Richard D. Horsley

An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers

Recent advances in high‐throughput genotyping have made it easier to combine information from different mapping populations into consensus genetic maps, which provide increased marker density and genome coverage compared to individual maps. Previously, a single nucleotide polymorphism (SNP)‐based genotyping platform was developed and used to genotype 373 individuals in four barley (Hordeum vulgare L.) mapping populations. This led to a 2943 SNP consensus genetic map with 975 unique positions. In this work, we add data from six additional populations and more individuals from one of the original populations to develop an improved consensus map from 1133 individuals. A stringent and systematic analysis of each of the 10 populations was performed to achieve uniformity. This involved reexamination of the four populations included in the previous map. As a consequence, we present a robust consensus genetic map that contains 2994 SNP loci mapped to 1163 unique positions. The map spans 1137.3 cM with an average density of one marker bin per 0.99 cM. A novel application of the genotyping platform for gene detection allowed the assignment of 2930 genes to flow‐sorted chromosomes or arms, confirmed the position of 2545 SNP‐mapped loci, added chromosome or arm allocations to an additional 370 SNP loci, and delineated pericentromeric regions for chromosomes 2H to 7H. Marker order has been improved and map resolution has been increased by almost 20%. These increased precision outcomes enable more optimized SNP selection for marker‐assisted breeding and support association genetic analysis and map‐based cloning. It will also improve the anchoring of DNA sequence scaffolds and the barley physical map to the genetic map.

Effect of population size and unbalanced data sets on QTL detection using genome-wide association mapping in barley breeding germplasm

Over the past two decades many quantitative trait loci (QTL) have been detected; however, very few have been incorporated into breeding programs. The recent development of genome-wide association studies (GWAS) in plants provides the opportunity to detect QTL in germplasm collections such as unstructured populations from breeding programs. The overall goal of the barley Coordinated Agricultural Project was to conduct GWAS with the intent to couple QTL detection and breeding. The basic idea is that breeding programs generate a vast amount of phenotypic data and combined with cheap genotyping it should be possible to use GWAS to detect QTL that would be immediately accessible and used by breeding programs. There are several constraints to using breeding program-derived phenotype data for conducting GWAS namely: limited population size and unbalanced data sets. We chose the highly heritable trait heading date to study these two variables. We examined 766 spring barley breeding lines (panel #1) grown in balanced trials and a subset of 384 spring barley breeding lines (panel #2) grown in balanced and unbalanced trials. In panel #1, we detected three major QTL for heading date that have been detected in previous bi-parental mapping studies. Simulation studies showed that population sizes greater than 384 individuals are required to consistently detect QTL. We also showed that unbalanced data sets from panel #2 can be used to detect the three major QTL. However, unbalanced data sets resulted in an increase in the false-positive rate. Interestingly, one-step analysis performed better than two-step analysis in reducing the false-positive rate. The results of this work show that it is possible to use phenotypic data from breeding programs to detect QTL, but that careful consideration of population size and experimental design are required.

The effect of grain storage conditions on the viability of Fusarium and deoxynivalenol production in infested malting barley.

A continuing outbreak of Fusarium head blight occurred on barley in the upper Midwest from 1993 to 1995. This resulted in barley with levels of the mycotoxin deoxynivalenol (DON) reaching levels of concern for maltsters and brewers. This study evaluated the effect of 7 months of storage under different conditions (ambient outdoor temperature from October to April), -20 degrees C, 4 degrees C, 24 degrees C with quiescent air, and 24 degrees C with forced air) on the viability of Fusarium and Alternaria infesting stored grain. Additionally, the ability of Fusarium to produce DON after storage and during malting was evaluated. Initial levels of infestation of barley by Fusarium and Alternaria were 85 and 75%, respectively. All storage condition reduced the viability of both molds slightly and significantly for Fusarium. Forced air ventilation at 24 degrees C was the type of storage most effective in reducing the viability of Fusarium, dropping the percentage of infected kernels to 66%. DON levels did not change after 7 months with respect to storage conditions. However, DON levels were lower in malt produced from barley stored at 24 degrees C with or without aeration. On-farm storage of infected barley at elevated temperatures may provide a means to reduce the level of DON in finished malts.

Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild × Cultivated Barley.

