Detection of linkage between restriction fragment length polymorphism markers and quantitative traits

Summary Methodologies commonly used to detect linkage of marker loci to loci affecting quantitative traits are discussed. It is shown that variances for the quantitative trait differ among marker genotypes when using F₂ or pooled backcross data if linkage exists. Hence, to analyze this type of data by single factor ANOVA or other statistical techniques that assume a common variance is inadequate. Restriction fragment length polymorphism (RFLP) markers are a powerful tool in plant breeding but cost is an important drawback; hence, a methodology is suggested to obtain the minimum number of plants in F₂ populations to detect such linkage.     

Heterosis for chiasma frequency and quantitative traits in common beans (Phaseolus vulgaris L.)

Summary Ten genotypes, including inbreds, hybrids, and advanced populations, were examined in order to elucidate the relationship between position and frequency distribution of chiasmata and quantitative traits, including yield heterosis in common beans. The hybrid and advanced population groups were determined to possess 83% and 54% increased chiasma frequency, respectively in contrast to inbred lines. The increase in chiasma frequency of these populations was further manifested in a high number of interstitial chiasmata. The regular and superior chromosome behaviour of the hybrids was found to be positively associated with quantitative measures on bean yield, harvest index and bean yield efficiency. The results were discussed from the point of view that: a) increased interstitial chiasmata may provide an effective mechanism for maintaining genetic diversity and heterosis in hybrid populations; and b) heterosis for chiasma frequency and quantitative traits may be due to dispersed genes on the chromosomes having combined intra-and interallelic interactions. The data provide evidence for the existence of positive associations between interstitially localized chiasmata with its recombination potential and regular chromosome behaviour to bean yield heterosis. The role of enhanced interstitial chiasmata to promote higher levels of genetic variation and heterozygous advantage is discussed.     

Mutation load and mutation-selection-balance in quantitative genetic traits

Haldane (1937) showed that the reduction of equilibrium mean fitness in an infinite population due to recurrent deleterious mutations depends only on the mutation rate but not on the harmfulness of mutants. His analysis, as well as more recent ones (cf. Crow 1970), ignored back mutation. The purpose of the present paper is to extend these results to arbitrary mutation patterns among alleles and to quantitative genetic traits. We derive first-order approximations for the equilibrium mean fitness (and the mutation load) and determine the order of the error term. For a metric trait under mutation-stabilizing-selection balance our result differs qualitatively from that of Crow and Kimura (1964), whose analysis is based on a Gaussian assumption. Our general approach also yields a mathematical proof that the variance under the usual mutation-stabilizing-selection model is, to first order, µ/s (the house-of-cards approximation) as µ/s tends to zero. This holds for arbitrary mutant distributions and does not require that the population mean coincide with the optimum. We show how the mutant distribution determines the order of the error term, and thus the accuracy of the house-of-cards approximation. Upper and lower bounds to the equilibrium variance are derived that deviate only to second order as µ/s tends to zero. The multilocus case is treated under the assumption of global linkage equilibrium.     

Quantitative genetic variance associated with chromosomal markers in segregating populations

Summary Use of chromosomal markers can accelerate genetic progress for quantitative traits in pedigree selection programs by providing early information on Mendelian segregation effects for individual progeny. Potential effectiveness of selection using markers is determined by the amount of additive genetic variance traced from parents to progeny by the markers. Theoretical equations for the amount of additive genetic variance associated with a marker were derived at the individual level and for a segregating population in joint linkage equilibrium. Factors considered were the number of quantitative trait loci linked to the marker, their individual effects, and recombination rates with the marker. Subsequently, the expected amount of genetic variance associated with a marker in a segregating population was derived. In pedigree selection programs in segregating populations, a considerable fraction of the genetic variance on a chromosome is expected to be associated with a marker located on that chromosome. For an average chromosome in the bovine, this fraction is approximately 40% of the Mendelian segregation variance contributed by the chromosome. The effects of interference and position of the marker on this expectation are relative small. Length of the chromosome has a large effect on the expected variance. Effectiveness of MAS is, however, greatly reduced by lack of polymorphism at the marker and inaccuracy of estimation of chromosome substitution effects. The size of the expected amount of genetic variance associated with a chromosomal marker indicates that, even when the marker is not the active locus, large chromosome substitution effects are not uncommon in segregating populations.     

