Doubled haploids for estimating genetic variances in presence of linkage and gene association

Summary The effect of gene association (or dispersion) and linkage on the estimation of genetic variances in a diallel experiment involving doubled haploid lines is evaluated. It is shown that the estimates of the additive and the additive X additive genetic variances, as obtained by Choo et al. (1979), are biased if genes are linked or are not independently distributed in the parents. However, this bias only occurs in the presence of interaction between homozygous loci. Gene association (or dispersion) and linkage, if present, can be detected by comparing the parental vs the crosses mean, the parental vs the doubled haploid lines variance, and the among vs the within crosses variance.     

Genetic analysis of blood pressure in the Milan hypertensive strain of rat (Rattus norvegicus)

Estimates of heritability (h2) of blood pressure level and the number of loci controlling the trait were derived from two genetic crosses involving the Milan hypertensive strain of rat and its control with normal blood pressure. In the genetic cross involving backcrosses, the estimates were h2 = 64% and the number of loci was two or three; there was some evidence of dominance of the alleles for normal blood pressures. In the other cross with only F2's, the degree of genetic determination (heritability in the broad sense) was 45%, involving at least three loci.     

Gene action for adult-plant resistance to powdery mildew in wheat.

Gene action for adult-plant resistance to powdery mildew was studied using generation mean analyses of parents and of F1, F2, and backcross populations derived from a diallel cross of one susceptible and three adult-plant resistant wheat cultivars. Joint scaling tests showed that an additive-dominance model was sufficient to explain the variability in the expression of adult-plant resistance in one cross, while digenic epistasis was involved in the other five crosses. Additive gene effects were predominant; however, dominance was significant in four crosses, additive x additive interaction was significant in three crosses, additive x dominance interaction was significant in three crosses, and dominance x dominance interaction was significant in one cross. Therefore, selection for adult-plant resistance would likely be most effective in advanced generations derived from crosses among the adult-plant resistant cultivars Redcoat, Houser, and Massey.     

Genetics of tassel branch number in maize and its implications for a selection program for small tassel size

Summary Tassel branch numbers of six crosses of maize (Zea mays L.) were analyzed to determine inheritance of this trait. Generation mean analyses were used to estimate genetic effects, and additive and nonadditive components of variance were calculated and evaluated for bias due to linkage. Both narrow-sense and broad-sense heritabilities were estimated. Additive genetic variance estimates were significant in five of the six crosses, whereas estimates of variance due to nonadditive components were significant in only three crosses. Additionally, estimates of additive variance components usually were larger than corresponding nonadditive components. There was no evidence for linkage bias in these estimates. Estimates of additive genetic effects were significant in four of six crosses, but significant dominance, additive × additive and additive × dominance effects also were detected. Additive, dominance, and epistatic gene action, therefore, all influenced the inheritance of tassel branch number, but additive gene action was most important. Both narrow-sense and broadsense heritability estimates were larger than those reported for other physiological traits of maize and corroborated conclusions concerning the importance of additive gene action inferred from analyses of genetic effects and variances. We concluded that selection for smalltasseled inbreds could be accomplished most easily through a mass-selection and/or pedigree-selection system. Production of a small-tasseled hybrid would require crossing of two small-tasseled inbreds. We proposed two genetic models to explain unexpected results obtained for two crosses. One model involved five interacting loci and the other employed two loci displaying only additive and additive × additive gene action.Journal Paper No. J-9231 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa 50011. Project No. 2152     

Genetics of Heading Time in Wheat (TRITICUM AESTIVUM L.). I. the Inheritance of Photoperiodic Response

The inheritance of photoperiodic response was studied in crosses involving four spring wheats (Sonora 64, Pitic 62, Justin and Thatcher) and three winter wheats (Blackhull, Early Blackhull and Extra Early Blackhull). The parental cultivars were classified into a photoperiod-sensitive group (Justin, Thatcher, Blackhull and Early Blackhull) and a relatively photoperiod-insensitive group (Sonora 64, Pitic 62 and Extra Early Blackhull) based on their heading response when vernalized and grown under different daylength regimes.-F(1) data indicated that daylength insensitivity is not always dominant over day-length sensitivity and that the dominance relationship with respect to photoperiodic response depends on the alleles present in the parents. The heading patterns after vernalization and growth under short days of F(1), F(2), F(3) and backcross generations of a 4-parent diallel cross involving Justin, Sonora 64, Extra Early Blackhull and Blackhull could be satisfactorily explained on the basis of two major loci with three alleles at each locus. The genotype for each parent was suggested in terms of these loci. Genes with minor effects also influenced the photoperiodic response in a quantitative manner.-Diallel cross analysis of the number of days to heading (log scale) indicated significant additive and dominance genetic variances, a high average degree of dominance for earliness (photoperiod insensitivity) and a preponderance of recessive alleles in the parents acting in the direction of lateness (photoperiod sensitivity). Estimation of the genetic components of variation contained in the generation means of individual crosses (untransformed data) showed that, besides additivity and dominance, epistasis was also an important factor in the genetic control of photoperiodic response in wheat.     

