Maize (Zea mays L.) serves as model plant for heterosis research and is the crop where hybrid breeding was pioneered. We analyzed genomic and phenotypic data of 1254 hybrids of a typical maize hybrid ...breeding program based on the important Dent × Flint heterotic pattern. Our main objectives were to investigate genome properties of the parental lines (e.g., allele frequencies, linkage disequilibrium, and phases) and examine the prospects of genomic prediction of hybrid performance. We found high consistency of linkage phases and large differences in allele frequencies between the Dent and Flint heterotic groups in pericentromeric regions. These results can be explained by the Hill-Robertson effect and support the hypothesis of differential fixation of alleles due to pseudo-overdominance in these regions. In pericentromeric regions we also found indications for consistent marker-QTL linkage between heterotic groups. With prediction methods GBLUP and BayesB, the cross-validation prediction accuracy ranged from 0.75 to 0.92 for grain yield and from 0.59 to 0.95 for grain moisture. The prediction accuracy of untested hybrids was highest, if both parents were parents of other hybrids in the training set, and lowest, if none of them were involved in any training set hybrid. Optimizing the composition of the training set in terms of number of lines and hybrids per line could further increase prediction accuracy. We conclude that genomic prediction facilitates a paradigm shift in hybrid breeding by focusing on the performance of experimental hybrids rather than the performance of parental lines in test crosses.
Doubled haploid (DH) production is an important step in varietal development in maize (Zea mays L.), and the success rate of chromosome doubling determines a major portion of the production costs per ...DH line. Colchicine, the standard chemical used for chromosome doubling, is highly toxic and requires special disposal. In comparison, nitrous oxide (N2O) is a relatively safe gas with simple disposal requirements. Therefore, the objective of this study was to compare chromosome doubling treatment of maize seedlings with N2O with the standard colchicine treatment and a recently proposed alternative herbicide treatment containing amiprophos‐methyl and pronamide in two environments suitable for DH production (DH nursery and greenhouse). Various treatment factors, including different pressures and concentrations of N2O, O2, and air in the treatment chamber, imbibition duration, and treatment duration were analyzed for their effect on survival rate of germinated seedlings, reproduction rate measured as the proportion of haploid (D0) plants with seed set, and overall success rate (OSR) measured as the proportion of D0 plants with seed set obtained from the germinated seedlings. The OSR of the best N2O treatment ranged from 6.4 to 33.3%, whereas the OSR of colchicine ranged from 5.0 to 28.1%, depending on the year and environment. Nitrous oxide treatment did not have a significantly different OSR than herbicide treatment. In conclusion, N2O treatment is a competitive alternative to colchicine and herbicide treatments for chromosome doubling and offers safety and disposal‐related benefits.
Key message
Selected doubled haploid lines averaged similar testcross performance as their original landraces, and the best of them approached the yields of elite inbreds, demonstrating their ...potential to broaden the narrow genetic diversity of the flint germplasm pool.
Maize landraces represent a rich source of genetic diversity that remains largely idle because the high genetic load and performance gap to elite germplasm hamper their use in modern breeding programs. Production of doubled haploid (DH) lines can mitigate problems associated with the use of landraces in pre-breeding. Our objective was to assess in comparison with modern materials the testcross performance (TP) of the best 89 out of 389 DH lines developed from six landraces and evaluated in previous studies for line per se performance (LP). TP with a dent tester was evaluated for the six original landraces, ~ 15 DH lines from each landrace selected for LP, and six elite flint inbreds together with nine commercial hybrids for grain and silage traits. Mean TP of the DH lines rarely differed significantly from TP of their corresponding landrace, which averaged in comparison with the mean TP of the elite flint inbreds ~ 20% lower grain yield and ~ 10% lower dry matter and methane yield. Trait correlations of DH lines closely agreed with the literature; correlation of TP with LP was zero for grain yield, underpinning the need to evaluate TP in addition to LP. For all traits, we observed substantial variation for TP among the DH lines and the best showed similar TP yields as the elite inbreds. Our results demonstrate the high potential of landraces for broadening the narrow genetic base of the flint heterotic pool and the usefulness of the DH technology for exploiting idle genetic resources from gene banks.
