Characteristic of the gene candidate SecARS encoding alkylresorcinol synthase in Secale.

BACKGROUND: Alkylresorcinols (ARs) are compounds belonging to the class of phenolic lipids. A rich source of ARs are cereal grains such as rye, wheat, triticale or barley. ARs found in plants are characterized by a variety of biological properties such as antimicrobial, antifungal and cytotoxic activity. Moreover, they are proven to have a positive influence on human health. Here, we aimed to find and characterize the gene with ARs synthase activity in the species Secale cereale. METHODS AND RESULTS: Using BAC library screening, two BAC clones containing the gene candidate were isolated and sequenced. Bioinformatic analyses of the resulting contigs were used to examine the structure and other features of the gene, including promoter, intron, 3'UTR and 5'UTR. Mapping using the FISH procedure located the gene on the 4R chromosome. Comparative analysis showed that the gene is highly similar to sequences coding for type III polyketide synthase. The level of gene expression in various parts of the plant was investigated, and the biochemical function of the gene was confirmed by heterologous expression in yeast. CONCLUSIONS: The conducted analyses contributed to a better understanding of the processes related to ARs synthesis. Although the research concerned the rye model, the knowledge gained may help in understanding the genetic basis of ARs biosynthesis in other species of the Poaceae family as well.

Multiplexed SSR and agronomic data used in an investigation of obsolete diversity of rye (Secale cereale L.).

Rye (Secale cereale L.) is one of the most important cereal crops cultivated in the world due to its ability to produce high yields even when grown under environmental stress conditions. About 27,000 Secale accessions have been collected and preserved in 70 gene banks worldwide. Although the germplasm represents a great source of genetic diversity, the molecular characteristics refers only to the part of them. Here, we present data obtained by the Simple Sequence Repeat markers (SSR) analysis of 100 rye accessions preserved in the gene bank of the Polish Academy of Sciences Botanical Garden - Center for Biological Diversity Conservation in Powsin. Additionally, the data presented in this article refers to evaluation of agronomoic traits and weather conditions measured for 14 years. The data was used in the research article "Investigation of obsolete diversity of rye (Secale cereale L.) using multiplexed SSR fingerprinting and evaluation of agronomic traits" [1].

Investigation of obsolete diversity of rye (Secale cereale L.) using multiplexed SSR fingerprinting and evaluation of agronomic traits.

Common rye (Secale cereale L.) is one of the most important cereals in Europe. Nevertheless, its germplasm collections are among the least numerous compared with cereals. There are only about 27,000 Secale accessions in 70 gene banks around the world. Despite extensive research on the molecular characterization of genetic resources, only a fraction of this collection has been described. The main objective of the presented study was to perform genotypic and phenotypic characterization of an obsolete gene pool represented by 100 accessions originated from 28 countries around the world and preserved in the gene bank of the Polish Academy of Sciences Botanical Garden - Center for Biological Diversity Conservation in Powsin. Genetic analysis using simple sequence repeat markers showed that the obsolete gene pool is relatively large. This indicates that different sources of variability were used in breeding programs. However, the genetic variation is in no way related to the place of origin. Despite the great differences in the genetic make-up, the collection showed a broadly common phenotype. This could result in a low level of interest among breeders in the stored germplasm, undervalued as a source of important but not easily observable traits, e.g., high disease resistance, which was found in some accessions.

Effective BAC clone anchoring with genotyping-by-sequencing and Diversity Arrays Technology in a large genome cereal rye.

Identification of bacterial artificial chromosome (BAC) clones containing specific sequences is a prerequisite for many applications, such as physical map anchoring or gene cloning. Existing BAC library screening strategies are either low-throughput or require a considerable initial input of resources for platform establishment. We describe a high-throughput, reliable, and cost-effective BAC library screening approach deploying genotyping platforms which are independent from the availability of sequence information: a genotyping-by-sequencing (GBS) method DArTSeq and the microarray-based Diversity Arrays Technology (DArT). The performance of these methods was tested in a very large and complex rye genome. The DArTseq approach delivered superior results: a several fold higher efficiency of addressing genetic markers to BAC clones and anchoring of BAC clones to genetic map and also a higher reliability. Considering the sequence independence of the platform, the DArTseq-based library screening can be proposed as an attractive method to speed up genomics research in resource poor species.

Identification of Single Nucleotide Polymorphisms Associated with Brown Rust Resistance, α-Amylase Activity and Pre-harvest Sprouting in Rye (Secale cereale L.).

Rye is a crop with relatively high resistance to biotic and abiotic stresses. However, the resistance to brown rust (Puccinia recondita f. sp. secalis) and pre-harvest sprouting are still not satisfactory. High α-amylase activity is also among the main disadvantages of this species. Therefore, effective tools, e.g. molecular markers, allowing precise and environmentally independent selection of favourable alleles are desirable. In the present study, two kinds of association mapping-genome-wide association mapping (GWAM) based on sequences of DArTSeq markers and candidate gene association mapping (CGAM) based on sequences of ScBx genes-were chosen for development of molecular markers fulfilling these criteria. The analysed population consisted of 149 diverse inbred lines (DILs). Altogether, 67 and 11 single nucleotide polymorphisms (SNPs) identified in, respectively, GWAM and CGAM, were significantly associated with the investigated traits: 2 SNPs with resistance to brown rust, 71 SNPs with resistance to pre-harvest sprouting and 5 SNPs with α-amylase activity in the grain. Fifteen SNPs were stable across all environments. The highest number (13) of environmentally stable SNPs was associated with pre-harvest sprouting resistance. The test employing the Kompetitive Allele Specific PCR method proved the versatility of four markers identified in both GWAM and CGAM.