Analysis of sugarcane mosaic virus resistance in maize in an isogenic dihybrid crossing scheme and implications for breeding potyvirus-resistant maize hybrids.

The gene action of 2 sugarcane mosaic virus (SCMV) resistance loci in maize, Scmv1 and Scmv2, was evaluated for potyvirus resistance in an isogenic background. All 4 homozygous and 5 heterozygous isogenic genotypes were produced for introgressions of the resistant donor (FAP1360A) alleles at both loci into the susceptible parent (F7) genetic background using simple sequence repeat markers. For SCMV and maize dwarf mosaic virus (MDMV), virus symptoms appeared rapidly in the 3 homozygous genotypes, with susceptibility alleles fixed at 1 or both loci. Although the 9 isogenic genotypes revealed a high level of resistance to Zea mosaic virus (ZeMV), the same 3 homozygous genotypes were only partially resistant. This indicates that 1 resistance gene alone is not sufficient for complete resistance against SCMV, MDMV, and ZeMV. Scmv1 showed strong early and complete dominant gene action to SCMV, but it gradually became partially dominant. Scmv2 was not detected at the beginning, showing dominant gene action initially and additive gene action at later stages. Both genes interacted epistatically (for a high level of resistance, at least 1 resistance allele at each of both loci is required). This implies that double heterozygotes at the 2 loci are promising for producing SCMVresistant hybrids. Results are discussed with respect to prospects for isolation of SCMV and MDMV resistance genes.     

Use of a novel outbred by inbred F1 cross to detect genetic markers for growth

A unique outbred by inbred F1 resource population was established. The population structure facilitated the unique opportunity of examining gene by genetic background interaction through crossing two modern broiler sires with dams from two unrelated inbred lines, with no selection for growth rate, to produce about 600 F1 chicks. Pools of DNA were generated from the phenotypic extremes (20% high and low) for 8-week body weight for each of the four combinations of sire and dam line. For one sire family, pools were also separately generated for each sex. The pools were genoyped with 25 informative (segregating) microsatellites. This unique F1 cross between outbred and inbred populations allowed use of the inbred alleles as an 'internal control' for polymerase chain reaction amplification quality in DNA pools. Ten microsatellites showed marked differences (P < 0.05) in allele frequencies between high and low pools, suggesting an association between marker and quantitative trait loci (QTL). These differences were verified using selective genotyping. For many markers, differences in allele frequencies between the high and the low pools, or marker effect, varied between the two dam lines and the two sexes, suggesting an interaction between some genes and the genetic background as represented by different dam lines or sexes. The suggestive marker-QTL associations identified in this F1 population demonstrate the efficiency of this population design while different QTL effects in different genetic line crosses and sexes highlight the importance of gene by genetic background interaction in QTL detection.     

Transmission ratio distortion in Arabidopsis lyrata: effects of population divergence and the S-locus

We investigated transmission ratio distortion within an Icelandic population of Arabidopsis lyrata using 16 molecular markers unlinked to the S-locus. Transmission ratio distortion was found more often than expected by chance at the gametic level, but not at the genotypic or zygotic level. The gametic effect may be due to meiotic drive or selection acting postmeiotically. At the gametic level, 10.9% of the tests were significant, which is substantially lower than earlier observed in an interpopulation cross (allowing for differences in power)-suggesting that the high level of transmission ratio distortion in the interpopulation cross is due to population divergence. It is also substantially lower than previously observed in intrapopulation crosses at the self-incompatibility locus, suggesting inherent fitness differences of the self-incompatibility alleles. We discuss the possible role of deleterious alleles accumulating at loci under balancing selection. Zygotic effects play a larger role in the interpopulation cross than in the intrapopulation crosses suggesting that Dobzhansky-Muller incompatibilities may be accumulating between the widely diverged populations.     

Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. II. Grain yield components

The genetic basis underlying inbreeding depression and heterosis for three grain yield components of rice was investigated in five interrelated mapping populations using a complete RFLP linkage map, replicated phenotyping, and the mixed model approach. The populations included 254 F(10) recombinant inbred lines (RILs) derived from a cross between Lemont (japonica) and Teqing (indica), two backcross (BC) and two testcross populations derived from crosses between the RILs and the parents plus two testers (Zhong413 and IR64). For the yield components, the RILs showed significant inbreeding depression and hybrid breakdown, and the BC and testcross populations showed high levels of heterosis. The average performance of the BC or testcross hybrids was largely determined by heterosis. The inbreeding depression values of individual RILs were negatively associated with the heterosis measurements of the BC or testcross hybrids. We identified many epistatic QTL pairs and a few main-effect QTL responsible for >65% of the phenotypic variation of the yield components in each of the populations. Most epistasis occurred between complementary loci, suggesting that grain yield components were associated more with multilocus genotypes than with specific alleles at individual loci. Overdominance was also an important property of most loci associated with heterosis, particularly for panicles per plant and grains per panicle. Two independent groups of genes appeared to affect grain weight: one showing primarily nonadditive gene action explained 62.1% of the heterotic variation of the trait, and the other exhibiting only additive gene action accounted for 28.1% of the total trait variation of the F(1) mean values. We found no evidence suggesting that pseudo-overdominance from the repulsive linkage of completely or partially dominant QTL for yield components resulted in the overdominant QTL for grain yield. Pronounced overdominance resulting from epistasis expressed by multilocus genotypes appeared to explain the long-standing dilemma of how inbreeding depression could arise from overdominant genes.     

Cleft palate: more genetic lessons from mice

Cleft palate occurred in high frequency (14%) in the F2 generation of the cross between two stocks of mice, LGG and SELH, neither of which produces more than 2% cleft palate. The cleft palate trait results from a new combination of alleles that is not present in either parental stock. The lack of cleft palate in the F2 generation after outcrosses of both parental stocks to other strains shows that this new combination of alleles has specific contributions from both parental strains, and also that there must be at least two loci involved. A deficiency of Mod-1 homozygotes in the SELH/LGG F2 adults suggests that one of the loci involved may be linked to Mod-1 and that the number of loci involved is few. Significantly more F2 males (19%) than females (9%) were affected with cleft palate. The data can be explained by a two-locus epistatic model with a dominant mutation (P) at one locus that causes cleft palate when not suppressed by or compensated for by a dominant allele (S) at a second locus. The parental stocks would be PPSS and ppss. In the F2 generation, the new combinations PPss and Ppss would express cleft palate, a total expected of 19%. Similar new combinations of alleles at two loci may explain some instances of high occurrence of cleft palate or other developmental threshold traits in previously unaffected human families.     

Isolation and Genetic Analysis of Mutations at the SerH Immobilization Antigen Locus of TETRAHYMENA THERMOPHILA

Multiple alleles at the SerH locus specify the major cell surface protein (immobilization antigen) of the ciliate Tetrahymena thermophila. Following mutagenesis of SerH1 homozygotes, two mutations, H1-1 and H1-2, were recovered in heterozygous form. Mutant homozygotes do not express H1 antigen, nor is H1 expressed in F1 progeny of crosses to wild-type strains homozygous for SerH2 or SerH3. H1-1 and H1-2 segregate without recombination from these wild-type alleles in expected F2 and testcross Mendelian ratios. H1-1 and H1-2 do, however, complement each other to express H1 antigen. Experiments suggest this complementation is due neither to recombination during macronuclear development nor to interallelic complementation of defective SerH1 gene products. These results suggest that SerH1 is intact in one mutant, and possibly both, although no such allele has been segregated in testcross progeny (N = 205). The hypothesis is presented that complementation between H1-1 and H1-2 is due to interaction between allele-specific regulators closely linked to the SerH1 gene.     

The nature of gene action in a Nicotiana rustica cross revealed by the recombinant inbred and second-cycle hybrid analysis

 A unique set of data recorded on 60 randomly extracted single-seed-descent (F_∞) lines of a highly heterotic cross between two varieties of Nicotiana rustica and their 870 reciprocally produced pairwise crosses, the second-cycle hybrids (SCH), are analysed to investigate the true nature of genetical control in the cross and the results are compared with those in earlier publications. The analysis revealed that epistasis, genotype-by-micro-environmental interaction, maternal effects and linkage are significant for several characters and the additive and non-additive components of variation take large values for all of the traits. Epistasis is predominantly duplicate and not complementary. Dominance is high but partial, all estimates of dominance ratio lying between 0.5 and 0.9. Dominance is predominantly unidirectional for leaf length, leaf width and final height, while for the remaining traits, some genes show ambidirectional dominance, although the incidence of unidirectional dominance is much higher throughout. The direction of dominance is predominantly for the increased score, except for flowering time where alleles conferring earliness are up to five times more frequently dominant. The present study has also confirmed that the F₂ and SCH_i distributions are very similar and that the former can be used to predict the transgression in the latter with confidence. The reduced range of the SCH _i families compared to the recombinant inbreds, further indicated that heterosis among many of the SCH_i is due to gene dispersion and there is little evidence for the presence of over-dominance. Received: 8 July 1996 / Accepted: 8 November 1996     

