Limagrain Cereal Seeds

Fort Collins, CO, United States

Limagrain Cereal Seeds

Fort Collins, CO, United States
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Oliver R.E.,General Mills Crop Biosciences | Tinker N.A.,Agriculture and Agri Food Canada | Lazo G.R.,Albany Research Center | Chao S.,U.S. Department of Agriculture | And 33 more authors.
PLoS ONE | Year: 2013

A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.

Babiker E.M.,U.S. Department of Agriculture | Gordon T.C.,U.S. Department of Agriculture | Jackson E.W.,General Mills Inc. | Chao S.,U.S. Department of Agriculture | And 4 more authors.
Phytopathology | Year: 2015

Developing oat cultivars with partial resistance to crown rust would be beneficial and cost-effective for disease management. Two recombinant inbred-line populations were generated by crossing the susceptible culti-var Provena with two partially resistant sources, CDC Boyer and breeding line 94197A1-9-2-2-2-5. A third mapping population was generated by crossing the partially resistant sources to validate the quantitative trait locus (QTL) results. The three populations were evaluated for crown rust severity in the field at Louisiana State University (LSU) in 2009 and 2010 and at the Cereal Disease Laboratory (CDL) in St. Paul, MN, in 2009, 2010, and 2011. An iSelect platform assay containing 5,744 oat single nucleotide polymorphisms was used to genotype the populations. From the 2009 CDL test, linkage analyses revealed two QTLs for partial resistance in the Provena/CDC Boyer population on chromosome 19A. One of the 19A QTLs was also detected in the 2009 LSU test. Another QTL was detected on chromosome 12D in the CDL 2009 test. In the Provena/94197A1-9-2-2-2-5 population, only one QTL was detected, on chromosome 13A, in the CDL 2011 test. The 13A QTL from the Provena/94197A1-9-2-2-2-5 population was validated in the CDC Boyer/94197A1-9-2-2-2-5 population in the CDL 2010 and 2011 tests. Comparative analysis of the significant marker sequences with the rice genome database revealed 15 candidate genes for disease resistance on chromosomes 4 and 6 of rice. These genes could be potential targets for cloning from the two resistant parents. © 2015 The American Phytopathological Society.

Oliver R.E.,North Dakota State University | Islamovic E.,U.S. Department of Agriculture | Obert D.E.,Limagrain Cereal Seeds | Wise M.L.,U.S. Department of Agriculture | And 9 more authors.
PLoS ONE | Year: 2014

Tocochromanols are recognized for nutritional content, plant stress response, and seed longevity. Here we present a systems biological approach to characterize and develop predictive assays for genes affecting tocochromanol variation in barley. Major QTL, detected in three regions of a SNP linkage map, affected multiple tocochromanol forms. Candidate genes were identified through barley/rice orthology and sequenced in genotypes with disparate tocochromanol profiles. Gene-specific markers, designed based on observed polymorphism, mapped to the originating QTL, increasing R2 values at the respective loci. Polymorphism within promoter regions corresponded to motifs known to influence gene expression. Quantitative PCR analysis revealed a trend of increased expression in tissues grown at cold temperatures. These results demonstrate utility of a novel method for rapid gene identification and characterization, and provide a resource for efficient development of barley lines with improved tocochromanol profiles. © 2014 Oliver et al.

Islamovic E.,U.S. Department of Agriculture | Obert D.E.,Limagrain Cereal Seeds | Oliver R.E.,U.S. Department of Agriculture | Oliver R.E.,General Mills Inc. | And 7 more authors.
Molecular Breeding | Year: 2013

High beta-glucan (BG) barleys (Hordeum vulgare L.) have major potential as food ingredients due to their well-known health benefits. Quantitative trait loci (QTL) associated with BG have been reported in traditional barley varieties with intermediate levels of BG, but no QTL studies have been reported in hull-less barley varieties with high BG levels. In this study, QTL analysis was performed to identify markers linked to high BG and amylose in the hull-less barley varieties Falcon (4-5 % BG) and Azhul (8-9 % BG) using a newly developed recombinant inbred line (RIL) mapping population. The population was grown over 3 years (2007-2009) at sites in Yuma, AZ, USA; Leeston, New Zealand; Aberdeen, ID, USA; and Tetonia, ID, USA. We identified 17 QTL associated with either BG or amylose content. QTL contributing to high BG were located on chromosomes 3H, 4H, 5H, 6H and 7H, while QTL contributing to amylose were located on chromosomes 1H, 5H and 7H. Additionally, we identified QTL affecting both BG and amylose content located on chromosomes 1H and 7H. Transgressive segregation was observed in some of the RILs and exceptions were discovered contradicting an inverse relationship between BG and amylose. This work will provide the basis for gene cloning and marker-assisted selection in combination with traditional field selection to improve barley breeding for high BG content. © 2012 Springer Science+Business Media B.V. (outside the USA).

