Grain yield and grain protein content are two very important traits in bread wheat. They are controlled by genetic factors, but environmental conditions considerably affect their expression. The aim ...of this study was to determine the genetic basis of these two traits by analysis of a segregating population of 194 F(7) recombinant inbred lines derived from a cross between two wheat varieties, grown at six locations in France in 1999. A genetic map of 254 loci was constructed, covering about 75% of the bread wheat genome. QTLs were detected for grain protein-content (GPC), yield and thousand-kernel weight (TKW). 'Stable' QTLs (i.e. detected in at least four of the six locations) were identified for grain protein-content on chromosomes 2A, 3A, 4D and 7D, each explaining about 10% of the phenotypic variation of GPC. For yield, only one important QTL was found on chromosome 7D, explaining up to 15.7% of the phenotypic variation. For TKW, three QTLs were detected on chromosomes 2B, 5B and 7A for all environments. No negative relationships between QTLs for yield and GPC were observed. Factorial Regression on GxE interaction allowed determination of some genetic regions involved in the differential reaction of genotypes to specific climatic factors, such as mean temperature and the number of days with a maximum temperature above 25 degrees C during grain filling.
Key message
Trait-assisted genomic prediction approach is a way to improve genetic gain by cost unit, by reducing budget allocated to phenotyping or by increasing the program’s size for the same ...budget.
This study compares different strategies of genomic prediction to optimize resource allocation in breeding schemes by using information from cheaper correlated traits to predict a more expensive trait of interest. We used bread wheat baking score (BMS) calculated for French registration as a case study. To conduct this project, 398 lines from a public breeding program were genotyped and phenotyped for BMS and correlated traits in 11 locations in France between 2000 and 2016. Single-trait (ST), multi-trait (MT) and trait-assisted (TA) strategies were compared in terms of predictive ability and cost. In MT and TA strategies, information from dough strength (
W
), a cheaper trait correlated with BMS (
r
= 0.45), was evaluated in the training population or in both the training and the validation sets, respectively. TA models allowed to reduce the budget allocated to phenotyping by up to 65% while maintaining the predictive ability of BMS. TA models also improved the predictive ability of BMS compared to ST models for a fixed budget (maximum gain: + 0.14 in cross-validation and + 0.21 in forward prediction). We also demonstrated that the budget can be further reduced by approximately one fourth while maintaining the same predictive ability by reducing the number of phenotypic records to estimate BMS adjusted means. In addition, we showed that the choice of the lines to be phenotyped can be optimized to minimize cost or maximize predictive ability. To do so, we extended the mean of the generalized coefficient of determination (CD
mean
) criterion to the multi-trait context (CD
multi
).
Flour and dough quality are very important breeding traits for wheat (
Triticum aestivum L.) the selection of which would benefit from linked molecular markers. Association analysis allows the ...identification of genes or quantitative trait loci (QTL) related to target traits. The effectiveness of this approach depends on the availability of a densely genotyped population with large genetic variability for the traits of interest. Our objective was to identify chromosomal regions associated with flour and dough quality traits using a core collection built by maximizing the genetic diversity and phenotypic variability. We investigated the association of DArT, SSR and SNP markers with grain protein content, grain hardness, water-extractable arabinoxylan (WEAX) viscosity, wholemeal flour color and dough rheology.
Out of 803 markers tested, 130 markers spread over the genome were associated with at least one trait, varying from 20 associated with WEAX viscosity to 60 associated with dough quality. Most chromosome regions known to determine wheat quality from the study of several bi-parental recombinant inbred lines were confirmed here and some new regions were identified. Associations were found for each trait studied, demonstrating that the core collection is a useful tool for QTL association mapping of these and other traits of interest.
► We investigated a global population to study genetic determinism of wheat quality. ► We searched molecular markers genetically associated with flour and dough traits. ► We mapped numerous regions involved in quality, some already known and some new. ► We demonstrated that this population is a useful tool for QTL association mapping.
