Linking Markers, Molecules, and Morphology in DNA Biology & Bioinformatics summer camp

Jaiswal laboratory at Oregon State University (OSU) organized a weeklong summer camp on DNA Biology & Bioinformatics from 7th-11th July 2014. The participants included 7 female and 8 male high school students from local area.

The focus of the camp activities was on linking concepts of genetics and molecular biology to their relevance and applications in plant breeding. Dr. Sushma Naithani, Outreach Coordinator of Gramene project at OSU, introduced students with Mendel’s principles of inheritance, and supervised hands on laboratory exercise using wolf-barley double haploid population aiming at testing Mendel’s Laws.

The Oregon Wolfe-barley lines (http://barleyworld.org) were developed in the laboratory of Prof. Patrick Hayes, at OSU. To generate this population, first Hordeum vulgare stock Wolfe Dominant × Wolfe Recessive parents were crossed and F1 population was generated. The F1 heterozygous H. vulgare plants (phenotypically like dominant parent) were then crossed to Hordeum bulbosum. Inter-specific cross can be made between these two species, however fertilization triggers embryo formation and spontaneous elimination of H. bulbosum chromosomes. The embryo with haploid set of chromosomes is equivalent to the pollen grains or gametes. Under natural conditions these embryo with haploid set of chromosomes do not survive, but in laboratory these embryos can be rescued to create haploid plants, which are generally sterile. The haploid plants were treated with colchicines to create double haploid plants, which can be propagated by seeds. In essence double haploid plants are a set of homozygous genotypes representing a random sample of F2 gametes. Sets of doubled haploid lines, like this one, are the equivalent of test cross populations (with the important exception that they can be maintained by saving seed).

The students were asked to score dominant or recessive phenotypes corresponding to four known genes in 96 double haploid plants and then to find out if their data supports Mendel's second law, the law of independent assortment. The four gene chosen for this study were: VRS1, phenotype; 2-row (OWB-D allele = A) vs. 6-row (OWB-R allele = B). Zeo, phenotype; Dwarf-head (OWB D allele) vs. tall head (OWB R allele). Kap, phenotype; hooded (OWB D allele) vs. awn (OWB R allele). Pre 2, phenotype: purple lemma (OWB D allele) or light color lemma (R allele)

The students analyzed phenotypes in 96 F2 double-haploids and found that their results do not fit into Mendel’s principle of segregation and independent assortment.
We discussed various scenarios in which the data could fail to support ‘principle of segregation and independent assortment’ and discussed location of these four genes on barley chromosomes. The three genes VRS1, PRE2 and Zeo1 are located in the chromosome 2 of Barley and thus do not follow the Mendel’s law of independent segregation.

Students were introduced to the concept of linkage and how often it breaks during meiosis due to recombination event. It was also discussed how using the data from F2 population can be used to map distances between two genes on the same chromosomes. The discussion was initiated about how Linkage is exploited by plant breeders for developing new plant varieties, when a breeder might want to "break" a linkage between a desirable gene and an undesirable one. How knowledge of the map distance between the desirable and the undesirable loci can help to estimate how many progeny plants should be analyzed to have a high probability of having at least one individual in which linkage has been broken.

The sequence of Vrs1 gene of barley, available from the NCBI, was used for various exercises using online tools including BLAST, Artemis, Pfam, Cn3D, etc. to annotate genes, gene products (proteins), assign function to proteins, compare to other well-known homologous proteins, and model protein 3D structures. Dr. Justin Elser, and Justin Preece and DR. Sam Fox introduced various bioinformatics tools for DNA/gene analysis to students.

Dr. Pankaj Jaiswal, Associate Professor at Oregon State University led the instruction, planning and coordination of the course and Cathy Law, Director, STEM academy at OSU coordinated student enrollment, and their transportation, housing etc. The funds for the course were provided by the National Science Foundation (NSF) funded projects, The Plant Ontology (IOS:0822201) and Gramene: A Comparative Genomics Database (IOS: 1127112).