Molecular markers are employed for doubled haploid (DH) technology by researchers and applied plant breeders in many crops. In the 1990s, isozymes and RFLPs were commonly used marker technologies to characterize DHs and were later replaced by PCR- based markers (e.g., RAPDs, AFLPs, ISSRs, SSRs) and today by SNPs. Markers are used for multiple purposes in DH production, that is, for the study of genes underlying haploid induction and confirming homozygous plants of gametophytic origin. Furthermore, they are tools for investigating segregation in DH populations and for mapping simple and complex traits using DHs. The deployment of DHs and markers for developing trait-linked markers are demonstrated with examples from rapeseed, wheat, and barley. Marker development for resistance to viruses derived from genetic resources and their use in, for example, pyramiding of resistance genes, are given as an example for the combination of DH-technology and marker development in research. Today, marker systems amenable to automation are frequently used in applied plant breeding. Practical examples are given from Lantmännen (LM) ( https://Lantmannen.com ) using large-scale genotyping for variety development based on SSRs and SNPs.

The northwards expansion of barley production requires adaptation to longer days, lower temperatures and stronger winds during the growing season. We have screened 169 lines of the current barley breeding gene pool in the Nordic region with regards to heading, maturity, height, and lodging under different environmental conditions in nineteen field trials over 3 years at eight locations in northern and central Europe. Through a genome-wide association scan we have linked phenotypic differences observed in multi-environment field trials (MET) to single nucleotide polymorphisms (SNP). We have identified an allele combination, only occurring among a few Icelandic lines, that affects heat sum to maturity and requires 214 growing degree days (GDD) less heat sum to maturity than the most common allele combination in the Nordic spring barley gene pool. This allele combination is beneficial in a cold environment, where autumn frost can destroy a late maturing harvest. Despite decades of intense breeding efforts relying heavily on the same germplasm, our results show that there still exists considerable variation within the current breeding gene pool and we identify ideal allele combinations for regional adaptation, which can facilitate the expansion of cereal cultivation even further northwards.

The objectives of this study were to generate molecular passport data for identification and differentiation of Baltic spring barley accessions (cultivars, landraces and breeding lines) and to estimate the genetic variation within and among these accessions. Allelic profiles of 21 microsatellite and 8 isoenzyme loci were obtained and analysed for 64 Baltic spring barley accessions. The microsatellite data was successfully used to separate all of the accessions by individual allelic pattern and frequencies, whereas only 30 of the studied accessions could be distinguished by isozyme data. Variation was detected both among and within the accessions and was significant. The variation within accessions accounted for 20.6% and 14.3% of the total variation, based on microsatellite and isozyme data, respectively. The six-rowed and two-rowed material was well differentiated by both types of marker data: according to AMOVA this differentiation accounted for 16.9% of the microsatellite variation and 26.8% of isozyme variation. Differentiation of accessions based on the country of origin could be detected only by isozyme markers and accounted for 9% of the total izozyme variation. Both isozyme and microsatellite data showed that accessions of Latvian origin had the highest total diversity values, while material from Estonia was the least diverse.

Genetic profiles and diversity of Baltic spring barley material The objectives of this study were to generate molecular passport data for identification and differentiation of Baltic spring barley accessions (cultivars, landraces and breeding lines) and to estimate the genetic variation within and among these accessions. Allelic profiles of 21 microsatellite and 8 isoenzyme loci were obtained and analysed for 64 Baltic spring barley accessions. The microsatellite data was successfully used to separate all of the accessions by individual allelic pattern and frequencies, whereas only 30 of the studied accessions could be distinguished by isozyme data. Variation was detected both among and within the accessions and was significant. The variation within accessions accounted for 20.6% and 14.3% of the total variation, based on microsatellite and isozyme data, respectively. The six-rowed and two-rowed material was well differentiated by both types of marker data: according to AMOVA this differentiation accounted for 16.9% of the microsatellite variation and 26.8% of isozyme variation. Differentiation of accessions based on the country of origin could be detected only by isozyme markers and accounted for 9% of the total izozyme variation. Both isozyme and microsatellite data showed that accessions of Latvian origin had the highest total diversity values, while material from Estonia was the least diverse.

Background: Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT).Results: Approximately 19,000 genomic clones were isolated from complexity-reduced genomic representations of pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays, with more than 2000 polymorphic markers being identified for use in this study, and approximately 2700 potentially polymorphic markers being identified for use in future studies. DNA sequence was obtained for 2573 clones and assembled into a non-redundant set of 1770 contigs and singletons. Of these, 705 showed highly significant (Expectation < 10E-10) BLAST similarity to gene sequences in public databases. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the 'Kanota' x 'Ogle' genetic map. DArT markers provided map coverage approximately equivalent to existing markers. After binning markers from similar clones, as well as those with 99% scoring similarity, a set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of worldwide origin. Results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to the presence of major breeding programs within geographical regions. Secondary clusters revealed groups that were often related to known pedigree structure.Conclusion: These markers will provide a solid basis for future efforts in genomic discovery, comparative mapping, and the generation of an oat consensus map. They will also provide new opportunities for directed breeding of superior oat varieties, and guidance in the maintenance of oat genetic diversity.

