Research internship on DArT marker characterization and detection for BX2 gene presence in native and inbred corn

Carlo M. Briz

Date

6-2016

Degree

Bachelor of Science in Agricultural Biotechnology

College

College of Agriculture and Food Science (CAFS)

Adviser/Committee Chair

Antonio C. Laurena

Abstract

The research internship was conducted in Crop Science Cluster-Institute of Plant Breeding, College of Agriculture, University of the Philippines Los Baños from August 2015 to May 2016. The in silico part of the experiment was conducted with the use of a laptop or a desktop computer. While the second part of the internship, which consisted of experiments in the lab, was conducted at the Physiology Laboratory-Institute of Plant Breeding, University of the Philippines Los Baños. The internship aimed to develop skills in doing in silico study as well as in DNA amplification techniques. Diversity Arrays Technology (DArT) offers an opportunity for studying whole genome profiling because it is low-cost and high throughput. In this study, sequenced DArT markers were identified in silico through homology search using Basic Local Alignment Search Tool (BLAST). The resulting homologues are then grouped according to their accession numbers in the Genbank. The 485 sequences were clustered into six groups. Those sequences without BLAST hits were grouped as ABSENT. Two hundred fifty seven (53%) sequences were included in this group. Predicted non-coding models have an accession number prefixed by "XM_". Ninety one (21%) sequences belonged to this group. Those sequences that have an accession prefixed by "GB_" are sequences not categorized by Reference sequence. This group included clones, cDNA clones, probe DNA, gene clusters, and insertion sites. Forty eight (10%) sequences were classified under GB_. Sequences producing BLAST results from organisms other than maize are grouped as non-maize. Forty four (9%) sequences belonged to this group. Only a small part, 2 (5%) of the sequences provided are coding mRNAs, grouped as "NM_". The sequences under the group XR_ predicted non-coding mRNAs are the fewest. There are 19 (4%) sequences under XR_. 2,4-dihydroxy-7-methoxyl-1,4-benzoxazin-3-one (DIMBOA) is a secondary defense compound belonging to the group of hydroxamic acids. Hydroxamic acids are chemicals with insecticidal property, and they are produced by grasses (Frey et al., 1997). In corn, DIMBOA plays an important part on insect and microbial defense. As suggested by the results of this experiment, DIMBOA, synthesized by protein products of BX genes, is present in native corn Tiniguib A, Kabagtik A, Bulldog A, and San Jose White and inbred corn lines P-17-1, P-17-6 P-17-7, P-17-8, and p-17-9. Presence of DIMBOA is proven by the detection of BX2 gene.

Language

English

Location

UPLB Main Library Special Collections Section (USCS)

Call Number

LG 993 2016 A127 /B75

Notes

major in Crop Biotechnology

Document Type

Thesis

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