Association and genome analyses to propose putative candidate genes for malt quality traits.

BACKGROUND: We studied the genetics of nine malt quality traits using association genetics in a panel of North Dakota, ICARDA, and Ethiopian barley lines. Grain samples harvested from Bekoji in 2011 and 2012 were used. RESULTS: The mapping panel revealed strong population structure explained by inflorescence-type, geographic origin, and breeding history. North Dakota germplasm were superior in malt quality traits and they can be donors to improve malt quality properties. We identified 106 marker-trait associations (MTAs) for the nine traits, representing 81 genomic regions across all barley chromosomes. Chromosomes 3H, 5H, and 7H contained most of the MTAs (58.5%). Nearly 18.5% of these genomic regions contained two to three malt quality traits. Within ±250 kb of 81 genomic regions, we recovered 348 barley genes, with some potential impacting malt quality. These include invertase, ß-fructofuranosidase, α-glucosidase, serine carboxypeptidase, and bidirectional sugar transporter SWEET14-like protein. Eighteen of these genes were also previously reported in the Hordeum Toolbox, and 17 of them highly expressed during the germination process. CONCLUSION: The results from this study invite further follow-up functional characterization experiments to relate the genes with individual malt quality traits with higher confidence. It also provides germplasm resources for malt barley improvement. © 2018 Society of Chemical Industry.

Multi-environment multi-QTL association mapping identifies disease resistance QTL in barley germplasm from Latin America.

KEY MESSAGE: Multi-environment multi-QTL mixed models were used in a GWAS context to identify QTL for disease resistance. The use of mega-environments aided the interpretation of environment-specific and general QTL. Diseases represent a major constraint for barley (Hordeum vulgare L.) production in Latin America. Spot blotch (caused by Cochliobolus sativus), stripe rust (caused by Puccinia striiformis f.sp. hordei) and leaf rust (caused by Puccinia hordei) are three of the most important diseases that affect the crop in the region. Since fungicide application is not an economically or environmentally sound solution, the development of durably resistant varieties is a priority for breeding programs. Therefore, new resistance sources are needed. The objective of this work was to detect genomic regions associated with field level plant resistance to spot blotch, stripe rust, and leaf rust in Latin American germplasm. Disease severities measured in multi-environment trials across the Americas and 1,096 SNPs in a population of 360 genotypes were used to identify genomic regions associated with disease resistance. Optimized experimental design and spatial modeling were used in each trial to estimate genotypic means. Genome-Wide Association Mapping (GWAS) in each environment was used to detect Quantitative Trait Loci (QTL). All significant environment-specific QTL were subsequently included in a multi-environment-multi-QTL (MEMQ) model. Geographical origin and inflorescence type were the main determinants of population structure. Spot blotch severity was low to intermediate while leaf and stripe rust severity was high in all environments. Mega-environments were defined by locations for spot blotch and leaf rust. Significant marker-trait associations for spot blotch (9 QTL), leaf (6 QTL) and stripe rust (7 QTL) and both global and environment-specific QTL were detected that will be useful for future breeding efforts.

CGIAR Barley Breeding Toolbox: A diversity panel to facilitate breeding and genomic research in the developing world.

Breeding programs in developing countries still cannot afford the new genotyping technologies, hindering their research. We aimed to assemble an Association Mapping panel to serve as CGIAR Barley Breeding Toolbox (CBBT), especially for the Developing World. The germplasm had to be representative of the one grown in the Developing World; with high genetic variability and be of public domain. For it, we genotyped with the Infinium iSelect 50K chip, a Global Barley Panel (GBP) of 530 genotypes representing a wide range of row-types, end-uses, growth habits, geographical origins and environments. 40,342 markers were polymorphic with an average polymorphism information content of 0.35 and 66% of them exceeding 0.25. The analysis of the population structure identified 8 subpopulations mostly linked to geographical origin, four of them with significant ICARDA origin. The 16 allele combinations at 4 major flowering genes (HvVRN-H3, HvPPD-H1, HvVRN-H1 and HvCEN) explained 11.07% genetic variation and were linked to the geographic origins of the lines. ICARDA material showed the widest diversity as revealed by the highest number of polymorphic loci (99.76% of all polymorphic SNPs in GBP), number of private alleles and the fact that ICARDA lines were present in all 8 subpopulations and carried all 16 allelic combinations. Due to their genetic diversity and their representativity of the germplasm adapted to the Developing World, ICARDA-derived lines and cultivated landraces were pre-selected to form the CBBT. Using the Mean of Transformed Kinships method, we assembled a panel capturing most of the allelic diversity in the GBP. The CBBT (N=250) preserves good balance between row-types and good representation of both phenology allelic combinations and subpopulations of the GBP. The CBBT and its genotypic data is available to researchers worldwide as a collaborative tool to underpin the genetic mechanisms of traits of interest for barley cultivation.