Plant breeders constantly need to adapt their research to the ever-changing market needs and agricultural practices. To achieve these goals, they need to competently combine different genetically-governed characters in a genotype, this is a complex, time-consuming and labour intensive task. In modern plant breeding, molecular markers are of increasing importance, and it is today undeniable that their application inhold tremendous possibilities to increase plant breeding efficiency. While the methods are more widely adopted, the capacity for high-throughput analyses at low cost becomes crucial for their practical use. To be attractive it is necessary that molecular technology is able to promptly handle sufficiently large amounts of material at reduced costs. Automation of the analysis processes is a way to meet these requirements. In that purpose, the specific needs of molecular applications in practical plant breeding are investigated in this chapter. The particular approach of a plant breeding company to automate them, in order to increase their availability to breeding programs, is described.

The breeding companies and laboratories involved in this article cover a wide range of crops grown in the temperate climate zone: small grain cereals, oilseed crops, forage crops, turf, vegetables and potato. Speed and efficiency are becoming increasingly important in variety breeding and doubled haploids (DH) and genetic markers are important biotechnological tools to accelerate materials to market. Collaborative research between universities, research institutions and breeding companies has resulted in the routine use of DH technology and molecular markers in practical breeding of barley, wheat and rapeseed. DH populations have been established not only for barley, wheat and rapeseed, but for rye, oat and triticale, where DH technology is less developed. A driver here is the value of the crop e.g. although wheat is less responsive to DH production the value of the end product makes the effort worthwhile. Simple and rapid DNA extraction methods used in high-throughput marker assisted selection (MAS) systems are essential for routine use of markers. MAS is used both to monitor the presence of genes of interest and also to monitor the genetic background. DH technology in forage, turf and vegetables is still in progress and the practical use of markers in all crops is limited by access to trait linked markers. Collaboration and technology transfer with universities, research institutions and breeding companies is essential for the improvement of both DH protocols in recalcitrant crops and marker technology in all crops.

A non-destructive, quick DNA extraction method for barley seed is described. The method is simple and consists of drilling out a sample from the seed, adding sodium hydroxide, heating in a microwave oven and neutralizing with Tris-HCl. The seed DNA extract can be used directly for PCR with extra cycles added to the PCR programme compared to PCR programmes used for leaf extracts. This protocol was developed in particular for a micro satellite marker genetically linked to barley yellow mosaic virus resistance, but it can be applied toother markers of interest for barley breeding. The quick seed extraction protocol makes it possible to handle thousands of samples per day. Extraction of DNA from seed also facilitates transfer of plant material compared to the long-distance transfer of leaf samples.

Accessions of cultivated barley ( Hordeum vulgare ssp. vulgare ) and its wild progenitor Hordeum vulgare ssp. spontaneum ( H. ssp. spont. ) were screened for gramine content at the seedling stage. H. ssp. spont. generally had higher gramine concentration compared with cultivated spring barley. Thus gramine concentrations might be raised in modern barley through crossings with selected H. ssp. spont. accessions and repeated back-crossings (BC) of selected offspring to cultivated barley. In the present study, the barley cultivar Lina was used as the recurrent parent. Lina was exceptional among the two-rowed barleys in that it contained moderate levels of gramine, whereas most of the others were very low in gramine. Chromosome-doubled haploid lines (DHs) from the first generation (F 1 ) had a skewed distribution towards higher gramine concentrations and so had the first back-cross generation (BC 1 F 1 -DHs). A hairy plant surface, another character proposed to confer resistance to aphids, was also found among some of the plants in the breeding material. BC 1 F 1 -DHs with a high proportion of the Lina genome, as determined in an analysis of PCR-based molecular markers, in addition to high gramine concentrations and hairy plant bases in two cases were tested for resistance to the barley pest Rhopalosiphum padi. However, based on aphid performance and preference tests, there were no indications that either high gramine concentrations or hairiness conferred resistance to R. padi when compared with Lina and a variety very low in gramine (Golf). The pattern was the same when the F 1 generation was evaluated in aphid performance tests along with Lina, Golf, and the six H. ssp. spont. parents. Aphid weight was consistently low on only one of the six H. ssp. spont. parents. Since previous reports of a positive relationship between gramine concentrations and resistance to R. padi were based on studies in Chile and Japan, a Chilean R. padi population was compared with three Swedish populations, but the responses of all four populations were similar.