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Extensive exotic introgression could significantly enlarge the genetic distance of hybrid parental populations to promote strong heterosis. The goal of this study was to investigate whether genome-wide prediction can support pre-breeding in populations with exotic introgressions. We evaluated seed yield, seed yield related traits and seed quality traits of 363 hybrids of Brassica napus (AACC) derived from two parental populations divergent on massive exotic introgression of related species in three environments. The hybrids presented strong heterosis on seed yield, which was much higher than other investigated traits. Five genomic best linear unbiased prediction models considering the exotic introgression and different marker effects (additive, dominance, and epistatic effects) were constructed to test the prediction ability for different traits of the hybrids. The analysis showed that the trait complexity, exotic introgression, genetic relationship between the training set and testing set, training set size, and environments affected the prediction ability. The models with best prediction ability for different traits varied. However, relatively high prediction ability (e.g., 0.728 for seed yield) was also observed when the simplest models were used, excluding the effects of the special exotic introgression and epistasis effect by 5-fold cross validation, which would simplify the prediction for the trait with complex architecture for hybrids with exotic introgression. The results provide novel insights and strategies for genome-wide prediction of hybrids between genetically distinct parent groups with exotic introgressions.

Crop domestication and breeding considerably increased productivity over centuries but unconsciously lowered 'selfish plant behavior' or individual plant fitness. Paradoxically, enhancing individual plant fitness is mistakenly equated with crop improvement. Because agriculture relies on community performance, embracing an agroecological genetics and genomics viewpoint might maximize communal yield by matching crop genotypes to target environments.

Combining ability is crucial for parent selection in crop hybrid breeding. Many studies have attempted to provide reliable and quick methods to identify genome regions in parental lines correlating with improved hybrid performance. The local haplotype patterns surrounding densely spaced DNA markers include a large amount of genetic information, and analysis of the relationships between haplotypes and hybrid performance can provide insight into the underlying genome regions which might contribute to enhancing combining ability. Here, we generated 24,403 single-copy, genome-wide SNP loci and calculated the general combining ability (GCA) of 950 hybrids from a diverse panel of 475 pollinators of spring-type canola inbred lines crossed with two testers for days to flowering (DTF) and seed glucosinolate content (GSL). We performed a genome-wide analysis of the haplotypes and detected eight and seven haplotype regions that were significantly associated with the GCA values for DTF and seed GSL, respectively. Additionally, two haplotype blocks containing orthologs of flowering time genes FLOWERING LOCUS T (FT) and FLOWERING LOCUS C (FLC) on chromosome A02 showed additive epistatic interactions influencing flowering time. Moreover, two homoeologous haplotype regions on chromosomes A02 and C02 corresponded to major quantitative trait loci (QTL) for GSL which showed additive effects related to reduction of seed GSL in F1 hybrids. Our study showed that haplotype analysis has the potential to substantially improve the efficiency of hybrid breeding programs.

Chlorophyll levels provide important information about plant growth and physiological plasticity in response to changing environments. The stay-green gene NON-YELLOWING 1 (NYE1) is believed to regulate chlorophyll degradation during senescence, concomitantly affecting the disassembly of the light-harvesting complex and hence indirectly influencing photosynthesis. We identified Brassica napus accessions carrying an NYE1 deletion associated with increased chlorophyll content, and with upregulated expression of light-harvesting complex and photosynthetic reaction center (PSI and PSII) genes. Comparative analysis of the seed oil content of accessions with related genetic backgrounds revealed that the B. napus NYE1 gene deletion (bnnye1) affected oil accumulation, and linkage disequilibrium signatures suggested that the locus has been subject to artificial selection by breeding in oilseed B. napus forms. Comparative analysis of haplotype diversity groups (haplogroups) between three different ecotypes of the allopolyploid B. napus and its A-subgenome diploid progenitor, Brassica rapa, indicated that introgression of the bnnye1 deletion from Asian B. rapa into winter-type B. napus may have simultaneously improved its adaptation to cooler environments experienced by autumn-sown rapeseed.

Sorghum is regarded a promising bioenergy crop and may be an alternative to maize for biogas use in temperate Europe in the near future. Presently, the principal shortcoming compared to maize besides chilling sensitivity during juvenile development is that current sorghum varieties fail to combine a high dry matter yield with adequate dry matter content for silage and satisfying methane yield. Our major goal was to evaluate whether early-maturing silage type Sorghum bicolor hybrids with a higher contribution of panicles and grains to total dry matter may allow an improvement of methane yield, representing a novel, alternative variety type for biogas use in temperate Europe. Our results indicate that under adequate conditions, they reach higher dry matter contents. Due to enhanced methane yields per dry matter unit which offset slightly lower dry matter yields, their methane yield per area unit is similar or superior to existing biomass type varieties. Since panicles account for up to 50% of total dry matter yield, seed set and maturity in cool environments represent critical factors for yield stability. Breeding efforts focus on chilling tolerance during flowering to avoid male sterility and on the development of appropriate parental lines combining earliness and adequate height. While selection for maturity can be reliably conducted on per se performance of parental lines, hybrid yield is predominantly determined by general combining ability.

The diploid species Brassica rapa (genome AA) and B. oleracea (genome CC) were compared by full-scale proteome analyses of seedling. A total of 28.2% of the proteins was common to both species, indicating the existence of a basal or ubiquitous proteome. However, a number of discriminating proteins (32.0%) and specific proteins (39.8%) of the Brassica A and C genomes, respectively, were identified, which could represent potentially species-specific functions. Based on these A or C genome-specific proteins, a number of PCR-based markers to distinguish B. rapa and B. oleracea species were also developed.

In view of the effects of global climate changes on plant growth conditions in Europe, specific traits of sorghum make it a promising candidate for a future bioenergy crop in this region. The main limiting factor seems to be low tolerance of sorghum seedlings to chilling temperature and possible damage caused by cold spells in April and May. Seedlings of six sorghum genotypes (M71/SS79/Etian/Keller/Ji2731/Btx623) at third-leaf stage were exposed to five-day chilling (13/10 °C, day/night) in a growth chamber and then recovered for five days at control temperature (25/20 °C). Before and during cold treatment as well as during recovery, photosynthetic efficiency (PE), stomata status, and osmotic potential (OP) were measured for the first three leaves. As early as after 4 h of chilling there was a significant drop in PE measured as chlorophyll a fluorescence parameters, which decreased further in the course of chilling with significant genotypic differences. These were particularly pronounced after five- day recovery – M71 and Ji2731 recovered almost fully while SS79, Keller, and Btx623 – to a very limited degree. In these susceptible lines a significantly bigger drop in PE was observed for the first (oldest) leaf compared to the third (youngest) one, whereas in the tolerant lines these differences were not significant. All genotypes exhibited stomata closure as late as the fifth chilling or first recovery day and a drop in leaf OP after 52 h of chilling. The results show that the fast and significant drop in PE of sorghum seedlings under chilling conditions is caused by metabolic (non-stomatal) limitations during exposure to low temperature and by stomatal limitations after its cessation. The most pronounced genotypic differences in the reaction of sorghum seedlings to chilling stress were in the extent of osmotic adjustment and the capability for PE recovery after chilling treatment. Research supported by NCBR, Poland, ERA-NET-BIOENERGY-3/2013.