The ability to access alleles from unadapted germplasm collections is a long-standing problem for geneticists and breeders. Here we developed, characterized, and demonstrated the utility of a wild barley advanced backcross-nested association mapping (AB-NAM) population. We developed this population by backcrossing 25 wild barley accessions to the six-rowed malting barley cultivar Rasmusson. The 25 wild barley parents were selected from the 318 accession Wild Barley Diversity Collection (WBDC) to maximize allelic diversity. The resulting 796 BC2F4:6 lines were genotyped with 384 SNP markers, and an additional 4022 SNPs and 263,531 sequence variants were imputed onto the population using 9K iSelect SNP genotypes and exome capture sequence of the parents, respectively. On average, 96% of each wild parent was introgressed into the Rasmusson background, and the population exhibited low population structure. While linkage disequilibrium (LD) decay (r2 = 0.2) was lowest in the WBDC (0.36 cM), the AB-NAM (9.2 cM) exhibited more rapid LD decay than comparable advanced backcross (28.6 cM) and recombinant inbred line (32.3 cM) populations. Three qualitative traits: glossy spike, glossy sheath, and black hull color were mapped with high resolution to loci corresponding to known barley mutants for these traits. Additionally, a total of 10 QTL were identified for grain protein content. The combination of low LD, negligible population structure, and high diversity in an adapted background make the AB-NAM an important tool for high-resolution gene mapping and discovery of novel allelic variation using wild barley germplasm.

DON occurrence in grains: A North American perspective

In agricultural commodities, the occurrence of deoxynivalenol (DON) has been reported all over the world, with levels varying among grain types and years of production. The grain supply chain, including growers, buyers, and end users, have effectively managed DON with strategies to control this issue systematically. The safety of consumers is ensured through use of these management strategies. This is observed in this review of the North American systems. This article describes the occurrence and management of DON in North America, which is accomplished by 1) a review of the toxicological effects of DON; 2) a review of publically available data and introduction of new information regarding the occurrence of DON in wheat, maize, and barley in North America, including variability due to growing regions, grain varieties, and year of production; 3) an overview of industry practices to reduce DON contamination from field through milling when necessary; 4) a review of how all in the value chain, including growe...

A new semi-dwarfing gene identified by molecular mapping of quantitative trait loci in barley.

Semi-dwarfing genes have been widely used in spring barley (Hordeum vulgare L.) breeding programs in many parts of the world, but the success in developing barley cultivars with semi-dwarfing genes has been limited in North America. Exploiting new semi-dwarfing genes may help in solving this dilemma. A recombinant inbred line population was developed by crossing ZAU 7, a semi-dwarf cultivar from China, to ND16092, a tall breeding line from North Dakota. To identify quantitative trait loci (QTL) controlling plant height, a linkage map comprised of 111 molecular markers was constructed. Simple interval mapping was performed for each of the eight environments. A consistent QTL for plant height was found on chromosome 7HL. This QTL is not associated with maturity and rachis internode length. We suggest the provisional name Qph-7H for this QTL. Qph-7H from ZAU 7 reduced plant height to about 3/4 of normal; thus, Qph-7H is considered a semi-dwarfing gene. Other QTLs for plant height were found, but their expression was variable across the eight environments tested.

Impact of tillage on field pea following spring wheat

Tillage is being reduced in semiarid regions. The impact of changing tillage practices on field pea (Pisum sativum L.) performance has not been considered in a major pea-producing area within the US northern Great Plains. A study was conducted from 2000 through 2005 to determine how field pea performance compared following spring wheat (Triticum aestivum L.) in clean-till (CT), reduced-till (RT), and no-till (NT) systems arranged in a randomized complete block at Dickinson in southwestern North Dakota. Seed yield increased over 1600 kg ha-1 in 2000 and almost 400 kg ha-1 in 2003 under NT compared with CT, and by 960 kg ha-1 in 2000 under NT compared with RT (P < 0.05). Differences in seed yield were not detected between tillage systems in other years. Plant establishment was improved as tillage was reduced, averaging 66 plants m-2 under NT and RT compared with 60 plants m-2 under CT management. The soil water conservation that can occur after adopting NT may explain the increased seed yields that occurred...

