Association of protein amount polymorphism (PAP) among maize lines with performances of their hybrids

Summary It has been suggested that molecular foundations of phenotypic diversity reside in the variability of genome expression. This variability can be appraised through the polymorphism of individual protein amounts (PAP: protein amount polymorphism). Eight maize inbred lines and ten of their single-cross hybrids were analyzed by two-dimensional polyacrylamide gel electrophoresis in order to examine the potential of PAP for predicting hybrid vigor. The 28 possible pairs of lines were characterized for: (i) the number, H of expected heterozygous structural loci in their hybrid, in the sample of loci revealed by 2D-PAGE; (ii) four distance indices based on PAP; (iii) the hybrid values for five agromorphological characters measured in four different year/locations. For the subset of ten hybrids analyzed by 2D-PAGE, the number of cases of nonadditive inheritance (NA) was also counted. Whereas H appeared to be related neither to the PAP indices, nor to NA, nor to hybrid performances, PAP indices were correlated to NA, and both were positively associated to hybrid performances. The possibility that PAP is responsible for quantitative trait variation is discussed. This could result in the definition of biological predictors of heterosis.     

Identification of Indica rice chromosome segments for the improvement of Japonica inbreds and hybrids

Exploitation of heterosis has brought significant advance in plant breeding and agricultural production, although its genetic basis is still poorly understood. In this study, a total of 66 chromosome segment substitution (CSS) lines, derived from a cross between japonica rice inbred line Asominori (as the recurrent parent) and indica rice inbred line IR24 (as the donor parent), were used to investigate the genetic basis of heterosis in indica × japonica inter-subspecific rice hybrids. Each CSS line was crossed with the background parent Asominori, and the heterosis of F(1) hybrids was estimated by comparing the F(1) performance with its two parental lines. Field experiments were carried out across six different environments to evaluate yield and yield-related traits in the 66 CSS lines and their 66 corresponding F(1) hybrids. Quantitative trait loci (QTL) analyses were conducted using a likelihood ratio test based on the stepwise regression. Thirty-six QTL were identified with significant effects in CSSL, 21 with significant effects in hybrids and 13 with significant effects in both. On the basis of average dominance degree, of all the 70 QTL affecting yield-related agronomic traits, 28.6% (20) showed an overdominance, 35.7% (25) a partial dominance and 30% (21) an additive effect, indicating that all effects contribute to trait variation in japonica-indica rice hybrids. Effects of these QTL were examined to identify Indica rice chromosome segments of interest for the improvement of japonica inbred lines and hybrids.     

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.     

Genetic diversity for restriction fragment length polymorphisms and heterosis for two diallel sets of maize inbreds

Summary Changes that may have occurred over the past 50 years of hybrid breeding in maize (Zea maize L.) with respect to heterosis for yield and heterozygosity at the molecular level are of interest to both maize breeders and quantitative geneticists. The objectives of this study were twofold: The first, to compare two diallels produced from six older maize inbreds released in the 1950's and earlier and six newer inbreds released during the 1970's with respect to (a) genetic variation for restriction fragment length polymorphisms (RFLPs) and (b) the size of heterosis and epistatic effects, and the second, to evaluate the usefulness of RFLP-based genetic distance measures in predicting heterosis and performance of single-cross hybrids. Five generations (parents, F₁; F₂, and backcrosses) from the 15 crosses in each diallel were evaluated for grain yield and yield components in four Iowa environments. Genetic effects were estimated from generation means by ordinary diallel analyses and by the Eberhart-Gardner model. Newer lines showed significantly greater yield for inbred generations than did older lines but smaller heterosis estimates. In most cases, estimates of additive x additive epistatic effects for yield and yield components were significantly positive for both groups of lines. RFLP analyses of inbred lines included two restriction enzymes and 82 genomic DNA clones distributed over the maize genome. Eighty-one clones revealed polymorphisms with at least one enzyme. In each set, about three different RFLP variants were typically found per RFLP locus. Genetic distances between inbred lines were estimated from RFLP data as Rogers' distance (RD), which was subdivided into general (GRD) and specific (SRD) Rogers' distances within each diallel. The mean and range of RDs were similar for the older and newer lines, suggesting that the level of heterozygosity at the molecular level had not changed. GRD explained about 50% of the variation among RD values in both sets. Cluster analyses, based on modified Rogers' distances, revealed associations among lines that were generally consistent with expectations based on known pedigree and on previous research. Correlations of RD and SRD with f₁ performance, specific combining ability, and heterosis for yield and yield components, were generally positive, but too small to be of predictive value. In agreement with previous studies, our results suggest that RFLPs can be used to investigate relationships among maize inbreds, but that they are of limited usefulness for predicting the heterotic performance of single crosses between unrelated lines.Joint contribution from Cereal and Soybean Research Unit, USDA, Agricultural Research Service and Journal Paper no. J-13929 of the Iowa Agric and Home Economics Exp Stn, Ames, IA 50011. Projects no. 2818 and 2778A.E.M. is presently at the Iowa State University on leave from University of Hohenheim, D-7000 Stuttgart 70, Federal Republic of Germany     

