Model training across multiple breeding cycles significantly improves genomic prediction accuracy in rye (Secale cereale L.).

KEY MESSAGE: Genomic prediction accuracy can be significantly increased by model calibration across multiple breeding cycles as long as selection cycles are connected by common ancestors. In hybrid rye breeding, application of genome-based prediction is expected to increase selection gain because of long selection cycles in population improvement and development of hybrid components. Essentially two prediction scenarios arise: (1) prediction of the genetic value of lines from the same breeding cycle in which model training is performed and (2) prediction of lines from subsequent cycles. It is the latter from which a reduction in cycle length and consequently the strongest impact on selection gain is expected. We empirically investigated genome-based prediction of grain yield, plant height and thousand kernel weight within and across four selection cycles of a hybrid rye breeding program. Prediction performance was assessed using genomic and pedigree-based best linear unbiased prediction (GBLUP and PBLUP). A total of 1040 S2 lines were genotyped with 16 k SNPs and each year testcrosses of 260 S2 lines were phenotyped in seven or eight locations. The performance gap between GBLUP and PBLUP increased significantly for all traits when model calibration was performed on aggregated data from several cycles. Prediction accuracies obtained from cross-validation were in the order of 0.70 for all traits when data from all cycles (N CS = 832) were used for model training and exceeded within-cycle accuracies in all cases. As long as selection cycles are connected by a sufficient number of common ancestors and prediction accuracy has not reached a plateau when increasing sample size, aggregating data from several preceding cycles is recommended for predicting genetic values in subsequent cycles despite decreasing relatedness over time.

Biology, genetics, and management of ergot (Claviceps spp.) in rye, sorghum, and pearl millet.

Ergot is a disease of cereals and grasses caused by fungi in the genus Claviceps. Of particular concern are Claviceps purpurea in temperate regions, C. africana in sorghum (worldwide), and C. fusiformis in pearl millet (Africa, Asia). The fungi infect young, usually unfertilized ovaries, replacing the seeds by dark mycelial masses known as sclerotia. The percentage of sclerotia in marketable grain is strictly regulated in many countries. In winter rye, ergot has been known in Europe since the early Middle Ages. The alkaloids produced by the fungus severely affect the health of humans and warm-blooded animals. In sorghum and pearl millet, ergot became a problem when growers adopted hybrid technology, which increased host susceptibility. Plant traits reducing ergot infection include immediate pollination of receptive stigmas, closed flowering (cleistogamy), and physiological resistance. Genetic, nonpollen-mediated variation in ergot susceptibility could be demonstrated in all three affected cereals. Fungicides have limited efficacy and application is weather dependent. Sorting out the sclerotia from the harvest by photocells is expensive and time consuming. In conclusion, molecular-based hybrid rye breeding could improve pollen fertility by introgressing effective restorer genes thus bringing down the ergot infection level to that of conventional population cultivars. A further reduction might be feasible in the future by selecting more resistant germplasm.

Genetic structure and diversity of wild sorghum populations (Sorghum spp.) from different eco-geographical regions of Kenya.

Wild sorghums are extremely diverse phenotypically, genetically and geographically. However, there is an apparent lack of knowledge on the genetic structure and diversity of wild sorghum populations within and between various eco-geographical regions. This is a major obstacle to both their effective conservation and potential use in breeding programs. The objective of this study was to assess the genetic diversity and structure of wild sorghum populations across a range of eco-geographical conditions in Kenya. Sixty-two wild sorghum populations collected from the 4 main sorghum growing regions in Kenya were genotyped using 18 simple sequence repeat markers. The study showed that wild sorghum is highly variable with the Coast region displaying the highest diversity. Analysis of molecular variance showed a significant variance component within and among wild sorghum populations within regions. The genetic structure of wild sorghum populations indicated that gene flow is not restricted to populations within the same geographic region. A weak regional differentiation was found among populations, reflecting human intervention in shaping wild sorghum genetic structure through seed-mediated gene flow. The sympatric occurrence of wild and cultivated sorghums coupled with extensive seed-mediated gene flow, suggests a potential crop-to-wild gene flow and vice versa across the regions. Wild sorghum displayed a mixed mating system. The wide range of estimated outcrossing rates indicate that some environmental conditions may exist where self-fertilisation is favoured while others cross-pollination is more advantageous.