Effects of marked chromosome sections on quantitative traits in the mouse

Summary An investigation of the influences of marked chromosome sections on quantitative traits in a backcross-generation with 2321 mice (C57BL/6JHan × (AKR/NHan×C57BL/6JHan)) is described. In the animals the chromosomes 1, 4, 7, and 8 were marked by the gene loci Idh-1, Gpd-1, Gpi-1s, Es-1, resp. Within the backcross-generation, for Idh-1 and Es-1, more heterozygous genotypes were found than expected under random conditions. By comparing animal-groups with different homologous sections of the marked chromosomes, effects were observed on quantitative traits (body length and weight, dry weight and matter, fat weight and content). The results indicate that a few chromosome sections influence to a major extent the genetic variation of some quantitative traits.This investigation was supported by the Deutsche Forschungsgemeinschaft (Sonderforschungsbereich 146)     

Genetic markers linked to quantitative traits in poultry

This study utilized DNA fingerprints and crosses of two genetically distinct lines of layer-type chickens to identify genetic markers linked to quantitative trait loci (QTL). In phase I, back-cross (BC¹) hens were separately ranked for each of eight traits and then blood pools were produced in groups along each phenotypic distribution. The DNA was isolated from the blood pools and used in a gradient analysis to screen for DNA fingerprint bands that exhibited intensity gradients associated with the phenotypic traits. To identify linkage of bands with QTL and to estimate band effects, F₂ progeny were produced in phase II from the phase I BC, population. A single-trait animal model was used for analysis of associations of all individual DNA fingerprint bands of sires and their progeny phenotypic performance. Twenty fingerprint bands, only two of which had shown trait-associated gradients in phase I, were identified by the animal model analysis of the progeny test as QTL linked (P≤005) to specific traits of growth, reproduction and egg quality. These 20 bands warrant further study as potentially valuable molecular markers for QTL.     

Genetic and molecular dissection of quantitative traits in rice

Recent progress in the generation of a molecular genetic map and markers for rice has made possible a new phase of mapping individual genes associated with complex traits. This type of analysis is often referred to as quantitative trait locus (QTL) analysis. Increasing numbers of QTL analyses are providing enormous amounts of information about QTLs, such as the numbers of loci involved, their chromosomal locations and gene effects. Clarification of genetic bases of complex traits has a big impact not only on fundamental research on rice plant development, but it also has practical benefits for rice breeding. In this review, we summarize recent progress of QTL analysis of several complex traits in rice. A strategy for positional cloning of genes at QTLs is also discussed.     

A mixed model for the effects of single gene,polygenes and their interaction on quantitative traits

Summary A model for the effects of single gene (SG), polygenes (PG) and their interaction on quantitative traits was developed. It is a mixed model where the SG is a fixed effect and the PG is a random effect. A two-way factorial experiment, in which the SG and the PG are the main effects, is proposed. The experimental material is comprised of F₃ families derived from F₂ plants heterozygous for the SG. For this experiment an ANOVA table with expected mean square is proposed, which facilitates estimation of the components of the model and testing of their significance. A detailed method for the interpretation of results from such an experiment is proposed, with emphasis on the analysis of the SG × PG interaction. Theoretical and applied aspects of SG × PG interaction is discussed.This paper is part of a Ph.D. Thesis of the senior author to be submitted to the Hebrew University of Jerusalem     

Association of genetic polymorphism inGH gene with milk production traits in Beijing Holstein cows

Associations were analysed between polymorphisms of the growth hormone gene (GH-MspI) (localized in intron 3) and milk production traits of Beijing Holstein cows (a total of 543 cows). Polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) method was used for identification of various geno-types. Frequencies of genotypes were 0.77, 0,21 and 0.02 for A/A, A/B and B/B, respectively. The frequency of theGH ^A allele is 0.875. The results of the least squares means show that in all three lactations, theGH A/A cows yielded more milk (P < 0.01 for lactation I andP 0.05 for lactations II and III), whereas A/B cows showed higher milk fat content than A/A individuals (P < 0.05 for lactations I and II, andP < 0.01 for lactation III). The A/A cows yielded more fat than A/B individuals (P < 0.01 only in lactation I). The A/A cows yielded more milk protein than A/B individuals (P < 0.01 for lactations I, II, and III). The A/A cows produced milk of higher protein content than of A/B individuals (P < 0.05 only in lactation II).     