Relationship of restriction fragment length polymorphisms to single-cross hybrid performance of maize

Summary Isozymes and restriction fragment length polymorphisms (RFLPs) have been proposed for use in varietal identification and selection for agronomic traits. Although the use of isozymes for these purposes has been well documented, evaluation of the efficacy of RFLP technology as applied to crop improvement is far from complete. This investigation was conducted to study the relationship between RFLP-derived genotypes and heterotic patterns of a group of maize (Zea mays L.) inbred lines. A total of 22 inbreds was crossed to four testers (B73, B76, Mo17, and Va26) in combinations that minimized crossing within heterotic groups. Forty-seven single-cross progeny were subsequently evaluated for several agronomic traits (including grain yield and moisture, ear height, and root lodging) over 2–4 consecutive years at two to four Iowa locations in a randomized complete-block design. The inbred lines were subjected to RFLP analysis, which involved 47 genomic clones and the restriction enzymes EcoRI and HindIII. Hybrid RFLP patterns were predicted from their inbred parents. Modified Roger's distances were computed to estimate genetic distance among the inbred lines. Principal component analysis facilitated ascertainment of relative dispersion of the inbreds based on the frequency of variants at specific RFLP loci. Evident associations of variants with genes affecting agronomic traits were identified by principal component regression analysis, in which adjusted hybrid means were regressed on the matrix of hybrid variants frequencies. The hybrid means were adjusted by removing environmental effects, using residuals as dependent variables in the regression analysis. Results from this study suggest that RFLP analysis may be of value in allocating maize inbreds to heterotic groups, but no relationship between RFLP-based genetic distance and hybrid performance was apparent. Principal component regression identified variants potentially linked to genes that control specific agronomic traits.Joint contribution: USDA-ARS and Journal Paper No. J-13590 of the Iowa Agriculture and Home Economics Experiment Station, Ames, IA 50011, USA. Projects No. 2818 and 2778     

Prediction of heterosis in crosses between inbred lines of Drosophila melanogaster

Summary The aim of the experiment was to determine if the estimated genetic distance between two populations could be used to predict the amount of heterosis that would occur when they were crossed. Eight lines of known relatedness to each other were produced by eight generations of sib mating and sub-lining. This produced lines that varied in coefficient of coancestry from zero to 0.78. Fourteen reciprocal crosses of these lines were used to measure heterosis for larval viability and adult fecundity. Gene frequencies at six polymorphic enzyme loci were used to estimate the genetic distances between lines, which were then compared with the known degrees of coancestry. The estimated genetic differences were poorly correlated with the known coancestry coefficients (r=0.4), possibly due to the small number of loci typed. Also genetic distances were only about 1/3 of what was expected. Selection acting on blocks of genes linked to the enzyme loci probably prevented the expected increase in homozygosity. Coancestry coefficient was correlated with heterosis (r=0.44–0.71). This level of correlation implied differences in heterosis among parent lines with the same level of coancestry. This variability is expected if a small number of loci explain most of the heterosis. The average level of heterosis was less than expected after eight generations of sib mating. This is most likely due to selection opposing the increase in homozygosity caused by inbreeding. The combination of these two imperfect correlations resulted in no significant correlation between genetic distance estimated from markers and heterosis.     

