Differential Expression and Detection of Transcripts in Sweetpotato (Ipomoea Batatas (L.) Lam.) Using CDNA Microarrays
Microarray protocols were developed for sweetpotato (Ipomoea batatas (L.) Lam.) and then used to study issues of importance in sweetpotato physiology and production. The effect of replication number and image analysis software was compared with results obtained by quantitative real-time PCR. The results indicated that reliable results could be obtained using six replicates and UCSF Spot image analysis software. These methodologies were employed to elucidate aspects of sweetpotato development, physiology and response to virus infection. Storage root formation is the most economically important process in sweetpotato development. Gene expression levels were compared between fibrous and storage roots of the cultivar Jewel. Sucrose synthase, ADP-glucose pyrophosphorylase, and fructokinase were up-regulated in storage roots, while hexokinase was not differentially expressed. A variety of transcription factors were differentially expressed as well as several auxin-related genes. The orange flesh color of sweetpotato is due to ?-carotene stored in chromoplasts of root cells. ?-carotene is important because of its role in human health. To elucidate biosynthesis and storage of ?-carotene in sweetpotato roots, microarray analysis was used to investigate genes differentially expressed between White Jewel and Jewel storage roots. ?-carotene content calculated for Jewel and White Jewel were 20.66 mg/100 g fresh weight (FW) and 1.68 mg/100 g FW, respectively. Isopentenyl diphosphate isomerase was down-regulated in White Jewel, but three other genes in the ?-carotene biosynthetic pathway were not differentially expressed. Several genes associated with chloroplasts were differentially expressed, indicating probable differences in chromoplast development of White Jewel and Jewel. Sweet potato virus disease (SPVD) is caused by the co-infection of plants with a potyvirus, Sweet potato feathery mottle virus (SPFMV), and a crinivirus, Sweet potato chlorotic stunt virus (SPCSV). Expression analysis revealed that the number of differentially expressed genes in plants infected with SPFMV alone and SPCSV alone compared to virus-tested plants was only three and 14, respectively. In contrast, more than 200 genes from various functional categories were differentially expressed between virus-tested and SPVD-affected plants. Microarray analysis has proved to be a useful tool to study important aspects of sweetpotato physiology and production.
Advisor:Don R. LaBonte; James H. Oard; Charles E. Johnson; Christopher A. Clark; Craig Hart; Manjit S. Kang
School:Louisiana State University in Shreveport
School Location:USA - Louisiana
Source Type:Master's Thesis
Date of Publication:05/10/2006