DNA-Based Genetic Markers for Rapid Cycling Brassica Rapa (Fast Plants Type) Designed for the Teaching Laboratory

We have developed DNA-based genetic markers for rapid cycling Brassica rapa (RCBr), also known as Fast Plants. Although markers for B. rapa already exist, ours were intentionally designed for use in a teaching laboratory environment. The qualities we selected for were robust amplification in PCR, polymorphism in RCBr strains, and alleles that can be easily resolved in simple agarose slab gels. We have developed two single nucleotide polymorphism (SNP) based markers and 14 variable number tandem repeat (VNTR)-type markers spread over four chromosomes. The DNA sequences of these markers represent variation in a wide range of genomic features. Among the VNTR-type markers, there are examples of variation in a non-genic region, variation within an intron, and variation in the coding sequence of a gene. Among the SNP-based markers there are examples of polymorphism in intronic DNA and synonymous substitution in a coding sequence. Thus these markers can serve laboratory exercises in both transmission genetics and molecular biology

Mapping the Anthocyaninless (anl) Locus in Rapid-Cycling Brassica rapa (RBr) to Linkage Group R9

<p>Abstract</p> <p>Background</p> <p>Anthocyanins are flavonoid pigments that are responsible for purple coloration in the stems and leaves of a variety of plant species. <it>Anthocyaninless </it>(<it>anl</it>) mutants of <it>Brassica rapa </it>fail to produce anthocyanin pigments. In rapid-cycling <it>Brassica rapa</it>, also known as Wisconsin Fast Plants, the anthocyaninless trait, also called non-purple stem, is widely used as a model recessive trait for teaching genetics. Although anthocyanin genes have been mapped in other plants such as <it>Arabidopsis thaliana</it>, the <it>anl </it>locus has not been mapped in any <it>Brassica </it>species.</p> <p>Results</p> <p>We tested primer pairs known to amplify microsatellites in <it>Brassicas </it>and identified 37 that amplified a product in rapid-cycling <it>Brassica rapa</it>. We then developed three-generation pedigrees to assess linkage between the microsatellite markers and <it>anl</it>. 22 of the markers that we tested were polymorphic in our crosses. Based on 177 F₂offspring, we identified three markers linked to <it>anl </it>with LOD scores ≥ 5.0, forming a linkage group spanning 46.9 cM. Because one of these markers has been assigned to a known <it>B. rapa </it>linkage group, we can now assign the <it>anl </it>locus to <it>B. rapa </it>linkage group R9.</p> <p>Conclusion</p> <p>This study is the first to identify the chromosomal location of an anthocyanin pigment gene among the <it>Brassicas</it>. It also connects a classical mutant frequently used in genetics education with molecular markers and a known chromosomal location.</p

The First Data Release of the Sloan Digital Sky Survey

The Sloan Digital Sky Survey has validated and made publicly available its First Data Release. This consists of 2099 square degrees of five-band (u, g, r, i, z) imaging data, 186,240 spectra of galaxies, quasars, stars and calibrating blank sky patches selected over 1360 square degrees of this area, and tables of measured parameters from these data. The imaging data go to a depth of r ~ 22.6 and are photometrically and astrometrically calibrated to 2% rms and 100 milli-arcsec rms per coordinate, respectively. The spectra cover the range 3800--9200 A, with a resolution of 1800--2100. Further characteristics of the data are described, as are the data products themselves.Comment: Submitted to The Astronomical Journal. 16 pages. For associated documentation, see http://www.sdss.org/dr

Genes in the interval containing <i>anthocyaninless</i>.

<p>Genes in the interval containing <i>anthocyaninless</i>.</p

Genetic linkage map of chromosome A09 including DNA markers tightly linked to the <i>anthocyaninless</i> (<i>ANL</i>) locus.

<p>Genotype data are from 126 BC1 progeny. Distances are in Kosambi centimorgans and all linkages have a LOD > 3.0.</p

Non-purple strains bear an insertion mutation in exon 4 of the <i>DFR</i> gene.

<p>(A) Diagram of predicted intron/exon structure of <i>DFR</i> with the insertion shown. Positions of primers used in this study are also shown. (B) PCR with primers pr7F and PR which are anchored in the 5^th exon of the gene identifies an insertion mutation. (C) Nucleotide sequence of the insertion (GenBank accession KX379243). Flanking direct repeats are underlined. The two halves of the perfect palindrome are shaded. An in-frame stop codon is indicated with double underline. (D) PCR assay for wild type and mutant alleles of the <i>DFR</i> gene. In the top panel, PCR primers were prCF and prNR which amplify a product (N) in alleles with the insertion. In the bottom panel, PCR primers were prCF and prPR which amplify a product (P) from the wild type allele. In all reactions, primers pr1F and pr10R, which amplify a segment from a different part of the <i>DFR</i> gene (+), were included to serve as a positive control. The DNA samples used were (1) Non-purple Stem Yellow Green Leaf, (2) Purple Hairy, (3) hybrid of 1 and 2, (4) DWRCBr57, (5) DWRCBr76, (6) hybrid of 4 and 5, (7) no template control.</p