Genetic distance of inbred lines and prediction of maize single-cross performance using RAPD markers

 To evaluate the genetic diversity of 18 maize inbred lines, and to determine the correlation between genetic distance and single-cross hybrid performance, we have used random amplified polymorphic DNA (RAPD), a PCR-based technique. Eight of these lines came from a Thai synthetic population (BR-105), and the others derived from a Brazilian composite population (BR-106). Thirty two different primers were used giving a total of 325 reproducible amplification products, 262 of them being polymorphic. Genetic divergence was determinated using Jaccard’s similarity coefficient, and a final dendrogram was constructed using an unweighted pair-group method with arithmetical averages (UPGMA). Cluster analysis divided the samples into three distinct groups (GI, GII and GIII) that were confirmed by principal-coordinate analysis. The genetic distances (GD) were correlated with important agronomic traits for single-cross hybrids and heterosis. No correlation was found when group division was not considered, but significant correlations were detected between GI×GII and GI×GIII GDs with their respective single-cross hybrid grain-yield values. Three groups were identified; that is, the BR-106 population was divided in two different groups and the BR-105 population remained mostly as one group. The results indicated that RAPD can be used as a tool for determining the extent of genetic diversity among tropical maize inbred lines, for allocating genotypes into different groups, and also to aid in the choice of the superior crosses to be made among maize inbred lines, so reducing the number of crosses required under field evaluation. Received: 24 May 1996 / Accepted: 22 November 1996     

Association between SCMV Resistance and Macroarray-based Expression Patterns in Maize Inbreds

Recent advances in RNA profiling offer an opportunity to establish functional links between genotype and phenotype for complex traits such as SCMV resistance. The change of RNA profiles was monitored on a macroarray containing SSH (suppression subtractive hybridization) clones. The number of differentially expressed genes (SCMV infected vs. non-infected) in individual lines was 177, 163, 165, 62, 47, 37, and 93, for FAP1360A, D21, D32, Pa405, F7, D145, and D408, respectively. All inbreds were divided into two groups by hierarchical cluster analysis: D32, D21, FAP1360A and D408 formed one; Pa405, D145, and F7 another group. Due to the genetic structure among the seven inbreds, genetic background and resistance response are confounded. With or without the resistant U.S. inbred line Pa405, 22 and 112 genes were identified by t tests between resistant (D21, D32, and FAP1360A) and susceptible (D145, D408, and F7) inbred lines, respectively. The 112 candidate genes were divided into three clusters by K-means clustering and analyzed in more detail, e.g., five genes were in silico mapped surrounding Scmv2 QTLs. These candidate genes provide a better understanding of signal transduction pathway for SCMV resistance and have the potential to develop functional markers to distinguish resistant and susceptible genotypes.     

Progressive heterosis in genetically defined tetraploid maize

Progressive heterosis, i.e., the additional hybrid vigor in double-cross tetraploid hybrids not found in their single-cross tetraploid parents, has been documented in a number of species including alfalfa,potato, and maize. In this study, four artificially induced maize tetraploids, directly derived from standard inbred lines, were crossed in pairs to create two single-cross hybrids. These hybrids were then crossed to create double-cross hybrids containing genetic material from all four original lines. Replicated fieldbased phenotyping of the materials over four years indicated a strong progressive heterosis phenotype in tetraploids but not in their diploid counterparts. In particular, the above ground dry weight phenotype of double-cross tetraploid hybrids was on average 34% and 56% heavier than that of the single-cross tetraploid hybrids and the double-cross diploid counterparts, respectively. Additionally,whole-genome resequencing of the original inbred lines and further analysis of these data did not show the expected spectrum of alleles to explain tetraploid progressive heterosis under the complementation of complete recessive model. These results underscore the reality of the progressive heterosis phenotype,its potential utility for increasing crop biomass production, and the need for exploring alternative hypothesis to explain it at a molecular level.     

