David J Hole

Association Mapping of Agronomic QTLs in U.S. Spring Barley Breeding Germplasm

The use of genome‐wide association studies (GWAS) to detect quantitative trait loci (QTL) controlling complex traits has become a popular approach for studying key traits in crop plants. The goal of this study was to identify the genomic regions of barley (Hordeum vulgare L.) that impact five agronomic and one quality trait in U.S. elite barley breeding lines, as well as to identify markers tightly linked with these loci for further use in barley improvement. Advanced recombinant inbred lines submitted to the U.S. Barley Coordinated Agricultural Project (CAP) were genotyped using a platform of 3072 single nucleotide polymorphism (SNP) markers from the barley oligonucleotide pool assays (BOPAs) 1 and 2. In each of 4 yr, approximately 770 lines were evaluated in a replicated, randomized complete block design under both irrigated and dryland conditions. This gave an overall population size of >3000 lines, which we analyzed in a hierarchical fashion, including analyzing the lines in aggregate using a mixed model to account for population structure and relatedness among the lines. We identified 41 significant marker–trait associations, of which 31 had been previously reported as QTL using biparental mapping techniques; 10 novel marker‐trait associations were identified. The results of this work show that genes with major effects are still segregating in U.S. barley germplasm and demonstrate the utility of GWAS in barley breeding populations.

Identification of roots of woody species using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis

Within the last two decades, substantial progress has been made in understanding seed‐bank dynamics and the contribution of the soil seed bank to a postdisturbance plant community. There has been relatively little progress, however, in understanding perennial bud‐bank dynamics and the contribution of the soil bud bank to secondary succession. This lack of information is due primarily to the inability to reliably identify roots, rhizomes and lignotubers that lie dormant beneath the soil surface. This investigation addressed the issue of identification of below‐ground woody structures. The first objective was to develop a method that used molecular tools to identify woody plant species from subsoil tissue samples. The second objective was to develop a key in which molecular markers served as criteria for the identification and differentiation of selected tree and shrub species common to the mountains of northeast Oregon and southeast Washington. Application of restriction fragment length polymorphism (RFLP) analysis of polymerase chain reaction (PCR)‐amplified rbcL appears to be a reliable method to identify and differentiate 15 plants to the genus level. Two restriction enzymes, DpnII and HhaI, provided restriction site polymorphisms in the PCR product. The fragment number and length were used to develop an identification key. However, plants not analysed in this ‘exploratory key’ might share the same banding patterns, resulting in a false identification of unknowns.

Expression and functional analysis of NUCLEAR FACTOR-Y, subunit B genes in barley

NUCLEAR FACTOR-Y, subunit B (NF-YB) comprises a multigene family in plants and has been shown to play important roles in growth, development, and response to environmental stress. In this study, five NF-YBs containing the full-length coding region were obtained from barley (Hordeum vulgare) through database sequence analysis, cloning, and sequencing. Sequence alignment and phylogenetic analysis showed that HvNF-YB3 and HvNF-YB1 were clustered with NF-YB2 and NF-YB3 in Arabidopsis, suggesting these NF-YBs are evolutionary and functionally related. To test this hypothesis, HvNF-YB3 and HvNF-YB1 were overexpressed in Arabidopsis. Overexpression of HvNF-YB1 greatly promoted early flowering in Arabidopsis, supporting that HvNF-YB1may have conserved gene function in flowering time control as NF-YB2 and NF-YB3 in Arabidopsis. Overexpression of HvNF-YB3 in Arabidopsis had no effect on flowering time. An analysis of barley single-nucleotide polymorphism (SNP) data, however, revealed a significant association between an HvNF-YB3 SNP and heading date. While it is unknown whether HvNF-YB3 directly contributes to heading date regulation, the results implied that HvNF-YB3 may also have conserved function in flowering time (heading date in barley) control. Further studies are needed to directly verify these gene functions in barley. Barley NF-YBs showed different expression patterns associated with tissue types, developmental stages, and response to different stress treatments, suggesting that barley NF-YBs may be involved in other physiological processes.

