Barley Populations Research Articles

Adaptive evolution of α‐amylase genes in wild barley (Hordeum spontaneum) on micro and macro scales

AbstractAlpha‐amylases play essential roles in germination, and the malting and brewing processes, by hydrolyzing starch granules present in the endosperm of barley. Hordeum spontaneum C. Koch, the progenitor of cultivated barley that harbors rich genetic diversity, was collected from seven different environments. To investigate the influence of microclimatic ecological divergence on α‐amylase, single nucleotide polymorphisms (SNPs) in amy genes from these populations were determined. A total of 16 and 17 SNPs were detected in the coding sequences of amy1 and amy2, respectively, from the seven wild barley populations. Among these SNPs, three in amy1‐2 and nine in amy2‐2 were significantly associated with ecological factors. The genetic divergence of amy sequences was significantly different among the populations. Natural microclimatic selection was apparently the major evolutionary driving force causing interslope divergence and adaptive evolution of these genes. The genetic variation in amy1‐2 and amy2‐2 was at least partly ecologically determined in these populations, representing adaptive patterns generated by natural selection. The SNPs were apparently generated by natural selection in climatic environmental patterns at both the micro (“Evolution Canyon”) and macro (across Israel, Galilee, and Negev) scales.

Evaluation of genetic diversity of wild-type barley (Hordeum vulgare L. sub sp. Spontaneum) based on storage proteins polymorphism

Today, most scientists have accepted that cultivated barley was originated from wild-type barley, Hordeum spontaneum. By the way, this is unclear whether domestication processes just occurred in Fertile Crescent or simultaneously in different areas all over the world. Additionally, there are disagreements in relation to center or main diversity centers of this plant. In the present study, in order to evaluate genetic and geographic diversity and also determining of barley populations phylogenic relations, 266 wild-type, H. spantaneum, from areas located in or out of Fertile Crescent and also 44 samples of cultivated barley from different world areas were studied. Barley samples storage proteins were analyzed by SDS-PAGE method and were assessed in three hordein groups including D, C and B. Genetic parameters, such as patterns number and genetic diversity index showed that by getting away from Fertile Crescent, barley genetic diversity was reduced, However, North Africa and East Asia could be considered as a secondary centers of diversity of the plant. The study of genetic distances showed that wild barley genotypes of Iraq and Turkey could be the nearest populations to modern cultivated barley samples. Based on these results, Fertile Crescent especially Iran, Iraq, South East of Turkey and Jordan could be main centers of diversity of wild barley H. Spontaneum.

QTL for chlorophyll fluorescence of barley plants grown at low oxygen concentration in hydroponics to simulate waterlogging

Abstract Waterlogging is a major factor limiting barley grain yield worldwide. Climate change will likely increase this water stress in Northern Europe. Breeding for waterlogging tolerance (WLT), as for other abiotic stresses, is difficult, but identification of genetic markers linked to genes affecting WLT could facilitate the breeding process. To identify a suitable marker population, parents of 14 double-haploid (DH) barley populations were tested for segregation of biomass growth reduction in waterlogged soil. The most interesting was found in the offspring from crossing cv. Psaknon and breeding line (SLUdt1398 × Mona4). Hence, 120 DH-lines derived from this cross were phenotyped for the chlorophyll fluorescence parameter quantum yield (QY) of electron transport of PSII from leaves of hypoxia-stressed plants and further genotyped with 384-SNP Illumina GoldenGate Bead Array. Five quantitative trait loci (QTL) for QY, with a narrow sense heritability of 0.87, were identified on chromosomes 4, 6 and 7H. They had additive effects ranging from 0.74 to 1.35 % with LOD scores from 3 to 12 and explained variance from 6 to 29 %. The major alleles for high QY were from cv. Psaknon; i.e., QY was low if the alleles from cv. Psaknon were not present. Based on leaf necrosis and residual biomass data, the four most interesting QTL may be also in two other populations with completely different progeny, which shows a certain stability of these QTL. The possibility of using marker assistant selection for WLT is discussed, as is possible concurrent improvement of drought tolerance and grain yield.

