Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

<p>Abstract</p> <p>Background</p> <p>Considerations in applying association mapping (AM) to plant breeding are population structure and size: not accounting for structure and/or using small populations can lead to elevated false-positive rates. The principal determinants of population structure in cultivated barley are growth habit and inflorescence type. Both are under complex genetic control: growth habit is controlled by the epistatic interactions of several genes. For inflorescence type, multiple loss-of-function alleles in one gene lead to the same phenotype. We used these two traits as models for assessing the effectiveness of AM. This research was initiated using the CAP Core germplasm array (n = 102) assembled at the start of the Barley Coordinated Agricultural Project (CAP). This array was genotyped with 4,608 SNPs and we re-sequenced genes involved in morphology, growth and development. Larger arrays of breeding germplasm were subsequently genotyped and phenotyped under the auspices of the CAP project. This provided sets of 247 accessions phenotyped for growth habit and 2,473 accessions phenotyped for inflorescence type. Each of the larger populations was genotyped with 3,072 SNPs derived from the original set of 4,608.</p> <p>Results</p> <p>Significant associations with SNPs located in the vicinity of the loci involved in growth habit and inflorescence type were found in the CAP Core. Differentiation of true and spurious associations was not possible without <it>a priori </it>knowledge of the candidate genes, based on re-sequencing. The re-sequencing data were used to define allele types of the determinant genes based on functional polymorphisms. In a second round of association mapping, these synthetic markers based on allele types gave the most significant associations. When the synthetic markers were used as anchor points for analysis of interactions, we detected other known-function genes and candidate loci involved in the control of growth habit and inflorescence type. We then conducted association analyses - with SNP data only - in the larger germplasm arrays. For both vernalization sensitivity and inflorescence type, the most significant associations in the larger data sets were found with SNPs coincident with the synthetic markers used in the CAP Core and with SNPs detected via interaction analysis in the CAP Core.</p> <p>Conclusions</p> <p>Small and highly structured collections of germplasm, such as the CAP Core, are cost-effectively phenotyped and genotyped with high-throughput markers. They are also useful for characterizing allelic diversity at loci in germplasm of interest. Our results suggest that discovery-oriented exercises in AM in such small arrays may generate a large number of false-positives. However, if haplotypes in candidate genes are available, they may be used as anchors in an analysis of interactions to identify other candidate regions harboring genes determining target traits. Using larger germplasm arrays, genome regions where the principal genes determining vernalization sensitivity and row type are located were identified.</p

The Relationships between Development and Low Temperature Tolerance in Barley Near Isogenic Lines Differing for Flowering Behavior

Flowering time, vernalization requirement, photoperiod sensitivity and low temperature tolerance are key traits in the Triticeae. We characterized a set of isogenic genetic stocks—representing single and pairwise substitutions of spring alleles at the VRN-H1, VRN-H2 and VRN-H3 loci in a winter barley background—at the structural, functional and phenotypic levels. High density mapping with reference to the barley genome sequence confirmed that in all cases target VRN alleles were present in the near isogenic lines (NILs) and allowed estimates of introgression size (at the genetic and physical levels) and gene content. Expression data corroborated the structural and phenotypic results. The latter confirmed that substitution of a spring allele at any of the VRN loci is sufficient to eliminate vernalization requirement. There was no significant change in low temperature tolerance with substitution of a spring allele at VRN-H2, but there were significant losses in cold tolerance with substitutions at VRN-H1 and VRN-H3. Reductions in cold tolerance are ascribed to an accelerated transition from the vegetative to reproductive state. The set of NILs will be a rich resource for understanding the genetics of vernalization, low temperature tolerance and other traits encoded/regulated by genes within the introgressed intervals

Malt modification and its effects on the contributions of barley genotype to beer flavor

Based on prior research that showed significant genetic differences between barley genotypes for beer sensory descriptors, the effects of degree of malt modification on these descriptors were assessed in two experiments. The first experiment involved sensory assessment of nano-beers made from micro-malts of Golden Promise, Full Pint, 34 doubled haploid progeny, and a check CDC Copeland. Average degree of modification was assessed by sampling grain from each of the 37 genotypes stored for three post-harvest intervals prior to malting and brewing. The second experiment involved sensory assessment of pilot beers made from intentionally under-properly-and over-modified pilot malts of two barley varieties: Full Pint and CDC Copeland. In both experiments, genotypes were the principal sources of significant variation in sensory descriptors. Degree of modification and genotype x modification interactions were also significant for some descriptors. Based on the results of this study, the genetic characterization of and selection for barley contributions to beer flavor is warranted, even with under-modified malts. The contribution of barley variety to beer flavor will likely be modest compared to the flavors developed during the malting process, and the flavors contributed by hops and yeast. However, in certain beer styles, the contributions of barley genotype may be worth the attention of maltsters, brewers, and consumers

Effects of Barley (<i>Hordeum Vulgare</i> L.) Variety and Growing Environment on Beer Flavor

<p>This research tested the hypothesis that barley genotype can affect beer flavor and assessed the relative contributions of genotype and location to beer sensory descriptors. Golden Promise, Full Pint, 34 of their doubled haploid progeny, and CDC Copeland were grown at three locations in Oregon, U.S.A. Grain from these trials was micromalted and the resulting malts used for nano-brewing. Sensory evaluations were conducted on the nano-brews. Barley genotype had significant effects on many sensory descriptors. The most significant sensory descriptors—when comparing barley genotypes—were cereal, color, floral, fruity, grassy, honey, malty, toasted, toffee, and sweet. Golden Promise was significantly higher in fruity, floral, and grassy flavors, whereas Full Pint was significantly higher in malty, toffee, and toasted flavors. CDC Copeland was closest to neutral for most flavor traits. There were notable differences for some descriptors between locations. New combinations of parental flavor attributes were observed in the progeny. Multitrait analysis revealed regions of the barley genome with significant effects on malting quality and flavor traits. These findings are, of course, applicable only to the barley germplasm tested, the environment sampled, and the protocols used for micromalting and brewing. The necessary larger-scale experiments involving optimized malts and larger volumes of beer are in process.</p

Effects of barley (Hordeum vulgare L.) variety and growing environment on beer flavor

​This research tested the hypothesis that barley genotype can affect beer flavor and assessed the relative contributions of genotype and location to beer sensory descriptors. Golden Promise, Full Pint, 34 of their doubled haploid progeny, and CDC Copeland were grown at three locations in Oregon, U.S.A. Grain from these trials was micromalted and the resulting malts used for nano-brewing. Sensory evaluations were conducted on the nano-brews. Barley genotype had significant effects on many sensory descriptors. The most significant sensory descriptors—when comparing barley genotypes—were cereal, color, floral, fruity, grassy, honey, malty, toasted, toffee, and sweet. Golden Promise was significantly higher in fruity, floral, and grassy flavors, whereas Full Pint was significantly higher in malty, toffee, and toasted flavors. CDC Copeland was closest to neutral for most flavor traits. There were notable differences for some descriptors between locations. New combinations of parental flavor attributes were observed in the progeny. Multitrait analysis revealed regions of the barley genome with significant effects on malting quality and flavor traits. These findings are, of course, applicable only to the barley germplasm tested, the environment sampled, and the protocols used for micromalting and brewing. The necessary larger-scale experiments involving optimized malts and larger volumes of beer are in process