The genetic basis of naturally occurring pollen color dimorphisms in Nigella degenii (Ranunculaceae)

Nigella degenii ssp. barbro and ssp. jenny differ from related taxa in being dimorphic for pollen color, with some plants having dark pollen and others light pollen. In this study we performed experimental crosses to determine whether the difference in pollen color is governed by few or many loci and whether the two subspecies utilize the same gene to control pollen color. Patterns of segregation in crosses between morphs show that dark pollen is dominant over light pollen and that a single major gene is responsible for most of the variation in pollen color. Consequently it should be relatively easy for pollen color dimorphisms to establish and spread in these subspecies. Aberrant segregation ratios were attributed to genetic factors that reduced the expression of the allele conferring dark pollen or processes that sorted between color morphs during seed development. Crosses between dark pollen plants from different subspecies showed signs of complementation in the F2 generation, but the frequency of the light morph was too low to support a model involving complementary action of recessive alleles at two separate loci. Based on this and other observations, we hypothesize that the pollen color difference is controlled by the same major locus in the two subspecies.     

Self-incompatibility in passionfruit: evidence of gametophytic-sporophytic control

Self-incompatibility in passionfruit was studied in families originated from crosses among plants that presented differences in reciprocal crosses. The three families, obtained by crossing S(3) plants, exhibited one incompatible group; no reciprocal differences were observed. The phenotype of the families was the same as the parent plants, S(3). These results suggest the presence of a gene ( G), gametophytic in its action, associated to the sporophytic gene S, modifying the incompatibility reaction in passionfruit. The reciprocal difference exhibited in the crosses among the parents could be explained as a matching between plants homozygous for S, but homozygous and heterozygous for G. Actually this would be a partially compatible cross, not detectable when the evaluation is done based on fruit set data. As the family originated from this kind of cross is homozygous for S and heterozygous for G, no reciprocal differences are expected, and the phenotype should be the same as the parental plants, as observed in the present work.     

Genetics of nodulation in Chickpea (Cicer arietinum L.)

Combining ability, components of genetic variance and graphic analysis revealed that nodulation in the cultivars of Chickpea (Cicer arietinum L.) under study, was predominantly under the control of non-additive gene action although substantial additive effect was also present. The crosses giving high specific combining ability effects also manifested highly significant positive heterosis. The parents F-61, Giza and Annegiri possessed mostly dominant alleles while Phule G-5, NEC-249 and N-31 possessed mostly recessive alleles having positive effect on nodule weight.     

Linkage Group Selection--a fast approach to the genetic analysis of malaria parasites

Genetic analysis of malaria parasites has shown that the mechanisms of inheritance in these organisms are classically Mendelian. In other words, alleles of genes at different loci recombine, and alleles at the same gene locus segregate, in the progeny of a genetic cross between two genetically distinct lines of malaria parasite. Importantly, such progeny are haploid in the first filial generation following genetic crossing. Consequently, genetic analysis, including linkage analysis, can be done directly upon the cloned cross progeny. Linkage analysis conducted upon the progeny of genetic crosses between malaria parasites can lead to the location of a single gene controlling a specific phenotype, as has been achieved to identify the gene for chloroquine resistance in Plasmodium falciparum. The work involved, however, is extremely labour intensive. It involves the generation of many hundreds, to a thousand or so, of independent recombinant clones from the cross progeny and the biological characterisation, and genetic typing for hundreds of molecular genetic markers of each such clone. We discuss here a fast-track method for identifying genes controlling specific phenotypes, e.g. drug resistance/sensitivity. It involves the mass screening with quantitative molecular genetic markers of the uncloned progeny of a genetic cross following its growth under a selection pressure representing the phenotype of interest. We have called the method Linkage Group Selection.     

Inheritance of partial resistance to powdery mildew in spring wheat

Summary Four spring wheat (Triticum aestivum L.) cultivars exhibiting partial resistance to powdery mildew induced by Erysiphe graminis f.sp. tritici were crossed to a common susceptible cultivar to study the inheritance of resistance. The genetic parameters contributing to resistance were estimated by generation means analyses. Additive gene action was the most important genetic component of variation among generation means in all four crosses. Additive by additive effects were significant in one cross and both additive by additive and additive by dominance effects were significant in another. Dominance effects were not significant. The F2/F3 correlations in three crosses ranged from 0.27 to 0.43. Three additional crosses among resistant cultivars were employed to study the effectiveness of selection in improving resistance. By selecting the most resistant plants from the F2 and evaluating the progenies in the F4, increases in resistance ranging from 21% to 31% were obtained. In all crosses, there was transgressive segregation in both directions indicating that the genes conferring resistance to these cultivars differ and exhibit additive effects.     