Cover crop and conidia delivery system impacts on soil persistence of Metarhizium anisopliae (Hypocreales: Clavicipitaceae) in sugarbeet

Abstract The sugarbeet root maggot, Tetanops myopaeformis (Röder), is a major North American pest of sugarbeet, Beta vulgaris L. Previous research suggests that moderate T. myopaeformis control is possible with the entomopathogen Metarhizium anisopliae (Metch.) Sorok. We conducted a three-year (2002–2004) experiment to assess impacts of oat, Avena sativa L. and rye, Secale cereale L., cover crops on persistence of corn grit-based granular or spray formulations of M. anisopliae isolate ATCC 62176 (i.e. MA 1200) applied at 8×1012 viable conidia/ha in sugarbeet. More colony forming units (CFUs) were detected immediately after application [0 days after treatment (DAT)] in spray plots than granule-treated plots. However, 76–92% declines in CFUs per gram of soil occurred in spray plots within 30 DAT. Substantially (i.e. 83–560%) more rainfall occurred in June 2002 than during June of any other year. Subsequently, 71–670% increases in CFU concentrations occurred by 60 DAT in M. anisopliae granule-treated plots with oat or rye cover crops that year. CFU density increases were higher in cover crops in 2002, but no significant cover crop effects were detected. Conidia persisted for up to 30 DAT in M. anisopliae spray plots and 60 DAT in granule-treated plots in 2002; however, no increases occurred in the years with less June rainfall. Trends suggest that M. anisopliae aqueous sprays result in greater conidia concentrations than granules at sugarbeet plant bases in June during T. myopaeformis oviposition and larval establishment on host plants. Increases are possible when delivering conidia via granules, but high post-application rainfall could be necessary for conidia production.

Malting of Fusarium Head Blight-Infected Rye (Secale cereale): Growth of Fusarium graminearum, Trichothecene Production, and the Impact on Malt Quality

This project was initiated with the goal of investigating the malt quality of winter rye cultivars and hybrids grown in the United States in 2014 and 2015, but high levels of deoxynivalenol (DON) were subsequently found in many of the malt samples. DON levels in 75% of the investigated rye samples (n = 117) were actually below 1.0 mg/kg, as quantified by a gas chromatography combined with electron capture detector (GC-ECD). However, 83% of the samples had DON in excess of 1.0 mg/kg following malting, and the average DON level in malted rye was 10.6 mg/kg. In addition, relatively high levels of 3-acetate DON (3-ADON), 15-acetate DON (15-ADON), nivalenol (NIV), and DON-3-glucoside (D3G) were observed in some rye malts. Our results show that rye grain DON is likely a poor predicator of type B trichothecenes in malt in practice, because high levels of malt DON, 15-ADONm and D3G were produced, even when the rye samples with DON levels below 0.50 mg/kg were processed. Fusarium Tri5 DNA content in rye was highly associated with malt DON levels (r = 0.83) in a small subset of samples (n = 55). The impact of Fusarium infection on malt quality was demonstrated by the significant correlations between malt DON levels and wort viscosity, β-glucan content, wort color, wort p-coumaric acid content, and total phenolic content. Additional correlations of rye Fusarium Tri5 DNA contents with malt diastatic power (DP), wort free amino nitrogen (FAN) content, and arabinoxylan content were observed.

Barley Cultivar Performance Following Canola, Corn, Pea, and Spring Wheat

Patrick M. Carr,* Richard D. Horsley, Glenn B. Martin, and Martin R. Hochhalter Abstract High-residue farming and crop diversification practices are replacing conventional tillage and crop-fallow in the Great Plains. Our objective was to determine if cultivar ranking changed when six barley (Hordeum vulgare L.) cultivars were grown following canola (Brassica napus L.), corn (Zea mays L.), pea (Pisum sativum L. subsp. sativum), and spring wheat (Triticum aestivum L. emend. Thell.) from 2010 through 2013 in southwestern North Dakota. An interaction between the previous crop and barley cultivar was detected in 2011 and 2013 for grain yield (P < 0.10). However, one cultivar in 2011 and three cultivars in 2013 produced equal or greater yields than those produced by other cultivars, regardless of previous crop. Grain yield was comparable with or greater following field pea to that following other crops in 2010 and 2012 when a previous crop cultivar interaction did not exist. Interactions between the previous crop and barley cultivar occurred in only 2 of 12 instances for grain quality traits, and even then at least one cultivar was among the top performers consistently after each previous crop treatment. These results suggest that the previous crop is not an important consideration when making barley cultivar recommendations.