Wild sorghum from different eco-geographic regions of Kenya display a mixed mating system.

Knowledge of mating systems is required in order to understand the genetic composition and evolutionary potential of plant populations. Outcrossing in a population may co-vary with the ecological and historical factors influencing it. However, literature on the outcrossing rate is limited in terms of wild sorghum species coverage and eco-geographic reference. This study investigated the outcrossing rates in wild sorghum populations from different ecological conditions of Kenya. Twelve wild sorghum populations were collected in four sorghum growing regions. Twenty-four individuals per population were genotyped using six polymorphic simple sequence repeat (SSR) markers to compute their indirect equilibrium estimates of outcrossing rate as well as population structure. In addition, the 12 populations were planted in a field in a randomised block design with five replications. Their progeny (250 individuals per population) were genotyped with the six SSR markers to estimate multi-locus outcrossing rates. Equilibrium estimates of outcrossing rates ranged from 7.0 to 75.0%, while multi-locus outcrossing rates (t (m)) ranged from 8.9 to 70.0% with a mean of 49.7%, indicating that wild sorghum exhibits a mixed mating system. The wide range of estimated outcrossing rates in wild sorghum populations indicate that environmental conditions may exist under which fitness is favoured by outcrossing and others under which selfing is more advantageous. The genetic structure of the populations studied is concordant with that expected for a species displaying mixed mating system.

DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits.

BACKGROUND: Association mapping is receiving considerable attention in plant genetics for its potential to fine map quantitative trait loci (QTL), validate candidate genes, and identify alleles of interest. In the present study association mapping in barley (Hordeum vulgare L.) is investigated by associating DNA polymorphisms with variation in grain quality traits, plant height, and flowering time to gain further understanding of gene functions involved in the control of these traits. We focused on the four loci BLZ1, BLZ2, BPBF and HvGAMYB that play a role in the regulation of B-hordein expression, the major fraction of the barley storage protein. The association was tested in a collection of 224 spring barley accessions using a two-stage mixed model approach. RESULTS: Within the sequenced fragments of four candidate genes we observed different levels of nucleotide diversity. The effect of selection on the candidate genes was tested by Tajima's D which revealed significant values for BLZ1, BLZ2, and BPBF in the subset of two-rowed barleys. Pair-wise LD estimates between the detected SNPs within each candidate gene revealed different intra-genic linkage patterns. On the basis of a more extensive examination of genomic regions surrounding the four candidate genes we found a sharp decrease of LD (r2<0.2 within 1 cM) in all but one flanking regions.Significant marker-trait associations between SNP sites within BLZ1 and flowering time, BPBF and crude protein content and BPBF and starch content were detected. Most haplotypes occurred at frequencies <0.05 and therefore were rejected from the association analysis. Based on haplotype information, BPBF was associated to crude protein content and starch content, BLZ2 showed association to thousand-grain weight and BLZ1 was found to be associated with flowering time and plant height. CONCLUSIONS: Differences in nucleotide diversity and LD pattern within the candidate genes BLZ1, BLZ2, BPBF, and HvGAMYB reflect the impact of selection on the nucleotide sequence of the four candidate loci.Despite significant associations, the analysed candidate genes only explained a minor part of the total genetic variation although they are known to be important factors influencing the expression of seed quality traits. Therefore, we assume that grain quality as well as plant height and flowering time are influenced by many factors each contributing a small part to the expression of the phenotype. A genome-wide association analysis could provide a more comprehensive picture of loci involved in the regulation of grain quality, thousand grain weight and the other agronomic traits that were analyzed in this study. However, despite available high-throughput genotyping arrays the marker density along the barely genome is still insufficient to cover all associations in a whole genome scan. Therefore, the candidate gene-based approach will further play an important role in barley association studies.

