Significance of Linkage Disequilibrium and Epistasis on the Genetic Variances in Non- Inbred and Inbred Populations

Background The influence of linkage disequilibrium (LD), epistasis, and inbreeding on the genotypic variance continues to be an important area of investigation in genetics and evolution. Although the current knowledge about biological pathways and gene networks imply that epistasis is important in determining quantitative traits, the empirical evidence for a range of species and traits is that the genetic variance is most additive. This is confirmed by some recent theoretical studies. However, because these investigations have assumed linkage equilibrium, only additive effects, or simplified assumptions for the two- and high-order epistatic effects, the objective of this investigation was to provide additional information about the impact of LD and epistasis on the genetic variances in non-inbred and inbred populations, using a simulated data set.Results The epistatic variance in generation 0 corresponded to 1 to 10% of the genotypic variance, with 30% of epistatic genes, but it corresponded to 5 to 45% assuming 100% of epistatic genes. After 10 generations of random cross or selfing the ratio epistatic variance/genotypic variance increased in the range of 15 to 1,079%. The epistatic variances are maximized assuming dominant epistasis, duplicate genes with cumulative effects, and non-epistatic gene interaction. A minimization occurs with complementary, recessive, and dominant and recessive epistasis. In non-inbred populations, the genetic covariances have negligible magnitude compared with the genetic variances. In inbred populations, excepting for duplicate epistasis, the sum of the epistatic covariances was in general negative and with magnitude higher than the non-additive variances, especially under 100% of epistatic genes.Conclusions The LD level for genes, even under a relatively low gene density, has a significant effect on the genetic variances in non-inbred and inbred populations. Assuming digenic epistasis, the additive variance is in general the most important component of the genotypic variance in non-inbred and inbred populations. The ratio epistatic variance/genotypic variance is proportional to the percentage of interacting genes and increases with random cross and selfing. In general, the additive x additive variance is the most important component of the epistatic variance. The maximization of the epistatic variance depends on the allele frequency, LD level, and epistasis type.

Significance of Linkage Disequilibrium and Epistasis on the Genetic Variances in Non-Inbred and Inbred Populations

Background The influence of linkage disequilibrium (LD), epistasis, and inbreeding on the genotypic variance continues to be an important area of investigation in genetics and evolution. Although the current knowledge about biological pathways and gene networks imply that epistasis is important in determining quantitative traits, the empirical evidence for a range of species and traits is that the genetic variance is most additive. This is confirmed by some recent theoretical studies. However, because these investigations have assumed linkage equilibrium, only additive effects, or simplified assumptions for the two- and high-order epistatic effects, the objective of this investigation was to provide additional information about the impact of LD and epistasis on the genetic variances in non-inbred and inbred populations, using a simulated data set.Results The epistatic variance in generation 0 corresponded to 1 to 10% of the genotypic variance, with 30% of epistatic genes, but it corresponded to 5 to 45% assuming 100% of epistatic genes. After 10 generations of random cross or selfing the ratio epistatic variance/genotypic variance increased in the range of 15 to 1,079%. The epistatic variances are maximized assuming dominant epistasis, duplicate genes with cumulative effects, and non-epistatic gene interaction. A minimization occurs with complementary, recessive, and dominant and recessive epistasis. In non-inbred populations, the genetic covariances have negligible magnitude compared with the genetic variances. In inbred populations, excepting for duplicate epistasis, the sum of the epistatic covariances was in general negative and with magnitude higher than the non-additive variances, especially under 100% of epistatic genes.Conclusions The LD level for genes, even under a relatively low gene density, has a significant effect on the genetic variances in non-inbred and inbred populations. Assuming digenic epistasis, the additive variance is in general the most important component of the genotypic variance in non-inbred and inbred populations. The ratio epistatic variance/genotypic variance is proportional to the percentage of interacting genes and increases with random cross and selfing. In general, the additive x additive variance is the most important component of the epistatic variance. The maximization of the epistatic variance depends on the allele frequency, LD level, and epistasis type.

Suitability of Pedigree Method for Improving Seed Cotton Yield and Fiber Quality Traits

Background: Cotton is grown around the globe for its fiber, which consists of unicellular seed trichome. Converging decent fiber quality and good fiber yield in cotton varieties is crucial for textile industry of any country. Pedigree method is mostly used for developing cotton varieties in Pakistan. Suitability of pedigree method for developing cotton variety is accessed in an experiment. Genotypic variance, phenotypic variance, heritability, co-heritability, genetic advance, mean comparison and correlation analysis was carried out of nine breeding lines of in fifth filial generation. Gene action was thus determined to target the traits for further yield and quality improvement of cotton fiber. Results: Substantial genetic variability existed in F5 lines. Genotypic and phenotypic variances had less differences and phenotypic variances were higher than genotypic variance indicating influence of environment on the final expression of the traits. All traits had medium to high heritability. Seed cotton yield per plant came up with high genetic advance and high heritability indicating additive gene action and can be improved by selection. Mean comparison indicated more variation for GOT% compared to other traits. Correlation analysis indicated selecting more sympodial branches for improving seed cotton yield per plant and selecting more monopodial branches for improving fiber fineness and fiber length. However, co-heritability had high value indicating that all the traits are in balance for improvement. Conclusion: Pedigree method is suitable for improving seed cotton yields and fiber quality. However, statistical check points are recommended with each proceeding generation to apply suitable selection pressure and monitor the gene action for each trait in each generation.