Dominance Is the Major Genetic Basis of Heterosis in Rice as Revealed by Qtl Analysis Using Molecular Markers

A set of 194 F(7) lines derived from a subspecific rice cross showing strong F(1) heterosis was backcrossed to the two parents. The materials (388 BC(1)F(7) lines, 194 F(8) lines, two parents, F(1)) were phenotyped for 12 quantitative traits. A total of 37 significant QTLs (LOD >/= 2.0) was detected through 141 RFLP markers in the BC(1)F(7) populations. Twenty-seven (73%) quantitative trait loci (QTLs) were detected in only one of the BC(1)F(7) populations. In 82% of these cases, the heterozygotes were superior to the respective homozygotes. The remaining 10 (27%) QTLs were detected in both BC(1)F(7) populations, and the heterozygote had a phenotype falling between those of the two homozygotes and in no instances were the heterozygotes found to be superior to both homozygotes. These results suggest that dominance complementation is the major genetic basis of heterosis in rice. This conclusion was strengthened by the finding that there was no correlation between most traits and overall genome heterozygosity and that there were some recombinant inbred lines in the F(8) population having phenotypic values superior to the F(1) for all of the traits evaluated--a result not expected if overdominance was a major contributor to heterosis. Digenic epistasis was not evident.     

The Effect of Level of Heterozygosity on the Performance of Hybrids between Isogenic Lines of Barley

Sixteen "isogenic" lines of Atlas 46 barley differing in one to four short chromosome segments, and 16 heterozygotes obtained by crossing these lines to male-sterile Atlas, were used to study the effect of level of heterozygosity on performance. In field tests conducted in four environments (two planting dates in two years) significant differences were found among the homozygous isogenic lines for the traits seed yield, kernel weight, tiller number, plant height, and heading time; thus each of the marked chromosome segments carries genes which, when homozygous, affect these quantitative characters. It was also found that heterozygotes produced more and heavier kernels and were taller and earlier than homozygotes but there was no clear indication that the degree of heterosis increased as the number of heterozygous segments increased from one to five. Degree of heterosis was, however, strongly affected by the environment, by allelic state at each segment (especially the segment marked by the two-row, six-row spike locus), and also by genotype for other marked segments. These results indicate that heterosis in barley has a more complex structure than can be adequately represented by simple models, such as the multiplicative model in which fitnesses are the product of fitnesses at individual loci, or threshold models in which optimum fitness is approached asymptotically as the number of heterozygous loci increases.     

Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two backcross populations

To understand the types of gene action controlling seven quantitative traits in rice, we carried out quantitative trait locus (QTL) mapping in order to distinguish between the main-effect QTLs (M-QTLs) and digenic epistatic QTLs (E-QTLs) responsible for the trait performance of 254 recombinant inbred lines (RILs) from rice varieties Lemont/Teqing and two backcross hybrid (BCF₁) populations derived from these RILs. We identified 44 M-QTL and 95 E-QTL pairs in the RI and BCF₁ populations as having significant effects on the mean values and mid-parental heterosis of heading date, plant height, flag leaf length, flag leaf width, panicle length, spikelet number and spikelet fertility. The E-QTLs detected collectively explained a larger portion of the total phenotypic variation than the M-QTLs in both the RI and BCF₁ populations. In both BCF₁ populations, over-dominant (or under-dominant) loci were more important than additive and complete or partially dominant loci for M-QTLs and E-QTL pairs, thereby supporting prior findings that overdominance resulting from epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice.     

Heterosis, sex and maternal interactions in crosses among inbred lines of mice.

All possible crosses and reciprocals were made among four inbred lines (F = 92%) developed from 12 generations of full-sib mating. All lines originated from a common outbred base population of ICR-albino mice. Data were obtained from 356 litter containing 2,734 mice to evaluate heterosis, reciprocal effects, sex effects and their interactions as they affect body weight and weight gain. Heterosis was significant for most of the postweaning traits (42- and 56-day weight and gain from 21 to 42 days). Nonadditive gene action may have included overdominance and epistasis since both reciprocal linecrosses were generally heavier than those of the better inbred lines. Although significant differences in reciprocals and inbred lines were not frequent, there were sufficient differences to indicate that lines varied in the fixation of loci during inbreeding. Sex-heterosis interactions were significant for 12 of 30 possible cases. However, eight of the 12 significant interactions occurred in crosses involving only one of the lines. The interactions were of the divergent type and arose from males exhibiting more heterosis than females. Overdominance in genes on the sex chromosomes modified by other loci (epistasis) was proposed as a possible explanation for these results. Some sex-linkage affecting growth was evident from the interaction of sex with reciprocal effects.     