In an elite cross of maize a major quantitative trait locus controls one-fourth of the genetic variation for grain yield

Quantitative trait loci (QTLs) for grain yield, dry matter content and test weight were identified in an F₂ segregating population derived from a single cross between two elite maize lines (B73 and A7) and testcrossed to two genetically divergent in breds. Most of the QTLs inferred were consistent across locations, indicating that the expression of the genes influencing the traits under investigation was largely independent of the environment. By using two different tester lines we found that QTLs exhibited by one tester may not necessarily be detected with the second one. Only loci with larger effects were consistent across testers, suggesting that interaction with tester alleles may contribute to the identification of QTLs in a specific fashion. Analysis across both testers revealed four significant QTLs for grain yield that explained more than 35% of the phenotypic variation and showed an overall phenotypic effect of more than 2t/ha. The major QTL for grain yield, located in the proximity of the Nucleolus Organiser Region, accounted for 24.5% of the phenotypic variation for grain yield and showed an average effect of allele substitution of approximately 1 t/ha. Marker-assisted introgression of the superior A7 allele at this locus in the B73 genetic background will not differ from qualitative trait introgression and will eventually lead to new lines having superior testcross performance.     

Fine mapping quantitative trait loci affecting milk production traits on bovine chromosome 6 in a Chinese Holstein population

To fine map the previously detected quantitative trait loci （QTLs） affecting milk production traits on bovine chromosome 6 （BTA6）, 15 microsatellite markers situated within an interval of 14.3 cM spanning from BMS690 to BM4528 were selected and 918 daughters of 8 sires were genotyped. Two mapping approaches, haplotype sharing based LD mapping and single marker regression mapping, were used to analyze the data. Both approaches revealed a quantitative trait locus （QTL） with significant effects on milk yield, fat yield and protein yield located in the segment flanked by markers BMS483 and MNB209, which spans a genetic distance of 0.6 cM and a physical distance of 1.5 Mb. In addition, the single marker regression mapping also revealed a QTL affecting fat percentage and protein percentage at marker DIK2291. Our fine mapping work will facilitate the cloning of candidate genes underlying the QTLs for milk production traits.     

The use of quantitative traits in the study of human population structure

Studies of human population structure and history have tended to use demographic and/or serological data for analysis. This paper reviews the methods and studies that incorporate quantitative traits (usually polygenic traits) in such analyses. Methods of assessing the degree and pattern of among-group variation are discussed, and are characterized as being model-free or model-bound. Model-free methods deal with the measure of overall populational differentiation and with comparative methods for describing the pattern of differentiation. Model-bound methods are used for direct incorporation into theoretical models of population structure in order to estimate genetic parameters, such as those in admixture and isolation by distance models. To date, studies have indicated that quantitative traits may often be used successfully in studies of human population structure, and show effects of microevolutionary forces on quantitative variation among populations.     

Identification of an RFLP marker tightly linked to theHt1 gene in maize

Summary We have identified tight linkage of an RFLP marker to theHt1 gene of maize that confers resistance to the fungal pathogenHelminthosporium turcicum race 1. This was accomplished by the use of four pairs of near isogenic lines (NILs; B73, A619, W153R, and CM105), each differing by the presence or the absence of the geneHt1. SinceHt1 maps to chromosome 2, 26 clones already mapped to this chromosome were labeled and probed against Southern blots of these NILs DNA digested with three restriction enzymes:EcoRI,BamHI, andHindIII. Six markers exhibited an RFLP for at least one pair of NILs. Presumptive linkage was further tested by analyzing the segregation of five of the six markers (one was monomorphic in the cross studied) and resistance toH. turcicum race 1 on 95 F₂ individuals from the cross DF20 × LH146Ht. The results indicate a tight linkage between one of the DNA markers,UMC150B, and theHt1 gene.     

Power analysis for quantitative trait locus mapping in populations derived by multiple backcrosses

 Populations derived by multiple backcrosses are potentially useful for quantitative trait locus (QTL) mapping studies. Comparisons of relative power to detect QTL using populations derived by multiple back-crosses are needed to make decisions when mapping projects are initiated. The objective of this study was to theoretically compare the power to detect QTL in populations derived by multiple backcrosses relative to mapping in a recombinant inbred population of equal size. Backcrossing results in a reduction in genetic variance with each generation and also results in an increasing frequency of the recurrent parent marker genotype. The relevant outcome for QTL mapping is a reduction in genetic variance to partition between marker genotype classes and increasing unbalance of the number of individuals contributing to the mean of the marker genotypes. Both of these factors lead to a decrease in the power to detect a QTL as the number of backcross generations increases. Experimental error was held constant with the populations compared. From a theoretical standpoint, backcross-derived populations offer few advantages for QTL detection. If, however, a backcrossing approach is the most efficient method to achieve a desired breeding objective and if QTL detection is an objective of equal or less importance, backcross-derived populations are a reasonable approach to QTL detection. Received: 4 August 1996 / Accepted: 4 April 1997     

