Dissection of the genetic basis of heterosis in an elite maize hybrid by QTL mapping in an immortalized F2 population

The genetic basis of heterosis for grain yield and its components was investigated at the single- and two-locus levels using molecular markers with an immortalized F₂ (IF₂) population, which was developed by pair crosses among recombinant inbred lines (RILs) derived from the elite maize hybrid Yuyu22. Mid-parent heterosis of each cross in the IF₂ population was used to map heterotic quantitative trait loci. A total of 13 heterotic loci (HL) were detected. These included three HL for grain yield, seven for ear length, one for ear row number and two for 100-kernel weight. A total of 143 digenic interactions contributing to mid-parent heterosis were detected at the two-locus level involving all three types of interactions (additive × additive = AA, additive × dominance = AD or DA, dominance × dominance = DD). There were 25 digenic interactions for grain yield, 36 for ear length, 31 for ear row number and 51 for 100-kernel weight. Altogether, dominance effects of HL at the single-locus level as well as AA interactions played an important role in the genetic basis of heterosis for grain yield and its components in Yuyu22.     

Potential genetic variance and the domestication of maize

Since Darwin, there has been a long and arduous struggle to understand the source and maintenance of natural genetic variation and its relationship to phenotype. The reason that this task is so difficult is that it requires integration of detailed, and as yet incomplete, knowledge from several biological disciplines, including evolutionary, population, and developmental genetics. In this 'post-genomic' era, it is relatively easy to identify differences in the DNA sequence between individuals. However, the task remains to delineate how this abundant genetic diversity actually contributes to phenotypic diversity. This necessitates tackling the problem of hidden genetic variation. Genetic polymorphisms can be conditionally cryptic, but have the potential to contribute to phenotypic variation in particular genetic backgrounds or under specific environmental conditions. A recent paper by Lauter and Doebley highlights the contribution of hidden genetic variation to traits characterizing the morphological evolution of modern maize from its wild grass-like progenitor teosinte.1 This work is the first to demonstrate hidden variance for selected (agronomically 'adaptive') traits in a well-characterized model for morphological evolution.     

Increased genetic variance after a population bottleneck

A conventional view holds that population bottlenecks cause massive losses of genetic variability, thus endangering the viability of the derived population. Although some alleles that were infrequent in the parent population may be lost new empirical evidence from Drosophila and housefly populations has demonstrated that genetic variance available to selection may actually increase following a single severe bottleneck. Several theoretical models support this view, and suggest that the increase may result from conversion of balanced epistatic variance to additive variance that becomes immediately available to selection. These effects appear to be greatest on the inheritance of quantitative characters, releasing new variance through the disruption of covariance matrices that underlie and interrelate quantitative traits. Thus, character change in adaptation and speciation may, in some instances, be promoted by founder events.     

Heritabilities and genetic correlations for reproductive traits in an F2 reciprocal cross chicken population

Studies estimating genetic parameters for reproductive traits in chickens can be useful for understanding and improvement of their genetic architecture. A total of 1276 observations of fertility (FERT), hatchability of fertile eggs (HFE) and hatchability of total eggs (HTE) were used to estimate the genetic and phenotypic parameters of 467 females from an F2 population generated by reciprocal crossing between a broiler line and a layer line, which were developed through a poultry genetics breeding program, maintained by Embrapa Swine and Poultry, Concordia, Santa Catarina, Brazil. Estimates of heritability and genetic and phenotypic correlations were obtained using restricted maximum likelihood calculations under the two-trait animal model, including the fixed effect of group (hatching of birds from the same genetic group) and the random additive genetic and residual effects. The mean percentages for FERT, HFE and HTE were 87.91 ± 19.77, 80.07 ± 26.81 and 70.67 ± 28.55%, respectively. The highest heritability estimate (h(2)) was 0.28 ± 0.04 for HTE. Genetic correlations for FERT with HFE (0.43 ± 0.17), HFE with HTE (0.98 ± 0.02) and FERT with HTE (0.69 ± 0.10) were positive and significant. Individuals with high breeding value for HTE would have high breeding values for HFE and FERT because of the high genetic association between them. These results suggest that HTE should be included as a selection criterion in genetic breeding programs to improve the reproductive performance of chickens, because HTE had the highest heritability estimate and high genetic correlation with FERT and HFE, and it is the easiest to measure.     

