Barley Germplasm Collection Research Articles

Genome‐wide association study of adult plant resistance to spot blotch in an elite Canadian two‐row barley germplasm collection

AbstractSpot blotch, caused by Bipolaris sorokiniana, is a growing concern for barley (Hordeum vulgare) production in most humid, temperate growing regions of the world. Under epidemic conditions, this disease can reduce yields significantly. Reduction of kernel plumpness is associated with lower malt extract and consequently grain quality. Enhanced resistance to this disease is a major goal of western Canadian two‐row barley breeding programmes; however, two‐row barley is considered to be more susceptible than six‐row barley. Plant–pathogen interactions observed for Canadian germplasm are polygenic, where quantitative breeding methods could be beneficial for the development of resistant germplasm. A germplasm panel consisting of 200 two‐row, spring barley genotypes with differential reaction to spot blotch was evaluated at Brandon, Manitoba (MB), and Melfort, Saskatchewan (SK), over eight site years. Genome‐wide association study was conducted using a 50k single‐nucleotide polymorphism (SNP) Illumina iSelect genotyping array. The most‐resistant germplasm was found to carry Midwest Six‐rowed Durable Resistant Haplotype (MSDRH) alleles at the loci located on chromosomes 1H (Rcs‐qtl‐1H‐11_10764), 3H (Rcs‐qtl‐3H‐11_10565) and 7H (Rcs‐qtl‐7H‐11_20162, Rcs5 locus), where the 3H locus was found to be the most under‐represented in Canadian germplasm. Additional marker‐trait associations within nurseries were identified on chromosomes 1H, 2H and 4H. Several of the SNP markers identified were found to be polymorphic within the Canadian two‐row germplasm panel and thus could be useful for enhancing spot blotch resistance in two‐row barley for development of resistant cultivars.

The effect of responses to vernalization, photoperiodism, and earliness per se of barley accessions from Dagestan on the duration of the period from shooting to heading

Background. Paratypic variability of the development rates of barley accessions from the Republic of Dagestan was analyzed for five years in the Northwe st of Russia (Pushkin, St. Petersburg) and in the North Caucasus (Derbent, Dagestan). Responses to vernalization, photoperiodism and earliness per se were tested in contrasting environments to assess their effect on barley development. Such studies make it possible to identify valuable adaptable plant forms in the barley germplasm collection for further use in breeding practice.Materials and methods. In Dagestan, the duration of the period from shooting to heading was measured for 12 samples of barley accessions in winter and spring sowing trials. Twenty samples sown in spring in both regions were compared. An empirical indicator of plant development rate was used for barley: the criterion “the number of days by which the period from shooting to heading of an accession exceeds the minimum across a sample” (DPSH).Results and conclusions. Early barley accessions with a low norm of responsiveness were identified: k-3772, k-15013, k-15034, k-15036, k-15186, k-15192, k-21803 and k-23785 – they combined weak sensitivity to a short photoperiod and vernalizing temperatures, so they are promising for breeding in regions where the length of the growing season is a limiting factor. The effect of the responses of barley accessions from Dagestan to vernalization and a short photoperiod on the duration of the period from shooting to heading was on average 8 (5.1–10.6) days and on their earliness per se 6 (4.8–8.2) days. Paratypic variability reflects the range of variation for these indicators. In Dagestan, vernalization temperatures and insensitivity to a short day are the main factors determining the earliness of local barleys in their native environment.

Genome-wide association analysis of natural variation in seed tocochromanols of barley.

Tocochromanols (tocols for short), commonly called Vitamin E, are lipid-soluble plant antioxidants vital for regulating lipid peroxidation in chloroplasts and seeds. Barley (Hordeum vulgare L.) seeds contain all eight different isoforms of tocols; however, the extent of natural variation in their composition and their underlying genetic basis is not known. Tocol levels in barley seeds were quantified in diverse H. vulgare panels comprising 297 wild lines from a diversity panel and 160 cultivated spring-type accessions from the mini-core panel representing the genetic diversity of the USDA barley germplasm collection. Significant differences were observed in the concentration of tocols between the two panels. To identify the genes associated with tocols, genome-wide association analysis was conducted with single nucleotide polymorphisms (SNPs) from Illumina arrays for the mini-core panel and genotyping-by-sequencing for the wild barley panel. Forty unique SNPs in the wild barley and 27 SNPs in the mini-core panel were significantly associated with various tocols. Marker-trait associations (MTAs) were identified on chromosomes 1, 6, and 7 for key genes in the tocol biosynthesis pathway, which have also been reported in other studies. Several novel MTAs were identified on chromosomes 2, 3, 4 and 5 and were found to be in proximity to genes involved in the generation of precursor metabolites required for tocol biosynthesis. This study provides a valuable resource for barley breeding programs targeting specific isoforms of seed tocols and for investigating the physiological roles of these metabolites in seed longevity, dormancy, and germination.