Landraces are valuable genetic resources for broadening the genetic base of elite germplasm in maize. Extensive exploitation of landraces has been hampered by their genetic heterogeneity and heavy ...genetic load. These limitations may be overcome by the in-vivo doubled haploid (DH) technique. A set of 132 DH lines derived from three European landraces and 106 elite flint (EF) lines were genotyped for 56,110 single nucleotide polymorphism (SNP) markers and evaluated in field trials at five locations in Germany in 2010 for several agronomic traits. In addition, the landraces were compared with synthetic populations produced by intermating DH lines derived from the respective landrace. Our objectives were to (1) evaluate the phenotypic and molecular diversity captured within DH lines derived from European landraces, (2) assess the breeding potential (usefulness) of DH lines derived from landraces to broaden the genetic base of the EF germplasm, and (3) compare the performance of each landrace with the synthetic population produced from the respective DH lines. Large genotypic variances among DH lines derived from landraces allowed the identification of DH lines with grain yields comparable to those of EF lines. Selected DH lines may thus be introgressed into elite germplasm without impairing its yield level. Large genetic distances of the DH lines to the EF lines demonstrated the potential of DH lines derived from landraces to broaden the genetic base of the EF germplasm. The comparison of landraces with their respective synthetic population showed no yield improvement and no reduction of phenotypic diversity. Owing to the low population structure and rapid decrease of linkage disequilibrium within populations of DH lines derived from landraces, these would be an ideal tool for association mapping. Altogether, the DH technology opens new opportunities for characterizing and utilizing the genetic diversity present in gene bank accessions of maize.
Key message
Association mapping with immortalized lines of landraces offers several advantages including a high mapping resolution, as demonstrated here in maize by identifying the causal variants ...underlying QTL for oil content and the metabolite allantoin.
Landraces are traditional varieties of crops that present a valuable yet largely untapped reservoir of genetic variation to meet future challenges of agriculture. Here, we performed association mapping in a panel comprising 358 immortalized maize lines from six European Flint landraces. Linkage disequilibrium decayed much faster in the landraces than in the elite lines included for comparison, permitting a high mapping resolution. We demonstrate this by fine-mapping a quantitative trait locus (QTL) for oil content down to the phenylalanine insertion F469 in
DGAT1-2
as the causal variant. For the metabolite allantoin, related to abiotic stress response, we identified promoter polymorphisms and differential expression of an allantoinase as putative cause of variation. Our results demonstrate the power of this approach to dissect QTL potentially down to the causal variants, toward the utilization of natural or engineered alleles in breeding. Moreover, we provide guidelines for studies using ancestral landraces for crop genetic research and breeding.
The importance of phosphorus (P) in agriculture contrasts with the negative environmental impact and the limited resources worldwide. Reducing P fertilizer application by utilizing more efficient ...genotypes is a promising way to address these issues. To approach this, a large panel of maize (
L.) comprising each 100 Flint and Dent elite lines and 199 doubled haploid lines from six landraces was assessed in multi-environment field trials with and without the application of P starter fertilizer. The treatment comparison showed that omitting the starter fertilizer can significantly affect traits in early plant development but had no effect on grain yield. Young maize plants provided with additional P showed an increased biomass, faster growth and superior vigor, which, however, was only the case under environmental conditions considered stressful for maize cultivation. Importantly, though the genotype-by-treatment interaction variance was comparably small, there is genotypic variation for this response that can be utilized in breeding. The comparison of elite and doubled haploid landrace lines revealed a superior agronomic performance of elite material but also potentially valuable variation for early traits in the landrace doubled haploid lines. In conclusion, our results illustrate that breeding for P efficient maize cultivars is possible towards a reduction of P fertilizer in a more sustainable agriculture.
In vivo production of doubled‐haploid (DH) lines in maize (Zea mays L.) routinely involves artificial chromosome doubling by colchicine treatment of seedlings. Because colchicine is a hazardous ...chemical, replacing it by less‐toxic alternatives would be highly desirable. Our objectives were to (i) test the efficacy of various herbicides alone or in combination with other herbicides or phytohormones as chromosome doubling agents, (ii) evaluate the efficacy of application of these chemicals for different durations and methods of delivery to meristems, and (iii) compare colchicine treatment with the most promising alternative treatment under economic aspects. Several antimitotic herbicides with different modes of action and two phytohormones were tested in various combinations and concentrations in four experiments for survival rate (SR) of germinated seedlings, reproduction rate (RR) measured as the proportion of D0 plants with seed set, and overall success rate (OSR) measured as the proportion of D1 ears with seed set obtained from the germinated seedlings. Amiprophos‐methyl (APM) and pronamid, applied with the seedling soaking method, outperformed all other alternative treatments tested and reached almost the same OSR as colchicine. Cost comparison between the best treatment, containing APM and pronamid, and the colchicine control showed that the total production cost per D0 plant with seed set was about 10% higher than for colchicine as a result of slightly lower OSR. In conclusion, APM combined in an optimum dosage with pronamid is a promising alternative to colchicine in view of the lower toxicity and similar rate of chromosome doubling in maize.
