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1.  Sequencing of Chloroplast Genomes from Wheat, Barley, Rye and Their Relatives Provides a Detailed Insight into the Evolution of the Triticeae Tribe 
PLoS ONE  2014;9(3):e85761.
Using Roche/454 technology, we sequenced the chloroplast genomes of 12 Triticeae species, including bread wheat, barley and rye, as well as the diploid progenitors and relatives of bread wheat Triticum urartu, Aegilops speltoides and Ae. tauschii. Two wild tetraploid taxa, Ae. cylindrica and Ae. geniculata, were also included. Additionally, we incorporated wild Einkorn wheat Triticum boeoticum and its domesticated form T. monococcum and two Hordeum spontaneum (wild barley) genotypes. Chloroplast genomes were used for overall sequence comparison, phylogenetic analysis and dating of divergence times. We estimate that barley diverged from rye and wheat approximately 8–9 million years ago (MYA). The genome donors of hexaploid wheat diverged between 2.1–2.9 MYA, while rye diverged from Triticum aestivum approximately 3–4 MYA, more recently than previously estimated. Interestingly, the A genome taxa T. boeoticum and T. urartu were estimated to have diverged approximately 570,000 years ago. As these two have a reproductive barrier, the divergence time estimate also provides an upper limit for the time required for the formation of a species boundary between the two. Furthermore, we conclusively show that the chloroplast genome of hexaploid wheat was contributed by the B genome donor and that this unknown species diverged from Ae. speltoides about 980,000 years ago. Additionally, sequence alignments identified a translocation of a chloroplast segment to the nuclear genome which is specific to the rye/wheat lineage. We propose the presented phylogeny and divergence time estimates as a reference framework for future studies on Triticeae.
doi:10.1371/journal.pone.0085761
PMCID: PMC3948623  PMID: 24614886
2.  Evolutionary History of Wild Barley (Hordeum vulgare subsp. spontaneum) Analyzed Using Multilocus Sequence Data and Paleodistribution Modeling 
Genome Biology and Evolution  2014;6(3):685-702.
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.
doi:10.1093/gbe/evu047
PMCID: PMC3971598  PMID: 24586028
phylogeography; genetic diversity; population genetics; species distribution models; population structure; domestication
3.  Diversity of Macro- and Micronutrients in the Seeds of Lentil Landraces 
The Scientific World Journal  2012;2012:710412.
Increasing the amount of bioavailable mineral elements in plant foods would help to improve the nutritional status of populations in developing countries. Legume seeds have the potential to provide many essential nutrients. It is important to have information on genetic variations among different lentil populations so that plant breeding programs can use new varieties in cross-breeding programs. The main objective of this study was to characterize the micro- and macronutrient concentrations of lentil landraces seeds collected from South-Eastern Turkey. We found impressive variation in the micro- and macroelement concentrations in 39 lentil landraces and 7 cultivars. We investigated the relationships of traits by correlation analysis and principal component analysis (PCA). The concentrations of several minerals, particularly Zn, were positively correlated with other minerals, suggesting that similar pathways or transporters control the uptake and transport of these minerals. Some genotypes had high mineral and protein content and potential to improve the nutritional value of cultivated lentil. Cross-breeding of numerous lentil landraces from Turkey with currently cultivated varieties could improve the levels of micro- and macronutrients of lentil and may contribute to the worldwide lentil quality breeding program.
doi:10.1100/2012/710412
PMCID: PMC3444848  PMID: 22997502
4.  Heterotic Trait Locus (HTL) Mapping Identifies Intra-Locus Interactions That Underlie Reproductive Hybrid Vigor in Sorghum bicolor 
PLoS ONE  2012;7(6):e38993.
Identifying intra-locus interactions underlying heterotic variation among whole-genome hybrids is a key to understanding mechanisms of heterosis and exploiting it for crop and livestock improvement. In this study, we present the development and first use of the heterotic trait locus (HTL) mapping approach to associate specific intra-locus interactions with an overdominant heterotic mode of inheritance in a diallel population using Sorghum bicolor as the model. This method combines the advantages of ample genetic diversity and the possibility of studying non-additive inheritance. Furthermore, this design enables dissecting the latter to identify specific intra-locus interactions. We identified three HTLs (3.5% of loci tested) with synergistic intra-locus effects on overdominant grain yield heterosis in 2 years of field trials. These loci account for 19.0% of the heterotic variation, including a significant interaction found between two of them. Moreover, analysis of one of these loci (hDPW4.1) in a consecutive F2 population confirmed a significant 21% increase in grain yield of heterozygous vs. homozygous plants in this locus. Notably, two of the three HTLs for grain yield are in synteny with previously reported overdominant quantitative trait loci for grain yield in maize. A mechanism for the reproductive heterosis found in this study is suggested, in which grain yield increase is achieved by releasing the compensatory tradeoffs between biomass and reproductive output, and between seed number and weight. These results highlight the power of analyzing a diverse set of inbreds and their hybrids for unraveling hitherto unknown allelic interactions mediating heterosis.
doi:10.1371/journal.pone.0038993
PMCID: PMC3382592  PMID: 22761720
5.  Genome-wide association studies for agronomical traits in a world wide spring barley collection 
BMC Plant Biology  2012;12:16.