Berger G.L.,Virginia Polytechnic Institute and State University | Liu S.,Texas AgriLife Research Center | Hall M.D.,Limagrain Cereal Seeds | Brooks W.S.,Virginia Polytechnic Institute and State University | And 5 more authors.
Theoretical and Applied Genetics | Year: 2013

Genome-wide association studies (GWAS) provide an opportunity to examine the genetic architecture of quantitatively inherited traits in breeding populations. The objectives of this study were to use GWAS to identify chromosome regions governing traits of importance in six-rowed winter barley (Hordeum vulgare L.) germplasm and to identify single-nucleotide polymorphisms (SNPs) markers that can be implemented in a marker-assisted breeding program. Advanced hulled and hulless lines (329 total) were screened using 3,072 SNPs as a part of the US. Barley Coordinated Agricultural Project (CAP). Phenotypic data collected over 4 years for agronomic and food quality traits and resistance to leaf rust (caused by Puccinia hordei G. Otth), powdery mildew [caused by Blumeria graminis (DC.) E. O. Speer f. sp. hordei Em. Marchal], net blotch (caused by Pyrenophora teres), and spot blotch [caused by Cochliobolus sativus (Ito and Kuribayashi) Drechsler ex Dastur] were analyzed with SNP genotypic data in a GWAS to determine marker-trait associations. Significant SNPs associated with previously described quantitative trait loci (QTL) or genes were identified for heading date on chromosome 3H, test weight on 2H, yield on 7H, grain protein on 5H, polyphenol oxidase activity on 2H and resistance to leaf rust on 2H and 3H, powdery mildew on 1H, 2H and 4H, net blotch on 5H, and spot blotch on 7H. Novel QTL also were identified for agronomic, quality, and disease resistance traits. These SNP-trait associations provide the opportunity to directly select for QTL contributing to multiple traits in breeding programs. © 2012 Springer-Verlag Berlin Heidelberg.

Obert D.E.,Limagrain Cereal Seeds | Hang A.,U.S. Department of Agriculture | Hu G.,U.S. Department of Agriculture | Burton C.,U.S. Department of Agriculture | And 4 more authors.
Journal of Plant Registrations | Year: 2011

Studies on the effects of β-glucan on humans have shown that food containing high concentrations of β-glucans from barley (Hordeum vulgare L.) reduced total cholesterol levels. β-Glucan has been shown to be beneficial for the regulation of blood-glucose levels, and high β-glucan has been found to reduce glucose intolerance and insulin resistance. High β-glucan barley varieties with good agronomic traits are few and have reduced yield potential compared with feedand malting-barley cultivars. 'Transit' (Reg. No. CV-348, PI 660128), a two-rowed, spring, high β-glucan barley, was developed and submitted for release in 2009 by the USDA-ARS, Aberdeen, ID in cooperation with the University of Idaho Agricultural Experiment Station. Transit is a selection from the cross 10/'Azhul'//'CDC Alamo'. 10 is a selection from composite cross XXXII. Azhul is a six-rowed, high β-glucan cultivar released by the ARS and Arizona Agricultural Experiment Station and is the progenitor of most high β-glucan cultivars and germplasm. Azhul was developed by the mutation of line 76-19-7 with diethyl sulfate. Line 76-19-7 has the pedigree CCXXXII/'Arimont'//'Westbar'. CDC Alamo, tested as HB340, has the pedigree SB85750/Azhul. Transit has a reduced yield potential compared with the best feed and malting types, but its high level of β-glucan provides enough added value to allow it to be economically competitive with current malting-barley cultivars. The release of Transit will provide producers with a variety having improved yield potential and β-glucan content compared with the current varieties CDC Alamo and Azhul. Transit is expected to be adapted to both irrigated and rainfed regions in Idaho. © Crop Science Society of America.

Mohammadi M.,University of Minnesota | Blake T.K.,Montana State University | Budde A.D.,U.S. Department of Agriculture | Chao S.,U.S. Department of Agriculture | And 5 more authors.
Theoretical and Applied Genetics | Year: 2015

