Prediction of testcross means and variances among F3 progenies of F1 crosses from testcross means and genetic distances of their parents in maize

 Prediction of the means and genetic variances in segregating generations could help to assess the breeding potential of base populations. In this study, we investigated whether the testcross (TC) means and variances of F₃ progenies from F₁ crosses in European maize can be predicted from the TC means of their parents and F₁ crosses and four measures of parental genetic divergence: genetic distance (GD) determined by 194 RFLP or 691 AFLP^{TM 1} markers, mid-parent heterosis (MPH), and absolute difference between the TC means of parents (∣P₁−P₂∣). The experimental materials comprised six sets of crosses; each set consisted of four elite inbreds from the flint or dent germplasm and the six possible F₁ crosses between them, which were evaluated for mid-parent heterosis. Testcross progenies of these materials and 20 random F₃ plants per F₁ cross were produced with a single-cross tester from the opposite heterotic group and evaluated in two environments. The characters studied were plant height, dry matter content and grain yield. The genetic distance between parent lines ranged between 0.17 and 0.70 for RFLPs and between 0.14 and 0.57 for AFLPs in the six sets. Testcross-means of parents, F₁ crosses, and F₃ populations averaged across the six crosses in a particular set generally agreed well for all three traits. Bartlett’s test revealed heterogeneous TC variances among the six crosses in all sets for plant height, in four sets for grain yield and in five sets for dry matter content. Correlations among the TC means of the parents, F₁ crosses, and F₃ populations were highly significant and positive for all traits. Estimates of the TC variance among F₃ progenies for the 36 crosses showed only low correlations with the four measures of parental genetic divergence for all traits. The results demonstrated that for our material, the TC means of the parents or the parental F₁ cross can be used as predictors for the TC means of F₃ populations. However, the prediction of the TC variance remains an unsolved problem. Received: 4 August 1997 / Accepted: 17 November 1997     

QTL analysis of early stage heterosis for biomass in Arabidopsis

The main objective of this study was to identify genomic regions involved in biomass heterosis using QTL, generation means, and mode-of-inheritance classification analyses. In a modified North Carolina Design III we backcrossed 429 recombinant inbred line and 140 introgression line populations to the two parental accessions, C24 and Col-0, whose F ₁ hybrid exhibited 44% heterosis for biomass. Mid-parent heterosis in the RILs ranged from ?31 to 99% for dry weight and from ?58 to 143% for leaf area. We detected ten genomic positions involved in biomass heterosis at an early developmental stage, individually explaining between 2.4 and 15.7% of the phenotypic variation. While overdominant gene action was prevalent in heterotic QTL, our results suggest that a combination of dominance, overdominance and epistasis is involved in biomass heterosis in this Arabidopsis cross.     

Molecular marker assisted broadening of the Central European heterotic groups in rye with Eastern European germplasm

Broadening the genetic base of heterotic pools is a key to ensure continued genetic gains in hybrid breeding and extend hybrid cultivation to new areas. In the present study, two Central European heterotic pools (Carsten and Petkus) and five Eastern European open-pollinated varieties (OPVs, Pop-1 to Pop-5) were studied with the objectives to (1) investigate the genetic diversity in OPVs and the heterotic pools using molecular and field data, (2) evaluate the molecular diversity among OPVs, (3) examine the combining ability for grain yield of the OPVs when crossed with testers in field trials, and (4) develop a strategy for targeted introgression of OPV germplasm into the heterotic pools. In total, 610 S₀ plants, 347 from OPVs and 263 from heterotic pools, were developed. Clones of the S₀ plants of OPVs were crossed with two testers belonging to each heterotic pool, while clones of heterotic pools were crossed with only the opposite tester. Testcrosses were evaluated for grain yield in multi-location trials. In addition, 589 S₀ plants were fingerprinted with 30 SSR markers. The data revealed that the Carsten pool has a narrow genetic base and should be the primary target for broadening the established heterotic pattern. Mean and genetic variance suggested that Pop-2 and Pop-4 are good candidates for introgression in Petkus pool and Pop-5 in Carsten pool. Nevertheless, introgression of Pop-5 in Carsten could reduce the genetic diversity between heterotic pools. Therefore, we suggest that either selected plants of Pop-5 should be introgressed or more Eastern European germplasm should be fingerprinted and field evaluated to identify promising germplasm for broadening the established heterotic pattern.     

Broadening the genetic base of European maize heterotic pools with US Cornbelt germplasm using field and molecular marker data

Maize (Zea mays L.) breeders are concerned about the narrowing of the genetic base of elite germplasm. To reverse this trend, elite germplasm from other geographic regions can be introgressed, but due to lack of adaptation it is difficult to assess their breeding potential in the targeted environment. The objectives of this study were to (1) investigate the relationship between European and US maize germplasm, (2) examine the suitability of different mega-environments and measures of performance to assess the breeding potential of exotics, and (3) study the relationship of genetic distance with mid-parent heterosis (MPH). Eight European inbreds from the Dent and Flint heterotic groups, 11 US inbreds belonging to Stiff Stalk (SS), non-Stiff Stalk (NSS), and CIMMYT Pool 41, and their 88 factorial crosses in F₁ and F₂ generations were evaluated for grain yield and dry matter concentration. The experiments were conducted in three mega-environments: Central Europe (target mega-environment), US Cornbelt (mega-environment where donor lines were developed), and Southeast Europe (an intermediate mega-environment). The inbreds were also fingerprinted with 266 SSR markers. Suitable criteria to identify promising exotic germplasm were F₁ hybrid performance in the targeted mega-environment and F₁ and parental performance in the intermediate mega-environment. Marker-based genetic distances reflected relatedness among the inbreds, but showed no association with MPH. Based on genetic distance, MPH, and F₁ performance, we suggest to introgress SS germplasm into European Dents and NSS into European Flints, in order to exploit the specific adaptation of European flint germplasm and the excellent combining ability of US germplasm in European maize breeding programs.     

