scholarly journals The impact of linkage disequilibrium and epistasis in the studies of inheritance based on Hayman’s diallel and generation mean analysis

2021 ◽  
Author(s):  
José Marcelo Soriano Viana
Keyword(s):  
Linkage Disequilibrium ◽  
Diallel Analysis ◽  
Variable Degree ◽  
Generation Mean Analysis ◽  
Dominance Model ◽  
Partial Dominance ◽  
Genetic Components ◽  
Recessive Genes ◽  
High Heritability ◽  
The Impact

Abstract This simulation-based study assessed the impact of linkage disequilibrium (LD) and epistasis on Hayman’s diallel and generation mean analysis, assuming hundreds of genes, variable degree of dominance, and seven types of digenic epistasis. The diallel parents were 15 doubled-haploid lines from a high LD population. The generation mean analysis was based on seven generations, assuming association. Under low LD and no epistasis, the diallel analysis provided confident results about the inheritance of the quantitative trait and high correlation between number of recessive genes and Wr + Vr, but biased estimates of the dominance components and genetic parameters. The additional consequences of high LD under no epistasis were rejection of the additive-dominance model assuming high heritability and lower correlation. Assuming 100% of epistatic genes, for four epistasis types there was evidence of inadequacy of the additive-dominance model. Assuming 30% of epistatic genes, there was a tendency for accepting the additive-dominance model for low heritability traits and for rejecting for high heritability traits. Linkage and epistasis affects the estimates of the genetic components of the generation means. Even assuming 100% of interacting genes, for most epistasis types there was no statistical evidence of epistasis. Assuming positive partial dominance, the signs of the epistatic components do not allow discriminate complementary, recessive, dominant and recessive, duplicate genes with cumulative effects, and non-epistatic genic interaction. Negative epistatic components evidence dominant epistasis. When the additive x additive and dominance x dominance components are positive and the additive x dominance component is negative, there is duplicate epistasis.

scholarly journals A study of gene action for yield and quality traits of Basmati rice (Oryza sativa L.) following Hayman's graphical approach

2021 ◽  
Vol 58 (1) ◽  
pp. 8-14
Author(s):  
Aarti Sharma ◽  
Hemant Kumar Jaiswal
Keyword(s):  
Oryza Sativa L ◽  
Genetic System ◽  
Numerical Approach ◽  
Grain Weight ◽  
Basmati Rice ◽  
Dominance Model ◽  
Partial Dominance ◽  
Genetic Components ◽  
Diallel Mating Design ◽  
High Heritability

The present study was conducted on 36 crosses obtained by carrying out a crossing program in nine Basmati rice genotypes following half-diallel mating design. Following, Hayman's graphical and numerical approach to comprehend the genetic system involved in the inheritance of traits, it was concluded that, out of 18 traits, only two traits viz., 100-grain weight, and aroma fulfilled the adequacy of additive-dominance model indicating absence of epistasis. Further, Vr/Wr graph was plotted and genetic components w ere estimated for these two traits only. By plotting Vr/Wr graph for 100-grain weight and aroma, partial dominance and over-dominance were observed in the inheritance, respectively. The ratio of KD/Kr implied influence of more of recessive alleles in inheritance of 100-grain weight among parents and dominant alleles for aroma genes among parents. Estimates of genetic components indicated the role of both additive and dominance effect in the inheritance of 100-grain weight and aroma. High heritability in narrow sense was observed for the traits.

scholarly journals PENDUGAAN PARAMETER GENETIK PADA PERSILANGAN DIALEL BEBERAPA TETUA CABAI (Capsicum annuum L.)

2015 ◽  
Vol 24 (1) ◽  
pp. 1
Author(s):  
Sri Romaito Dalimunthe
Keyword(s):  
Combining Ability ◽  
Block Design ◽  
Diallel Analysis ◽  
Inbred Lines ◽  
Fruit Weight ◽  
High Genetic Diversity ◽  
Diallel Crossing ◽  
Recessive Genes ◽  
High Heritability ◽  
Materials Used