Heterosis in early seed development: a comparative study of F1 embryo and endosperm tissues 6 days after fertilization.

Heterosis specifies the superior performance of heterozygous individuals and although used in plant breeding the underlying molecular mechanisms still remain largely elusive. In this study, we demonstrate the manifestation of heterosis in hybrid maize embryo and endosperm tissue 6 days after fertilization in crosses of several inbred lines. We provide a comparative analysis of heterosis-associated gene expression in these tissues by a combined approach of suppression subtractive hybridization and microarray hybridizations. Non-additive expression pattern indicated a trans-regulatory mechanism to act early after fertilization in hybrid embryo and endosperm although the majority of genes showed mid-parental expression levels in embryo and dosage dependent expression levels in endosperm. The consistent expression pattern within both tissues and both inbred line genotype combinations of genes coding for chromatin related proteins pointed to heterosis-related epigenetic processes. These and genes involved in other biological processes, identified in this study, might provide entry points for the investigation of regulatory networks associated with the specification of heterosis.

Association mapping reveals gene action and interactions in the determination of flowering time in barley.

The interaction between members of a gene network has an important impact on the variation of quantitative traits, and can influence the outcome of phenotype/genotype association studies. Three genes (Ppd-H1, HvCO1, HvFT1) known to play an essential role in the regulation of flowering time under long days in barley were subjected to an analysis of nucleotide diversity in a collection of 220 spring barley accessions. The coding region of Ppd-H1 was highly diverse, while both HvCO1 and HvFT1 showed a rather limited level of diversity. Within all three genes, the extent of linkage disequilibrium was variable, but on average only moderate. Ppd-H1 is strongly associated with flowering time across four environments, showing a difference of five to ten days between the most extreme haplotypes. The association between flowering time and the variation at HvFT1 and HvCO1 was strongly dependent on the haplotype present at Ppd-H1. The interaction between HvCO1 and Ppd-H1 was statistically significant, but this association disappeared when the analysis was corrected for the geographical origin of the accessions. No association existed between flowering time and allelic variation at HvFT1. In contrast to Ppd-H1, functional variation at both HvCO1 and HvFT1 is limited in cultivated barley.

High level of conservation between genes coding for the GAMYB transcription factor in barley (Hordeum vulgare L.) and bread wheat (Triticum aestivum L.) collections.

The transcription factor GAMYB is involved in gibberellin signalling in cereal aleurone cells and in plant developmental processes. Nucleotide diversity of HvGAMYB and TaGAMYB was investigated in 155 barley (Hordeum vulgare) and 42 wheat (Triticum aestivum) accessions, respectively. Polymorphisms defined 18 haplotypes in the barley collection and 1, 7 and 3 haplotypes for the A, B, and D genomes of wheat, respectively. We found that (1) Hv- and TaGAMYB genes have identical structures. (2) Both genes show a high level of nucleotide identity (>95%) in the coding sequences and the distribution of polymorphisms is similar in both collections. At the protein level the functional domain is identical in both species. (3) GAMYB genes map to a syntenic position on chromosome 3. GAMYB genes are different in both collections with respect to the Tajima D statistic and linkage disequilibrium (LD). A moderate level of LD was observed in the barley collection. In wheat, LD is absolute between polymorphic sites, mostly located in the first intron, while it decays within the gene. Differences in Tajima D values might be due to a lower selection pressure on HvGAMYB, compared to its wheat orthologue. Altogether our results provide evidence that there have been only few evolutionary changes in Hv- and TaGAMYB. This confirms the close relationship between these species and also highlights the functional importance of this transcription factor.

MBP (version 1.0): a software package to optimize maize breeding procedures based on doubled haploid lines.