Genome-Wide Association Studies and Prediction of Tan Spot (Pyrenophora tritici-repentis) Infection in European Winter Wheat via Different Marker Platforms

Tan spot, caused by the fungus Pyrenophoratritici-repentis (Ptr), is a severe foliar disease of wheat (Triticumaestivum L.). Improving genetic resistance is a durable strategy to reduce Ptr-related losses. Here, we dissected Ptr-infection’s genetic basis in 372 European wheat varieties via simple sequence repeats (SSRs) plus 35k and 90k single nucleotide polymorphism (SNP) marker platforms. In our phenotypic data analyses, Ptr infection showed a significant genotypic variance and a significant negative correlation with plant height. Genome-wide association studies revealed a highly quantitative nature of Ptr infection and identified two quantitative trait loci (QTL), viz., QTs.ipk-7A and QTs.ipk-7B, which imparted 21.23 and 5.84% of the genotypic variance, respectively. Besides, the Rht-D1 gene showed a strong allelic influence on the infection scores. Due to the complex genetic nature of the Ptr infection, the potential of genome-wide prediction (GP) was assessed via three different genetic models on individual and combined marker platforms. The GP results indicated that the marker density and marker platforms do not considerably impact prediction accuracy (~40–42%) and that higher-order epistatic interactions may not be highly pervasive. Our results provide a further understanding of Ptr-infection’s genetic nature, serve as a resource for marker-assisted breeding, and highlight the potential of genome-wide selection for improved Ptr resistance.

Significance of linkage disequilibrium and epistasis on the genetic variances and covariance between relatives in non-inbred and inbred populations

Because no feasible theoretical model can depict the complexity of phenotype development from a genotype, the joint significance of linkage disequilibrium (LD), epistasis, and inbreeding on the genetic variances remains unclear. The objective of this investigation was to assess the impact of LD and epistasis on the genetic variances and covariances between relatives in non-inbred and inbred populations using simulated data. We provided the theoretical background and simulated grain yield assuming 400 genes in 10 chromosomes of 200 and 50 cM. We generated five populations with low to high LD levels, assuming 10 generations of random cross and selfing. The analysis of the parametric LD in the populations shows that the LD level depends mainly on the gene density. The significance of the LD level is impressive on the magnitude of the genotypic and additive variances, which is the most important component of the genotypic variance, regardless of the LD level and the degree of inbreeding. Regardless of the type of epistasis, the ratio epistatic variance/genotypic variance is proportional to the percentage of the epistatic genes. For the epistatic variances, except for duplicate epistasis and dominant and recessive epistasis, with 100% of epistatic genes, their magnitudes are much lower than the magnitude of the additive variance. The additive x additive variance is the most important epistatic variance. Our results explain why LD for genes and relationship information are key factors affecting the genomic prediction accuracy of complex traits and the efficacy of association studies.

Genetic Variation, Heritability and Genetic Advance in Some Promising Rice Hybrids

Eleven rice hybrids including two check varieties were evaluated to approximate their genetic variability, heritability and genetic advance for ten quantitative traits. The analysis of variance illustrated that all the quantitative traits differed significantly indicating that enough variation is presenting the studied materials. Among the desirable quantitative traits number of filled spikelet’s per panicle was found to have highest both phenotypic and genotypic variance followed by total number of spikelet’s per panicle. Almost all the characters showed a little variation between PCV and GCV revealing little influence of the environment on the expression of traits. High phenotypic and genotypic variance coupled with high heritability and high genetic advance was observed for number of filled spikelet’s per panicle, total number of spikelet’s per panicle, plant height and number of unfilled spikelet’s per panicle. Such findings stipulated that these traits were governed by additive gene actions which are fixable and these traits may be accounted for reliable index of selection. The genotypes G3 (IR79156A × EL108R) and G6 (IR79156A × EL253R) were selected as high response superior promising rice hybrids for achievable yield advantage 49% and 23%, respectively over best check varieties. Therefore, the G3 and G6 are proposed to be extensively evaluated for further trial of variety release. SAARC J. Agri., 18(2): 39-49 (2020)

Genetic analysis in mango (Mangifera indica L.) based on fruit characteristics of 400 genotypes

The analysis of variance for 6 quantitative traits and 30 qualitative traits showed significant differences among the 400 genotypes of mango which indicates the existence of high heterozygosity. Among the 18 clusters formed, the highest fruit weight of 1404.27 g was recorded in cluster 10 followed by cluster 15 with 1280.67g whereas the lowest fruit weight was recorded in cluster 16 (30.94g). The highest fruit length (22.03 cm) was recorded in cluster 10 followed by 17.80 cm in cluster 14. Similarly, the fruit diameter was highest (12.18 cm) in cluster 10 followed by 12.03 cluster 4. The fruit thickness was highest (10.60 cm) in cluster 15 followed by cluster 4 with 9.96 cm. The pulp recovery was maximum (87.16%) in cluster-14 followed by clusters 4 and 18 with 79.28 and 78.41 %, respectively. Clusters 15 had the varieties meant for pickle making and possessed less TSS whereas the TSS of above 19°B was recorded in cluster 2. The maximum inter-cluster (D2) value was obtained between cluster 10 and cluster 11. These clusters may be used for hybridization programs due to wide variability and the possibility of transgressive sergeants. Estimates of phenotypic variance and genotypic variance had only a narrow difference for all six characters studied indicating that these characters are not much influenced by environmental factors and highly heritable which can be exploited by adopting clonal selection or selection of chance seedlings and selection as parents for breeding purpose.