High genetic diversity in chili is the basis for a chili breeding program. One of the methods to increase diversity is through crossing. There are several crossing designs in order to produce new varieties, such as diallel crossing. Diallel analysis is a method for studying the inheritance of characteristics from various crossings. The aim of this research was to estimate the genetic parameters, the general combining ability (GCA) and specific combining ability (SCA) of six inbred lines of chili. The research was conducted in November 2008-May 2009 at the Experimental Farm Leuwikopo IPB. Genetic materials used were six inbred lines of chili (IPB C2, IPB C9, IPB C10, IPB C14, IPB C15 and IPB C20) and the F1s of the combination of six inbred lines. The experimental design was Randomized Complete Block Design with a single factor, namely genotype. The number of genotypes were 36 with three replications, so there were 108 units of experiment. The crossing design used was diallel crossing design. The results showed that there were no interaction between genes on the dichotomous height and fruit weight, significant additive effects, the control genes spread unevenly, and relatively high heritability values. Genotype which carried recessive genes the most was IPB C14 and genotype which carried the most dominant genes was IPB C10. IPB C10 showed the highest GCA for dichotomous height and IPB C2 showed the highest GCA on fruit weight. The crossing between IPB C2 x IPB C10 showed the highest SCA for dichotomous height. For fruit weight, crossing of IPB C2x IPB C14 had the highest SCA. Crossing combination of IPB C2 x IPB C14 was the best hybrid.

scholarly journals Theory and analysis of partial diallel crosses

1999 ◽  
Vol 22 (4) ◽  
pp. 591-599 ◽  
Author(s):  
José Marcelo Soriano Viana ◽  
Cosme Damião Cruz ◽  
Antonio Américo Cardoso
Keyword(s):  
Relative Number ◽  
Diallel Analysis ◽  
F1 Hybrids ◽  
Genotypic Differences ◽  
Diallel Crosses ◽  
Genetic Components ◽  
Recessive Genes ◽  
Using Data ◽  
Dominant Genes ◽  
Partial Diallel

This study presents theory and analysis of partial diallel crosses based on Hayman's methods. This genetic design consists of crosses among two parental groups. It should be used when there are two groups of parents, for example, dent and flint maize inbred lines, and the breeder is not interested in the assessment of crosses between parents of the same group. Analyses are carried out using data from the parents and their F1 hybrids allowing a detailed characterization of the polygenic systems under study and the choice of parents for hybridization. Diallel analysis allows the estimation of genetic and non-genetic components of variation and genetic parameters and to assess the following: genetic variability in each group; genotypic differences between parents of distinct groups; if a parent has a common or a rare genotype in the group to which it does not belong; if there is dominance; if dominant genes increase or decrease trait expression (direction of dominance); average degree of dominance in each group; the relative importance of mean effects of genes and dominance in determining a trait; if, in each group, the allelic genes have the same frequency; if genes are equally frequent in the two groups; the group with the greatest frequency of favorable genes; the group in which dominant genes are most frequent; the relative number of dominant and recessive genes in each parent; if a parent has a common or a rare genotype in the group to which it belongs, and the genotypic differences between parents of the same group. An example with common bean varieties is considered.

scholarly journals GENETIC COMPONENTS OF GRAIN CHARACTERS IN RICE (Oryza sativa L.)

2008 ◽  
Vol 21 (1) ◽  
pp. 36-41
Author(s):  
K. M. Iftekharuddaula ◽  
M. A. Newaz ◽  
P. S. Biswas ◽  
M. K. Bashar
Keyword(s):  
Genetic Model ◽  
Oryza Sativa L ◽  
Gene Interaction ◽  
Components Of Variance ◽  
Partial Dominance ◽  
Complete Dominance ◽  
Genetic Components ◽  
Kernel Length ◽  
Glume Length ◽  
Recessive Genes

Hayman’s analysis of variance (ANOVA) indicated importance of both additive and non-additive genetic components for all the grain characters. The ANOVA showed unidirectional dominance for the characters viz. kernel breadth, upper empty glume length and endosperm-embryo ratio, asymmetrical gene distribution for the characters viz. grain length, grain breadth, kernel length, kernel breadth and kernel thickness and residual dominance effects for all the grain characters studied. Five out of nine grain characters viz. grain breadth, grain thickness, kernel breadth, kernel thickness and upper empty glume length followed the simple additive-dominance genetic model. The rest of the grain characters showed nonallelic gene interaction or epistasis. According to Vr-Wr graph, partial dominance was involved in the action of genes governing the inheritance of grain breadth, grain thickness, kernel breadth and kernel thickness while complete dominance was involved in the inheritance of upper empty glume length. BR4828-54-4-1-4-9 contained the most of the recessive genes for four characters except upper empty glume length while Amol3 appeared to possess most of the recessive genes. On the other hand, Minikit for grain breadth, Amol3 for grain thickness and BRRI dhan29 for kernel breadth, kernel thickness and upper empty glume length possessed most of the dominant genes for the respective characters. The components of variance demonstrated involvement of both additive and dominant components in the inheritance of grain breadth, grain thickness, kernel breadth, kernel thickness and endosperm-embryo ratio. The distribution of dominant and recessive genes was unequal in the parents for grain breadth, kernel breadth, grain thickness, kernel thickness and upper empty glume length. Again, net dominance effects were in the negative direction for all the grain characters. There was drastic influence of environment on all the five grain characters following simple additive-dominance genetic model. Heritability in narrow sense (h2 n) was very high for grain breadth, grain thickness, kernel breadth and kernel thickness. However, h2 n for upper empty glume length was moderate. DOI: http://dx.doi.org/10.3329/bjpbg.v21i1.17047

scholarly journals Diallel analysis of seven quantitative traits in deshi jute (Corchorus capsularis L.)