Pleiotropic effects of the sdw1 locus in barley populations representing different rounds of recombination

Background: Short-stature cultivars have been developed by breeders worldwide to reduce lodging and increase grain yield. In barley, the effort to achieve short stature genotypes has relied in part on the sdw1 / denso gene. In the present study populations, representing different rounds of recombination were used for the analysis of phenotypic effects associated with the sdw1 / denso locus. Other studies have mostly focused only on one type of population. Many different QTLs mapped at the same position as the sdw1/denso locus may indicate a pleiotropy of this gene or a tight linkage between genes conditioning quantitative traits. To date, results of studies have not unequivocally proven either of these two phenomena. Results: In this study, both breeding and molecular mapping experiments were undertaken to examine 200 single seed descent (SSD) and 60 doubled haploid (DH) lines obtained from the Maresi (with a semi-dwarfing gene) and Pomo cross combination. These lines and their parental forms were evaluated for the type of juvenile growth habit and certain agronomic traits were measured after harvesting. The estimates of mean values, standard errors and significance of effects were analyzed. In terms of the analyzed characteristics, the greatest variability was obtained for genotypes with the prostrate growth habit. Microsatellite markers (SSR) were also used to identify co-segregation with the sdw1/denso locus and Bmag0013, Bmag0877, Bmag0306b markers were linked the closest. A partial linkage map of chromosome 3H with the sdw1/denso semi-dwarfing gene was constructed and QTLs were identified. Conclusions: Our experiments confirmed the impact of the semi-dwarfing gene on plant height, heading and flowering date both in SSD and DH populations, which may indicate pleiotropy. On the other hand, a partial linkage between sdw1 / denso locus and grain weight per spike and 1000-grain weight was found in the SSD population. A combination of a biometric approach with molecular analyses of different populations may present the opportunity to solve the problem of the distinction between the pleiotropic effects of semi-dwarfing genes and linkage effects. Normal 0 21 false false false ES X-NONE X-NONE

A Weighted AMMI Algorithm to Study Genotype‐by‐Environment Interaction and QTL‐by‐Environment Interaction

ABSTRACTGenotype‐by‐environment (G × E) interaction (GEI) and quantitative trait locus (QTL)‐by‐environment interaction (QEI) are common phenomena in multiple‐environment trials and represent a major challenge to breeders. The additive main effects and multiplicative interaction (AMMI) model is a widely used tool for the analysis of multiple‐environment trials, where the data are represented by a two‐way table of G × E means. For complete tables, least squares estimation for the AMMI model is equivalent to fitting an additive two‐way ANOVA model for the main effects and applying a singular value decomposition to the interaction residuals, thereby implicitly assuming equal weights for all G × E means. However, multiple‐environment data with strong GEI are often also characterized by strong heterogeneous error variation. To improve the performance of the AMMI model in the latter situation, we introduce a generalized estimation scheme, the weighted AMMI or W‐AMMI algorithm. This algorithm is useful for studying GEI and QEI. For QEI, the W‐AMMI algorithm can be used to create predicted values per environment that are subjected to QTL analysis. We compare the performance of this combined W‐AMMI and QTL mapping strategy to direct QTL mapping on G × E means and to QTL mapping on AMMI‐predicted values, again with QTL analyses for individual environments. Finally, we compare the W‐AMMI QTL mapping strategy, with a multi‐environment mixed model QTL mapping approach. Two data sets are used: (i) data from a simulated pepper (Capsicum annuum L.) back cross population using a crop growth model to relate genotypes to phenotypes in a nonlinear way, and (ii) the doubled‐haploid Steptoe × Morex barley (Hordeum vulgare L.) population. The QTL analyses on the W‐AMMI‐predicted values outperformed the QTL analyses on the G × E means and on the AMMI‐predicted values, and were very similar to the mixed model QTL mapping approach with regard to the number and location of the true positive QTLs detected, especially for QTLs associated with the interaction and for environments with higher error variance. W‐AMMI analysis for GEI and QEI provides an easy‐to‐use and robust tool with wide applicability.