Genetic diversity and population structure assessment of Western Canadian barley cooperative trials.

Studying the population structure and genetic diversity of historical datasets is a proposed use for association analysis. This is particularly important when the dataset contains traits that are time-consuming or costly to measure. A set of 96 elite barley genotypes, developed from eight breeding programs of the Western Canadian Cooperative Trials were used in the current study. Genetic diversity, allelic variation, and linkage disequilibrium (LD) were investigated using 5063 high-quality SNP markers via the Illumina 9K Barley Infinium iSelect SNP assay. The distribution of SNPs markers across the barley genome ranged from 449 markers on chromosome 1H to 1111 markers on chromosome 5H. The average polymorphism information content (PIC) per locus was 0.275 and ranged from 0.094 to 0.375. Bayesian clustering in STRUCTURE and principal coordinate analysis revealed that the populations are differentiated primarily due to the different breeding program origins and ear-row type into five subpopulations. Analysis of molecular variance based on PhiPT values suggested that high values of genetic diversity were observed within populations and accounted for 90% of the total variance. Subpopulation 5 exhibited the most diversity with the highest values of the diversity indices, which represent the breeding program gene pool of AFC, AAFRD, AU, and BARI. With increasing genetic distance, the LD values, expressed as r2, declined to below the critical r2 = 0.18 after 3.91 cM, and the same pattern was observed on each chromosome. Our results identified an important pattern of genetic diversity among the Canadian barley panel that was proposed to be representative of target breeding programs and may have important implications for association mapping in the future. This highlight, that efforts to identify novel variability underlying this diversity may present practical breeding opportunities to develop new barley genotypes.

Perspectives on Low Temperature Tolerance and Vernalization Sensitivity in Barley: Prospects for Facultative Growth Habit.

One option to achieving greater resiliency for barley production in the face of climate change is to explore the potential of winter and facultative growth habits: for both types, low temperature tolerance (LTT) and vernalization sensitivity are key traits. Sensitivity to short-day photoperiod is a desirable attribute for facultative types. In order to broaden our understanding of the genetics of these phenotypes, we mapped quantitative trait loci (QTLs) and identified candidate genes using a genome-wide association studies (GWAS) panel composed of 882 barley accessions that was genotyped with the Illumina 9K single-nucleotide polymorphism (SNP) chip. Fifteen loci including 5 known and 10 novel QTL/genes were identified for LTT-assessed as winter survival in 10 field tests and mapped using a GWAS meta-analysis. FR-H1, FR-H2, and FR-H3 were major drivers of LTT, and candidate genes were identified for FR-H3. The principal determinants of vernalization sensitivity were VRN-H1, VRN-H2, and PPD-H1. VRN-H2 deletions conferred insensitive or intermediate sensitivity to vernalization. A subset of accessions with maximum LTT were identified as a resource for allele mining and further characterization. Facultative types comprised a small portion of the GWAS panel but may be useful for developing germplasm with this growth habit.

Genetic variability in elite barley genotypes based on the agro-morphological characteristics evaluated under irrigated system / Variabilidade genética de genótipos elite de cevada com base em características morfo agronômicas avaliadas em sistema de produção irrigado

ABSTRACT Recently, researches have shown that the Brazilian savannah has a great potential to supply the demand for barley grains. The purpose of this study was to assess the genetic variability in 39 elite barley (Hordeum vulgare L.) genotypes based on the agro-morphological traits of a crop irrigated in the savannah system. An irrigation experiment in the design of complete randomized block with four replicates was conducted at Federal District - Brazil. The evaluated traits were: distance from the last knot to the rachis, distance from the flag leaf to rachis, spike length, number of grains by ear, flag leaf area, plant height, silking, lodging, grain yield, thousand-seed weight, protein content and grain commercial classification. After using analysis of variance the means were used to estimate the genetic dissimilarity among all genotypes pairs based on the Mahalanobis' generalized distance. Cluster analysis using genetic distance matrix was performed having Unweighted Pair Group Method using Arithmetic Means method (UPGMA) as the criteria. Highly significant differences were found among the genotypes for all traits evaluated. The high coefficient of genetic variation indicates the possibility of having genetic gains for all traits. The traits that most contributed to the variability were the flag leaf area and silking, while the protein content and lodging were the traits that contributed the least. Based on the cluster analysis, at least three major groups of similarity were found. There was a clustering trend of two and six-rowed materials. The most divergent genotypes were PFC 2005123, Antártica-1, Nandi and FM 404.

