High levels of nucleotide diversity and fast decline of linkage disequilibrium in rye (Secale cereale L.) genes involved in frost response

<p>Abstract</p> <p>Background</p> <p>Rye (<it>Secale cereale </it>L.) is the most frost tolerant cereal species. As an outcrossing species, rye exhibits high levels of intraspecific diversity, which makes it well-suited for allele mining in genes involved in the frost responsive network. For investigating genetic diversity and the extent of linkage disequilibrium (LD) we analyzed eleven candidate genes and 37 microsatellite markers in 201 lines from five Eastern and Middle European rye populations.</p> <p>Results</p> <p>A total of 147 single nucleotide polymorphisms (SNPs) and nine insertion-deletion polymorphisms were found within 7,639 bp of DNA sequence from eleven candidate genes, resulting in an average SNP frequency of 1 SNP/52 bp. Nucleotide and haplotype diversity of candidate genes were high with average values <it>π </it>= 5.6 × 10^-3and <it>Hd </it>= 0.59, respectively. According to an analysis of molecular variance (AMOVA), most of the genetic variation was found between individuals within populations. Haplotype frequencies varied markedly between the candidate genes. <it>ScCbf14</it>, <it>ScVrn1</it>, and <it>ScDhn1 </it>were dominated by a single haplotype, while the other 8 genes (<it>ScCbf2</it>, <it>ScCbf6</it>, <it>ScCbf9b</it>, <it>ScCbf11</it>, <it>ScCbf12</it>, <it>ScCbf15</it>, <it>ScIce2</it>, and <it>ScDhn3</it>) had a more balanced haplotype frequency distribution. Intra-genic LD decayed rapidly, within approximately 520 bp on average. Genome-wide LD based on microsatellites was low.</p> <p>Conclusions</p> <p>The Middle European population did not differ substantially from the four Eastern European populations in terms of haplotype frequencies or in the level of nucleotide diversity. The low LD in rye compared to self-pollinating species promises a high resolution in genome-wide association mapping. SNPs discovered in the promoters or coding regions, which attribute to non-synonymous substitutions, are suitable candidates for association mapping.</p

Allele Mining in Barley Genetic Resources Reveals Genes of Race-Non-Specific Powdery Mildew Resistance

Race-non-specific, or quantitative, pathogen resistance is of high importance to plant breeders due to its expected durability. However, it is usually controlled by multiple quantitative trait loci (QTL) and therefore difficult to handle in practice. Knowing the genes that underlie race-non-specific resistance (NR) would allow its exploitation in a more targeted manner. Here, we performed an association-genetic study in a customized worldwide collection of spring barley accessions for candidate genes of race-NR to the powdery mildew fungus Blumeria graminis f. sp. hordei (Bgh) and combined data with results from QTL mapping as well as functional-genomics approaches. This led to the identification of 11 associated genes with converging evidence for an important role in race-NR in the presence of the Mlo gene for basal susceptibility. Outstanding in this respect was the gene encoding the transcription factor WRKY2. The results suggest that unlocking plant genetic resources and integrating functional-genomic with genetic approaches can accelerate the discovery of genes underlying race-NR in barley and other crop plants

Haplotyping, linkage mapping and expression analysis of barley genes regulated by terminal drought stress influencing seed quality

<p>Abstract</p> <p>Background</p> <p>The increasingly narrow genetic background characteristic of modern crop germplasm presents a challenge for the breeding of cultivars that require adaptation to the anticipated change in climate. Thus, high priority research aims at the identification of relevant allelic variation present both in the crop itself as well as in its progenitors. This study is based on the characterization of genetic variation in barley, with a view to enhancing its response to terminal drought stress.</p> <p>Results</p> <p>The expression patterns of drought regulated genes were monitored during plant ontogeny, mapped and the location of these genes was incorporated into a comprehensive barley SNP linkage map. Haplotypes within a set of 17 starch biosynthesis/degradation genes were defined, and a particularly high level of haplotype variation was uncovered in the genes encoding sucrose synthase (types I and II) and starch synthase. The ability of a panel of 50 barley accessions to maintain grain starch content under terminal drought conditions was explored.</p> <p>Conclusion</p> <p>The linkage/expression map is an informative resource in the context of characterizing the response of barley to drought stress. The high level of haplotype variation among starch biosynthesis/degradation genes in the progenitors of cultivated barley shows that domestication and breeding have greatly eroded their allelic diversity in current elite cultivars. Prospective association analysis based on core drought-regulated genes may simplify the process of identifying favourable alleles, and help to understand the genetic basis of the response to terminal drought.</p