The ability to predict the agronomic performance of single-crosses with high precision is essential for selecting superior candidates for hybrid breeding. With recent technological advances, ...thousands of new parent lines, and, consequently, millions of new hybrid combinations are possible in each breeding cycle, yet only a few hundred can be produced and phenotyped in multi-environment yield trials. Well established prediction approaches such as best linear unbiased prediction (BLUP) using pedigree data and whole-genome prediction using genomic data are limited in capturing epistasis and interactions occurring within and among downstream biological strata such as transcriptome and metabolome. Because mRNA and small RNA (sRNA) sequences are involved in transcriptional, translational and post-translational processes, we expect them to provide information influencing several biological strata. However, using sRNA data of parent lines to predict hybrid performance has not yet been addressed. Here, we gathered genomic, transcriptomic (mRNA and sRNA) and metabolomic data of parent lines to evaluate the ability of the data to predict the performance of untested hybrids for important agronomic traits in grain maize. We found a considerable interaction for predictive ability between predictor and trait, with mRNA data being a superior predictor for grain yield and genomic data for grain dry matter content, while sRNA performed relatively poorly for both traits. Combining mRNA and genomic data as predictors resulted in high predictive abilities across both traits and combining other predictors improved prediction over that of the individual predictors alone. We conclude that downstream "omics" can complement genomics for hybrid prediction, and, thereby, contribute to more efficient selection of hybrid candidates.
Key message
Inclusion of historical training data improved the genomics-based prediction of performance of maize hybrids, the extent depending on the phenotypic trait and genotype-by-year ...interaction.
Prediction of hybrid performance using existing phenotypic data on previous hybrids combined with molecular data collected on the parent lines allows to identify the most promising candidates from a huge number of possible hybrids at an early stage. Phenotypic data on yield and dry matter of 1970 grain maize hybrids from 19 years of a public breeding program were aggregated considering the underlying structure of factorial sets of hybrids. Pedigree records and 50 K SNP data were collected on their 170 Dent and 127 Flint parent lines. The performance of untested hybrids was predicted by best linear unbiased predictors (BLUP) on basis of pedigree or genomic data. For composition of training sets (TRN) and test sets (TST), three schemes for collecting factorials from specific years were employed which resulted in 490 scenarios. For each scenario, the predictive ability and genomic relationship between TRN and TST hybrids were determined. For extended TRNs, where earlier years were successively added to the TRN, the maximum relationship increased and the predictive ability improved, with the extent of the latter depending on the phenotypic trait and its genotype-by-year interaction. Genomic BLUP outperformed pedigree BLUP and better utilized the early years’ data, especially for prediction of hybrids from factorials in a more distant future. This study on hybrid prediction in grain maize illustrated that including historical phenotypic data for training, although consisting of less related genotypes, can improve genomic prediction and enables optimization of hybrid variety development.
One of the critical limitations for the in vivo production of doubled haploid (DH) lines in maize (Zea mays L.) is the inability to effectively identify haploids in a significant proportion of ...induction crosses due to the possibility of complete or partial inhibition of the currently used R1‐nj (Navajo) color marker. In this study, we demonstrate that the R1‐nj marker could result in a high proportion of false positives among the haploids identified, besides being ineffective in germplasm with natural anthocyanin expression in pericarp tissue. To address these limitations, we developed haploid inducer lines with triple anthocyanin color markers, including the expression of anthocyanin coloration in the seedling roots and leaf sheaths, in addition to the Navajo marker on the seed. Although these inducers show acceptable haploid induction rates ranging from 8.6 to 10.2%, they exhibited relatively poor agronomic performance compared with tropicalized haploid inducers within tropical environments. The addition of the red root marker more accurately identified haploids among the germinating seedlings, including four tropical inbred lines and eight breeding populations that showed complete inhibition of R1‐nj. We also demonstrate that the red root marker can be used for haploid identification in germplasm with natural anthocyanin expression in the pericarp. A survey of 546 tropical inbreds and 244 landraces showed that anthocyanin accumulation in the roots of germinating seedlings is very rare compared with anthocyanin accumulation in the seed and leaf sheath tissues. As a result, the red root marker can serve as a highly complementary marker to R1‐nj to enable effective identification of haploids within a wide range of tropical maize germplasm.
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