Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley.

Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi-environment common garden trials. Then we applied refined statistical methods, including some based on exomic haplotype states, for genotype-by-environment (G×E) modelling. Sub-populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G×E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock-related genes, associated with the environmentally adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large-effect alleles. Our analysis supports a gene-level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses.

Flow cytometric chromosome sorting from diploid progenitors of bread wheat, T. urartu, Ae. speltoides and Ae. tauschii.

KEY MESSAGE: Chromosomes 5A (u) , 5S and 5D can be isolated from wild progenitors, providing a chromosome-based approach to develop tools for breeding and to study the genome evolution of wheat. The three subgenomes of hexaploid bread wheat originated from Triticum urartu (A(u)A(u)), from a species similar to Aegilops speltoides (SS) (progenitor of the B genome), and from Ae. tauschii (DD). Earlier studies indicated the potential of chromosome genomics to assist gene transfer from wild relatives of wheat and discover novel genes for wheat improvement. This study evaluates the potential of flow cytometric chromosome sorting in the diploid progenitors of bread wheat. Flow karyotypes obtained by analysing DAPI-stained chromosomes were characterized and the contents of the chromosome peaks were determined. FISH analysis with repetitive DNA probes proved that chromosomes 5A(u), 5S and 5D could be sorted with purities of 78-90 %, while the remaining chromosomes could be sorted in groups of three. Twenty-five conserved orthologous set (COS) markers covering wheat homoeologous chromosome groups 1-7 were used for PCR with DNA amplified from flow-sorted chromosomes and genomic DNA. These assays validated the cytomolecular results as follows: peak I on flow karyotypes contained chromosome groups 1, 4 and 6, peak II represented homoeologous group 5, while peak III consisted of groups 2, 3 and 7. The isolation of individual chromosomes of wild progenitors provides an attractive opportunity to investigate the structure and evolution of the polyploid genome and to deliver tools for wheat improvement.

Electrical Capacitance versus Minirhizotron Technique: A Study of Root Dynamics in Wheat-Pea Intercrops.

This study evaluated the concurrent application and the results of the root electrical capacitance (CR) and minirhizotron (MR) methods in the same plant populations. The container experiment involved three winter wheat cultivars, grown as sole crops or intercropped with winter pea under well-watered or drought-stressed conditions. The wheat root activity (characterized by CR) and the MR-based root length (RL) and root surface area (RSA) were monitored during the vegetation period, the flag leaf chlorophyll content was measured at flowering, and the wheat shoot dry mass (SDM) and grain yield (GY) were determined at maturity. CR, RL and RSA exhibited similar seasonal patterns with peaks around the flowering. The presence of pea reduced the maximum CR, RL and RSA. Drought significantly decreased CR, but increased the MR-based root size. Both intercropping and drought reduced wheat chlorophyll content, SDM and GY. The relative decrease caused by pea or drought in the maximum CR was proportional to the rate of change in SDM or GY. Significant linear correlations (R2: 0.77-0.97) were found between CR and RSA, with significantly smaller specific root capacitance (per unit RSA) for the drought-stress treatments. CR measurements tend to predict root function and the accompanying effect on above-ground production and grain yield. The parallel application of the two in situ methods improves the evaluation of root dynamics and plant responses.

Development of a New Am -Genome-Specific Single Nucleotide Polymorphism Marker Set for the Molecular Characterization of Wheat-Triticum monococcum Introgression Lines.

CORE IDEAS: We identified 1247 polymorphic single nucleotide polymorphisms between Triticum monococcum and wheat. We identified 191 markers validated across all seven chromosomes of T. monococcum. Detected a T. monococcum introgression in leaf-rust-resistant lines. Cultivated einkorn wheat (Triticum monococcum L. subsp. monococcum, 2n = 2x = 14, Am Am ) and its wild relative T. monococcum subsp. aegilopoides are important sources of economically useful genes that can be exploited for wheat (Triticum aestivum L.) breeding. Einkorn has excellent resistance to fungal diseases and gene transfer is relatively simple via standard breeding methods. To fulfill the growing demand by modern prebreeding programs for a cost-effective high-throughput procedure for accurately detecting introgressed chromosomes or chromosome segments from T. monococcum into wheat, we used the Axiom Wheat-Relative Genotyping Array and developed a set of Am genome-specific exome-based single nucleotide polymorphism (SNP) markers suitable for rapid identification of T. monococcum chromatin in a wheat background. We identified 1247 polymorphic SNPs between T. monococcum and wheat. We identified 191 markers across all seven chromosomes of T. monococcum that are also present on an existing Triticum urartu Thum. ex Gandil. genetic map and potentially ordered them on the basis of the high macrocollinearity and conservation of marker order between T. monococcum and T. urartu. The marker set has been tested on leaf-rust-resistant BC3 F4 progenies of wheat-T. monococcum hybrids. Two markers (AX-94492165, AX-95073542) placed on the distal end of the chromosome arm 7AL detected a T. monococcum introgression into wheat. The SNP marker set thus proved highly effective in the identification of T. monococcum chromatin in a wheat background, offering a reliable method for screening and selecting wheat-T. monococcum introgression lines, a procedure that could significantly speed up prebreeding programs.

