than genotypic coefficient of variability for all studied traits, suggesting that there was an influence by environments in the expression of these traits. Recorded heritability percentage in broad sense ranged from low for (ear position%, no. of ears/100 plants, ear diameter and grain yield) traits, medium for (days to 50% silking, plant height, ear height and no. of kernels/row) traits to moderate high for ear length trait.ConclusionOur investigation concluded that most of the studied lines exhibited highly general combiners and the superior crosses were as a result of a good × good combiner for most of yield components traits.

Studies on genetic evaluation of first lactation traits in crossbred cattle

The present investigation was carried on crossbred cattle maintained at Instructional Dairy Farm, Nagla of G.B. Pant University of Agriculture and Technology, Pantnagar. The study was conducted on 700 crossbred cattle, the progeny of 68 sires which were born over a period of 28 years from 1990-2017. The overall least squares means along with standard errors of AFC, FLMY, FLP, FDP, FCI, FSP and FL305DMY were observed as 1186.45±8.66 days, 2846.16±46.92 kg, 326.51±3.09 days, 124.29±3.67 days, 450.80±4.5 days, 261.34±1.77 days and 2631.07±35.68 kg, respectively. The effect due to sire was found significant on AFC, FLMY, FCI and FL305DMY. The effect of the genetic group was non-significant on all the traits under study. The significant effect of season of calving was found on AFC, FLMY, FDP, FSP and FL305DMYwhile non-significant effect of season of calving on FLP and FCI was observed. The effect of the period of calving was observed significant on FLMY and FL305DMY, however, a non-significant effect of the period of calving was observed on AFC, FLP, FDP, FCI and. FSP. The heritability estimates for AFC, FLMY, FLP, FDP, FCI, FSP and FL305DMY were observed as 0.429±0.127, 0.267±0.110, 0.078± 0.087, 0.048±0.083, 0.096±0.089, 0.114±0.09 and 0.273±0.110, respectively. The results of the present study showed that most of the variations in the traits were due to non-additive genetic and environmental variances. Therefore, improvement in these traits can be made through better managemental practices at the farm. Keywords: First lactation milk yield, Least square means, Heritability, Crossbred cattle.

Heterosis response and combining ability (variance and effect) analysis for seed yield and its components in Indian mustard (Brassica juncea L.) under timely sown condition

Diallel analysis excluding reciprocal crosses comprising of seven parents and their 21 specific hybrids was carried out to identifyhigh heterotic combinations and their relationship in terms of general and specific combining ability (GCA and SCA) in Indian mustard. Highest economic heterosis for yield was observed in crosses namely; NRCHB-101 x Pusa M-21, Urvashi x Pusa Bold, NRCDR-2 x Urvashi, Maya x Pusa Bold, and Maya x NRCDR-2. The economic parents Urvashi, Pusa Bold, NRCHB-101, Pusa M-21, NRCDR-2, Maya and RGN-73 were the best parents for majority of the characters with Urvashi and Pusa Bold being the best economic parents for seed yield/plant and its contributing characters as their GCA and per se performances were high. Analysis of variance for GCA and SCA signified differences for majority of the characters. Ratio of GCA and SCA variances was below unity for majority of the characters except Days to 50% flowering and Days to maturity, which suggested superior role of non-additive genetic variance in the inheritance of these traits. The crosses namely Maya x NRCDR-2, Maya x Pusa Bold, NRCDR-2 x Urvashi, NRCHB-101 x Pusa M-21 and Urvashi x Pusa Bold showed high per se performance as well as SCA effects for seed yield and its contributing characters. The above best parents and best crosses could be used in hybridization and heterosis breeding respectively.

Little heterosis found in diploid hybrid potato: The genetic underpinnings of a new hybrid crop.

Hybrid potato breeding has become a novel alternative to conventional potato breeding allowing breeders to overcome intractable barriers (e.g. tetrasomic inheritance, masked deleterious alleles, obligate clonal propagation) with the benefit of seed-based propagule, flexible population design, and the potential of hybrid vigor. Until now, however, no formal inquiry has adequately examined the relevant genetic components for complex traits in hybrid potato populations. In this present study, we use a 2-step multivariate modeling approach to estimate the variance components to assess the magnitude of the general and specific combining abilities in diploid hybrid potato. Specific combining ability effects were identified for all yield components studied here warranting evidence of nonadditive genetic effects in hybrid potato yield. However, the estimated general combining ability effects were on average 2 times larger than their respective specific combining ability quantile across all yield phenotypes. Tuber number general combining abilities and specific combining abilities were found to be highly correlated with total yield’s genetic components. Tuber volume was shown to have the largest proportion of additive and nonadditive genetic variation suggesting under-selection of this phenotype in this population. The prominence of additive effects found for all traits presents evidence that the mid-parent value alone is useful for hybrid potato evaluation. Heterotic vigor stands to be useful in bolstering simpler traits but this will be dependent on target phenotypes and market requirements. This study represents the first diallel analysis of its kind in diploid potato using material derived from a commercial hybrid breeding program.