Minimizing ergot infection in hybrid rye by a SMART breeding approach

In Hybridsorten bei Winterroggen führt das Restorergen Rfp1 zu einer vollständigen Restauration der männlichen Fertilität und trägt dazu bei, die Kontamination des Erntegutes mit Mutterkorn zu minimieren. Wir beschreiben Ergebnisse zur Validierung neuer Rfp1-Selektionsmarker an Elitezuchtmaterial des Roggens. Für alle per molekularer Markeranalyse genotypisierten Individuen wurde eine perfekte Übereinstimmung zwischen der postulierten genetischen Konstitution am Restorerlocus Rfp1 und dem Pollenschüttungsvermögen in den Testkreuzungsnachkommenschaften beobachtet. Rekombination zwischen den untersuchten Rfp1-Markern zeigt, dass die neuen Selektionsmarker dazu geeignet sind, rekombinativ verkleinerte, Rfp1-tragende Genomsegmente zu identifizieren. Es konnte gezeigt werden, dass die mit Rfp1 assoziierten, eng gekoppelten Markerallele diagnostisch für Rfp1 sind. Die vorgestellten Ergebnisse belegen, dass die neuen Selektionsmarker eine effiziente Genotypisierung aktueller Elitezuchtlinien im Hinblick auf das Rfp1-Restorergen ermöglichen. Für die mit Rfp1 assoziierten Selektionsmarker konnte in der vorliegenden Studie auch Kopplung mit dem Restorergen Rfc1 nachgewiesen werden. Diese Kopplungsbeziehungen lassen die validierten Marker daher für eine indirekte Selektion von Maintainer-Genotypen des C-Plasmas geeignet erscheinen. Die beobachtete Kopplung von STS-Markern zu Rfp1 bzw. Rfc1 bestätigt frühere Vermutungen, dass in dieser Region auf Chromosom 4RL entweder mehrere Restorergene lokalisiert sind oder es sich bei den betreffenden Restorergenen um Allele desselben Genortes handelt.The restorer gene Rfp1 results in an almost complete restoration of male fertility in hybrid rye varieties and, thus, contributes to minimize harvest contamination with ergot. Here, we report on the validation of recently established Rfp1 markers located on chromosome 4RL in elite breeding lines of rye. The Rfp1 genotypes, as deduced by molecular-marker analysis, perfectly corresponded with the degree of male fertility assessed in test crosses of individual genotpes with male sterile testers. Recombination could be observed between Rfp1 markers indicating their potential to reduce the donor chromosome segment carrying Rfp1. These marker alleles proved to be diagnostic for Rfp1 in current breeding lines. Taken together, results presented qualify the novel markers as efficent molecular tools to assess the restorer gene Rfp1 in elite breeding lines of rye. In addition, we have observed linkage of the Rfp1 markers to the restorer gene Rfc1. Thus, the validated markers should be applicable for marker-assisted selection strategies of maintainer genotypes of the male sterility inducing C cytoplasm, which occur at low frequency in European rye populations as well. The observed linkage of the STS markers to both Rfp1 and Rfc1 supports the assumption that the restorer genes identified on chromosome 4RL are either alleles of a single restorer gene or represent different linked genes located in this sub-genomic region

Addressing Research Bottlenecks to Crop Productivity

Asymmetry of investment in crop research leads to knowledge gaps and lost opportunities to accelerate genetic gain through identifying new sources and combinations of traits and alleles. On the basis of consultation with scientists from most major seed companies, we identified several research areas with three common features: (i) relatively underrepresented in the literature; (ii) high probability of boosting productivity in a wide range of crops and environments; and (iii) could be researched in ‘precompetitive’ space, leveraging previous knowledge, and thereby improving models that guide crop breeding and management decisions. Areas identified included research into hormones, recombination, respiration, roots, and source–sink, which, along with new opportunities in phenomics, genomics, and bioinformatics, make it more feasible to explore crop genetic resources and improve breeding strategies.We acknowledge Renee Lafitte (Bill and Melinda Gates Foundation) for helpful feedback on the manuscript and Fatima Escalante for valuable assistance in coordinating edits to the manuscript and its formatting. M.R. acknowledges the International Wheat Yield Partnership (https://iwyp.org/) for establishing a precedent of integrating different research strands in wheat for targeted prebreeding and the Foundation for Food and Agricultural Research (https://foundationfar.org/) for supporting a translational research and prebreeding pipeline at CIMMYT to identify and stack climate resilience traits in wheat