Temporal changes in allele frequencies in two European F2 flint maize populations under modified recurrent full-sib selection

Selection and random genetic drift are the two main forces affecting the selection response of recurrent selection (RS) programs by changes in allele frequencies. Therefore, detailed knowledge on allele frequency changes attributable to these forces is of fundamental importance for assessing RS programs. The objectives of our study were to (1) estimate the number, position, and genetic effect of quantitative trait loci (QTL) for selection index and its components in the base populations, (2) determine changes in allele frequencies of QTL regions due to the effects of random genetic drift and selection, and (3) predict allele frequency changes by using QTL results and compare these predictions with observed values. We performed QTL analyses, based on restriction fragment length polymorphisms (RFLPs) and simple sequence repeats (SSRs), in 274 F_2:3 lines of cross KW1265 × D146 (A × B) and 133 F_3:4 lines of cross D145 × KW1292 (C × D) originating from two European flint maize populations. Four (A × B) and seven (C × D) cycles of RS were analyzed with SSRs for significant allele frequency changes due to selection. Several QTL regions for selection index were detected with simple and composite interval mapping. In some of them, flanking markers showed a significant allele frequency change after the first and the final selection cycles. The correlation between observed and predicted allele frequencies was significant only in A × B. We attribute these observations mainly to (1) the high dependence of the power of QTL detection on the population size and (2) the occurrence of undetectable QTL in repulsion phase. Assessment of allele frequency changes in RS programs can be used to detect marker alleles linked to QTL regions under selection pressure. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Potential causes of linkage disequilibrium in a European maize breeding program investigated with computer simulations

Knowledge about the forces generating and conserving linkage disequilibrium (LD) is important for drawing conclusions about the prospects and limitations of association mapping. The objectives of our research were to examine the importance of (1) selection, (2) mutation, and (3) genetic drift for generating LD in a typical maize breeding program. We conducted computer simulations based on genotypic data of Central European maize open-pollinated varieties which have played an important role as founders of the European flint heterotic group. The breeding scheme and the dimensioning underlying our simulations reflect essentially the maize breeding program of the University of Hohenheim. Results suggested that in a plant breeding program of the examined dimension and breeding scheme, genetic drift and selection are major forces generating LD. The currently used population-based association mapping tests do not explicitly correct for LD caused by these two forces. Therefore, increased type I error rates are expected if these tests are applied to plant breeding populations. As a consequence, we recommend to use family-based association tests for association mapping approaches in plant breeding populations.     

Chilling tolerance of Central European maize lines and their factorial crosses

BACKGROUND AND AIMS: Chilling-stress tolerance is a prerequisite for maize production under cool climatic conditions. The main goal of this study was to evaluate the Central European dent and flint pools for chilling tolerance during heterotrophic and early autotrophic growth in field trials and growth chamber experiments. METHODS: Five European flint and five dent inbreds and their 25 factorial crosses were evaluated in six natural environments, where chilling occurred, for chlorophyll concentration and plant height at the three-leaf stage, and plant height and fresh weight at the seven-leaf stage. In growth chambers, leaf 3 growth was analysed under cold and control conditions. KEY RESULTS: Comparing the field and growth chamber data, the strongest association was found between leaf elongation rate during cold nights and plant height at the three-leaf stage, with a weaker association with the seven-leaf stage. In the field, moderate correlations were observed between plant height at the three-leaf stage, and plant height and fresh weight at the seven-leaf stage, respectively. Furthermore, mid-parent and hybrid performance were only moderately correlated. CONCLUSIONS: The results suggest that heterotrophic and early autotrophic growth stages are controlled by different genetic factors or that maternal effects play a role. In addition, the findings showed that mid-parent performance is a poor predictor of hybrid performance. Consequently, test cross performance should be the target in quantitiative trait locus (QTL) mapping studies with the final goal of establishing marker-assisted breeding programmes for chilling-tolerant hybrids.     

Linkage disequilibrium in European elite maize germplasm investigated with SSRs

Information about the extent and genomic distribution of linkage disequilibrium (LD) is of fundamental importance for association mapping. The main objectives of this study were to (1) investigate genetic diversity within germplasm groups of elite European maize (Zea mays L.) inbred lines, (2) examine the population structure of elite European maize germplasm, and (3) determine the extent and genomic distribution of LD between pairs of simple sequence repeat (SSR) markers. We examined genetic diversity and LD in a cross section of European and US elite breeding material comprising 147 inbred lines genotyped with 100 SSR markers. For gene diversity within each group, significant (P<0.05) differences existed among the groups. The LD was significant (P<0.05) for 49% of the SSR marker pairs in the 80 flint lines and for 56% of the SSR marker pairs in the 57 dent lines. The ratio of linked to unlinked loci in LD was 1.1 for both germplasm groups. The high incidence of LD suggests that the extent of LD between SSR markers should allow the detection of marker-phenotype associations in a genome scan. However, our results also indicate that a high proportion of the observed LD is generated by forces, such as relatedness, population stratification, and genetic drift, which cause a high risk of detecting false positives in association mapping.