New DArT markers for oat provide enhanced map coverage and global germplasm characterization

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' × '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

Isolation of a cDNA Encoding a Granule-Bound 152-Kilodalton Starch-Branching Enzyme in Wheat

Screening of a wheat (Triticum aestivum) cDNA library for starch-branching enzyme I (SBEI) genes combined with 5′-rapid amplification of cDNA ends resulted in isolation of a 4,563-bp composite cDNA, Sbe1c. Based on sequence alignment to characterized SBEI cDNA clones isolated from plants, the SBEIc predicted from the cDNA sequence was produced with a transit peptide directing the polypeptide into plastids. Furthermore, the predicted mature form of SBEIc was much larger (152 kD) than previously characterized plant SBEI (80–100 kD) and contained a partial duplication of SBEI sequences. The first SBEI domain showed high amino acid similarity to a 74-kD wheat SBEI-like protein that is inactive as a branching enzyme when expressed in Escherichia coli. The second SBEI domain on SBEIc was identical in sequence to a functional 87-kD SBEI produced in the wheat endosperm. Immunoblot analysis of proteins produced in developing wheat kernels demonstrated that the 152-kD SBEIc was, in contrast to the 87- to 88-kD SBEI, preferentially associated with the starch granules. Proteins similar in size and recognized by wheat SBEI antibodies were also present in Triticum monococcum, Triticum tauschii, and Triticum turgidum subsp. durum

Modeling Climate Suitability of the Western Blacklegged Tick in California

Ixodes pacificus Cooley &amp; Kohls (Acari: Ixodidae), the primary vector of Lyme disease spirochetes to humans in the far-western United States, is broadly distributed across Pacific Coast states, but its distribution is not uniform within this large, ecologically diverse region. To identify areas of suitable habitat, we assembled records of locations throughout California where two or more I. pacificus were collected from vegetation from 1980 to 2014. We then employed ensemble species distribution modeling to identify suitable climatic conditions for the tick and restricted the results to land cover classes where these ticks are typically encountered (i.e., forest, grass, scrub-shrub, riparian). Cold-season temperature and rainfall are particularly important abiotic drivers of suitability, explaining between 50 and 99% of the spatial variability across California among models. The likelihood of an area being classified as suitable increases steadily with increasing temperatures &gt;0°C during the coldest quarter of the year, and further increases when precipitation amounts range from 400 to 800 mm during the coldest quarter, indicating that areas in California with relatively warm and wet winters typically are most suitable for I. pacificus. Other consistent predictors of suitability include increasing autumn humidity, temperatures in the warmest month between 23 and 33°C, and low-temperature variability throughout the year. The resultant climatic suitability maps indicate that coastal California, especially the northern coast, and the western Sierra Nevada foothills have the highest probability of I. pacificus presence