1970 ◽  
Vol 39 (2) ◽  
pp. 137-141
Author(s):  
Rahima Khatun ◽  
RH Sarker ◽  
MA Sobhan
Keyword(s):  
Dominance Effect ◽  
Diallel Analysis ◽  
Diallel Cross ◽  
Genetic System ◽  
Genetic Constitution ◽  
Base Diameter ◽  
Partial Dominance ◽  
Corchorus Capsularis ◽  
Recessive Genes ◽  
Additive Gene

Genetic constitution of yield and its associated traits of Corchorus capsularis L. was investigated using a 10 × 10 full diallel cross experiment. Additive gene action system with partial dominance was predominat for plant height, technical height, base diameter and number of nodes in F1. Non-allellic interaction was involved in the inheritance of bark weight and stick weight in F2. The Vr - Wr graph for bark weight and fibre weight of F1 and F2 showed an additive genetic system with dominance effect. The parents Acc. 4087 and var. A-38 possessed maximum number of dominant alleles for most of the characters. Acc.1833 possessed an excess of recessive genes for all the characters. Key words: Diallel analysis; Inheritance; Dominance effect; Corchorus capsularisDOI: 10.3329/bjb.v39i2.7299 Bangladesh J. Bot. 39(2): 137-141, 2010 (December)

GENETIC ANALYSIS OF SEED SIZE IN PIGEON PEA CAJANUS CAJAN

1972 ◽  
Vol 14 (3) ◽  
pp. 545-548
Author(s):  
D. Sharma ◽  
Laxman Singh ◽  
S. S. Baghel ◽  
H. K. Sharma
Keyword(s):  
Seed Size ◽  
Cajanus Cajan ◽  
Diallel Analysis ◽  
Pigeon Pea ◽  
Gene Effects ◽  
Partial Dominance ◽  
Degree Of Dominance ◽  
Wide Range ◽  
Additive Gene ◽  
High Heritability

Diallel analysis for seed size on 10 varieties of pigeon pea or arhar Cajanus cajan L. Millsp., representing different maturity groups and wide range of variability in seed size, was conducted to determine genetic parameters. The D and H1 components indicated a predominance of additive gene effects and the degree of dominance was in the partial dominance range. Seed size was simply inherited with a high heritability value of 0.82. The scatter of parental arrays in a Wr, Vr graph suggested that the genes controlling smaller seed size were dominant over the genes controlling larger seed size. The analysis indicated the possibility of improving seed size by simple selection procedures.

Genetics of Cercospora Leaf Spot Resistance in Mungbean [Vigna radiata (L.) Wilczek] through Generation Mean Analysis

2021 ◽  
Author(s):  
Priyanka Choudhary ◽  
Ramesh Chand ◽  
Anil Kumar Singh
Keyword(s):  
Latent Period ◽  
Leaf Spot ◽  
Vigna Radiata ◽  
Generation Mean Analysis ◽  
Cercospora Leaf Spot ◽  
Progress Curve ◽  
High Heritability ◽  
Efficient Breeding ◽  
Important Disease ◽  
Selection Of

Background: Cercospora leaf spot (CLS) is a fungal disease of mungbean [Vigna radiata (L.) Wilczek] caused by Cercospora canescens and now emerged as an important biotic stress. A better understanding of the genetics of CLS resistance will help in formulating efficient breeding procedures in mungbean.Methods: The present investigation focused on genetics of CLS resistance through generation mean analysis (six parameter model) in two intra-specific mungbean crosses namely, Kopergaon × HUM12 and Kopergaon × ML1720. Four quantitative disease resistance components, viz., Area under disease progress curve (AUDPC), Incubation period (IP), Latent period (LP) and degree of sporulation (SP) were studied.Result: A high correlation of AUDPC with latent period (r = –0.68 to –0.79, P less than 0.0001) and SP (r = 0.72 to -0.81, P less than 0.0001) advocated that both are main contributor for CLS disease development. High heterosis along with high heritability in terms of AUDPC ( greater than 0.09) indicated the importance of genetic factor(s) in controlling CLS resistance. Generation mean analysis of both the crosses revealed duplicate epistatic interaction and involvement of two genes for CLS resistance in terms of AUDPC. This study supports oligogenic nature of inheritance, advocating AUDPC along with IP, LP and SP as important disease indicator for selection of CLS resistance in mungbean.