Hybrid wheat: quantitative genetic parameters and consequences for the design of breeding programs

Key message

Commercial heterosis for grain yield is present in hybrid wheat but long-term competiveness of hybrid versus line breeding depends on the development of heterotic groups to improve hybrid prediction.

Abstract

Detailed knowledge of the amount of heterosis and quantitative genetic parameters are of paramount importance to assess the potential of hybrid breeding. Our objectives were to (1) examine the extent of midparent, better-parent and commercial heterosis in a vast population of 1,604 wheat (Triticum aestivum L.) hybrids and their parental elite inbred lines and (2) discuss the consequences of relevant quantitative parameters for the design of hybrid wheat breeding programs. Fifteen male lines were crossed in a factorial mating design with 120 female lines, resulting in 1,604 of the 1,800 potential single-cross hybrid combinations. The hybrids, their parents, and ten commercial wheat varieties were evaluated in multi-location field experiments for grain yield, plant height, heading time and susceptibility to frost, lodging, septoria tritici blotch, yellow rust, leaf rust, and powdery mildew at up to five locations. We observed that hybrids were superior to the mean of their parents for grain yield (10.7 %) and susceptibility to frost (?7.2 %), leaf rust (?8.4 %) and septoria tritici blotch (?9.3 %). Moreover, 69 hybrids significantly (P < 0.05) outyielded the best commercial inbred line variety underlining the potential of hybrid wheat breeding. The estimated quantitative genetic parameters suggest that the establishment of reciprocal recurrent selection programs is pivotal for a successful long-term hybrid wheat breeding.     

Genome‐wide association analyses reveal the genetic basis of combining ability in rice

Combining ability is a measure for selecting elite parents and predicting hybrid performance in plant breeding. However, the genetic basis of combining ability remains unclear and a global view of combining ability from diverse mating designs is lacking. We developed a North Carolina II (NCII) population of 96 Oryza sativa and four male sterile lines to identify parents of greatest value for hybrid rice production. Statistical analyses indicated that general combining ability (GCA) and specific combining ability (SCA) contributed variously to different agronomic traits. In a genome‐wide association study (GWAS) of agronomic traits, GCA and SCA, we identified 34 significant associations (P < 2.39 × 10^?7). The superior alleles of GCA loci (Ghd8, GS3 and qSSR4) accumulated in parental lines with high GCA and explained 30.03% of GCA variance in grain yield, indicating that molecular breeding of high GCA parental lines is feasible. The distinct distributions of these QTLs contributed to the differentiation of parental GCA in subpopulations. GWAS of SCA identified 12 more loci that showed dominance on corresponding agronomic traits. We conclude that the accumulation of superior GCA and SCA alleles is an important contributor to heterosis and QTLs that greatly contributed to combining ability in our study would accelerate the identification of elite inbred lines and breeding of super hybrids.     

Assembly of yield heterosis of an elite rice hybrid is promising by manipulating dominant quantitative trait loci

In the past, rice hybrids with strong heterosis have been obtained empirically, by developing and testing thousands of combinations. Here, we aimed to determine whether heterosis of an elite hybrid could be achieved by manipulating major quantitative trait loci. We used 202 chromosome segment substitution lines from the elite hybrid Shanyou 63 to evaluate single segment heterosis (SSH) of yield per plant and identify heterotic loci. All nine detected heterotic loci acted in a dominant fashion, and no SSH exhibited overdominance. Functional alleles of key yield-related genes Ghd7, Ghd7.1, Hd1, and GS3 were dispersed in both parents. No functional alleles of three investigated genes were expressed at higher levels in the hybrids than in the more desirable parents. A hybrid pyramiding eight heterotic loci in the female parent Zhenshan 97 background had a comparable yield to Shanyou 63 and much higher yield than Zhenshan 97. Five hybrids pyramiding eight or nine heterotic loci in the combined parental genome background showed similar yield performance to that of Shanyou 63. These results suggest that dominance underlying functional complementation is an important contributor to yield heterosis and that heterosis assembly might be successfully promised by manipulating several major dominant heterotic loci.     

