Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin

Population structure and genome-wide linkage disequilibrium (LD) were investigated in 192 Hordeum vulgare accessions providing a comprehensive coverage of past and present barley breeding in the Mediterranean basin, using 50 nuclear microsatellite and 1,130 DArT® markers. Both clustering and principal coordinate analyses clearly sub-divided the sample into five distinct groups centred on key ancestors and regions of origin of the germplasm. For given genetic distances, large variation in LD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at 50 cM separation still showing significant LD. Mean LD values across the whole population sample decayed below r 2 of 0.15 after 3.2 cM. By assaying 1,130 genome-wide DArT® markers, we demonstrated that, after accounting for population substructure, current genome coverage of 1 marker per 1.5 cM except for chromosome 4H with 1 marker per 3.62 cM is sufficient for whole genome association scans. We show, by identifying associations with powdery mildew that map in genomic regions known to have resistance loci, that associations can be detected in strongly stratified samples provided population structure is effectively controlled in the analysis. The population we describe is, therefore, shown to be a valuable resource, which can be used in basic and applied research in barle

The Genetic Potential of a Germplasm of Interspecific Crosses between Durum Wheats (Triticum turgidum L. ssp. durum (Desf.) Husn.) and their Relatives (T. dicoccum Schübl. and T. polonicum L.) in Five Glutenin Loci

Wheat endosperm storage proteins are the major components of gluten. They play an important role in dough properties and in bread making quality in various wheat varieties. In the present study, the different alleles encoded at the 5 glutenin loci were identified from a set of 38 tetraploid wheat germplasm obtained from interspecific crosses between durum wheats (Triticum turgidum L. ssp. durum (Desf.) Husn.) and their relatives (T. dicoccum Schübl. and T. polonicum L.) using SDS-PAGE. At Glu-A1 and Glu-B1, encoding high molecular weight glutenin subunits (HMW-GS), 2 and 4 alleles were observed, respectively. Low molecular weight glutenin subunits (LMW-GS) displayed similar polymorphism, as 3, 5 and 3 alleles were identified at loci Glu-A3, Glu-B3 and Glu-B2, respectively. One new allele was detected at Glu-B3 locus and appeared in nine accessions obtained from five crosses. This allele codes for five subunits (2 + 8 + 9 + 13 + 18), encoded by the Glu-B3b without subunit 16 plus subunits 2 and 18. A total of 38 patterns resulted from the genetic combination of the alleles encoding at the five glutenin loci. This led to a significantly higher Nei coefficient of genetic variation in Glu-1, Glu-3 and Glu-B2 loci (0.54). The germplasm analyzed exhibited allelic variation in HMW and LMW glutenin subunit composition and the variation differed from that of tetraploid wheats of other countries. The presence of high quality alleles in glutenin loci have led the accessions to be considered as an asset in breeding programs aimed for wheat quality

Mapping adaptation of barley to droughted environments

Identifying barley genomic regions influencing the response of yield and its components to water deficits will aid in our understanding of the genetics of drought tolerance and the development of more drought tolerant cultivars. We assembled a population of 192 genotypes that represented landraces, old, and contemporary cultivars sampling key regions around the Mediterranean basin and the rest of Europe. The population was genotyped with a stratified set of 50 genomic and EST derived molecular markers, 49 of which were Simple Sequence Repeats (SSRs), which revealed an underlying population sub-structure that corresponded closely to the geographic regions in which the genotypes were grown. A more dense whole genome scan was generated by using Diversity Array Technology (DArT®) to generate 1130 biallelic markers for the population. The population was grown at two contrasting sites in each of seven Mediterranean countries for harvest 2004 and 2005 and grain yield data collected. Mean yield levels ranged from 0.3 to 6.2 t/ha, with highly significant genetic variation in low-yielding environments. Associations of yield with barley genomic regions were then detected by combining the DArT marker data with the yield data in mixed model analyses for the individual trials, followed by multiple regression of yield on markers to identify a multi-locus subset of significant markers/QTLs. QTLs exhibiting a pre-defined consistency across environments were detected in bins 4, 6, 6 and 7 on barley chromosomes 3H, 4H, 5H and 7H respectivel

Mixed model association scans of multi-environmental trial data reveal major loci controlling yield and yield related traits in Hordeum vulgare in Mediterranean environments

An association panel consisting of 185 accessions representative of the barley germplasm cultivated in the Mediterranean basin was used to localise quantitative trait loci (QTL) controlling grain yield and yield related traits. The germplasm set was genotyped with 1,536 SNP markers and tested for associations with phenotypic data gathered over 2 years for a total of 24 year × location combinations under a broad range of environmental conditions. Analysis of multi-environmental trial (MET) data by fitting a mixed model with kinship estimates detected from two to seven QTL for the major components of yield including 1000 kernel weight, grains per spike and spikes per m2, as well as heading date, harvest index and plant height. Several of the associations involved SNPs tightly linked to known major genes determining spike morphology in barley (vrs1 and int-c). Similarly, the largest QTL for heading date co-locates with SNPs linked with eam6, a major locus for heading date in barley for autumn sown conditions. Co-localization of several QTL related to yield components traits suggest that major developmental loci may be linked to most of the associations. This study highlights the potential of association genetics to identify genetic variants controlling complex traits