Association between ovocalyxin-32 gene haplotypes and eggshell quality traits in an F2 intercross between two chicken lines divergently selected for eggshell strength

Broken and cracked eggshells contribute significantly to economic losses in the egg production industry. We previously identified ovocalyxin-32 as a potential gene influencing eggshell traits, by analysing an intercross between two parent lines developed from the same founder population by a two-way selection for eggshell strength with non-destructive deformation (DEF) conducted over 14 generations. We determined the nucleotide sequences of six ovocalyxin-32 exons in the parent individuals and analysed the association between ovocalyxin-32 and eggshell traits in the F₂ individuals. We identified three haplotypes (W, M and S) of ovocalyxin-32 in the parent individuals. A mismatch amplification mutation assay was performed to distinguish six diplotype individuals (WW, MM, SS, WM, MS and WS) in the F₂ population. The egg weight (EW) of SS-diplotype individuals was significantly higher than that of WW-, WM- and WS-diplotypes. Short length of the egg (SLE) of SS-diplotype individuals was significantly higher than that of WW-, WM- and MS-diplotypes. Long length of the egg (LLE) of SS-diplotype individuals was significantly higher than that of WM- and WS-diplotypes. DEF of WW-diplotype individuals was significantly higher than that of SS-, WM, MS and WM-diplotypes. Haplotypic effect analyses showed significant differences between the W-haplotype and the S-haplotypes in the EW, SLE, LLE and DEF. The DEF of M-haplotype was significantly lower than that of W- and S-haplotypes. These results suggest that S- and M-haplotypes are critical for high quality of eggshells in the F₂ population. In conclusion, ovocalyxin-32 is a useful marker of eggshell traits and can be used to develop strategies for improving eggshell traits in commercial layer houses.     

Detection of loci affecting milk production and health traits in an elite US Holstein population using microsatellite markers

Quantitative trait loci (QTL) affecting health and milk production traits were studied in seven large half-sib US Holstein families by using the granddaughter design. Genotyping for 16 markers was completed and marker allele differences within and pooled-across families were analysed. Potential QTL were identified for somatic cell score (SCS), fat yield, fat percentage, protein yield and protein percentage. Three markers (BM203, BM4505 and BM2078) were associated with significant effects for different traits and, after further analysis, may be useful in marker-assisted selection in specific families. Comparisons between these data and previously identified QTL support the location of a QTL for milk yield and protein yield on chromosome 21.     

Genetic analysis using trans-dominant linked markers in an F2 family

Trans-dominant linked markers pairs (trans referring to the repulsion linkage phase) provide a model for inferring the F₂ progeny genotype based upon both the conditional probabilities of F₂ genotypes, given the F₂ phenotype, and prior information on marker arrangement. Prior information of marker arrangement can be readily obtained from a linkage analysis performed on marker segregation data in a family resulting by crossing the F₁ individual to a tester parent or else can be obtained directly from the gametes of the F₁, or from recombinant inbred lines. We showed that a trans-dominant linked marker (TDLM) pair can be recoded as a co-dominant megalocus when the recombination fraction, r₁, for apair of TDLMs is less than 0.05. We obtained a maximum-likelihood estimator (MLE) of the recombination frequency, r₂, between a TDLM pair and a co-dominant marker in an F₂ family using the EM algorithm. The MLE was biased. Mean bias increased as r₁ and r₂ increased, and decreased as sample size increased. The information content for r₂ was compared to the information content of dominant and co-dominant markers segregating in an F₂ family. It was almost identical with two co-dominant markers when r₁0.01 and r₂0.05. For larger values of r₁, (0.05r₁0.15) a TDLM pair provided 75%–66% of the information content of two co-dominant markers. Although dominant markers can be converted to co-dominant markers by a laborious process of cloning, sequencing, and PCR, TDLM pairs could easily substitute for co-dominant markers in order to detect quantitative trait loci (QTLs) and estimate gene action in an F₂ family.