Partitioning of population genetic variance under multiplicative-epistatic gene action

Determining the way in which different QTLs interact (epistasis) in their effects on the phenotype is crucial to many areas in population genetics and evolutionary biology. For example, in the founder event, a separated population readapts to a new environment through the release of cryptic gene-gene interactions. In hybrid zones, hybrid speciation must be subjected to natural selection for epistasis resulting from genomic recombinations between different species. However, there is a severe shortage of relevant methodologies to estimate epistatic genetic effects and variances. A statistical model has recently been proposed to estimate the number of QTLs, their genetic effects and allelic frequencies in segregating populations. This model is based on multiplicative gene action and derived from a two-level intra- and interspecific mating design. In this paper, we formulate a statistical procedure for partitioning the genetic variance into additive, dominant and various kinds of epistatic components in an intra- or mixed intra- and interspecific hybrid population. The procedure can be used to study the genetic architecture of fragmented populations and hybrid zones, thus allowing for a better recognition of the role of epistasis in evolution and hybrid speciation. A real example for two Populus species, P. tremuloides and P. tremula, is provided to illustrate the procedure. In this example, we found that considerable new genetic variation is formed through genomic recombination between two aspen species. Received: 1 May 1999 / Accepted: 27 July 1999     

Argentine population genetic structure: large variance in Amerindian contribution

Argentine population genetic structure was examined using a set of 78 ancestry informative markers (AIMs) to assess the contributions of European, Amerindian, and African ancestry in 94 individuals members of this population. Using the Bayesian clustering algorithm STRUCTURE, the mean European contribution was 78%, the Amerindian contribution was 19.4%, and the African contribution was 2.5%. Similar results were found using weighted least mean square method: European, 80.2%; Amerindian, 18.1%; and African, 1.7%. Consistent with previous studies the current results showed very few individuals (four of 94) with greater than 10% African admixture. Notably, when individual admixture was examined, the Amerindian and European admixture showed a very large variance and individual Amerindian contribution ranged from 1.5 to 84.5% in the 94 individual Argentine subjects. These results indicate that admixture must be considered when clinical epidemiology or case control genetic analyses are studied in this population. Moreover, the current study provides a set of informative SNPs that can be used to ascertain or control for this potentially hidden stratification. In addition, the large variance in admixture proportions in individual Argentine subjects shown by this study suggests that this population is appropriate for future admixture mapping studies.     

Relative changes in genetic variability and correlations in an early-maturing maize population during recurrent selection

Four cycles of S(1) family recurrent selection to improve grain yield and resistance to Striga hermonthica have been completed in TZE-Y Pop STR C(0.) In order to determine whether or not to continue with the recurrent scheme, it was desirable to evaluate the amount of residual genetic variance and associated parameters in the population. The objective of this study was to characterize the relative changes in the levels of the genetic variances, heritability estimates and genetic correlation coefficients, and to predict future gains from selection for grain yield, Striga resistance and other agronomic traits. Fifty S(1) families, derived from each cycle, were evaluated under Striga-infested and Striga-free conditions at Mokwa, Ikenne and Abuja, Nigeria, in 2005 and 2007. Under Striga infestation, genetic variances for grain yield, days to anthesis, plant height and Striga damage generally increased in the advanced cycles of selection. In contrast, the genetic variances for days to silk, anthesis-silking interval, ears per plant, ear aspect and number of emerged Striga plants decreased with selection. The advanced cycles of selection significantly out-yielded the original cycle in both research environments. Heritabilities for grain yield, Striga damage and number of emerged Striga plants were significantly greater than zero. The realized gains from selection for grain yield under Striga infestation (52?kg?ha(-1)?cycle(-1)) and Striga-free conditions (130?kg?ha(-1)?cycle(-1)) were remarkably lower than the predicted gains (350 and 250?kg?ha(-1?)cycle(-1), respectively). Adequate genetic variability exists in cycle 4 of the scheme to ensure future gains from selection.     

Joint effect of selection, linkage and partial inbreeding on additive genetic variance in an infinite population

Under the inifinitesimal model of gene effects, selection reduces the additive genetic variance by inducing negative linkage disequilibrium among selected genes. If the selected genes are linked, the decay of linkage disequilibrium is delayed, and the reduction of additive genetic variance is enhanced. Inbreeding in an infinite population also alters the additive genetic variance through the generation of positive association among genes within a locus. In the present study, the joint effect of selection, linkage and partial inbreeding (partial selfing or partial full-sib mating) on the additive genetic variance was modeled. The recurrence relations of the additive genetic variance between successive generations and the prediction equation of the asymptotic additive genetic variance were derived. Numerical computation showed that although partially inbred populations initially maintain larger genetic variances, the accumulated effect of selection overrides the effect of inbreeding. Stochastic simulation was carried out to check the precision of prediction, showing that the obtained equations give a satisfactory prediction during initial generations. However, the predicted values always overestimate the simulated values, especially in later generations. Based on these results, possible extensions and perspectives of the assumed model were discussed.     