We developed MBP (version 1.0), a software package for optimizing maize (Zea mays L.) breeding procedures based on doubled haploid lines. This software accounts for both recurrent selection and the development of hybrid parent lines. Based on quantitative genetic model calculations, MBP (version 1.0) maximizes the expected genetic gain per year as a function of various genetic parameters and operational variables under the restriction of a given annual breeding budget. Exact formulae for the prediction of the effective population size are implemented, which allows to optimize breeding procedures under limited relative annual loss of genetic variance.

Quantitative trait loci for early plant vigour of maize grown in chilly environments.

Maize (Zea mays L.) is particularly sensitive to chilling in the early growth stages. The objective of this study was to determine quantitative trait loci (QTL) for early plant vigour of maize grown under cool and moderately warm conditions in Central Europe. A population of 720 doubled haploid (DH) lines was derived from a cross between two dent inbred lines contrasting in early vigour and were genotyped with 188 SSR markers. The DH lines per se and their testcrosses with a flint line were evaluated in field experiments across 11 environments in 2001 and 2002. Plants were harvested after six to eight leaves had been fully developed to assess fresh matter yield as a criterion of early vigour. Seven QTL were detected for line performance and ten QTL for testcross performance, explaining 64 and 49% of the genetic variance. Six out of seven QTL detected in the lines per se were also significant in their testcrosses. Significant QTL x environment interaction was observed, but no relationship existed between the size of the QTL effects and the mean temperature in the individual environment. The correlation between fresh matter yield and days to silking was non-significant, indicating that differences in early plant vigour were not simply caused by maturity differences. For three additional chilling-related traits, leaf chlorosis, leaf purpling, and frost damage seven, six, and five QTL were detected, respectively. Three QTL for leaf chlorosis, two for leaf purpling, and two for frost damage co-localized with QTL for fresh matter yield. Results are considered as a reliable basis for further genetic, molecular, and physiological investigations.

Estimating the outcrossing rate of barley landraces and wild barley populations collected from ecologically different regions of Jordan.

The results of previous studies conducted at the University of Hohenheim and the International Center for Agricultural Research in the Dry Areas (ICARDA) indicated that the yielding ability and stability of barley (Hordeum vulgare L.) could be improved in environments with drought stress by increasing the level of heterozygosity. This would require increasing the outbreeding rate of locally adapted breeding materials. As a first step, we estimated the outcrossing rate of 12 barley landraces (Hordeum vulgare ssp. vulgare, in short H. vulgare) and 13 sympatrically occurring populations of its wild progenitor [Hordeum vulgare ssp. spontaneum (C. Koch), in short H. spontaneum] collected from semi-arid localities in Jordan during the 1999/2000 growing season. In each H. vulgare or H. spontaneum population 28-48 spikes were sampled, and up to six offspring (seeds) per spike (called a family) were used for PCR analyses. Collection sites covered high-low transects for rainfall and altitude in order to detect possible environmental effects on the outcrossing rate. Four microsatellite markers located on different chromosomes were used to genotype the samples for estimating the outcrossing rate. Low season-specific multilocus outcrossing rates (tm) were found in both cultivated and wild barley, ranging among populations from 0-1.8% with a mean of 0.34%. Outcrossing rates based on inbreeding equilibrium (te), indicating outcrossing averaged across years, were two- to threefold higher than the season-specific estimates. Under high rainfall conditions somewhat higher--though not significantly higher--outcrossing rates were observed in H. spontaneum than in H. vulgare. The season-specific outcrossing rate in H. spontaneum was positively correlated (r = 0.67, P = 0.01) with average annual precipitation and negatively correlated (r = 0.59, P = 0.05) with monthly average temperature during flowering. The results suggest that outcrossing may vary considerably among seasons and that high precipitation and cool temperatures during flowering tend to enhance outcrossing. The rather low levels of outcrossing detected indicate that increased vigour due to heterozygosity has not been a major fitness advantage in the evolution and domestication of H. spontaneum and H. vulgare, respectively. Stable seed production to secure survival under extreme heat and drought stress may have been more important. Cleistogamy may be considered as an effective mechanism to warrant pollination even in drought-stunted plants with non-extruding spikes.