Ariel J. Castro

Chapter 10 - Genetic diversity for quantitatively inherited agronomic and malting quality traits

This chapter reviews diversity in agronomic traits, diversity in malting quality traits, and the current status of Quantitative Trait Loci (QTL) analysis in barley and the application of QTL tools to the analysis of genetic diversity in barley and crop improvement. Agronomic and quality traits were undoubtedly key issues for the domesticators of barley. Crop productivity would clearly have been an attribute of key interest, and the selection of shattering-resistant mutants probably led to a quantum leap in yield. Because barley has been used both as a food and as a principal ingredient of fermented beverages from the earliest times, there may well have been conscious selection for end-use properties. The selection of hull-less mutants in areas of the world where barley was a principal foodstuff underscores the importance of end-use properties in domestication. The malting and brewing properties of wild barley accessions and landraces have not been welldescribed and are, in fact, extremely difficult to measure. Plant breeding efforts are directed primarily at traits exhibiting quantitative variation. Breeders and geneticists were now able to collaborate in developing and testing hypotheses regarding the number, location, effect, and interactions of genes influencing quantitative traits.

Mapping and pyramiding of qualitative and quantitative resistance to stripe rust in barley

Abstract The identification and location of sources of genetic resistance to plant diseases are important contributions to the development of resistant varieties. The combination of different sources and types of resistance in the same genotype should assist in the development of durably resistant varieties. Using a doubled haploid (DH), mapping population of barley, we mapped a qualitative resistance gene (Rpsx) to barley stripe rust in the accession CI10587 (PI 243183) to the long arm of chromosome 1(7H). We combined the Rpsx gene, through a series of crosses, with three mapped and validated barley stripe rust resistance QTL alleles located on chromosomes 4(4H) (QTL4), 5(1H) (QTL5), and 7(5H) (QTL7). Three different barley DH populations were developed from these crosses, two combining Rpsx with QTL4 and QTL7, and the third combining Rpsx with QTL5. Disease severity testing in four environments and QTL mapping analyses confirmed the effects and locations of Rpsx, QTL4, and QTL5, thereby validating the original estimates of QTL location and effect. QTL alleles on chromosomes 4(4H) and 5(1H) were effective in decreasing disease severity in the absence of the resistance allele at Rpsx. Quantitative resistance effects were mainly additive, although magnitude interactions were detected. Our results indicate that combining qualitative and quantitative resistance in the same genotype is feasible. However, the durability of such resistance pyramids will require challenge from virulent isolates, which currently are not reported in North America.

The Genetics of Winterhardiness in Barley: Perspectives from Genome-Wide Association Mapping

Winterhardiness is a complex trait that involves low temperature tolerance (LTT), vernalization sensitivity, and photoperiod sensitivity. Quantitative trait loci (QTL) for these traits were first identified using biparental mapping populations; candidate genes for all loci have since been identified and characterized. In this research we used a set of 148 accessions consisting of advanced breeding lines from the Oregon barley (Hordeum vulgare L. subsp vulgare) breeding program and selected cultivars that were extensively phenotyped and genotyped with single nucleotide polymorphisms. Using these data for genome‐wide association mapping we detected the same QTL and genes that have been systematically characterized using biparental populations over nearly two decades of intensive research. In this sample of germplasm, maximum LTT can be achieved with facultative growth habit, which can be predicted using a three‐locus haplotype involving FR‐H1, FR‐H2, and VRN‐H2. The FR‐H1 and FR‐H2 LTT QTL explained 25% of the phenotypic variation, offering the prospect that additional gains from selection can be achieved once favorable alleles are fixed at these loci.

Association Mapping of Malting Quality Quantitative Trait Loci in Winter Barley: Positive Signals from Small Germplasm Arrays

Malting quality comprises one of the most economically relevant set of traits in barley (Hordeum vulgare L.). It is a complex phenotype, expensive and difficult to measure, that would benefit from a marker‐assisted selection strategy. Malting quality is a target of the U.S. Barley Coordinated Agricultural Project (CAP) and development of winter habit malting barley varieties is a key objective of the U.S. barley research community. The objective of this work was to detect quantitative trait loci (QTL) for malting quality traits in a winter breeding program that is a component of the U.S. Barley CAP. We studied the association between five malting quality traits and 3072 single nucleotide polymorphisms (SNPs) from the barley oligonucleotide pool assay (BOPA) 1 and 2, assayed in advanced inbred lines from the Oregon State University (OSU) breeding program from three germplasm arrays (CAP I, CAP II, and CAP III). After comparing 16 models we selected a structured association model with posterior probabilities inferred from software STRUCTURE (QK) approach to use on all germplasm arrays. Most of the marker‐trait associations are germplasm‐ and environment‐specific and close to previously mapped genes and QTL relevant for malt and beer quality. We found alleles fixed by random genetic drift, novel unmasked alleles, and genetic‐background interaction. In a relatively small population size study we provide strong evidence for detecting true QTL.

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

Key messageMulti-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.AbstractDiseases 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.