Nonrandom mating in an open-pollinated maize population

Randomness of fertilization was studied in an open-pollinated population of maize (Zea mays L.) through allozyme assays of seedlings from open-pollinated seeds produced on both tasseled and detasseled plants. Mixed-mating-model estimates of the amount of outcrossing (t) were not significantly different from t = 1.00 for four enzyme loci ( Adh1, Idh2, Got1 and Acp1), indicating that fertilizations were at random in the population. However, for loci Prx1 and Est4 , estimates of t were significantly smaller than unity—0.80 and 0.70 for tasseled plants and 0.81 and 0.80 for detasseled plants. The excesses of homogametic fertilizations detected on the detasseled plants could not have been due to selffertilization, s = 1 - t, because the detasseled plants shed no pollen. Analyses of allelic frequencies in the pollen that produced seed on the detasseled plants established that different maternal plants sampled genetically different populations of pollen from the outcross pollen pool. It was suggested that the causes of the differential sampling were temporal variation in the pollen pool, and/or gametophytic selection, correlated with marker-locus genotype. Two-, three- and four-locus interactions among the marker loci were often statistically significant, indicating that the factors responsible for the nonrandom gametic unions observed in the maize population studied were complexly interactive.     

Artificial selection and maintenance of genetic variance in the global dairy cow population

Genetic improvement of dairy cows, which has increased the milk yield of cows in the UK by 1200 kg per lactation in 12 years, is an excellent example of the application of quantitative genetics to agriculture. The most important traits of dairy cattle are expressed only in females, but the main opportunity for selection is in males. Despite this, genetic improvement was achieved by the invention of a new statistical methodology, called 'best linear unbiased prediction' to estimate the breeding value of bulls. Intense selection of the best bulls, combined with the worldwide use of these bulls through artificial insemination and frozen semen, has created a global population and caused concern that the genetic variation available in the future will be reduced. Maintenance of genetic variation and long-term genetic gains would be aided by rational payment systems, use of crossbreeding where profitable, inclusion of all economically important traits in the breeding objective, recognition of genotype by environment interactions and the use of selection algorithms that balance estimated breeding value against the average relationship among the selected animals. Fortunately, all of these things are happening to some degree.     

Associations between quantitative traits and enzyme loci in the F2 population of a maize hybrid

Summary Univariate and multivariate analyses were used to identify associations between eight enzyme marker loci and 11 quantitative traits of maize (Zea mays L.). The material analyzed included inbred lines Wf9 and Pa405, single-cross hybrid Wf9 X Pa405, and the F2 generation of the selfed single-cross hybrid. Each enzyme locus assayed was associated with at least one quantitative trait, and all quantitative traits were associated with genotypes at particular enzyme loci. Significant associations also were found between the level of heterozygosity per individual and nine of 11 quantitative traits. The total contribution to heterosis, for seed yield per plant, of genes linked with the eight enzyme loci, was 27% of the F2 mean and 18% of the difference in mean between the F1 hybrid and the inbred parents. Genes linked with Glu1 accounted for nearly one third of the total dominance effect detected by the eight enzyme loci. The chromosome segments marked by loci with significant effects on seed yield were markedly overdominant. The large heterotic effects of chromosome segments marked by particular loci suggest that enzyme loci could be used to help transfer genes responsible for heterosis to inbred lines. We conclude that analyses of additional inbred lines, F1 hybrids, and F2 populations in more environments will halp identify specific associations between enzyme loci, or chromosome segments which they mark, and important agronomic traits.Cooperative investigations of the USDA, ARS and Dept. of Plant Sciences, South Dakota State Univ. (SDSU), Brookings, Journal Series No. 2039; and the Institute of Animal Resource Ecology, Univ. of British Columbia, Vancouver, B.C. V6T 1W5, Canada     

Identification of genetic variants associated with maize flowering time using an extremely large multi‐genetic background population

Flowering time is one of the major adaptive traits in domestication of maize and an important selection criterion in breeding. To detect more maize flowering time variants we evaluated flowering time traits using an extremely large multi‐ genetic background population that contained more than 8000 lines under multiple Sino‐United States environments. The population included two nested association mapping (NAM) panels and a natural association panel. Nearly 1 million single‐nucleotide polymorphisms (SNPs) were used in the analyses. Through the parallel linkage analysis of the two NAM panels, both common and unique flowering time regions were detected. Genome wide, a total of 90 flowering time regions were identified. One‐third of these regions were connected to traits associated with the environmental sensitivity of maize flowering time. The genome‐wide association study of the three panels identified nearly 1000 flowering time‐associated SNPs, mainly distributed around 220 candidate genes (within a distance of 1 Mb). Interestingly, two types of regions were significantly enriched for these associated SNPs – one was the candidate gene regions and the other was the approximately 5 kb regions away from the candidate genes. Moreover, the associated SNPs exhibited high accuracy for predicting flowering time.     