Genetic architecture of growth and body composition in unique chicken populations

A resource population was established by crossing one modern broiler sire from a commercial broiler breeder male line with dams from two unrelated highly inbred lines; F1 birds were intercrossed to produce two F2 populations. A variety of phe notypic measurements related to growth, muscling, internal organs, and skeleton were recorded for the F2 populations and contemporary pure inbred and broiler birds. Based on the means and phenotypic distributions of the F2 populations com pared to their parental lines, the effective number of genes affecting each trait and heterosis were estimated and discussed relative to the known genetic selection history for each trait. The results suggest that a high number of genes with small epistatic effects are involved in determining the phenotype for traits that broilers were traditionally selected for, and a lower number of genes with major effects are involved in determining the phenotype for traits related to fitness. The estimated number of genes and the phenotypic distributions of the different traits suggest that a quantitative trait loci (QTL) search might be more effectively applied for traits with a low number of involved genes and a high phenotypic distribution among the F2 birds than for traits that show a lower phenotypic distribution and a high number of genes.     

Genetic basis of grain yield heterosis in an “immortalized F2” maize population

Key message

Genetic basis of grain yield heterosis relies on the cumulative effects of dominance, overdominance, and epistasis in maize hybrid Yuyu22.

Abstract

Heterosis, i.e., when F₁ hybrid phenotypes are superior to those of the parents, continues to play a critical role in boosting global grain yield. Notwithstanding our limited insight into the genetic and molecular basis of heterosis, it has been exploited extensively using different breeding approaches. In this study, we investigated the genetic underpinnings of grain yield and its components using “immortalized F₂” and recombinant inbred line populations derived from the elite hybrid Yuyu22. A high-density linkage map consisting of 3,184 bins was used to assess (1) the additive and additive-by-additive effects determined using recombinant inbred lines; (2) the dominance and dominance-by-dominance effects from a mid-parent heterosis dataset; and (3) the various genetic effects in the “immortalized F₂” population. Compared with a low-density simple sequence repeat map, the bin map identified more quantitative trait loci, with higher LOD scores and better accuracy of detecting quantitative trait loci. The bin map showed that, among all traits, dominance was more important to heterosis than other genetic effects. The importance of overdominance/pseudo-overdominance was proportional to the amount of heterosis. In addition, epistasis contributed to heterosis as well. Phenotypic variances explained by the QTLs detected were close to the broad-sense heritabilities of the observed traits. Comparison of the analyzed results obtained for the “immortalized F₂” population with those for the mid-parent heterosis dataset indicated identical genetic modes of action for mid-parent heterosis and grain yield performance of the hybrid.     

Prediction of single-cross hybrid performance for grain yield and grain dry matter content in maize using AFLP markers associated with QTL

Prediction methods to identify single-cross hybrids with superior yield performance have the potential to greatly improve the efficiency of commercial maize (Zea mays L.) hybrid breeding programs. Our objectives were to (1) identify marker loci associated with quantitative trait loci for hybrid performance or specific combining ability (SCA) in maize, (2) compare hybrid performance prediction by genotypic value estimates with that based on general combining ability (GCA) estimates, and (3) investigate a newly proposed combination of the GCA model with SCA predictions from genotypic value estimates. A total of 270 hybrids was evaluated for grain yield and grain dry matter content in four Dent × Flint factorial mating experiments, their parental inbred lines were genotyped with 20 AFLP primer-enzyme combinations. Markers associated significantly with hybrid performance and SCA were identified, genotypic values and SCA effects were estimated, and four hybrid performance prediction approaches were evaluated. For grain yield, between 38 and 98 significant markers were identified for hybrid performance and between zero and five for SCA. Estimates of prediction efficiency (R ²) ranged from 0.46 to 0.86 for grain yield and from 0.59 to 0.96 for grain dry matter content. Models enhancing the GCA approach with SCA estimates resulted in the highest prediction efficiency if the SCA to GCA ratio was high. We conclude that it is advantageous for prediction of single-cross hybrids to enhance a GCA-based model with SCA effects estimated from molecular marker data, if SCA variances are of similar or larger importance as GCA variances.