Bayesian analysis of additive and non-additive genetic variances of body weight gain traits in crossbred population of Japanese quail

Aim of study: To select the appropriate model for body weight gain (BWG) traits in different ages and estimation of additive and non-additive genetic variances based on the best model, of a crossbred population of quail. Area of study: Zabol, Iran Materials and methods: Four strains of Japanese quail, including Italian Speckled, Tuxedo, Pharaoh, and A&M Texas, were used to create a crossbred population in a partial diallel design over 4 generations. BWG traits were calculated as the average growth performance of the bird in a 5-day period from hatch to 45 days of age. Analyses were performed using the Bayesian method by fitting 24 models including the additive and non-additive genetic effects. The deviance information criteria (DIC) was used for the selection of an appropriate model for each trait. Main results: Based on DIC, the maternal genetic, maternal permanent environmental, dominance and epistasis effects had a significant contribution to the best model for BWG traits before 25 days of age, whereas these effects were not significant on BWG traits at the end of ages. With the best model, direct heritability of BWG traits in different ages ranged from 0.037 (BWG15-20) to 0.199 (BWG5-10). The maternal genetic and maternal permanent environmental as a proportion of phenotypic variance was less than 10% and 5%, respectively. The ratio of dominance and epistasis variance was in the range of 0.016-0.019, and 0.016-0.019, respectively. Research highlights: Non- additive genetic effects are important for the early BWG traits and must be included in the evaluation models to have accurate estimates.

Genetic Control of Reproductive Traits under Different Temperature Regimes in Inbred Line Populations Derived from Crosses between S. pimpinellifolium and S. lycopersicum Accessions.

In the present work, we study the genetic control of reproductive traits under different heat stress conditions in two populations of inbred lines derived from crosses between two S. pimpinellifolium accessions and two tomato cultivars (E9×L5 and E6203×LA1589). The temperature increase affected the reproductive traits, especially at extremely high temperatures, where only a few lines were able to set fruits. Even though a relative modest number of QTLs was identified, two clusters of QTLs involved in the responses of reproductive traits to heat stress were detected in both populations on chromosomes 1 and 2. Interestingly, several epistatic interactions were detected in the E9×L5 population, which were classified into three classes based on the allelic interaction: dominant (one locus suppressed the allelic effects of a second locus), co-adaptive (the double-homozygous alleles from the same parent alleles showed a higher phenotypic value than the combination of homozygous alleles from alternative parents) and transgressive (the combination of double-homozygous alleles from different parents showed better performance than double-homozygous alleles from the same parents). These results reinforce the important role of non-additive genetic variance in the response to heat stress and the potential of the new allelic combinations that arise after wide crosses.

Elucidation of gene action and combining ability for grain and forage yield and contributing traits in sorghum [Sorghum bicolor (L.) Moench

The present investigation was undertaken to achieve information on gene action and combining ability in sorghum [Sorghum bicolor (L.) Moench]. The experimental material consisted of eleven parents and their 28 Line × Tester crosses. The evaluation was carried out during Kharif, 2020 at Sorghum Research Station, S. D. Agricultural University, Deesa. The ratio of σ2D/σ2H being more than unity was found for days to flowering, which suggested a more significant role of additive genetic variance in the inheritance of this trait. In contrast, the rest of the yield and its component traits showed non-additive genetic variance. The gca effects indicated that parents, SR 3019, CSV 31 and GJ 43 were found as good general combiners for grain yield per plant. While, parents DS 156, CSV 31 and SPV 2682 were good general combiners for dry fodder yield per plant and its contributing traits. Based on estimates of sca effects, the most promising hybrids for grain yield per plant were viz., SR 2980 × CSV 31, SR 3019 × SPV 2573 and DSF 117 × SPV 2682, whereas for dry fodder yield per plant were viz.,SR 3048 × CSV 31, GJ 43 × SPV 2573 and DSF 168 × SPV 2573. The good general combiners for 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. Keywords: L × T analysis, Gene action, combining ability, Grain yield, Dry fodder yield

Improving genomic predictions with inbreeding and nonadditive effects in two admixed maize hybrid populations in single and multienvironment contexts.