Association mapping for yield and yield-contributing traits in barley under drought conditions with genome-based SSR markers

Drought negatively affects plant development, growth, yield, and ultimately production of crop species. Association analysis of yield and yield-contributing traits was conducted for a barley germplasm collection consisting 107 wild (Hordeum spontaneum L.) genotypes, originating from 12 countries using 76 SSR markers. Phenotypic evaluations were performed for days to heading, plant height, number of tillers/plant, spike length, thousand kernel weight, single plant yield under well-watered and drought-stress conditions. Highly significant differences between well-watered and drought-stress conditions were observed in all measured traits. Association analysis revealed a total of 83 significant marker–trait associations for all six measured traits. The results revealed that several chromosomal regions significantly influence more than one trait, suggesting a possible existence of pleiotropic or indirect effects. The phenotypic variation explained by individual marker–trait associations ranged from 5.08 to 27.84%. The results demonstrated that wild barley is a valuable source for improving yield and yield-contributing traits for drought tolerance. Our data provide a tool kit for the potential application of marker-assisted selection for drought tolerance in barley.

Discovery of Novel Bmy1 Alleles Increasing β-Amylase Activity in Chinese Landraces and Tibetan Wild Barley for Improvement of Malting Quality via MAS

China has a large barley germplasm collection which has not been well characterized and is therefore underutilized. The Bmy1 locus encoding the β-amylase enzyme on chromosome 4H has been well characterized in the worldwide barley germplasm collections due to its importance in the malting and brewing industry. The Bmy1 locus was chosen as an indicator to understand genetic potential for improvement of malting quality in Chinese landraces and Tibetan wild barley. The genetic diversity of 91 barley accessions was assessed using allele specific Multiplex-ready molecular markers. Eight accessions were further sequenced, based on the Multiplex-ready marker diversity for Bmy1 in the germplasm. Six of the eight accessions clustered together in a unique group, and showed similarities to ‘Haruna Nijo’, wild barley accession PI296896 and ‘Ashqelon’. Sequence comparisons with the known Bmy1 alleles identified not only the existing 13 amino acid substitutions, but also a new substitution positioned at A387T from a Chinese landrace W127, which has the highest β-amylase activity. Two new alleles/haplotypes namely Bmy1-Sd1c and Bmy1-Sd5 were designated based on different amino acid combinations. We identified new amino acid combination of C115, D165, V233, S347 and V430 in the germplasm. The broad variation in both β-amylase activity and amino acid composition provides novel alleles for the improvement of malting quality for different brewing styles, which indicates the high potential value of the Chinese landraces and Tibetan wild barley.

Genome wide association analyses for drought tolerance related traits in barley ( Hordeum vulgare L .)

Genome wide association (GWA) analysis of yield, yield components, developmental, physiological and anatomical traits was conducted for a barley germplasm collection consisting of 185 cultivated ( Hordeum vulgare L.) and 38 wild ( Hordeum spontaneum L.) genotypes, originating from 30 countries of four continents. Phenotypic evaluations were performed at a dry (Breda) and wet (Tel Hadya) location in Syria. Genome wide association study was done with 816 markers comprised of 710 diversity array technology (DArT), 61 single nucleotide polymorphism (SNP) and 45 microsatellite or simple sequence repeat (SSR) markers. Diversity analysis revealed 5 groups of germplasm, related to origin (Middle East, North Africa), structural information (two-rows), and domestication (wild versus domesticated). Linkage disequilibrium (LD) decayed after 3 cM with a few exceptions at 10 and 15 cM. Although a few QTLs were identified that differed between the dry and wet site, these QTLs explained low phenotypic variation and could not unequivocally be related to drought tolerance when compared to earlier linkage mapping based QTL analysis studies. Therefore, GWA analysis seems to be not very effective for identification of major QTLs for complex traits like drought tolerance in highly structured germplasm collections.

