SECOBRA Saatzucht GmbH

Feldkirchen, Germany

SECOBRA Saatzucht GmbH

Feldkirchen, Germany
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Mora F.,University of Talca | Castillo D.,Institute Investigaciones Agropecuarias | Lado B.,Instituto Nacional Of Investigacion Agropecuaria | Matus I.,Institute Investigaciones Agropecuarias | And 4 more authors.
Molecular Breeding | Year: 2015

Association mapping has been proposed to identify polymorphisms involved in phenotypic variations and may prove useful in identifying interesting alleles for breeding purposes. Using this approach, a total of 382 cultivars and advanced lines of spring wheat obtained from three breeding programs (Chile, Uruguay and CIMMYT) were evaluated for plant height (PH), kernels per spike (KS), 1,000 kernel weight (TKW), grain yield and carbon isotope discrimination (Δ13C) and tested for genotyping-by-sequencing-derived SNP markers across the hexaploid wheat genome. A Bayesian clustering approach via Markov chain Monte Carlo was performed to examine the genetic differentiation (FST) among different genetic groups. The results indicated the existence of two distinct and strongly differentiated genetic groups. Cluster I contained 215 genotypes (56.3 %), over 60 % (137/215) of which were collected from CIMMYT. Cluster II showed the highest FST value, according to 95 % credible interval. Linkage disequilibrium (LD) among SNPs was calculated for the A, B and D genomes and at the whole-genome level. LD decayed over a longer genetic distance for the D genome than for the A and B genomes. In the A and B genomes, LD declined to 50 % of its initial value at about 2 cM. In the D genome, LD was much more extensive, declining to 50 % of its initial value only at 22 cM. In the whole genome, LD declined to 50 % of its initial value at an average of 4 cM. Important genomic regions associated with complex traits in spring wheat were identified. Selection on these regions may increase the efficiency of the current breeding programs. Although most of the associations were environment specific, some stable associations were detected for Δ13C, KS, PH and TKW. Chromosomes 1A, 3A, 4A and 5A were the most important chromosomes, as they comprised quantitative trait loci (QTL) for Δ13C, a trait that can be used as an indirect tool for increased water-use efficiency in wheat. Environment-specific genomic regions were detected, indicating the presence of QTL-by-environment interaction. To produce suitable genotypes under contrasting water availability conditions, QTL × E interactions (and genotype-by-environment interaction) should be considered in the current spring wheat breeding program. © 2015, Springer Science+Business Media Dordrecht.

Albrecht T.,Institute for Crop Science and Plant Breeding | Oberforster M.,Austrian Agency for Health and Food Safety AGES | Kempf H.,Secobra Saatzucht GmbH | Ramgraber L.,Saatzucht Josef Breun GmbH & Co. KG | And 6 more authors.
Journal of Applied Genetics | Year: 2015

Global wheat production will benefit from cultivars showing genetic resistance to preharvest sprouting (PHS). Working on PHS resistance is still challenging due to the lack of simple protocols for the provocation of symptoms for appropriate trait differentiation under highly variable environmental conditions. Therefore, the availability of molecular markers for enhancing PHS resistance in breeding lines is of utmost importance. Genome-wide association mapping was performed to unravel the genetics of PHS resistance in a diversity panel of 124 winter wheat genotypes using both random and targeted marker locus approaches. Data for grain germination tests, spike wetting treatments, and field sprouting damage measurements of grains were collected in 11, 12, and four environments, respectively. Twenty-two quantitative trait loci (QTL) linked with 40 markers were detected for the three traits commonly used for assessing the PHS resistance of cultivars. All but five QTL on chromosomes 1B, 1D (two QTL), 3D, and 5D showed locations similar to previous studies, including prominent QTL on chromosomes 2BS, 3AS, and 4AL. The highest retrieval rate across environments was found for QTL on chromosomes 1D, 2BS, 3D, 4AL, and 7B. The study identified genomic signatures useful for marker-assisted improvement of PHS resistance not only in European breeding programs, but of global significance. © 2015, Institute of Plant Genetics, Polish Academy of Sciences, Poznan.