Coincident quantitative trait loci effects for dormancy, water sensitivity and malting quality traits in the BCD47 × Baronesse barley mapping population

A degree of seed dormancy (SD) is required for malting barley varieties in Uruguay, and many other parts of the world, in order to prevent pre-harvest sprouting. Water sensitivity (WS) (a decrease in germination under excess water) is a related trait that can create problems at the malthouse. Both traits are affected by environmental conditions during grain filling. We used a population of 100 doubled haploid lines derived from the cross BCD47 × Baronesse to map quantitative trait loci (QTL) affecting SD, WS, and malting quality traits. Preliminary experiments revealed that BCD47 has low SD and Baronesse has high SD. WS for these accessions was not known before this research. A major SD QTL – detected in four experiments – is on chromosome 5H, with BCD47 contributing the low dormancy allele. Four other regions with QTL effects for SD were mapped, but these QTL were significant in data from only one or two environments. Four regions were detected with QTL effects for WS, but only two – in 5H coincident with the SD QTL, and 3H – were significant in more than one environment. SD and WS were affected by the average temperature at the end of the grain-filling period, with higher temperatures associated with lower values for SD. At the same region on 5H where SD and WS QTL were detected, we found significant QTL for malt extract, α-amylase activity, β-glucans, FAN, Kolbach index, wort turbidity and protein content, with BCD47 contributing favourable alleles for all traits. These results underscore the importance of environmental effects on both SD and WS as well as the difficulties of combining good malting quality with adequate levels of SD and WS.

Genome-Wide Association Mapping Identifies Disease-Resistance QTLs in Barley Germplasm from Latin America

Diseases are the main problem for barley 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 attack the crop in the region. Chemical control of those diseases is both economically and environmentally inappropriate, making the development of durable resistant varieties a priority for breeding programs. However, the availability of new resistance sources is a limiting factor. The objective of this work was to detect genomic regions associated to durable resistance to spot blotch, stripe rust, and leaf rust in Latin American germplasm. Associations between disease severities measured in several environments across the Americas and 1,536 SNPs (belonging to the barley OPA1) in a population of 360 genotypes were used to identify genomic regions associated with disease. Several models for association mapping with mixed models were compared. These models considered either the structure of the population (Q) through PCA analysis, the identity by descent through coancestry information (K), or both. Results show significant marker-trait associations for spot blotch and leaf and stripe rust. Associations are environment specific.

Ascertainment bias from imputation methods evaluation in wheat.

BackgroundWhole-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.ResultsIn 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.ConclusionsPoorer performance was found in GWAS analysis when an imputed marker score matrix was used, no reference panel is available, in a wheat GBS panel.

Genome-Wide Association Mapping of Malting Quality Traits in Relevant Barley Germplasm in Uruguay

Knowledge about the genetic components of major malting quality traits is needed for efficient barley breeding, and although some of these traits have been mapped, little information about germplasm-specific QTL is known for South American germplasm. The aim of this study was to determine by genome-wide association mapping the key genetic basis of malting quality traits in a population of 76 different genotypes consisting of historical varieties, commercial cultivars, and advanced lines representative of barley breeding in Uruguay. Samples obtained in five contrasting environments were micromalted in order to obtain a phenotypic database. The population was genotyped with 1,033 polymorphic SNPs using the Illumina BOPA1. Marker-trait associations were detected through linkage disequilibrium mapping using a mixed linear model (MLM) Q + K containing a structure matrix (PCA) and a kinship matrix (K). Preliminary results showed QTL effects detected for all traits, with some genomic regions showing a high concentration of significant associations. Most QTL were environment specific. We are presently studying the relationship between malting quality traits and linkage disequilibrium blocks found in the population. The results provide some of the first data regarding genetic basis of malting quality relevant traits in the germplasm used in the region.

Variety and N Management Effects on Grain Yield and Quality of Winter Barley

Winter malting barley (Hordeum vulgare L.) is a potential alternative crop for the dryland region of the Pacific Northwest. Nitrogen fertilization can increase grain yield but may also increase lodging and grain protein and reduce test weight. The objectives of this research were to determine the effect of N application rate and timing on grain yield and quality of winter feed and malting barley varieties. Field trials were conducted at Pendleton, OR (17 inches annual precipitation) and Moro, OR (12 inches annual precipitation). Nitrogen was applied at 0, 50, 100, or 150 lb N per acre in the fall and at 0 or 50 lb N per acre in the spring at Pendleton and at 0, 30, 60, or 90 lb N per acre in the fall and at 0 or 30 lb N per acre in the spring at Moro. Nitrogen fertilization increased grain yields at Pendleton to a maximum of 5,800 lb/acre in 2001 and 5,200 lb/acre in 2002 and at Moro to a maximum of 3,000 lb/acre. Nitrogen fertilization increased grain protein and reduced test weights. Yields of the advanced lines of malting barley were about 90% of the yields of feed type barley varieties. Spring N applications did not increase grain yield or protein more than fall N applications.