Genes controlling plant growth habit in Leymus (Triticeae): maize barren stalk1 (ba1), rice lax panicle, and wheat tiller inhibition (tin3) genes as possible candidates

Leymus cinereus and L. triticoides are large caespitose and rhizomatous perennial grasses, respectively. Previous studies detected quantitative trait loci (QTL) controlling rhizome spreading near the viviparous1 (vp1) gene markers on linkage groups LG3a and LG3b in two families, TTC1 and TTC2, derived from Leymus triticoides × Leymus cinereus hybrids. The wheat tiller inhibition gene (tin3) is located on Triticum monococcum chromosome 3 AmL near vp1. Triticeae group 3 is reportedly collinear with rice chromosome 1, which also contains the maize barren stalk1 and rice lax branching orthogene near vp1. However, previous studies lacked cross-species markers for comparative mapping and showed possible rearrangements of Leymus group 3 in wheat-Leymus racemosus chromosome addition lines. Here, we developed expressed sequence tag (EST) markers from Leymus tiller and rhizomes and mapped sequences aligned to rice chromosome 1. Thirty-eight of 44 informative markers detected loci on Leymus LG3a and LG3b that were collinear with homoeologous sequences on rice chromosome 1 and syntenous in homoeologous group 3 wheat-Leymus and wheat-Thinopyrum addition lines. A SCARECROW-like GRAS-family transcription factor candidate gene was identified in the Leymus EST library, which aligns to the Leymus chromosome group 3 growth habit QTL and a 324-kb rice chromosome 1 region thought to contain the wheat tin3 gene.

Variation in Kernel Hardness and Associated Traits in U.S. Barley Breeding Lines

ABSTRACTKernel hardness is an important trait influencing postharvest handling, processing, and food product quality in cereal grains. Though well-characterized in wheat, the basis of kernel hardness is still not completely understood in barley. Kernels of 959 barley breeding lines were evaluated for hardness using the Single Kernel Characterization System (SKCS). Barley lines exhibited a broad range of hardness index (HI) values at 30.1–91.9. Distribution of kernel diameter and weight were 1.7–2.9 mm and 24.9–53.7 mg, respectively. The proportion of hull was 10.2–20.7%. From the 959 breeding lines, 10 hulled spring barley lines differing in HI values (30.1–91.2) were selected to study the associations of HI with proportion of hull, kernel weight, diameter, vitreousness, protein, β-glucan, and amylose content. Vitreousness, evaluated visually using a light box, showed a clear distinction between hard and soft kernels. Hard kernels appeared translucent, while soft kernels appeared opaque when illuminated f...

Carbon isotope discrimination of two-rowed and six-rowed barley genotypes under irrigated and non-irrigated field conditions

Carbon isotope discrimination (Δ) has been widely used to estimate the water-use efficiency (WUE) of C3 cereals including barley (Hordeum vulgare L.). Genetic lines of barley belong to two phenotypic classes for ear morphology, either two-rowed or six-rowed, a simply inherited trait. We tested the value of Δ as a predictor of grain yield and WUE for these two types of barley under different conditions of water availability. We also investigated if differences in plant morphology and yield parameters between these two types resulted in different carbon dynamics and different Δ values for grain, awn and flag leaf. We conducted field experiments for 3 consecutive years with genetic lines of both ear types in northern Utah and southeastern Idaho under irrigated and non-irrigated conditions, including two line-source sprinkler experiments. Correlations between grain yield and Δ values of flag leaf, awn and grain were stronger in combined analyses across ear types than in analyses within two-rowed (2R) and six-...