Unlocking the Genetic Diversity and Population Structure of a Wild Gene Source of Wheat, Aegilops biuncialis Vis., and Its Relationship With the Heading Time.

Understanding the genetic diversity of Aegilops biuncialis, a valuable source of agronomical useful genes, may significantly facilitate the introgression breeding of wheat. The genetic diversity and population structure of 86 Ae. biuncialis genotypes were investigated by 32700 DArT markers with the simultaneous application of three statistical methods- neighbor-joining clustering, Principal Coordinate Analysis, and the Bayesian approach to classification. The collection of Ae. biuncialis accessions was divided into five groups that correlated well with their eco-geographic habitat: A (North Africa), B (mainly from Balkans), C (Kosovo and Near East), D (Turkey, Crimea, and Peloponnese), and E (Azerbaijan and the Levant region). The diversity between the Ae. biuncialis accessions for a phenological trait (heading time), which is of decisive importance in the adaptation of plants to different eco-geographical environments, was studied over 3 years. A comparison of the intraspecific variation in the heading time trait by means of analysis of variance and principal component analysis revealed four phenotypic categories showing association with the genetic structure and geographic distribution, except for minor differences. The detailed exploration of genetic and phenologic divergence provides an insight into the adaptation capacity of Ae. biuncialis, identifying promising genotypes that could be utilized for wheat improvement.

Cytomolecular discrimination of the Am chromosomes of Triticum monococcum and the A chromosomes of Triticum aestivum using microsatellite DNA repeats.

The cytomolecular discrimination of the Am- and A-genome chromosomes facilitates the selection of wheat-Triticum monococcum introgression lines. Fluorescence in situ hybridisation (FISH) with the commonly used DNA probes Afa family, 18S rDNA and pSc119.2 showed that the more complex hybridisation pattern obtained in T. monococcum relative to bread wheat made it possible to differentiate the Am and A chromosomes within homoeologous groups 1, 4 and 5. In order to provide additional chromosomal landmarks to discriminate the Am and A chromosomes, the microsatellite repeats (GAA)n, (CAG)n, (CAC)n, (AAC)n, (AGG)n and (ACT)n were tested as FISH probes. These showed that T. monococcum chromosomes have fewer, generally weaker, simple sequence repeat (SSR) signals than the A-genome chromosomes of hexaploid wheat. A differential hybridisation pattern was observed on 6Am and 6A chromosomes with all the SSR probes tested except for the (ACT)n probe. The 2Am and 2A chromosomes were differentiated by the signals given by the (GAA)n, (CAG)n and (AAC)n repeats, while only (GAA)n discriminated the chromosomes 3Am and 3A. Chromosomes 7Am and 7A could be differentiated by the lack of (GAA)n and (AGG)n signals on 7A. As potential landmarks for identifying the Am chromosomes, SSR repeats will facilitate the introgression of T. monococcum chromatin into wheat.

Molecular cytogenetic identification and phenotypic description of a new synthetic amphiploid, Triticum timococcum (AtAtGGAmAm).

A recently developed synthetic amphiploid, Triticum timococcum Kost., nom. nud. (2n = 6x = 42, AtAtGGAmAm) is described in the present study. This hexaploid taxon was developed by colchicine treatment in Martonvásár from the hybrid of a selected accession of Triticum timopheevii Zhuk. (2n = 4x = 28, AtAtGG) and a prebred semi-dwarf line of Triticum monococcum L. (2n = 2x = 14, AmAm). A detailed cytomolecular examination was carried out using the sequential multicolour fluorescence and genomic in situ hybridization techniques (FISH and mcGISH). It was proved that T. timococcum has 42 chromosomes originating from its parents. The chromosomes of the A genomes of T. monococcum and T. timopheevii could be distinguished in the amphiploid using FISH. The successful discrimination of the chromosomes was supported by the karyotypes of the three genomes and the successful optimization of the mcGISH technique for the A and G chromosomes achieved in the present study. A phenotypic evaluation was also carried out under natural and artificial growing conditions in 2012 and 2013. Based on the results, T. timococcum has intermediate characteristics in terms of spike (spikelet) shape and plant height, while it is similar to the female parent, T. timopheevii regarding pubescence. Like its parents, T. timococcum showed outstanding resistance to the main fungal diseases of wheat. T. timococcum headed later and developed longer and looser spikes, fewer tillers and only a third as many seeds than its parents. The third generation of T. timococcum was able to develop an acceptable number of seeds, even taking into account the reduced germination ability in the field.