Genomic approaches to understand sweetpotato root development in relation to abiotic factors

Storage root development is the most important physiological process in sweetpotato. Understanding the underlying genetics is the overall objective of this research. A secondary objective is examining the impact of abiotic stress on gene expression and storage root development. A comprehensive analysis of a high-throughput RNA sequencing data (sweetpotato root, stem, and leaf) and public Expressed Sequences Tags was done to generate a genome-wide transcriptome assembly. About 33 million sequences were assembled into 77,663 unigenes; 52,322 (69.55%) of these unigenes matched to a protein sequence from UniprotKB. Data from de novo root transcriptome enriched the existing sweetpotato gene index by 37,697 new sequences. Genes which control storage root formation under normal and drought and salt stress conditions were identified through a combination of (quantitative) reverse transcription polymerase chain reaction (qRT-RT-PCR) and microarray analysis. Global gene expression analysis using a custom sweetpotato oligo array, including ~ 14,000 unigenes derived from the de novo transcriptome, identified 1,111 differentially expressed transcripts between fibrous and young storage roots; the majority of these transcripts are involved in basic cellular processes as well as development and differentiation. A set of regulatory genes, such as BEL1-like (BELL), basic helix-loop-helix (bHLH) and HD-Zip homeobox, and signal transduction genes, such as those encoding calcium binding proteins (CBP), calcium dependent protein kinases (CDPK) and genes involved in post-transcriptional modifications (protein phosphatase 2A and a phosphatase associated protein) were up-regulated in early developing storage roots in comparison to fibrous roots. Thirteen out of 20 selected genes showed altered expression under drought stress and suppressed expression under salt stress. Interestingly, IbBEL1 and IbCRF1 (cytokinin response factor) were upregulated in two-week-old adventitious roots of the plants given drought stress at planting but were downregulated in storage roots as revealed from sequence-based digital gene expression and microarray analyses. Field and greenhouse studies showed a significant reduction in storage root number and size under drought stress. Altogether, this study furthers our knowledge in identification of new genes that are crucial in the physiological, metabolic, and molecular events during root organogenesis in sweetpotato under normal conditions and in response to external stimuli – drought and/or salt stress.

Name thesis:degree_name

Doctor of Philosophy (PhD)

Level thesis:degree_level

Dissertation

Grantor

Plant, Environmental Management and Soil Sciences

Year dc:date.available

2012

Author dc:creator

• Solis Sarmiento, Julio

• transcriptome
• de novo assembly
• functional genomics
• storage root development
• sweetpotato
• microarray
• drought stress
• salt stress

Statement dc:rights

• unrestricted
• Release the entire work immediately for access worldwide.

Identifier

etd-11142012-144543
https://repository.lsu.edu/gradschool_dissertations/1217

OAI identifier oai:identifier

oai:repository.lsu.edu:gradschool_dissertations-2216