Transfer of recessive skr crossability trait into well-adapted French wheat cultivar Barok through marker-assisted backcrossing method

In order to increase genetic diversity in cereals, interspecific or even intergeneric crosses are worthwhile, especially wheat by rye crosses for triticale production. However, these crosses often fail due to inhibiting genes. To overcome this obstacle, crossability trait, present in a few wheat cultivars, can be transferred into other wheat lines of agronomical interest. Nevertheless, this transfer remains tedious through conventional backcrossing methods because it is a recessive trait, which requires selfing generations and complex evaluation by many crosses. Here, we present a marker-assisted backcrossing method to transfer this trait more quickly and easily. We chose to introduce the recessive crossability skr, located on chromosome 5BS and originating from Asian wheat, into Barok, a non-crossable French wheat cultivar, with good agronomic characteristics. Six molecular markers, close to the Skr locus, were used to check the transfer of the gene at each of the three backcrosses, without selfing generation nor crosses with rye. Finally, we crossed the predicted crossable lines with rye to validate their crossability. We obtained sixteen lines, morphologically similar to Barok, exhibiting high crossability rate (30%). The markers were thus efficient to transfer the skr crossability but they remain too far from the Skr locus to be considered as diagnostic markers. Indeed, genotyping and phenotyping on other wheat cultivars showed some discrepancies. Nevertheless, this opens the way to enhance genetic diversity more easily and to improve traits of agronomic interest in triticale or wheat as well as to study further barriers to intergeneric crosses

An integrative genetic linkage map of winter wheat ( Triticum aestivum L.)

We constructed a genetic linkage map based on a cross between two Swiss winter wheat (Triticum aestivum L.) varieties, Arina and Forno. Two-hundred and forty F5 single-seed descent (SSD)-derived lines were analysed with 112 restriction fragment length polymorphism (RFLP) anonymous probes, 18 wheat cDNA clones coding for putative stress or defence-related proteins and 179 simple-sequence repeat (SSR) primer-pairs. The 309 markers revealed 396 segregating loci. Linkage analysis defined 27 linkage groups that could all be assigned to chromosomes or chromosome arms. The resulting genetic map comprises 380 loci and spans 3,086cM with 1,131cM for the A genome, 920cM for the B genome and 1,036cM for the D genome. Seventeen percent of the loci showed a significant (P < 0.05) deviation from a 1:1 ratio, most of them in favour of the Arina alleles. This map enabled the mapping of QTLs for resistance against several fungal diseases such as Stagonospora glume blotch, leaf rust and Fusarium head blight. It will also be very useful for wheat genetic mapping, as it combines RFLP and SSR markers that were previously located on separate map

Evaluation of the genetic variability of homoeologous group 3 SSRs in bread wheat

Thorough characterization of the genetic variability in bread wheat (Triticum aestivum L.) is important for a better improvement of this key crop and to increase cereal yield in the context of sustainable agriculture to face human needs in the next decades. To study the genetic variability of SSRs on wheat homoeologous group 3 chromosomes, we characterized 38 hexaploid and two tetraploid wheat lines using a set of 165 microsatellites that we cytogenetically assigned to the 17 deletion bins for chromosomes group 3.Изучали вариабельность МС-локусов третьей гомеологичной группы хромосом T. aestivum L., осуществили сопоставление изменчивости микросателлитов в дистальных и проксимальных областях хромосом и физическое картирование МС-локусов с помощью делеционных, дителосомных, нуллитетрасомных линий и провели сравнительный анализ вариабельности микросателлитных локусов хромосом 3А, 3B и 3D.Вивчали варіабельність МС-локусів третьої гомеологічної групи хромосом T. aestivum L., здійснили порівняння мінливості мікросателітів у дистальних та проксимальних областях хромосом, а також фізичне картування МС-локусів за допомогою делеційних, дітелосомних, нулітетрасомних ліній та провели порівняльний аналіз варіабельності мікросателітних локусів хромосом 3А, 3B і 3D

Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A

Background: Bread wheat (Triticum aestivum L.) is one of the most important crops worldwide and its production faces pressing challenges, the solution of which demands genome information. However, the large, highly repetitive hexaploid wheat genome has been considered intractable to standard sequencing approaches. Therefore the International Wheat Genome Sequencing Consortium (IWGSC) proposes to map and sequence the genome on a chromosome-by-chromosome basis. Methodology/Principal Findings: We have constructed a physical map of the long arm of bread wheat chromosome 1A using chromosome-specific BAC libraries by High Information Content Fingerprinting (HICF). Two alternative methods (FPC and LTC) were used to assemble the fingerprints into a high-resolution physical map of the chromosome arm. A total of 365 molecular markers were added to the map, in addition to 1122 putative unique transcripts that were identified by microarray hybridization. The final map consists of 1180 FPC based or 583 LTC based contigs. Conclusions/Significance: The physical map presented here marks an important step forward in mapping of hexaploid bread wheat. The map is orders of magnitude more detailed than previously available maps of this chromosome, and the assignment of over a thousand putative expressed gene sequences to specific map locations will greatly assist future functional studies. This map will be an essential tool for future sequencing of and positional cloning within chromosome 1A

Copy Number Variation Affecting the Photoperiod-B1 and Vernalization-A1 Genes Is Associated with Altered Flowering Time in Wheat (Triticum aestivum)

The timing of flowering during the year is an important adaptive character affecting reproductive success in plants and is critical to crop yield. Flowering time has been extensively manipulated in crops such as wheat (Triticum aestivum L.) during domestication, and this enables them to grow productively in a wide range of environments. Several major genes controlling flowering time have been identified in wheat with mutant alleles having sequence changes such as insertions, deletions or point mutations. We investigated genetic variants in commercial varieties of wheat that regulate flowering by altering photoperiod response (Ppd-B1 alleles) or vernalization requirement (Vrn-A1 alleles) and for which no candidate mutation was found within the gene sequence. Genetic and genomic approaches showed that in both cases alleles conferring altered flowering time had an increased copy number of the gene and altered gene expression. Alleles with an increased copy number of Ppd-B1 confer an early flowering day neutral phenotype and have arisen independently at least twice. Plants with an increased copy number of Vrn-A1 have an increased requirement for vernalization so that longer periods of cold are required to potentiate flowering. The results suggest that copy number variation (CNV) plays a significant role in wheat adaptation

A highly mutagenised barley (cv. Golden Promise) TILLING population coupled with strategies for screening-by-sequencing

Background:We developed and characterised a highly mutagenised TILLING population of the barley (Hordeum vulgare) cultivar Golden Promise. Golden Promise is the 'reference' genotype for barley transformation and a primary objective of using this cultivar was to be able to genetically complement observed mutations directly in order to prove gene function. Importantly, a reference genome assembly of Golden Promise has also recently been developed. As our primary interest was to identify mutations in genes involved in meiosis and recombination, to characterise the population we focused on a set of 46 genes from the literature that are possible meiosis gene candidates. Results:Sequencing 20 plants from the population using whole exome capture revealed that the mutation density in this population is high (one mutation every 154 kb), and consequently even in this small number of plants we identified several interesting mutations. We also recorded some issues with seed availability and germination. We subsequently designed and applied a simple two-dimensional pooling strategy to identify mutations in varying numbers of specific target genes by Illumina short read pooled-amplicon sequencing and subsequent deconvolution. In parallel we assembled a collection of semi-sterile mutants from the population and used a custom exome capture array targeting the 46 candidate meiotic genes to identify potentially causal mutations. Conclusions:We developed a highly mutagenised barley TILLING population in the transformation competent cultivar Golden Promise. We used novel and cost-efficient screening approaches to successfully identify a broad range of potentially deleterious variants that were subsequently validated by Sanger sequencing. These resources combined with a high-quality genome reference sequence opens new possibilities for efficient functional gene validation.Miriam Schreiber, Abdellah Barakate, Nicola Uzrek, Malcolm Macaulay, Adeline Sourdille, Jenny Morris, Pete E. Hedley, Luke Ramsay and Robbie Waug