Brandariz S.P.,University of the Republic of Uruguay | Gonzalez Reymundez A.,University of the Republic of Uruguay | Lado B.,University of the Republic of Uruguay | Malosetti M.,Wageningen University | And 9 more authors.
BMC Genomics | Year: 2016

Background: Whole-genome genotyping techniques like Genotyping-by-sequencing (GBS) are being used for genetic studies such as Genome-Wide Association (GWAS) and Genomewide Selection (GS), where different strategies for imputation have been developed. Nevertheless, imputation error may lead to poor performance (i.e. smaller power or higher false positive rate) when complete data is not required as it is for GWAS, and each marker is taken at a time. The aim of this study was to compare the performance of GWAS analysis for Quantitative Trait Loci (QTL) of major and minor effect using different imputation methods when no reference panel is available in a wheat GBS panel. Results: In this study, we compared the power and false positive rate of dissecting quantitative traits for imputed and not-imputed marker score matrices in: (1) a complete molecular marker barley panel array, and (2) a GBS wheat panel with missing data. We found that there is an ascertainment bias in imputation method comparisons. Simulating over a complete matrix and creating missing data at random proved that imputation methods have a poorer performance. Furthermore, we found that when QTL were simulated with imputed data, the imputation methods performed better than the not-imputed ones. On the other hand, when QTL were simulated with not-imputed data, the not-imputed method and one of the imputation methods performed better for dissecting quantitative traits. Moreover, larger differences between imputation methods were detected for QTL of major effect than QTL of minor effect. We also compared the different marker score matrices for GWAS analysis in a real wheat phenotype dataset, and we found minimal differences indicating that imputation did not improve the GWAS performance when a reference panel was not available. Conclusions: Poorer performance was found in GWAS analysis when an imputed marker score matrix was used, no reference panel is available, in a wheat GBS panel. © 2016 The Author(s).

Lado B.,Instituto Nacional Of Investigacion Agropecuaria | Matus I.,Institute Investigaciones Agropecuarias | Rodriguez A.,Institute Investigaciones Agropecuarias | Inostroza L.,Institute Investigaciones Agropecuarias | And 8 more authors.
G3: Genes, Genomes, Genetics | Year: 2013

In crop breeding, the interest of predicting the performance of candidate cultivars in the field has increased due to recent advances in molecular breeding technologies. However, the complexity of the wheat genome presents some challenges for applying new technologies in molecular marker identification with next-generation sequencing. We applied genotyping-by-sequencing, a recently developed method to identify single-nucleotide polymorphisms, in the genomes of 384 wheat (Triticum aestivum) genotypes that were field tested under three different water regimes in Mediterranean climatic conditions: rain-fed only, mild water stress, and fully irrigated. We identified 102,324 single-nucleotide polymorphisms in these genotypes, and the phenotypic data were used to train and test genomic selection models intended to predict yield, thousand-kernel weight, number of kernels per spike, and heading date. Phenotypic data showed marked spatial variation. Therefore, different models were tested to correct the trends observed in the field. A mixed-model using moving-means as a covariate was found to best fit the data. When we applied the genomic selection models, the accuracy of predicted traits increased with spatial adjustment. Multiple genomic selection models were tested, and a Gaussian kernel model was determined to give the highest accuracy. The best predictions between environments were obtained when data from different years were used to train the model. Our results confirm that genotyping-by-sequencing is an effective tool to obtain genome-wide information for crops with complex genomes, that these data are efficient for predicting traits, and that correction of spatial variation is a crucial ingredient to increase prediction accuracy in genomic selection models. © 2013 Lado et al.

Mohler V.,Institute for Crop Science and Plant Breeding | Bauer C.,Institute for Crop Science and Plant Breeding | Schweizer G.,Institute for Crop Science and Plant Breeding | Kempf H.,Secobra Saatzucht GmbH | Hartl L.,Institute for Crop Science and Plant Breeding
Journal of Applied Genetics | Year: 2013

Fungal diseases of wheat, including powdery mildew, cause significant crop, yield and quality losses throughout the world. Knowledge of the genetic basis of powdery mildew resistance will greatly support future efforts to develop and cultivate resistant cultivars. Studies were conducted on cultivated emmer-derived wheat line K2 to identify genes involved in powdery mildew resistance at the seedling and adult plant growth stages using a BC1 doubled haploid population derived from a cross between K2 and susceptible cultivar Audace. A single gene was located distal to microsatellite marker Xgwm294 on the long arm of chromosome 2A. Quantitative trait loci (QTL) analysis indicated that the gene was also effective at the adult plant stage, explaining up to 79.0 % of the variation in the progeny. Comparison of genetic maps indicated that the resistance gene in K2 was different from Pm4, the only other formally named resistance gene located on chromosome 2AL, and PmHNK54, a gene derived from Chinese germplasm. The new gene was designated Pm50. © 2013 Institute of Plant Genetics, Polish Academy of Sciences, Poznan.

