Like other crop species, barley, the fourth most important crop worldwide, suffers from the genetic bottleneck effect, where further improvements in performance through classical breeding methods ...become difficult. Therefore, indirect selection methods are of great interest. Here, genomic prediction (GP) based on 33,005 SNP markers and, alternatively, metabolic prediction (MP) based on 128 metabolites with sampling at two different time points in one year, were applied to predict multi-year agronomic traits in the nested association mapping (NAM) population HEB-25. We found prediction abilities of up to 0.93 for plant height with SNP markers and of up to 0.61 for flowering time with metabolites. Interestingly, prediction abilities in GP increased after reducing the number of incorporated SNP markers. The estimated effects of GP and MP were highly concordant, indicating MP as an interesting alternative to GP, being able to reflect a stable genotype-specific metabolite profile. In MP, sampling at an early developmental stage outperformed sampling at a later stage. The results confirm the value of GP for future breeding. With MP, an interesting alternative was also applied successfully. However, based on our results, usage of MP alone cannot be recommended in barley. Nevertheless, MP can assist in unravelling physiological pathways for the expression of agronomically important traits.
Metabolites play a key role in plants as they are routing plant developmental processes and are involved in biotic and abiotic stress responses. Their analysis can offer important information on the ...underlying processes. Regarding plant breeding, metabolite concentrations can be used as biomarkers instead of or in addition to genetic markers to predict important phenotypic traits (metabolic prediction). In this study, we applied a genome-wide association study (GWAS) in a wild barley nested association mapping (NAM) population to identify metabolic quantitative trait loci (mQTL). A set of approximately 130 metabolites, measured at early and late sampling dates, was analysed. For four metabolites from the early and six metabolites from the late sampling date significant mQTL (grouped as 19 mQTL for the early and 25 mQTL for the late sampling date) were found. Interestingly, all of those metabolites could be classified as sugars. Sugars are known to be involved in signalling, plant growth and plant development. Sugar-related genes, encoding mainly sugar transporters, have been identified as candidate genes for most of the mQTL. Moreover, several of them co-localized with known flowering time genes like Ppd-H1, HvELF3, Vrn-H1, Vrn-H2 and Vrn-H3, hinting on the known role of sugars in flowering. Furthermore, numerous disease resistance-related genes were detected, pointing to the signalling function of sugars in plant resistance. An mQTL on chromosome 1H in the region of 13 Mbp to 20 Mbp stood out, that alone explained up to 65% of the phenotypic variation of a single metabolite. Analysis of family-specific effects within the diverse NAM population showed the available natural genetic variation regarding sugar metabolites due to different wild alleles. The study represents a step towards a better understanding of the genetic components of metabolite accumulation, especially sugars, thereby linking them to biological functions in barley.
Caraway (
Carum carvi
) is a medicinal and aromatic plant of the Apiaceae family with a long history of cultivation. To this day, improvements in yield and essential oil content are desirable. In the ...past, line breeding was used to increase essential oil content with the final intention of combining inbred lines to a synthetic variety by outcrossing. Outcrossing should overcome inbreeding depression and exploit heterosis vice versa. In this study, we wanted to detect whether and to what extent heterosis can be exploited in caraway. In a randomized complete block design with two years of growing and four repetitions per year and genotype, we compared 18 inbred lines with 18 corresponding F
1
populations produced in a polycross. In addition to yield, we estimated the beginning of flowering, the end of flowering, maturity, height, thousand-grain weight, stalk attachment rate, shattering rate and essential oil content. Linear mixed models were used to compute variance components, heritability and best linear unbiased estimates. As major result, we detected the existence of better parent heterosis in caraway. To summarize, outcrossing led to a significant increase in yield, thousand-grain weight and height and to an earlier beginning of flowering, end of flowering and maturity. In two-year data, no effect of outcrossing on the essential oil content was observed, but single year data revealed slight effects. We found strong negative correlations between developmental traits and yield. Hence, selection of early developing genotypes seems highly recommendable. Results make us confident that improved annual varieties can be introduced soon.
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