Estimating the number of genes in a polygenic system by genotype assay.

A new method, genotype assay, is described for estimating k the number of genes or more strictly the number of effective factors responsible for variation of a continuous kind. The central feature is the determination of the proportion of individuals in the Fn generation of a cross between two pure breeding lines that are heterozygous at, at least, one locus by an assay of their Fn+2 grand progeny families. The observed proportion is then equated to a theoretical expectation which is a function of the number of genes involved. Expectations generalised to cover any generation n for experimental designs in which every Fn individual is assayed by comparing two Fn+2 grand progeny families have been derived for two limiting cases; one in which all genotypic differences are expressed as phenotypic differences and the other where the expression is minimised by imposing the maximum and relational balancing out of the contributions of individual gene loci. Equating the observed proportion of heterozygotes to these expectations therefore, leads to an upper and a lower estimate of k corresponding with these two limiting conditions. The reliability and sensitivity of the estimates depends primarily on n the generation chosen for study, the number of individuals (m) assayed from that generation and the number of individuals (l) raised in each Fn+2 grand progeny family. The two variables m and l being the principal determinants of the variances of the family means set the lower limit to the size of the gene effects that can be detected. The method is illustrated by assays of the F3 and F5 generations of two crosses between conditioned lines of Nicotiana rustica for three characters. The estimates are, without exception, as great as or greater than those obtained by alternative procedures. They show large, consistent increases between the F3 and F5 that cannot be traced to greater sensitivity of the latter generation and hence are presumably genuine.     

Genetic association of crown rust resistance gene Pc68, storage protein loci, and resistance gene analogues in oats

Segregating F(3) families, derived from a cross between oat cultivar Swan and the putative single gene line PC68, were used to determine the association of seed storage protein loci and resistance gene analogues (RGAs) with the crown rust resistance gene Pc68. SDS-PAGE analysis detected three avenin loci, AveX, AveY, and AveZ, closely linked to Pc68. Their diagnostic alleles are linked in coupling to Pc68 and were also detected in three additional lines carrying Pc68. Another protein locus was linked in repulsion to Pc68. In complementary studies, three wheat RGA clones (W2, W4, and W10) detected restriction fragment length polymorphisms (RFLPs) between homozygous resistant and homozygous susceptible F(3) DNA bulks. Four oat homologues of W2 were cloned and sequenced. RFLPs detected with two of them were mapped using F(3) and F(4) populations. Clone 18 detected a locus, Orga2, linked in repulsion to Pc68. Clone 22 detected several RFLPs including Orga1 (the closest locus to Pc68) and three RGA loci (Orga22-2, Orga22-3, and Orga22-4) loosely linked to Pc68. The diagnostic RFLPs linked in coupling to Pc68 were detected by clone 22 in three additional oat lines carrying Pc68 and have potential utility in investigating and improving crown rust resistance of oat.     

Healing quantitative trait loci in a combined cross analysis using related mouse strain crosses

Inbred mouse strains MRL and LG share the ability to fully heal ear hole punches with the full range of appropriate tissues without scarring. They also share a common ancestry, MRL being formed from a multi-strain cross with two final backcrosses to LG before being inbred by brother-sister mating. Many gene-mapping studies for healing ability have been performed using these two strains, resulting in the location of about 20 quantitative trait loci (QTLs). Here, we combine two of these crosses (N = 638), MRL/lpr × C57BL/6NTac and LG/J × SM/J, in a single combined cross analysis to increase the mapping power, decrease QTL support intervals, separate multiple QTLs and establish allelic states at individual QTL. The combined cross analysis located 11 QTLs, 6 affecting only one cross (5 LG × SM and 1 MRL × B6) and 5 affecting both crosses, approximately the number of common QTLs expected given strain SNP similarity. Amongst the five QTLs mapped in both crosses, three had significantly different genetic effects, additive in one cross and over or underdominant in the other. It is possible that allelic states at these three loci are different in SM and B6 because they lead to differences in dominance interactions with the LG and MRL alleles. QTL support intervals are 40% smaller in the combined cross analysis than in either of the single crosses. Combined cross analysis was successful in enhancing the interpretation of earlier QTL results for these strains.