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Previous studies have shown that there is considerable population structure in cultivated barley (Hordeum vulgareL.), with the strongest structure corresponding to differences in row number and growth habit. U.S. barley breeding programs include six‐row and two‐row types and winter and spring types in all combinations. To facilitate mapping of complex traits in breeding germplasm, 1816 barley lines from 10 U.S. breeding programs were scored with 1536 single nucleotide polymorphism (SNP) genotyping assays. The number of SNPs segregating within breeding programs varied from 854 to 1398. Model‐based analysis of population structure showed the expected clustering by row type and growth habit; however, there was additional structure, some of which corresponded to the breeding programs. The model that fit the data best had seven populations: three two‐row spring, two six‐row spring, and two six‐row winter. Average linkage disequilibrium (LD) within populations decayed over a distance of 20 to 30 cM, but some populations showed long‐range LD suggestive of admixture. Genetic distance (allele‐sharing) between populations varied from 0.11 (six‐row spring vs. six‐row spring) to 0.45 (two‐row spring vs. six‐row spring). Analyses of pairwise LD revealed that the phase of allelic associations was not well correlated between populations, particularly when their allele‐sharing distance was >0.2. These results suggest that pooling divergent barley populations for purposes of association mapping may be inadvisable.

Grain protein concentration is an important determinant of grain quality in many crops, including wheat (Triticum aestivumL.) and barley (Hordeum vulgareL.). While high grain protein percentage might be desirable in barley destined for monogastric feed, low grain protein concentration is desirable for malt and beer production. Low grain protein concentration is associated with increased levels of malt extract and reduced problems with beer chill haze. Molecular markers were used to map and characterize the genes responsible for low, stable grain protein concentration in a recombinant inbred line population developed from a cross between ‘Karl’ (CIho 15487), a low grain protein six‐rowed barley, and ‘Lewis’ (CIho 15856), a standard two‐rowed cultivar. Three major quantitative trait loci (QTL) were identified which impacted grain protein percentage. Two of these grain protein effects appeared to result from gene action impacting flowering date. This pleiotropic relationship may be the main reason agronomically acceptable, low protein cultivars have yet to be released.

The least ambiguous genetic markers are those based on completely characterized DNA sequence polymorphisms. Unfortunately, assaying allele states by allele sequencing is slow and cumbersome. The most desirable type of genetic marker would be unambiguous, inexpensive to assay and would be assayable singly or in parallel with hundreds of other markers (multiplexable). In this report we sequenced alleles at 54 barley (Hordeum vulgaressp. vulgare) loci, 38 of which contained single-nucleotide polymorphisms (SNPs). Many of these 38 loci contained multiple polymorphisms, and a total of 112 polymorphisms were scored in five barley genotypes. The polymorphism data set was analyzed both by using the individual mutations as cladistic characters and by reducing data for each locus to haplotypes. We compared the informativeness of these two approaches by consensus tree construction and bootstrap analysis. Both approaches provided similar results. Since some of the loci sequenced contained insertion/deletion events and multiple point mutations, we thought that these multiple-mutated loci might represent old alleles that predated the divergence of barley from H. spontaneum. We evaluated sequences from a sample of H. spontaneumaccessions from the Eastern Mediterranean, and observed similar alleles present in both cultivated barley and H. spontaneum, suggesting either multiple domestication events or multiple transfers of genes between barley and its wild ancestor.

Single-nucleotide polymorphisms (SNPs) represent the most prevalent class of genetic markers available for linkage disequilibrium or cladistic analyses. PCR primers may be labeled with fluorescent dyes and used to rapidly and accurately differentiate among alleles that are defined by a single-nucleotide differences. Here, we describe the primer-mediated detection of SNPs based on primer mismatch during allele-specific amplification of preamplified target sequences. Primers are labeled with different fluors at their 5′ nucleotides, with their 3′ termini at the transition mutation that defines allelic variation at the target locus. Each primer perfectly matches one of the two available alleles for each locus. Electrophoretic detection permits characterization of the product both by size and fluor. This report demonstrates some of the capabilities of this assay, including heterozygote determination and multiplexed analysis.

The F2 progeny of a cross between a chromosome 2 multiple marker stock and an adapted cultivar of barley were analyzed for four morphological markers and electrophoretic patterns of eight leaf isozymes. TheIdh-2 locus was linked to thePer-5 locus (27.96±5.07 cM) and to thee locus (10.26±3.13 cM). Also, thePer-5 ande loci were located on the short arm of chromosome 2. In additionIdh-2 was also located on barley chromosome 2 and was linked to thev locus (13.18±3.56 cM), which is located on the long arm of chromosome 2. Two other marker genes,li andwst,,B, were linked (26.50±5.24 cM) on chromosome 2 but segregate independently of the other loci evaluated.

Several variants of the replacement histone H3 genes from soybean, barley and wheat have been cloned and sequenced. Analysis of segregating populations in barley and soybean, as well as analysis of clones isolated from a soybean genomic library, suggested that these genes are dispersed throughout the genome. Several genes contain introns located in similar positions, but of different lengths and sequence. Comparison of mRNA levels in different tissues revealed that the intron-containing and intronless genes have different expression patterns. The distribution of the introns in the histone H3 genes across several plant species suggests that some of the introns might have been lost during the evolution of the gene family. Sequence divergence among introns and gene-flanking sequences in cloned gene variants allowed us to use them as specific probes for localizing individual gene copies and analyzing the genomic distribution of these variants across a range of genotypes.

‘Maverick’ spring oat (Avena sativaL.) (Reg. No. CV‐375, PI 652940) was developed cooperatively by the USDA‐ARS and the Idaho Agricultural Experiment Station (AES) and jointly released in 2007 by the USDA‐ARS, the Idaho AES, the Montana AES, and the Colorado AES. Maverick derives from the cross 80Ab988/‘Monida’ made in 1984 at Aberdeen, ID. Maverick was developed using a modified bulk selection program and selected as an F5:6head row at Aberdeen, ID, in 1990 and was given the selection designation of 90Ab1322. Maverick is a short‐strawed oat cultivar suited to irrigated and higher moisture areas in Colorado, Idaho, and Montana. It is a white hulled, high‐protein type favored in the equine industry.

‘Monico’ spring oat (Avena sativaL.) (Reg. No. CV‐376, PI 652941) was developed cooperatively by the USDA‐ARS and the Idaho Agricultural Experiment Station (AES) and jointly released by the USDA‐ARS, the Idaho AES, the Montana AES, and the Colorado AES in 2007. Monico was developed using a modified bulk selection program. It is a F4spaced‐plant selection from the cross 83Ab3119/‘Monida’ harvested in 1993 at Aberdeen, ID. The parent 83Ab3119 had the pedigree of ‘Cayuse’/76Ab6843 (‘Appaloosa’/3/‘Otana’ //Coker X848‐1‐1‐2/Cayuse). Monico is an early to midseason, relatively tall spring oat with excellent yield potential under both irrigated and rainfed conditions in Montana, Idaho, and Colorado.