MAPPING OF QTLs CONTROLLING RESISTANCE TO LEAF STRIPE (Pyrenophora graminea) IN EGYPTIAN BARLEY

Leaf stripe in barley, caused by Pyrenophora graminea, is an important seed-borne disease in organically grown as well as in conventionally grown Nordic and Mediterranean barley districts. In the present work, a QTL map for F2 barley and 7 LSLs) distributed on 8 linkage groups and spanning 2099.4 cM of the barley genome. The size of linkage groups varied from 117.8 cM for LG2 (2H) to 482.9 cM for LG6 (6H) with an average length of 262.4 cM. Based on the used anchor SSR markers, only four linkage groups were assigned to chromosomes, where LG2, LG5, LG6 and LG7 were assigned to chromosomes 2H, 5H, 6H and 7H, respectively. Single point analysis was used to identify genomic regions controlling the leaf stripe severity and plant height traits. A total of 40 QTL were identified for the disease severity (DS) and plant height (PH) traits (20 QTL for disease severity and 20 QTL for plant height). This work represents the first genetic linkage map for barley population derived from an intraspecific cross between At20 and At29 showing chromosomal regions associated with disease severity and plant height traits in barley.

Comparative QTL analysis of root lesion nematode resistance in barley.

This study demonstrates for the first time that resistance to different root lesion nematodes ( P. neglectus and P. penetrans ) is controlled by a common QTL. A major resistance QTL ( Rlnnp6H ) has been mapped to chromosome 6H using two independent barley populations. Root lesion nematodes (Pratylenchus spp.) are important pests in cereal production worldwide. We selected two doubled haploid populations of barley (Igri×Franka and Uschi×HHOR 3073) and infected them with Pratylenchus penetrans and Pratylenchus neglectus. Nematode multiplication rates were measured 7 or 10weeks after infection. In both populations, continuous phenotypic variations for nematode multiplication rates were detected indicating a quantitative inheritance of resistance. In the Igri×Franka population, four P. penetrans resistance QTLs were mapped with 857 molecular markers on four linkage groups (2H, 5H, 6H and 7H). In the Uschi×HHOR 3073 population, eleven resistance QTLs (P. penetrans and P. neglectus) were mapped with 646 molecular markers on linkage groups 1H, 3H, 4H, 5H, 6H and 7H. A major resistance QTL named Rlnnp6H (LOD score 6.42-11.19) with a large phenotypic effect (27.5-36.6%) for both pests was mapped in both populations to chromosome 6H. Another resistance QTL for both pests was mapped on linkage group5H (Igri×Franka population). These data provide first evidence for common resistance mechanisms against different root lesion nematode species. The molecular markers are a powerful tool for the selection of resistant barley lines among segregating populations because resistance tests are time consuming and laborious.

Population genetics and phylogenetic analysis of the vrs1 nucleotide sequence in wild and cultivated barley.

Spike morphology is a key characteristic in the study of barley genetics, breeding, and domestication. Variation at the six-rowed spike 1 (vrs1) locus is sufficient to control the development and fertility of the lateral spikelet of barley. To study the genetic variation of vrs1 in wild barley (Hordeum vulgare subsp. spontaneum) and cultivated barley (Hordeum vulgare subsp. vulgare), nucleotide sequences of vrs1 were examined in 84 wild barleys (including 10 six-rowed) and 20 cultivated barleys (including 10 six-rowed) from four populations. The length of the vrs1 sequence amplified was 1536 bp. A total of 40 haplotypes were identified in the four populations. The highest nucleotide diversity, haplotype diversity, and per-site nucleotide diversity were observed in the Southwest Asian wild barley population. The nucleotide diversity, number of haplotypes, haplotype diversity, and per-site nucleotide diversity in two-rowed barley were higher than those in six-rowed barley. The phylogenetic analysis of the vrs1 sequences partially separated the six-rowed and the two-rowed barley. The six-rowed barleys were divided into four groups.