Genetic admixture, resulting from the recombination between structural groups, is frequently encountered in breeding populations. In hybrid breeding, crossing admixed lines can generate substantial nonadditive genetic variance and contrasted levels of inbreeding which can impact trait variation. This study aimed at testing recent methodological developments for the modeling of inbreeding and nonadditive effects in order to increase prediction accuracy in admixed populations. Using two maize (Zea mays L.) populations of hybrids admixed between dent and flint heterotic groups, we compared a suite of five genomic prediction models incorporating (or not) parameters accounting for inbreeding and nonadditive effects with the natural and orthogonal interaction approach in single and multienvironment contexts. In both populations, variance decompositions showed the strong impact of inbreeding on plant yield, height, and flowering time which was supported by the superiority of prediction models incorporating this effect (+0.038 in predictive ability for mean yield). In most cases dominance variance was reduced when inbreeding was accounted for. The model including additivity, dominance, epistasis, and inbreeding effects appeared to be the most robust for prediction across traits and populations (+0.054 in predictive ability for mean yield). In a multienvironment context, we found that the inclusion of nonadditive and inbreeding effects was advantageous when predicting hybrids not yet observed in any environment. Overall, comparing variance decompositions was helpful to guide model selection for genomic prediction. Finally, we recommend the use of models including inbreeding and nonadditive parameters following the natural and orthogonal interaction approach to increase prediction accuracy in admixed populations.

Dominance Can Increase Genetic Variance After a Population Bottleneck: A Synthesis of the Theoretical and Empirical Evidence.

Drastic reductions in population size, or population bottlenecks, can lead to a reduction in additive genetic variance and adaptive potential. Genetic variance for some quantitative genetic traits, however, can increase after a population reduction. Empirical evaluations of quantitative traits following experimental bottlenecks indicate that non-additive genetic effects, including both allelic dominance at a given locus and epistatic interactions among loci, may impact the additive variance contributed by alleles that ultimately influences phenotypic expression and fitness. The dramatic effects of bottlenecks on overall genetic diversity have been well studied, but relatively little is known about how dominance and demographic events like bottlenecks can impact additive genetic variance. Herein, we critically examine how the degree of dominance among alleles affects additive genetic variance after a bottleneck. We first review and synthesize studies that document the impact of empirical bottlenecks on dominance variance. We then extend earlier work by elaborating on 2 theoretical models that illustrate the relationship between dominance and the potential increase in additive genetic variance immediately following a bottleneck. Furthermore, we investigate the parameters that influence the maximum level of genetic variation (associated with adaptive potential) after a bottleneck, including the number of founding individuals. Finally, we validated our methods using forward-time population genetic simulations of loci with varying dominance and selection levels. The fate of non-additive genetic variation following bottlenecks could have important implications for conservation and management efforts in a wide variety of taxa, and our work should help contextualize future studies (e.g., epistatic variance) in population genomics.

Non-additive QTL mapping of lactation traits in 124,000 cattle reveals novel recessive loci

BackgroundDeleterious recessive conditions have been primarily studied in the context of Mendelian diseases. Recently, several deleterious recessive mutations with large effects were discovered via non-additive genome-wide association studies (GWAS) of quantitative growth and developmental traits in cattle, which showed that quantitative traits can be used as proxies of genetic disorders when such traits are indicative of whole-animal health status. We reasoned that lactation traits in cattle might also reflect genetic disorders, given the increased energy demands of lactation and the substantial stresses imposed on the animal. In this study, we screened more than 124,000 cows for recessive effects based on lactation traits.ResultsWe discovered five novel quantitative trait loci (QTL) that are associated with large recessive impacts on three milk yield traits, with these loci presenting missense variants in the DOCK8, IL4R, KIAA0556, and SLC25A4 genes or premature stop variants in the ITGAL, LRCH4, and RBM34 genes, as candidate causal mutations. For two milk composition traits, we identified several previously reported additive QTL that display small dominance effects. By contrasting results from milk yield and milk composition phenotypes, we note differing genetic architectures. Compared to milk composition phenotypes, milk yield phenotypes had lower heritabilities and were associated with fewer additive QTL but had a higher non-additive genetic variance and were associated with a higher proportion of loci exhibiting dominance.ConclusionsWe identified large-effect recessive QTL which are segregating at surprisingly high frequencies in cattle. We speculate that the differences in genetic architecture between milk yield and milk composition phenotypes derive from underlying dissimilarities in the cellular and molecular representation of these traits, with yield phenotypes acting as a better proxy of underlying biological disorders through presentation of a larger number of major recessive impacts.