While two-rowed barley is usually preferred for malting and beer-making, six-rowed malting barley varieties appeared in Europe around 30 years ago, and several breeders have dedicated improvement ...programs on this specific germplasm. In this study, we evaluated the feasibility of genomic prediction for yield and malting related traits using 679 breeding lines from two French barley breeders, as well as a set of recently registered varieties. These lines were evaluated in five locations and two harvest years in an unbalanced design. Although the germplasm from the two breeders does show some trend towards differentiation, globally the whole panel did not show a clear-cut genetic structure. Predictive ability of GBLUP was evaluated through random cross-validation within and across breeder sets, and using cross-prediction between breeder sets. Results show moderate to high predictive ability (PA), particularly for malt friability and β-glucan content, for which predictive ability of 0.8 was obtained with training populations as small as 105 registered varieties and across breeding sets. The long range of useful linkage disequilibrium in this particular germplasm allows using as few as 2000 to 5000 markers to obtain high PA. Other prediction methods such as Bayesian LASSO, Bayes Cpi or EGBLUP did not improve predictive ability. These results are very encouraging for implementing genomic prediction of malting quality traits in applied breeding programs.
Four trials were conducted to study the grain magnesium (Mg), zinc (Zn) and iron (Fe) concentrations in bread wheat (
Triticum aestivum L.). These trials used different sources of genotypes, ...including old French landraces, a worldwide germplasm collection and elite breeding lines or modern cultivars, grown in different environments. Mg concentration ranged from 600 to 1400
ppm in modern material, and reached 1890
ppm in some exotic genotypes. There was a negative correlation between grain yield and Mg concentration, but despite this dilution effect enough variability remains useful for selection purposes. Analysis of variance showed high genotype effects and Spearman rank correlations indicated moderate genotype by environment (G
×
E) interactions, so breeding for high Mg concentration can reasonably be envisaged. Zn concentration generally ranged from 15 to 35
ppm, but increased to 43
ppm in some genetic resources. Variation in Zn was also partly explained by a dilution effect. There was a significant effect of genotype, but also high G
×
E interactions, which would make direct selection more difficult than for Mg. However, as Zn and Mg concentrations appeared to be positively correlated, Zn concentration should respond favorably to selection for high Mg concentration. Fe concentration ranged from 20 to 60
ppm, and reached 88
ppm in non-adapted material. There were no significant genotype effects, very high G
×
E interactions, and the trait was poorly correlated to other mineral concentrations. Breeding for high Fe concentration will thus probably prove illusory.
A core collection of 372 accessions representative of worldwide hexaploid bread wheat diversity Balfourier, F., Roussel, V., Strelchenko, P., Exbrayat-Vinson, F., Sourdille, P., Boutet, G., Koenig, ...J., Ravel, C., Mitrofanova, O., Beckert, M., Charmet, G., 2007. A worldwide bread wheat core collection arrayed in a 384-well plate. Theoretical and Applied Genetics 114, 1265–1275 was used to evaluate the available genetic diversity of agronomic and quality characteristics. The traits assessed during the vegetative period were date of ear-emergence, date of flowering, lodging, disease susceptibility and pre-harvest sprouting. Thousand kernel weight, test weight, grain hardness, grain protein content, pentosan viscosity and grain colour were also measured. The rheological properties of the derived white flours were estimated using mixograph and alveograph tests. For most of the traits, a wide phenotypic variation was observed across all the accessions. Several parameters (mixograph width parameters before and after peak time, alveograph dough tenacity and extensibility, near infrared measurements, like those for protein content, and absorbance measurements of palmitic acid and linoleic acid content) made it easier to discriminate between the cultivars. The largest ranges of variation were found in landraces and old cultivars rather than in more recent varieties. This is evidence that there is sufficient variability available for rare alleles, which have been eliminated in breeding modern varieties to be detected. Such a core collection will therefore be a useful resource for future genetic studies on wheat quality.