Features of SNP and SSR diversity in a set of ICARDA barley germplasm collection

Detection and utilization of genetic variation available in the germplasm collection for crop improvement have been the prime activities of breeders. Here a set of ICARDA barley germplasm collection comprising of 185 cultivated (Hordeum vulgare L.) and 38 wild (H. spontaneum L.) genotypes originated from 30 countries of four continents was genotyped with 68 single nucleotide polymorphism (SNP) and 45 microsatellite or simple sequence repeat (SSR) markers derived from genes (expressed sequence tags, ESTs). As two SNP markers provided 2 and 3 datapoints, a total of 71 SNPs were surveyed that yielded a total of 143 alleles. The number of SSR alleles per locus ranged from 3 to 22 with an average of 7.9 per marker. Average PIC (polymorphism information content) value for SSR and SNP markers were recorded as 0.63 and 0.38, respectively. Heterogeneity was recorded at both SNP and SSR loci in an average of 5.72 and 12.42% accessions, respectively. Genetic similarity matrices for SSR and SNP allelic data were highly correlated (r = 0.75, P < 0.005) and therefore allelic data for both markers were combined and analyzed for understanding the genetic relationships among the germplasm surveyed. Majority of clusters/subclusters were found to contain genotypes from the same geographic origins. While comparing the genetic diversity, the accessions coming from Middle East Asia and North East Asia showed more diversity as compared to that of other geographic regions. Majority of countries representing Africa, Middle East Asia, North East Asia and Arabian Peninsula included the genotypes that contained rare alleles. As expected, spontaneum accessions, as compared to vulgare accessions, showed a higher number of total alleles, higher number of alleles per locus, higher effective number of alleles and higher allelic richness and a higher number of rare alleles were observed. In summary, the examined ICARDA germplasm set showed ample natural genetic variation that can be harnessed for future breeding of barley as climate change and sustainability have become important throughout all growing areas of the world, drought/heat tolerance being the most important ones.

The production and characterisation of Hor 3 null lines of barley provides new information on the relationship of D hordein to malting performance

Abstract Six pairs of near isogenic lines, differing in the presence of absence of D hordein, were produced in backgrounds with different B and C hordein alleles by introducing a Hor 3 null gene discovered in a barley germplasm collection. Biochemical and cytochemical studies were performed on the harvested and malted grains. Statistical comparisons of the composition of the grains and their malting performance revealed that neither presence or absence of D hordein, nor gel protein levels related to differences in malting performance of the different lines. However, differences in hordein amount and in the grain ultrastructural characteristics could be related to some differences in malting performance between and within some pairs of lines.

Variation over time and environments in resistance to Erysiphe graminis hordei in samples from a barley germplasm collection

When germplasm is evaluated over a period of time and a range of environments, there is a danger that the basis of evaluation will change. The extent of such variation in samples from a germplasm collection was assessed using powdery mildew resistance in barley as an example. The changes found are believed to be representative of those commonly encountered by breeders when using samples from collections. Results show that substantial deviations from the original scores can occur. The implications of this variation are discussed.

Barley Stripe Mosaic Virus in the Western Australian Barley Germplasm Collection.

Barley stripe mosaic virus was detected using enzymelinked immunosorbent assay in the Western Australian barley germplasm collection in accessions originally introduced from Mexico, New Zealand and USA. The virus was also intercepted in one accession introduced from Japan into post-entry quarantine in the Australian Capital Territory. The extent to which the virus occurs in Australian cereal germplasm collections and in the field warrants further investigation.

The emergence of new centres of diversity: evidence from barley

Statistical analyses of data from a large barley germplasm collection of worldwide origins revealed that material from the USA now contains more variability in toto than material from any other country. In addition trends of overall diversity for other countries suggest that there is little association between high overall variability and what are considered as traditional "centres of origin" or "centres of diversity" for this crop. The five countries of highest overall diversity worldwide were found to be (in descending order): USA, Turkey, Japan, USSR and China. Cluster analyses revealed that relatedness of germplasm was by far strongest between certain European countries, which were also in general of a more intermediate diversity level. The data presented here suggests that the variability present in gene pools still varies substantially by country but according to patterns which appear different from those described previously.