Secondary Microseisms generated by typhoons in the Northwestern Pacific Ocean

vEGU21: Gather Online | 19-30 April 2021Secondary Microseisms (SM) are recorded by seismometers in the period band 3-10 s. They are generated by the interaction of ocean gravity waves of similar frequencies and coming from nearly opposite directions. Typhoons create such ocean waves, and the purpose of this study is to investigate the relationship between typhoons and microseism source characteristics. We focused our study on the Northwestern Pacific and we analyzed seismic signals recorded by the Alaska array and the corresponding storm catalog. While P body waves enable to characterize the amplitude and the localization of the sources, secondary microseisms are dominated by surface waves. Therefore, we apply beamforming technique to the vertical components in order to highlight the weaker body wave signals. This analysis permits us to track the localization of SM sources every 6 hours. Our results show three cases: In the case of one active typhoon, the positions of SM sources are localized close to the typhoon position. In the case of two nearby typhoons acting simultaneously, the SM sources are localized in between the typhoons. Finally, when the typhoon arrives close to the coast, we observe sources generated by ocean wave reflections. In conclusion, the three mechanisms proposed by Ardhuin et al., (2011) are necessary to explain secondary microseisms generated by typhoons

Genetic and Management Effects on Barley Yield and Phenology in the Mediterranean Basin

Heading time in barley is considered a key developmental stage controlling adaptation to the environment and it affects grain yield; with the combination of agronomy (planting dates) and genetics being some of the determinants of adaptation to environmental conditions in order to escape late frost, heat, and terminal drought stresses. The objectives of this study are (i) to apply a gene-based characterization of 118 barley doubled haploid recombinants for vernalization, photoperiod, and earliness per se; (ii) use such information to quantify the optimal combination of genotype/sowing date that escapes extreme weather events; and (iii) how water and nitrogen management impact on grain yield. The doubled haploid barley genotypes with different allelic combinations for vernalization, photoperiod, and earliness per se were grown in eight locations across the Mediterranean basin. This information was linked with the crop growth model parameters. The photoperiod and earliness per se alleles modify the length of the phenological cycle, and this is more evident in combination with the recessive allele of the vernalization gene VRN-H2. In hot environments such as Algeria, Syria, and Jordan, early sowing dates (October 30 and December15) would be chosen to minimize the risk of exposing barley to heat stress. To maintain higher yields in the Mediterranean basin, barley breeding activities should focus on allelic combinations that have recessive VRN-H2 and EPS2 genes, since the risk of cold stress is much lower than the one represented by heat stress

The impact of climate change on barley yield in the Mediterranean basin

Barley is an important cereal crop for the arid and semi-arid Mediterranean environments. Future climate projections show that Mediterranean countries will get drier and hotter. The objectives of the study are to: i) simulate the impacts of different climate projections and different sowing dates on yield; ii) quantify the importance of heat and drought on barley yield at different growth stages and sowing dates; iii) quantify the contributions of sources of uncertainty among inter-annual variability, adaptation options and climate projections. Nine locations across the Mediterranean basin were used to calibrate and evaluate the Decision Support System for Agrotechnology Transfer (DSSAT) model. At each location the 40 Global Circulation Model (GCM) outputs (RCP4.5, Mid of the Century) showed an increase in mean growing season temperature between 0.9 and 2.16 °C, while changes of growing season rainfall were between -24 and +24%. Therefore, at each location a drier (Dry), mid (Mid), and wetter (Wet) projection was selected. Overall, there was a 9% reduction in grain yield under climate change; but the mean yield change was -27%, +4%, +8%, for the Dry, Mid, and Wet scenarios, respectively. The results of the simulations under the Wet scenario showed a higher variability of yield response. There was an interaction between the soil type, the amount of rainfall, the extractable soil water content and the maximum air temperature. Because of these relationship water-stress during the vegetative stage was experienced, affecting expansive growth. At the same time, the high number of days with Tmax>34 °C caused higher soil water depletion by the plant and therefore lower yields under the Wet scenario. The inter-annual weather variability impacts barley yield irrespective of the sowing dates and the future projected climate. In conclusion, the impact of future climate on barley yield in the Mediterranean is negative but some locations will be less affected than others

Genetic and Management Effects on Barley Yield and Phenology in the Mediterranean Basin

Heading time in barley is considered a key developmental stage controlling adaptation to the environment and it affects grain yield; with the combination of agronomy (planting dates) and genetics being some of the determinants of adaptation to environmental conditions in order to escape late frost, heat, and terminal drought stresses. The objectives of this study are (i) to apply a gene-based characterization of 118 barley doubled haploid recombinants for vernalization, photoperiod, and earliness per se; (ii) use such information to quantify the optimal combination of genotype/sowing date that escapes extreme weather events; and (iii) how water and nitrogen management impact on grain yield. The doubled haploid barley genotypes with different allelic combinations for vernalization, photoperiod, and earliness per se were grown in eight locations across the Mediterranean basin. This information was linked with the crop growth model parameters. The photoperiod and earliness per se alleles modify the length of the phenological cycle, and this is more evident in combination with the recessive allele of the vernalization gene VRN-H2. In hot environments such as Algeria, Syria, and Jordan, early sowing dates (October 30 and December15) would be chosen to minimize the risk of exposing barley to heat stress. To maintain higher yields in the Mediterranean basin, barley breeding activities should focus on allelic combinations that have recessive VRN-H2 and EPS2 genes, since the risk of cold stress is much lower than the one represented by heat stress