scholarly journals Diallel Analysis for Area, Chlorophyll and Temperature of Flag Leaf in Bread Wheat under Well Watered and Drought Stress Conditions

2021 ◽  
Vol 13 (10) ◽  
pp. 45
Author(s):  
Naheif E. Mohamed ◽  
Ismail M. Bedawy ◽  
Yasser A. M. Hefny
Keyword(s):  
Drought Stress ◽  
Bread Wheat ◽  
Flag Leaf ◽  
Block Design ◽  
Diallel Analysis ◽  
Stress Conditions ◽  
F1 Hybrids ◽  
Gene Effects ◽  
Genetic Components ◽  
Additive Gene

To study genetic analysis of some physiological traits of drought stress in wheat using diallel techniques, an experiment was performed on ten bread wheat genotypes as parents and their 45 F1 hybrids in a randomized complete block design with three replicates under well-watered and drought stress conditions at the Research Farm of Faculty of Agriculture, Sohag University, Egypt during season of 2018/19. The results showed significant differences between the genotypes (G), Parents (P), F1 crosses, P vs. F1, GCA and SCA under well-watered and drought stress in the flag leaf area (FLA), flag leaf chlorophyll content (FLCC) and flag leaf temperature (FLT), except FLCC for F1 crosses exhibited insignificant differences. The significant differences were found in the interaction of SCA × Env., in all studied traits and GCA × Env., for FLT., indicating the involvement of both additive and dominance gene action in their inheritance. The most desirable heterotic effects were considered as the largest positive heterosis estimates for FLA and FLCC, and the lowest negative for FLT. The parent numbers P9, P8 and P3 were the best general combiner for FLA under normal irrigation and drought stress. While the parents P2, P7 and P9 were the best general combiner for FLCC, under normal irrigation and (P1, P2 and P3) under drought stress. Therefor the parents P1, P4 and P5 were the best general combiner for FLT under normal irrigation, also the P3, P4 and P5 were the best general combiner for FLT under drought stress conditions. Under normal irrigation and drought stress conditions as well as the combined data, the additive genetic components of variation (VA) in F1 ’s was much greater than dominance component (VD), as expressed by the (VA/VD) ratio which was more than unity for the FLA, and FLT under normal irrigation and their combined. This indicates that the additive gene effects in F1 crosses are more important than dominance and plays the major role in the inheritance of these studied traits.

scholarly journals An evaluation of the interpretability and predictive performance of the BayesR model for genomic prediction

2020 ◽  
Author(s):  
Fanny Mollandin ◽  
Andrea Rau ◽  
Pascal Croiseau
Keyword(s):  
Linkage Disequilibrium ◽  
Qtl Mapping ◽  
Effect Size ◽  
Genomic Prediction ◽  
Simulated Data ◽  
Predictive Performance ◽  
Real Data ◽  
Sliding Windows ◽  
Size Classes ◽  
The Impact

ABSTRACTTechnological advances and decreasing costs have led to the rise of increasingly dense genotyping data, making feasible the identification of potential causal markers. Custom genotyping chips, which combine medium-density genotypes with a custom genotype panel, can capitalize on these candidates to potentially yield improved accuracy and interpretability in genomic prediction. A particularly promising model to this end is BayesR, which divides markers into four effect size classes. BayesR has been shown to yield accurate predictions and promise for quantitative trait loci (QTL) mapping in real data applications, but an extensive benchmarking in simulated data is currently lacking. Based on a set of real genotypes, we generated simulated data under a variety of genetic architectures, phenotype heritabilities, and we evaluated the impact of excluding or including causal markers among the genotypes. We define several statistical criteria for QTL mapping, including several based on sliding windows to account for linkage disequilibrium. We compare and contrast these statistics and their ability to accurately prioritize known causal markers. Overall, we confirm the strong predictive performance for BayesR in moderately to highly heritable traits, particularly for 50k custom data. In cases of low heritability or weak linkage disequilibrium with the causal marker in 50k genotypes, QTL mapping is a challenge, regardless of the criterion used. BayesR is a promising approach to simultaneously obtain accurate predictions and interpretable classifications of SNPs into effect size classes. We illustrated the performance of BayesR in a variety of simulation scenarios, and compared the advantages and limitations of each.

Sign in / Sign up

Export Citation Format

Share Document