Understanding the genetic control and physiological traits associated with rhizosheath production by barley (Hordeum vulgare)

There is an urgent need for simple rapid screens of root traits that improve the acquisition of nutrients and water. Temperate cereals produce rhizosheaths of variable weight, a trait first noted on desert species sampled by Tansley over 100 yr ago. This trait is almost certainly important in tolerance to abiotic stress. Here, we screened association genetics populations of barley for rhizosheath weight and derived quantitative trait loci (QTLs) and candidate genes. We assessed whether rhizosheath weight was correlated with plant performance and phosphate uptake under combined drought and phosphorus deficiency. Rhizosheath weight was investigated in relation to root hair length, and under both laboratory and field conditions. Our data demonstrated that rhizosheath weight was correlated with phosphate uptake under dry conditions and that the differences in rhizosheath weight between genotypes were maintained in the field. Rhizosheath weight also varied significantly within barley populations, was correlated with root hair length and was associated with a genetic locus (QTL) on chromosome 2H. Putative candidate genes were identified. Rhizosheath weight is easy and rapid to measure, and is associated with relatively high heritability. The breeding of cereal genotypes for beneficial rhizosheath characteristics is achievable and could contribute to agricultural sustainability in nutrient- and water-stressed environments.

Evolutionary History of Wild Barley (Hordeum vulgare subsp. spontaneum) Analyzed Using Multilocus Sequence Data and Paleodistribution Modeling

Studies of Hordeum vulgare subsp. spontaneum, the wild progenitor of cultivated barley, have mostly relied on materials collected decades ago and maintained since then ex situ in germplasm repositories. We analyzed spatial genetic variation in wild barley populations collected rather recently, exploring sequence variations at seven single-copy nuclear loci, and inferred the relationships among these populations and toward the genepool of the crop. The wild barley collection covers the whole natural distribution area from the Mediterranean to Middle Asia. In contrast to earlier studies, Bayesian assignment analyses revealed three population clusters, in the Levant, Turkey, and east of Turkey, respectively. Genetic diversity was exceptionally high in the Levant, while eastern populations were depleted of private alleles. Species distribution modeling based on climate parameters and extant occurrence points of the taxon inferred suitable habitat conditions during the ice-age, particularly in the Levant and Turkey. Together with the ecologically wide range of habitats, they might contribute to structured but long-term stable populations in this region and their high genetic diversity. For recently collected individuals, Bayesian assignment to geographic clusters was generally unambiguous, but materials from genebanks often showed accessions that were not placed according to their assumed geographic origin or showed traces of introgression from cultivated barley. We assign this to gene flow among accessions during ex situ maintenance. Evolutionary studies based on such materials might therefore result in wrong conclusions regarding the history of the species or the origin and mode of domestication of the crop, depending on the accessions included.

Gain from marker‐based recurrent selection for increased heterozygosity in barley

AbstractBarley (Hordeum vulgare L.) is a highly adaptable cereal crop grown under a wide range of agro‐ecological conditions. Various literature reports demonstrate that heterozygosity may enhance the yielding level and stability of barley particularly in stress‐prone environments. The major aim of this study was to investigate whether recurrent selection (RS) for heterozygosity at highly polymorphic codominant molecular marker loci increases outcrossing in a genetically broad‐based population. Four to six SSR marker loci were used for this purpose. Selection was conducted over four cycles. Progress from selection was evaluated in a terminal experiment comprised of population samples from all four RS cycles. All experiments were conducted under greenhouse conditions. The starting population was composed of 201 gene bank accessions (178 lines, 12 landraces and 11 wild barley populations) sampled in West Asia and North Africa. Selection led to a stepwise increase in heterozygosity from 0.23% to 1.50%. Correspondingly, the estimated multilocus outbreeding rate rose from 1.4% to 3.5%. This positive selection response offers new perspectives for improving the productivity of barley in stress‐prone areas.

A novel morphometric method for differentiating wild and domesticated barley through intra-rachis measurements

The main methods used for determining whether cereal remains from archaeological site were domesticated or not are based on the type of rachis scars and grain size. However, both ways suffer from uncertainties, and more reliable methods are in need. In this work we suggest such a novel differentiating method. We developed two statistical equations, one for unburned and one for burned (charred) wild (Hordeum spontaneum) and domesticated (Hordeum distichum) barley triplets. These equations are based on clearly measurable characteristics of the upper scars of triplets from modern barley populations. The equations yield the probability (P) that a triplet is from a domesticated variety. Using different batches of barley collected in Israel, it was confirmed that at P > 0.8 and P > 0.7 for unburned and charred triplets, respectively, domesticated barley was correctly identified at a certainty of >99%.