RESUMO Recentemente, pesquisas tem demonstrado que o Cerrado tem grande potencial para suprir a demanda de cevada. O objetivo deste trabalho foi avaliar a variabilidade genética de 39 genótipos elite de cevada com base em características morfoagronômicas avaliadas em sistema de produção irrigado no Cerrado. O experimento foi conduzido num delineamento de blocos ao acaso com quatro repetições no Distrito Federal - Brasil. Avaliaram-se as características: distância do último nó à ráquis, distância da folha bandeira à ráquis, comprimento da espiga, número de grãos por espiga, área da folha bandeira, altura de plantas, espigamento, grau de acamamento, rendimento de grãos, peso de mil sementes, teor de proteína e classificação comercial de grãos. Após análise de variância as médias foram utilizadas para estimar a dissimilaridade genética, com base na distância generalizada de Mahalanobis. Utilizando a matriz de distâncias genéticas foram realizadas análises de agrupamento. Foram observadas diferenças altamente significativas entre os genótipos para todas as características avaliadas. O elevado coeficiente de variação genético evidencia a possibilidade de obter ganhos genéticos para todas características. Através das análises de agrupamento, verificou-se a formação de pelo menos três grandes grupos de similaridade. Houve tendência de agrupamento dos materiais dísticos e hexásticos. Os genótipos PFC 2005123, Antártica-1, Nandi e FM 404 foram os mais divergentes.

Genetic variability of elite barley genotypes for brazilian savanna irrigated systems based on RAPD markers / Variabilidade genética de acessos elite de cevada para sistemas irrigados no cerrado com base em marcadores RAPD

The objective of this work was to characterize and quantify the genetic variability of 39 barley elite genotypes from a Brazilian working collection belonging to Embrapa, using RAPD (Random Amplified Polymorphic DNA) molecular markers. Genomic DNA samples were extracted from leaves of each genotype and 15 decamer primers were used to obtain RAPD molecular markers. Molecular markers were converted in a binary data matrix utilized to estimate genetic dissimilarities between genotypes and to realize grouping and dispersion graphic analysis. A total of 160 RAPD markers were obtained, making 10.7 markers medium per primer. From all the markers, 141 (88.12%) were polymorphic. Genetic dissimilarities varied from 0.049 to 0.337 among the genotypes. PFC 2004033 and Prestige cultivar showed biggest genetic dissimilarities to others genetic materials. Grouping and dispersion graphic analysis showed a clustering tendency between the Mexican and American genotypes. Another clustering tendency was also found concerning the six-rowed materials. Accessions developed and used in Brazil and also in Germany, UK and Australia have shown the greatest genetic dissimilarity among themselves, being considered promising options to increase the genetic base of breeding programs.

O objetivo deste trabalho foi caracterizar e quantificar a variabilidade genética de 39 acessos de cevada elite da coleção de trabalho da Embrapa Cerrados, utilizando marcadores moleculares RAPD. Foram utilizados 15 iniciadores decâmeros para a obtenção dos marcadores RAPD, que foram convertidos em uma matriz de dados binários, a partir da qual foram estimadas as dissimilaridades genéticas entre os diferentes acessos e realizadas análises de agrupamento. Foram obtidos 160 marcadores RAPD, dos quais 141 (88,12%) foram polimórficos. As dissimilaridades genéticas variaram de 0,049 a 0,337, entre os acessos de cevada. A análise de agrupamento e de dispersão gráfica mostrou uma tendência de agrupamento entre os genótipos mexicanos e americanos. Outra tendência de agrupamento também foi encontrada entre os genótipos de seis fileiras de grãos. Acessos desenvolvidos e utilizados no Brasil e também os genótipos provenientes da Alemanha, Inglaterra e Austrália têm demonstrado a maior divergência genética entre si, sendo considerados opções interessantes para aumentar a base genética dos programas de melhoramento.