Silva P.,Instituto Nacional Of Investigacion Agropecuaria Inia | Calvo-Salazar V.,International Maize and Wheat Improvement Center | Condon F.,Instituto Nacional Of Investigacion Agropecuaria Inia | Quincke M.,Instituto Nacional Of Investigacion Agropecuaria Inia | And 6 more authors.
Euphytica | Year: 2015

Achieving durable resistance to leaf rust (LR), caused by Puccinia triticina, in wheat has been one of the main objectives of breeding programs. Durability of LR resistance is considered to be associated with adult plant resistance (APR) genes that are quantitatively inherited and whose expression is largely influenced by environment. Our objective was to study the effects and interactions of APR genes Lr34, Lr68 and Sr2 on LR response in Uruguay using two BC1F6 populations (‘LE2304*2/Parula’ and ‘ORL99192*2/Parula’). The experimental material was screened for LR in three artificially inoculated environments (La Estanzuela 2012 and 2013 and Young 2012). Linked molecular markers were used to detect the presence of the genes conferring resistance to LR. Gene Lr34 was fixed in the ‘LE2304*2/Parula’ population. Lr68+Sr2 resulted in a reduction of 79 % of the LR area under the disease progress curve (AUDPC), while the presence of Lr68 alone resulted in a reduction of 51 %. In the ‘ORL99192*2/Parula’ population, the combined effect of Lr34+Lr68+Sr2 led to the highest reduction of LR AUDPC (73 %). Individually, Lr34 and Lr68 resulted in a reduction of the LR AUDPC of 14 and 50 %, respectively. Sr2 alone did not reduce LR AUDPC but enhanced the effect of either Lr34 or Lr68. Unlike previous reports Lr68 conferred a higher level of LR resistance than Lr34 in Uruguay. © 2015, Springer Science+Business Media Dordrecht.

Wang G.,Oregon State University | Leonard J.M.,Oregon State University | von Zitzewitz J.,Oregon State University | von Zitzewitz J.,SECOBRA Saatzucht GmbH | And 4 more authors.
Molecular Breeding | Year: 2014

Identification of marker-trait associations is the first step towards marker-assisted selection in plant breeding. Here we assess genetic diversity and population structure of 94 diverse wheat elite lines and use genome-wide association mapping to identify marker-trait associations for five important traits: kernel hardness (KHA), thousand-kernel weight, grain protein content, test weight (TWT), and plant height (PHT). The 94 accessions employed in this study were grouped into three subpopulations based on the first three principal components, which accounted for 51.5 % of the variations. A mixed linear model was used to detect marker-trait associations incorporating covariance of population structure and relative kinship. A total of six marker loci was significantly associated with KHA, TWT, and PHT after the correction of false discovery rate (α c = 0.05). The gene pinB was found to be highly associated with KHA, and is reported to be a major determinant of KHA together with the gene pinA at the Ha locus on chromosome 5D. Marker XwPt-7187 on chromosome 2A was also significantly associated with KHA, two Diversity Arrays Technology markers XwPt-1250 and XwPt-4628 with TWT, and marker Xgwm512 with PHT, making the first report of marker-trait associations in these genomic regions. © 2014 Springer Science+Business Media Dordrecht.

Rudolphi S.,Secobra Saatzucht GmbH | Becker H.C.,University of Gottingen | Schierholt A.,University of Gottingen | Von Witzke-Ehbrecht S.,University of Gottingen
JAOCS, Journal of the American Oil Chemists' Society | Year: 2012

Near-infrared reflectance spectroscopy (NIRS) of intact seeds allows the non-destructive estimation of seed quality parameters which is highly desirable in plant breeding. Together with yield, oil content and quality, a main aim in safflower (Carthamus tinctorius L.) breeding is the selection of genotypes with a low percentage of empty seeds even under cooler climates. We developed NIRS calibrations for seed oil content, oleic and linoleic acid content, the seed hull fraction and the percentage of empty seeds using seed meal and intact seeds. For the different calibrations 108-534 samples from a safflower breeding program with lines adapted to German conditions, were analyzed with reference analyses (Soxhlet, gas chromatography), and scanned by NIRS as intact seeds and seed meal. Calibration equations were developed and tested through cross validation. The coefficient of determination of the calibration (R 2) for intact seeds ranged from 0.91(oil content), 0.90 (seed hull fraction), 0.84 (empty seeds), 0.73 (linoleic acid) to 0.68 (oleic acid). The coefficient of determination of the cross validation was higher for seed meal than for intact seeds except for the parameter seed hull fraction. The results show that NIRS calibrations are applicable in safflower breeding programs for a fast screening. © AOCS 2011.

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