Mapping-by-sequencing accelerates forward genetics in barley

Mapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing of phenotypic bulks of a mapping population of barley segregating for a mutant phenotype that increases the rate of leaf initiation. Read depth analysis identifies a candidate gene, which is confirmed by the analysis of independent mutant alleles. Our method illustrates how the genomic resources of barley together with exome resequencing can underpin mapping-by-sequencing.

Molecular detection of QTL controlling plant height components in a doubled haploid barley population.

Yield losses caused by lodging in barley can be partially controlled by reducing plant height. In order to understand dwarfing mechanisms and efficiently use new dwarf germplasms for a breeding program, it is important to identify QTL of plant height components. QTL analysis was performed for seven plant height component traits using a DH population of 122 lines derived from the cross of Huaai 11 x Huadamai 6. Composite interval mapping procedures detected 20 QTL, which were mapped onto chromosomes 2H, 3H, 5H, 6H, and 7H. Eleven QTL were detected in 3 years and four QTL were detected in 2 years. QTL controlling all seven plant height component traits were found near the dwarfing gene btwd1 on chromosome 7H. These QTL accounted for 27.19 to 59.73% of phenotypic variation in seven plant height component traits. Positive transgressive segregation was found for all traits. Some of the QTL identified in this study will be useful for understanding the dwarfing mechanism and for developing new dwarf varieties using marker-assisted selection.

Genetic characterization of wild barley populations (Hordeum vulgare ssp. spontaneum) from Kazakhstan based on genome wide SNP analysis.

The wild ancestral form of barley, Hordeum vulgare ssp. spontaneum, is a valuable source for gene enrichment of cultivated barley. The purpose of this work was to study the area of distribution as well as the extent and structure of genetic variation of wild barley populations grown in Kazakhstan. It was found that distribution of wild barley populations in Kazakhstan is restricted to the most southern province. A genome wide single nucleotide polymorphism (SNP) analysis was performed in order to study the level of the genetic diversity in 96 accessions representing 14 wild barley populations from Kazakhstan and 25 accessions from the Middle East which is the center of diversity of this subspecies. The oligonucleotide pooled assay was used to genotype 384 SNPs distributed throughout the genome. In total 233 polymorphic SNPs were selected for further statistical analysis. The level of genetic diversity of wild barley populations from Kazakhstan was predictably narrower (He = 0.19 ± 0.01) in comparison with wild barley samples from the Middle East (He = 0.29 ± 0.01). The results suggested that H. vulgare ssp. spontaneum populations in Kazakhstan probably represent a recent spread of a limited number of plants from the primary distribution area and might be well adapted to winter low temperature.

Assessment and Introduction of Quantitative Resistance to Fusarium Head Blight in Elite Spring Barley

Breeding for resistance is a key task to control Fusarium head blight (FHB), a devastating disease of small cereals leading to economic losses and grain contamination with mycotoxins harmful for humans and animals. In the present work, FHB resistance of the six-rowed spring barley 'Chevron' to FHB in Germany was compared with those of adapted German spring barley cultivars. Both under natural infection conditions and after spray inoculation with conidia of Fusarium culmorum, F. sporotrichioides, and F. avenaceum under field conditions, Chevron showed a high level of quantitative resistance to the infection and contamination of grain with diverse mycotoxins. This indicates that Chevron is not only a little susceptible to deoxynivalenol-producing Fusarium spp. but also to Fusarium spp. producing type A trichothecenes and enniatins. Monitoring the initial infection course of F. culmorum on barley lemma tissue by confocal laser-scanning microscopy provided evidence that FHB resistance of Chevron is partially mediated by a preformed penetration resistance, because direct penetration of floral tissue by F. culmorum was observed rarely on Chevron but was common on susceptible genotypes. Alternatively, F. culmorum penetrated Chevron lemma tissue via stomata, which was unusual for susceptible genotypes. We generated double-haploid barley populations segregating for the major FHB resistance quantitative trait loci (QTL) Qrgz-2H-8 of Chevron. Subsequently, we characterized these populations by spray inoculation with conidia of F. culmorum and F. sporotrichioides. This suggested that Qrgz-2H-8 was functional in the genetic background of European elite barley cultivars. However, the degree of achieved resistance was very low when compared with quantitative resistance of the QTL donor Chevron, and the introgression of Qrgz-2H-8 was not sufficient to mediate the cellular resistance phenotype of Chevron in the European backgrounds.

