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United States Department of Agriculture

Agricultural Research Service

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Research Project: Gene Expression Analysis in Sweet Potato

Location: Genomics and Bioinformatics Research Unit

2012 Annual Report


1a.Objectives (from AD-416):
To study gene expression in cultivated sweet potato and its diploid relatives.


1b.Approach (from AD-416):
Selected tissues from sweet potato and its diploid relatives will be collected and mRNA isolated and converted to cDNA to be sequenced by 454 technology at ARS Location.


3.Progress Report:

The Genomics and Bioinformatics Research Unit does not have the necessary facilities to grow plant material under different growing conditions nor does it have expertise in sweet potato physiology, whereas the scientists at Alcorn State University (ASU) specialize in sweet potato. Various sweet potato tissue samples have been collected and Robonucleic acid (RNA) isolated at the Biotech Center, ASU for the project.

For Objective 1: Preparation of sweet potato tissue samples and RNA extraction for gene expression analysis: and Objective 2: Preparation of total RNA from various tissues under different conditions for normalized complementary DNA (cDNA) libraries for deep-coverage of Expressed Sequence Tag (ESTs).

The objectives are complete. A total of 55 total RNA samples have been prepared in large scale (~1 mg) from various tissue types of a sweet potato breeding line SC1149 under different treatments, quantified and analyzed for integrity on Formaldehyde agrose gels. About 300 ug each of 43 of the RNA samples were aliquoted and combined for making a normalized cDNA library and sequencing (2 GS-FLX plates, completed) at University of Indiana. The following table summarizes the RNA samples. These RNA samples will be used for gene expression analysis later. Developmental stages/Treatments Leaves (19) Young, middle-aged, and old aged leaves from hydroponic plants under high or low nitrogen media (6 samples) Leaves of similar age from hydroponic plants with or without treatment of Apogee under low or high nitrogen media (5 samples) Mature leaves from field-grown plants (1 sample) Cold challenged or frosted leaves, leaf blade or petioles from field or pot-grown plants (5 samples) Leaves from drought challenged plants in pots (2 samples)

Vines (18) Young, middle, and old vines from hydroponic plants under high or low nitrogen media (9 samples) Vines of similar age from hydroponic plants with or without treatment of Apogee under low or high nitrogen media (4 samples) Vines from field-grown plants (1 sample) Cold challenged or frosted vines from field or pot-grown plants (2 samples) Vines from drought challenged plants in pots (2 samples)

Fibrous roots (7) Young, middle-aged, and old Fibrous roots from hydroponic plants under high or low nitrogen media (3 samples) Fibrous roots from hydroponic plants with or without treatment of Apogee under low or high nitrogen media (4 samples) Pencil roots (4) Pencil roots from hydroponic plants with or without treatment of Apogee under low or high nitrogen media (4 samples) Storage roots (7) Storage roots from filed-grown plants with or without treatment of Apogee (3 samples) Cured storage roots (1 sample) Storage of different developmental stages from hydroponic grown plants (3)

In addition, total RNA samples were prepared in large-scale (>1mg) from various tissues of a diploid and a tetraploid progenitor to the hexaploid sweet potato, Iris tenuissima (2x) and Ipomoea littoralis (4x). The RNA samples from each species were combined for making an normalized cDNA library, and for sequencing (1.5 GS-FLX plates for Ippomoea littoralis, and 1 for Iris tenuissima). Ipomoea littoralis (4x) Leaf Young, middle-aged and old leaves from pot-grown plants (4 samples) Vine Young and old vines (2 samples) Roots Young and old roots (2 samples) Iris tenuissima (2x) Leaf Young, middle-aged and old leaves from pot-grown plants (2 samples) Vine Young and old vines (2 samples) Roots Young and old roots (2 samples) Flowers 3 samples of mixed flower tissues.

The project objectives were expanded at a late stage of the project (October to December 14, 2011) to include preparations of total RNAs from fibrous and storage root tissues of sweet potato, and fibrous roots of its tetraploid and diploid relative for comparative analyses of root transcriptomes using RNAseq. A total of 15 total RNA samples in large scale (> 1mg) were prepared from biological triplicates of fibrous roots (grown in pots and hydroponic conditions) and storage roots of sweet potatoes, and fibrous roots of the tetraploid Ipomoea littoralis and diploid Iris tenuissima). They will be used for RNAseq analyses at ARS.


Last Modified: 9/29/2014
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