Modern wheat (Triticum aestivum L.) varieties in Western Europe have mainly been bred, and selected in conditions where high levels of nitrogen-rich fertilizer are applied. However, high input crop ...management has greatly increased the risk of nitrates leaching into groundwater with negative impacts on the environment. To investigate wheat nitrogen tolerance characteristics that could be adapted to low input crop management, we supplied 196 accessions of a wheat core collection of old and modern cultivars with high or moderate amounts of nitrogen fertilizer in an experimental network consisting of three sites and 2 years. The main breeding traits were assessed including grain yield and grain protein content. The response to nitrogen level was estimated for grain yield and grain number per m² using both the difference and the ratio between performance at the two input levels and the slope of joint regression. A large variability was observed for all the traits studied and the response to nitrogen level. Whole genome association mapping was carried out using 899 molecular markers taking into account the five ancestral group structure of the collection. We identified 54 main regions involving almost all chromosomes that influence yield and its components, plant height, heading date and grain protein concentration. Twenty-three regions, including several genes, spread over 16 chromosomes were involved in the response to nitrogen level. These chromosomal regions may be good candidates to be used in breeding programs to improve the performance of wheat varieties at moderate nitrogen input levels.
We made an update of the intervarietal molecular marker linkage map of the wheat genome developed using a doubled-haploid (DH) population derived from the cross between the cultivars "Courtot" and ..."Chinese Spring". This map was constructed using 187 DH lines and 659 markers. The genome was well covered (more than 95%) except for chromosomes from homoeologous group 4 and chromosomes 5D and 7D, which had gaps slightly larger than 50 cM. A core-map based on a set of 200 anchor loci (one marker each 18.4 cM) was developed. The total length of this map was 3,685 cM which is similar to the size of the international reference map of the ITMI population (3,551 cM). Map coverage was identical for the three genomes (A, B and D) and for the number of anchor loci, as well as for the size of the map. Using this map, QTLs for several agronomic traits were detected on phenotypic data from the population grown in Clermont-Ferrand (France) under natural field conditions over 6 years, and in Norwich (UK) in controlled conditions and under natural field conditions in 1 year. Almost all of the 21 chromosomes were involved in at least one trait. However, several regions seemed to contain gene clusters either for grain traits (and thus bread-making quality) or plant development traits.
Microsatellites were isolated from a Aegilops tauschii (the D-genome donor of bread wheat) library enriched for various motifs. Primers generated from the flanking region of the microsatellites were ...used successfully to amplify the corresponding loci in the D genome of bread wheat. Additional amplification sometimes also occurred from the A and B genomes. The majority of the microsatellites contained (GA)(n) and (GT)(n) motifs. GA and GT repeats appeared to be both more abundant in this library and more polymorphic than other types of repeats. The allele number for both types of dinucleotide repeats fitted a Poisson distribution. Deviance analysis showed that GA and GT were more polymorphic than other motifs in bread wheat. Within each motif type (di-, tri- and tetra-nucleotide repeats), repeat number has no influence on polymorphism. The microsatellites were mapped using the Triticum aestivum Courtot x Chinese Spring mapping population. A total of 100 markers was developed on this intraspecific map, mainly on the D genome. For polyploid species, isolation of microsatellites from an ancestral diploid donor seems to be an efficient way of developing markers for the corresponding genome in the polyploid plant.
In many wheat ( Triticum aestivumL.) growing areas, pre-harvest sprouting (PHS) may cause important damage, and in particular, it has deleterious effects on bread-making quality. The relationship ...between PHS and grain color is well known and could be due either to the pleiotropic effect of genes controlling red-testa pigmentation ( R) or to linkage between these genes and other genes affecting PHS. In the present work, we have studied a population of 194 recombinant inbred lines from the cross between two cultivars, 'Renan' and 'Récital', in order to detect QTLs for both PHS resistance and grain color. The variety 'Renan' has red kernels and is resistant to PHS, while 'Récital' has white grain and is highly susceptible to PHS. A molecular-marker linkage map of this cross was constructed using SSRs, RFLPs and AFLPs. The population was evaluated over 2 years at Clermont-Ferrand (France). PHS was evaluated on mature spikes under controlled conditions and red-grain color was measured using a chromameter. Over the 2 years, we detected four QTLs for PHS, all of them being co-localized with QTLs for grain color. Three of them were located on the long arm of chromosomes 3 A, 3B and 3D, close to the loci where the genes R and taVp1 were previously mapped. For these three QTLs, the resistance to PHS is due to the allele of the variety 'Renan'. Another co-located QTL for PHS and grain color was detected on the short arm of chromosome 5 A. The resistance for PHS for this QTL is due to the allele of 'Récital'.
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