Estimation of epistasis in doubled haploid barley populations considering interactions between all possible marker pairs

AbstractEpistasis, is the interaction between alleles from two or more loci determining complex traits, and thus plays an important role in the development of quantitative traits of crops. In mapping studies of inbreeding species epistasis is usually defined as the interactions between quantitative trait loci with significant additive gene effects. Indeed, in many studies, genes with small effects do not come into the final model and thus the total epistasis interaction effect is biased. Many loci may not have a significant direct effect on the trait under consideration, but they may still affect trait expression by interacting with other loci. In this paper the benefits of using all loci, not only the loci with significant main effects, for estimation of the epistatic effects are presented. The particular examples are with doubled haploids lines and so are restricted to homozygotes and thus additive genetic effects and additive × additive interactions. Numerical analyses were carried out on three populations of doubled haploid lines of barley (Hordeum vulgare L.): 120 doubled haploid lines from the Clipper × Sahara 3771 cross, 145 doubled haploid lines from the Harrington × TR306 cross and 150 doubled haploid lines from the Steptoe × Morex cross. In total, 157 sets of observations were analyzed and altogether 728 pairs of loci were observed for the three datasets.

Cluster structure of barley (Hordeum vulgare L.) populations at hordein-coding loci in countries of Southwest Asia, North and Northeast Africa, the Middle East, and South Arabia

Cluster structure of barley (Hordeum vulgare L.) populations at hordein-coding loci in countries of Southwest Asia, North and Northeast Africa, the Middle East, and South Arabia

Quantitative trait loci for agronomic traits in an elite barley population for Mediterranean conditions

Advances in plant breeding through marker-assisted selection (MAS) are only possible when genes or quantitative trait loci (QTLs) can contribute to the improvement of elite germplasm. A population of recombinant inbred lines (RILs) was developed for one of the best crosses of the Spanish National Barley Breeding Program, between two six-row winter barley cultivars Orria and Plaisant. The objective of this study was to identify favourable QTLs for agronomic traits in this population, which may help to optimise breeding strategies for these and other elite materials for the Mediterranean region. A genetic linkage map was developed for 217 RILs, using 382 single nucleotide polymorphism markers, selected from the barley oligonucleotide pool assay BOPA1 and two genes. A subset of 112 RILs was evaluated for several agronomic traits over a period of 2 years at three locations, Lleida and Zaragoza (Spain) and Fiorenzuola d’Arda (Italy), for a total of five field trials. An important segregation distortion occurred during population development in the region surrounding the VrnH1 locus. A QTL for grain yield and length of growth cycle was also found at this locus, apparently linked to a differential response of the VrnH1 alleles to temperature. A total of 33 QTLs was detected, most of them for important breeding targets such as plant height and thousand-grain weight. QTL × environment interactions were prevalent for most of the QTLs detected, although most interactions were of a quantitative nature. Therefore, QTLs suitable for MAS for most traits were identified.

The detection of QTLs in barley associated with endosperm hardness, grain density, grain size and malting quality using rapid phenotyping tools

Using a barley mapping population, 'Vlamingh'×'Buloke' (V×B), whole grain analyses were undertaken for physical seed traits and malting quality. Grain density and size were predicted by digital image analysis (DIA), while malt extract and protein content were predicted using near infrared (NIR) analysis. Validation of DIA and NIR algorithms confirmed that data for QTL analysis was highly correlated (R (2)>0.82), with high RPD values (the ratio of the standard error of prediction to the standard deviation, 2.31-9.06). Endosperm hardness was measured on this mapping population using the single kernel characterisation system. Grain density and endosperm hardness were significantly inter-correlated in all three environments (r>0.22, P<0.001); however, other grain components were found to interact with the traits. QTL for these traits were also found on different genomic regions, for example, grain density QTLs were found on chromosomes 2H and 6H, whereas endosperm hardness QTLs were found on 1H, 5H, and 7H. In this study, the majority of the genomic regions associated with grain texture were also coincident with QTLs for grain size, yield, flowering date and/or plant development genes. This study highlights the complexity of genomic regions associated with the variation of endosperm hardness and grain density, and their relationships with grain size traits, agronomic-related traits, and plant development loci.