Partitioning the Nutrient and Nonnutrient Contributions Of Compost to Dryland-Organic Wheat

Organic materials supply nutrients to plants but may also have other, nonnutrient-related benefits which are more difficult to quantify. This study partitioned the winter wheat (Triticum aestivum L.) yield response from compost applications into nutrient and nonnutrient fractions. Composted dairy manure and wheat straw bedding was applied at five rates (0, 10, 25, 50, and 75 Mg dry weight ha−1) to dry-land wheat in an organic wheat-fallow farming system. The compost was fall-applied and incorporated prior to planting at adjacent sites in sequential years. Maximum grain yield increases from compost application ranged from 2,139 kg ha−1 in a year with 186% of average annual precipitation to 1,324 kg ha−1 in a year with 87% of average annual precipitation. The Mitscherlich equation was used to describe the yield response to compost rate. The nutrient and nonnutrient contributions of compost to grain yield were partitioned by solving the Mitscherlich equation for compost rates where applied nutrients were in surplus (≥25 Mg ha−1), calculating a non-nutrient Mitscherlich response function, and subtracting the nonnutrient response function from the full response to determine the nutrient contribution across compost rates. At the 10 Mg ha−1 compost rate, the nonnutrient to nutrient yield response ratio varied from 0.25:1 for the year with above average precipitation to 2.2:1 for the year with below average precipitation. Compost significantly increases dry-land wheat yields. These results suggest that nonnutrient benefits of compost applications may be significant and exceed nutrient benefits under dryland production in low rainfall years.

Wheat kernel dormancy and +abscisic acid level following exposure to fluridone

Summary Detached spikes from soft white winter wheat ( Triticum aestivum L.) cultivars that produce caryopses with high dormancy levels (Brevor) or low dormancy levels (Greer) were cultured from anthesis in basal media and media amended with fluridone or fluridone plus ABA. Effects of fluridone and exogenous ABA on kernel development and dormancy acquisition and maintenance were assessed by measuring fresh and dry mass of embryos and caryopses, ABA content in embryos and caryopses, and kernel post-desiccation dormancy levels. Caryopses and embryos exposed to fluridone accumulated very little ABA. Detached spike culture increased ABA concentration and reduced fresh and dry mass in both caryopses and embryos. Fluridone did not affect fresh and dry mass. Addition of ABA to culture media slightly reduced media uptake by detached spikes. During desiccation, ABA and dry matter decreased in caryopses whereas embryos continued to accumulate both. After 2d, 95 % of Greer kernels exposed to fluridone germinated while only 80 % of Brevor kernels were germinated after 4 d. Culture of detached spikes in media amended with fluridone and ABA induced higher dormancy levels in Brevor than in Greer. Results from this study support the hypothesis that ABA may be involved in acquisition of dormancy as well as maintenance of dormancy in wheat kernels.

Awn contribution to gas exchanges of barley ears

The effects of awn removal on ear gas exchange in four barley lines (Morex, Harrington, Steptoe, and TR306) were studied under a controlled environment using a Before-After Control-Impact Paired (BACIP) experimental design. From ear emergence to grain maturity, plants were grown in pots at either 60 or 90 % of soil water holding capacity. Gas-exchange measurements of ears were made 9 and 10 d after anthesis (DAA). On 11 DAA, awn removal was performed on half of the ears in each pot, followed by measurements on both intact and de-awned ears on 12 and 13 DAA. Net photosynthetic (PN) and transpiration (E) rates decreased significantly with awn removal, but dark respiration (RD) rate was not affected. We estimated for each ear a temperature-adjusted respiration rate (Ra) from RD. When we corrected PN with Ra, we found that rates of spikelet photosynthesis were largely underestimated. Moderate water stress had minimal effect on gas exchange of bracts and awns of the barley ear. Barley lines did not differ for any individual gas-exchange parameter.

Estimation of genetic diversity using SSR markers in sunflower.

Microsatellites or simple sequence repeats (SSRs) were used for the estimation of genetic diversity among a group of 40 sunflower lines developed at the research area of Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad. Total numbers of alleles amplified by 22 polymorphic primers were 135 with an average of 6.13 alleles per locus, suggesting that SSR is a powerful technique for assessment of genetic diversity at molecular level. The expected heterozygosity (PIC) ranged from 0.17 to 0.89. The highest PIC value was observed at the locus C1779. The genetic distances ranged from 9% to 37%. The highest genetic distance was observed between the lines L50 and V3. Genetic distances were low showing lesser amount of genetic diversity among the sunflower lines.