Background
Genome-wide association studies (GWAS) based on linkage disequilibrium (LD) provide a promising tool for the detection and fine mapping of quantitative trait loci (QTL) underlying complex agronomic traits. In this study we explored the genetic basis of variation for the traits heading date, plant height, thousand grain weight, starch content and crude protein content in a diverse collection of 224 spring barleys of worldwide origin. The whole panel was genotyped with a customized oligonucleotide pool assay containing 1536 SNPs using Illumina's GoldenGate technology resulting in 957 successful SNPs covering all chromosomes. The morphological trait "row type" (two-rowed spike vs. six-rowed spike) was used to confirm the high level of selectivity and sensitivity of the approach. This study describes the detection of QTL for the above mentioned agronomic traits by GWAS.
Results
Population structure in the panel was investigated by various methods and six subgroups that are mainly based on their spike morphology and region of origin. We explored the patterns of linkage disequilibrium (LD) among the whole panel for all seven barley chromosomes. Average LD was observed to decay below a critical level (r2-value 0.2) within a map distance of 5-10 cM. Phenotypic variation within the panel was reasonably large for all the traits. The heritabilities calculated for each trait over multi-environment experiments ranged between 0.90-0.95. Different statistical models were tested to control spurious LD caused by population structure and to calculate the P-value of marker-trait associations. Using a mixed linear model with kinship for controlling spurious LD effects, we found a total of 171 significant marker trait associations, which delineate into 107 QTL regions. Across all traits these can be grouped into 57 novel QTL and 50 QTL that are congruent with previously mapped QTL positions.
Conclusions
Our results demonstrate that the described diverse barley panel can be efficiently used for GWAS of various quantitative traits, provided that population structure is appropriately taken into account. The observed significant marker trait associations provide a refined insight into the genetic architecture of important agronomic traits in barley. However, individual QTL account only for a small portion of phenotypic variation, which may be due to insufficient marker coverage and/or the elimination of rare alleles prior to analysis. The fact that the combined SNP effects fall short of explaining the complete phenotypic variance may support the hypothesis that the expression of a quantitative trait is caused by a large number of very small effects that escape detection. Notwithstanding these limitations, the integration of GWAS with biparental linkage mapping and an ever increasing body of genomic sequence information will facilitate the systematic isolation of agronomically important genes and subsequent analysis of their allelic diversity.
doi:10.1186/1471-2229-12-16
PMCID: PMC3349577  PMID: 22284310
6.  NGS technologies for analyzing germplasm diversity in genebanks* 
More than 70 years after the first ex situ genebanks have been established, major efforts in this field are still concerned with issues related to further completion of individual collections and securing of their storage. Attempts regarding valorization of ex situ collections for plant breeders have been hampered by the limited availability of phenotypic and genotypic information. With the advent of molecular marker technologies first efforts were made to fingerprint genebank accessions, albeit on a very small scale and mostly based on inadequate DNA marker systems. Advances in DNA sequencing technology and the development of high-throughput systems for multiparallel interrogation of thousands of single nucleotide polymorphisms (SNPs) now provide a suite of technological platforms facilitating the analysis of several hundred of Gigabases per day using state-of-the-art sequencing technology or, at the same time, of thousands of SNPs. The present review summarizes recent developments regarding the deployment of these technologies for the analysis of plant genetic resources, in order to identify patterns of genetic diversity, map quantitative traits and mine novel alleles from the vast amount of genetic resources maintained in genebanks around the world. It also refers to the various shortcomings and bottlenecks that need to be overcome to leverage the full potential of high-throughput DNA analysis for the targeted utilization of plant genetic resources.