Heterosis and Combining Ability for Fruit Yield, Sweetness, β-Carotene, Ascorbic Acid, Firmness and Fusarium Wilt Resistance in Muskmelon (Cucumis melo L.) Involving Genetic Male Sterile Lines

Ten genetically diverse inbred lines, including two genic male sterile lines, of muskmelon (Cucumis melo L.) were crossed in a half-diallel to generate 45 F1 hybrids. These hybrids, along with the parental lines and commercial check, were evaluated for their fruit yield, level of phytochemicals and Fusarium wilt resistance. Both additive and non-additive genetic variances were important in governing the expression of all of the traits; however, the additive gene action for the fruit weight (g), flesh thickness (cm), rind thickness (mm), firmness (lb inch−2), β-carotene content (mg/100 g), non-additive variance for fruit yield (t ha−1), fruit number, total soluble solids (TSS, °Brix), ascorbic acid (mg/100 g) and reaction to Fusarium wilt were comparatively more important. The parental line MM-625 was the best general combiner for fruit yield, rind thickness and β-carotene content (mg/100 g). The exotic line Riogold was the best combiner for flesh thickness and firmness. The netted inbred line MM-610 was the best general combiner for fruit weight, ascorbic acid and reaction to Fusarium wilt. The inbred lines KP4HM-15 and MM-916 were the best general combiners for the number of fruits per vine and TSS. The best cross-combinations for fruit yield ha−1 and TSS were MS-1×M-610 and Kajri×MM-904, respectively. The hybrids KP4HM-15×MM Sel-103 and KP4HM-15×MM-1831 recorded the highest standard heterosis for fruit yield and TSS. The landrace-derived inbred lines Kajri, MM Sel-103 and KP4HM-15 produced moderate-to-highly FW-resistant hybrids. Out of the 121 SSR markers applied, 70 exhibited parental polymorphism. The markers DM0561, CMAAAGN14, TJ147, CMMS35_3, CMAGN45 and DE1337 identified specific/unique alleles in certain parental genotypes. Thus, the findings of this study revealed that the novel inbred lines can effectively be combined to generate heterotic F1 hybrids for yield and other traits, such as rind and flesh thickness, TSS, β-carotene content and firmness. Furthermore, SSR markers can potentially be utilized to confirm the genetic diversity among the parental lines, and for the DNA fingerprinting of F1 hybrids.

Rice (Oryza sativa L.) Breeding among Hassawi Landrace and Egyptian Genotypes for Stem Borer (Chilo agamemnon Bles.) Resistance and Related Quantitative Traits

Rice stem borer (Chilo agamemnon Bles.) is a primary insect pest of rice and is a major limiting factor to rice production. Breeding for insect-resistant crop varieties has been an economic way of integrated pest management (IPM) as it offers a viable and ecologically acceptable approach. This study was aimed to evaluate rice genotypes for their resistance against rice stem borer. Seven parental genotypes with twenty one F1 crosses were evaluated for genotypic variation in field experiments. Analysis of variance revealed significant differences for the studied traits in almost all crosses and parents. In addition, the mean squares of parents versus their crosses were signifi- cant for stem borer resistance and other associated traits. Moreover, both general combining ability (GCA) and specific combining ability (SCA) variances were highly significant for all characters studied in the F1 generation. Based on GCA, 4 genotypes (Sakha101, Gz6903-3-4-2-1, Gz9577-4-1-1 and Hassawi) exhibited highly significant negative values for stem borer resistance (–0.53, –1.06, –0.18 and –0.49, respectively) indicating they are the best combiners for stem borer resistance. Based on SCA analysis, nine cross combinations showed highly significant negative effects for stem borer resistance. Similarly, the cross Giza178 Hassawi was the best combination with significantly highest value for early maturity. In addition, seven crosses showed highly significant negative SCA for plant height trait. On the other hand, for panicle length, number of primary branches/panicle, panicle weight and 1000-grain weight, seven, four, eight and six crosses showed highly significant positive SCA, respectively. The result further revealed that the non-additive dominance genetic variance was higher than the additive variance for all evaluated traits indicating that non-additive genetic variances have a role in their inheritance. The broad-sense heritability estimates were high for all the studied traits. The stem borer resistance was significantly correlated with panicle weight and 1000-grain weight, which also showed a highly significant correlation with grain yield/plant. Thus these traits can be effectively employed in a breeding program to confer resistance against stem borer infestation in rice. It was further supported by biplot analysis, which clustered these potentially important traits into two quadrants showing their importance in any future breeding program to control stem borer infestation. This study has contributed valuable information for evaluation of genetic diversity in the local rice germplasm and its utilization in futuristic rice genetic improvement programs.

Genomic Prediction Methods Accounting for Nonadditive Genetic Effects.

The use of genomic information for prediction of future phenotypes or breeding values for the candidates to selection has become a standard over the last decade. However, most procedures for genomic prediction only consider the additive (or substitution) effects associated with polymorphic markers. Nevertheless, the implementation of models that consider nonadditive genetic variation may be interesting because they (1) may increase the ability of prediction, (2) can be used to define mate allocation procedures in plant and animal breeding schemes, and (3) can be used to benefit from nonadditive genetic variation in crossbreeding or purebred breeding schemes. This study reviews the available methods for incorporating nonadditive effects into genomic prediction procedures and their potential applications in predicting future phenotypic performance, mate allocation, and crossbred and purebred selection. Finally, a brief outline of some future research lines is also proposed.