Construction of a genetic linkage map of the model legume Lotus japonicus using an intraspecific F2 population.

Among leguminous plants, the model legume Lotus japonicus (Regel) Larsen has many biological and genetic advantages. We have developed a genetic linkage map of L. japonicus based on amplified fragment length polymorphism (AFLP), simple sequence repeat polymorphism (SSRP) and derived cleaved amplified polymorphic sequence (dCAPS). The F2 mapping population used was derived from a cross between two L. japonicus accessions Gifu B-129 and Miyakojima MG-20. These parental accessions showed remarkable cytological differences, particularly with respect to size and morphology of chromosomes 1 and 2. Using fluorescence in situ hybridization (FISH) with BAC clones from Gifu B-129 and TAC (Transformation-competent Artificial Chromosome) clones from Miyakojima MG-20, a reciprocal translocation was found to be responsible for the cytological differences between chromosomes 1 and 2. The borders of the translocations were identified by FISH and by alignment toward the L. filicaulis x L. japonicus Gifu B-129 linkage map. The markers from the main translocated region were located on linkage groups 1 and 2 of the two accessions, Gifu B-129 and Miyakojima MG-20, respectively. The framework of the linkage map was constructed based on codominant markers, and then dominant markers were integrated separately in each linkage group of the parents. The resulting linkage groups correspond to the six pairs of chromosomes of L. japonicus and consist of 287 markers with 487.3 cM length in Gifu B-129 and 277 markers with 481.6 cM length in Miyakojima MG-20. The map and marker information is available through the World Wide Web at http://www.kazusa.or.jp/lotus/.     

Association mapping in an elite maize breeding population

Association mapping (AM) is a powerful approach to dissect the genetic architecture of quantitative traits. The main goal of our study was to empirically compare several statistical methods of AM using data of an elite maize breeding program with respect to QTL detection power and possibility to correct for population stratification. These models were based on the inclusion of cofactors (Model A), cofactors and population effect (Model B), and SNP effects nested within populations (Model C). A total of 930 testcross progenies of an elite maize breeding population were field-evaluated for grain yield and grain moisture in multi-location trials and fingerprinted with 425 SNP markers. For grain yield, population stratification was effectively controlled by Model A. For grain moisture with a high ratio of variance among versus within populations, Model B should be applied in order to avoid potential false positives. Model C revealed large differences among allele substitution effects for trait-associated SNPs across multiple plant breeding populations. This heterogeneous SNP allele substitution effects have a severe impact for genomic selection studies, where SNP effects are often assumed to be independent of the genetic background.     

Genetic variance in the F2 generation of divergently selected parents

 Either by selective breeding for population divergence or by using natural population differences, F₂ and advanced generation hybrids can be developed with high variances. We relate the size of the genetic variance to the population divergence based on a forward and backward mutation model at a locus with two alleles with additive gene action. The effects of population size and initial gene frequency are also explored. Larger parental population sizes increase the F₂ genetic variance if the initial probability distribution is uniform or U-shaped. However, population size has the opposite effect if the initial distribution of gene frequencies is skewed such as it would be with newly arriving alleles. These alleles contribute to the genetic variance sooner when the selection pressure is higher or when the effective population size is smaller. Received: 5 April 1998 / Accepted: 22 April 1998     

Resistance of F1, F2 and BC1 generations to maize dwarf mosaic virus in maize

Computer simulations with GTLAUS 3.7 were performed to investigate the influence of different cases of increasing temperatures on the tritrophic wheat ‐ cereal aphid ‐ predator interaction. Two cases of a temperature increase were defined: (1) homogenous increase by adding 3°C, and (2) comparable increase with relatively wanner nights. Both cases of increasing temperatures with similar daily average values resulted in a significant reduction of aphid infestation, but this reduction was smaller in scenarios with relatively higher night temperatures. But the results indicate only relatively small differences deriving from this particularly high night temperatures.