Key message: We report malt quality QTLs relevant to breeding with greater precision than previous mapping studies. The distribution of favorable alleles suggests strategies for marker-assisted breeding and germplasm exchange.Abstract: This study leverages the breeding data of 1,862 barley breeding lines evaluated in 97 field trials for genome-wide association study of malting quality traits in barley. The mapping panel consisted of six-row and two-row advanced breeding lines from eight breeding populations established at six public breeding programs across the United States. A total of 4,976 grain samples were subjected to micro-malting analysis and mapping of nine quality traits was conducted with 3,072 SNP markers distributed throughout the genome. Association mapping was performed for individual breeding populations and for combined six-row and two-row populations. Only 16 % of the QTL we report here had been detected in prior bi-parental mapping studies. Comparison of the analyses of the combined two-row and six-row panels identified only two QTL regions that were common to both. In total, 108 and 107 significant marker-trait associations were identified in all six-row and all two-row breeding programs, respectively. A total of 102 and 65 marker-trait associations were specific to individual six-row and two-row breeding programs, respectively indicating that most marker-trait associations were breeding population specific. Combining datasets from different breeding program resulted in both the loss of some QTL that were apparent in the analyses of individual programs and the discovery of new QTL not identified in individual programs. This suggests that simply increasing sample size by pooling samples with different breeding history does not necessarily increase the power to detect associations. The genetic architecture of malting quality and the distribution of favorable alleles suggest strategies for marker-assisted selection and germplasm exchange. © 2015, Springer-Verlag Berlin Heidelberg.

Pauli D.,Montana State University | Muehlbauer G.J.,University of Minnesota | Smith K.P.,University of Minnesota | Cooper B.,Limagrain Cereal Seeds | And 4 more authors.
Plant Genome | Year: 2014

The use of genome-wide association studies (GWAS) to detect quantitative trait loci (QTL) controlling complex traits has become a popular approach for studying key traits in crop plants. The goal of this study was to identify the genomic regions of barley (Hordeum vulgare L.) that impact five agronomic and one quality trait in U.S. elite barley breeding lines, as well as to identify markers tightly linked with these loci for further use in barley improvement. Advanced recombinant inbred lines submitted to the U.S. Barley Coordinated Agricultural Project (CAP) were genotyped using a platform of 3072 single nucleotide polymorphism (SNP) markers from the barley oligonucleotide pool assays (BOPAs) 1 and 2. In each of 4 yr, approximately 770 lines were evaluated in a replicated, randomized complete block design under both irrigated and dryland conditions. This gave an overall population size of > 3000 lines, which we analyzed in a hierarchical fashion, including analyzing the lines in aggregate using a mixed model to account for population structure and relatedness among the lines. We identified 41 significant marker–trait associations, of which 31 had been previously reported as QTL using biparental mapping techniques; 10 novel marker-trait associations were identified. The results of this work show that genes with major effects are still segregating in U.S. barley germplasm and demonstrate the utility of GWAS in barley breeding populations. © Crop Science Society of America.

Hu G.,U.S. Department of Agriculture | Evans C.P.,U.S. Department of Agriculture | Satterfield K.,U.S. Department of Agriculture | Ellberg S.,U.S. Department of Agriculture | And 2 more authors.
Journal of Plant Registrations | Year: 2016

‘Kardia’(Reg.No.CV-360, PI 675999), a two-rowed spring hulled food barley (Hordeum vulgare L.) cultivar developed by the USDA-ARS, Aberdeen, ID, in cooperation with the University of Idaho Agricultural Experiment Station, was released in 2015.Kardia is derived from the cross 03AH3054/98Ab12019’ and was advanced through bulk pedigree F1– F5.Kardia was tested at the USDA-ARS and all other cooperative trials as line 2Ab09-X06F084-51.Kardia tested across 40 location years and has shown better yield in irrigated condition and similar yield in dryland comparing to the current two-rowed spring hulled food barley cultivar check ‘Salute’, but it has lower yield than ‘Baronesse’, a feed barley check.Kardia, however, has shown significantly higher b-glucan content than Salute.Kardia could be a good hulled cultivar and a better alternative than Salute in the food barley production market. © Crop Science Society of America.

Graybosch R.A.,University of Nebraska - Lincoln | James Peterson C.,Limagrain Cereal Seeds
Crop Science | Year: 2012

A previous investigation, using region-wide data from Great Plains wheat (Triticum aestivum L.) breeding trials, indicated a possible plateau in the rate of genetically determined yield potential. Data from the same USDA- Agricultural Research Service (ARS) coordinated long-term regional performance nurseries was used to further examine the rate of genetic improvement of Great Plains winter wheats in specific agroecological or production zones over the time period 1987 to 2010. The absolute grain yield of all entries and of the top five most productive entries increased in the majority of production zones over this time period. The relative rate of genetic improvement, obtained by comparing grain yields to those of the long-term control cultivar Kharkof, ranged from not significantly different from zero to 1.98% yr -1. This rate of change, however, was statistically significant (α = 0.05) in only two of the 12 zones evaluated. Variance components identified production zone and locations within production zone as being the largest sources of variation in grain yields. Variance due to either genotype or genotype × environmental factors remained both constant over the 24-yr time period and small, relative to the environmental variances. Genetic progress for enhanced wheat yield in the region might be limited by the magnitude of these environmental variances and by constraints arising from continuous evolution of pest and pathogen populations. © Crop Science Society of America.

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