doi:10.1093/bfgp/elr046
PMCID: PMC3281264  PMID: 22257472
genetic resources; next-generation sequencing; SNP; allele mining; genetic diversity; association analysis
7.  Association of barley photoperiod and vernalization genes with QTLs for flowering time and agronomic traits in a BC2DH population and a set of wild barley introgression lines 
The control of flowering time has important impacts on crop yield. The variation in response to day length (photoperiod) and low temperature (vernalization) has been selected in barley to provide adaptation to different environments and farming practices. As a further step towards unraveling the genetic mechanisms underlying flowering time control in barley, we investigated the allelic variation of ten known or putative photoperiod and vernalization pathway genes between two genotypes, the spring barley elite cultivar ‘Scarlett’ (Hordeum vulgare ssp. vulgare) and the wild barley accession ‘ISR42-8’ (Hordeum vulgare ssp. spontaneum). The genes studied are Ppd-H1, VRN-H1, VRN-H2, VRN-H3, HvCO1, HvCO2, HvGI, HvFT2, HvFT3 and HvFT4. ‘Scarlett’ and ‘ISR42-8’ are the parents of the BC2DH advanced backcross population S42 and a set of wild barley introgression lines (S42ILs). The latter are derived from S42 after backcrossing and marker-assisted selection. The genotypes and phenotypes in S42 and S42ILs were utilized to determine the genetic map location of the candidate genes and to test if these genes may exert quantitative trait locus (QTL) effects on flowering time, yield and yield-related traits in the two populations studied. By sequencing the characteristic regions of the genes and genotyping with diagnostic markers, the contrasting allelic constitutions of four known flowering regulation genes were identified as ppd-H1, Vrn-H1, vrn-H2 and vrn-H3 in ‘Scarlett’ and as Ppd-H1, vrn-H1, Vrn-H2 and a novel allele of VRN-H3 in ‘ISR42-8’. All candidate genes could be placed on a barley simple sequence repeat (SSR) map. Seven candidate genes (Ppd-H1, VRN-H2, VRN-H3, HvGI, HvFT2, HvFT3 and HvFT4) were associated with flowering time QTLs in population S42. Four exotic alleles (Ppd-H1, Vrn-H2, vrn-H3 and HvCO1) possibly exhibited significant effects on flowering time in S42ILs. In both populations, the QTL showing the strongest effect corresponded to Ppd-H1. Here, the exotic allele was associated with a reduction of number of days until flowering by 8.0 and 12.7%, respectively. Our data suggest that Ppd-H1, Vrn-H2 and Vrn-H3 may also exert pleiotropic effects on yield and yield-related traits.
doi:10.1007/s00122-010-1276-y
PMCID: PMC2859222  PMID: 20155245
8.  Genome size variation in diploid and tetraploid wild wheats 
AoB Plants  2010;2010:plq015.
Low but significant intraspecific genome size variations were found in diploid and tetraploid wild wheats. This limited variation is not correlated with geographical and climate variables. It can be concluded that the genome size of Triticum species is generally stable, despite of the presence of many potentially active retroelements.
Background and aims
Intra- and interspecific variations of C-values and the relationship between habitat factors and genome size were studied in natural populations of diploid and tetraploid wild wheats.
Methodology
The 1C nuclear DNA content of 376 individual plants representing 41 populations of diploid and tetraploid wild wheats was determined by flow cytometry (FCM) and correlated with geographical and bioclimate variables.
Principal results
Based on analysis of variance, significant differences between diploid and tetraploid Triticum species were found. Differences among populations of T. boeoticum and T. dicoccoides were also statistically significant and argue for isolation between populations, except for T. araraticum. However, the variation among individuals of the same population was not statistically significant. Maximum genome size differences among populations for T. boeoticum (0.143 pg; 2.32 %), T. dicoccoides (0.314 pg; 2.49 %) and T. araraticum (0.116 pg; 0.98 %) argue for genome constancy in these species. There was no significant correlation between intra-population variance and geographical and bioclimate variables for T. boeoticum and T. dicoccoides. In contrast to the limited genome size variation at the intraspecific level, the interspecific variation was large: ∼0.5 pg/1C (8 %) at the diploid level (T. boeoticum vs. T. urartu) and ∼1 pg/1C (9.7 %) at the tetraploid level (T. dicoccoides vs. T. araraticum).
Conclusions
Low intraspecific genome size variation occurs in diploid and tetraploid wild wheats, and this limited variation is not correlated with geographical and climate variables. However, interspecific variation is significant at the diploid and tetraploid level. It can be concluded that the genome size of wild self-fertilizing Triticum species is generally stable, despite the presence of many potentially active retroelements. In natural habitats, it is very difficult to distinguish wild wheats from each other. However, all four species can be distinguished easily, quickly and unambiguously by using the FCM technique.
doi:10.1093/aobpla/plq015
PMCID: PMC2992354  PMID: 22476073
9.  A catalogue of Triticum monococcum genes encoding toxic and immunogenic peptides for celiac disease patients 
Molecular Genetics and Genomics   2008;281(3):289-300.
The celiac disease (CD) is an inflammatory condition characterized by injury to the lining of the small-intestine on exposure to the gluten of wheat, barley and rye. The involvement of gluten in the CD syndrome has been studied in detail in bread wheat, where a set of “toxic” and “immunogenic” peptides has been defined. For wheat diploid species, information on CD epitopes is poor. In the present paper, we have adopted a genomic approach in order to understand the potential CD danger represented by storage proteins in diploid wheat and sequenced a sufficiently large number of cDNA clones related to storage protein genes of Triticum monococcum. Four bona fide toxic peptides and 13 immunogenic peptides were found. All the classes of storage proteins were shown to contain harmful sequences. The major conclusion is that einkorn has the full potential to induce the CD syndrome, as already evident for polyploid wheats. In addition, a complete overview of the storage protein gene arsenal in T. monococcum is provided, including a full-length HMW x-type sequence and two partial HMW y-type sequences.
Electronic supplementary material
The online version of this article (doi:10.1007/s00438-008-0412-8) contains supplementary material, which is available to authorized users.
doi:10.1007/s00438-008-0412-8
PMCID: PMC2757618  PMID: 19104838
Einkorn wheat; Celiac disease; Gluten; Gliadins; Glutenins; Epitopes

Results 1-9 (9)