Transcriptomics of Mature Rice (<i>Oryza Sativa</i> L. Koshihikari) Seed under Hot Conditions by DNA Microarray Analyses
Higher temperature conditions during the final stages of rice seed development (seed filling and maturation) are known to cause damage to both rice yield and rice kernel quality. The western and central parts of Japan especially have seen record high temperatures during the past decade, resulting in...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-05-01
|
| Series: | Atmosphere |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4433/11/5/528 |
| _version_ | 1797567452383543296 |
|---|---|
| author | Ranjith Kumar Bakku Randeep Rakwal Junko Shibato Kyoungwon Cho Soshi Kikuchi Masami Yonekura Abhijit Sarkar Seiji Shioda Ganesh Kumar Agrawal |
| author_facet | Ranjith Kumar Bakku Randeep Rakwal Junko Shibato Kyoungwon Cho Soshi Kikuchi Masami Yonekura Abhijit Sarkar Seiji Shioda Ganesh Kumar Agrawal |
| author_sort | Ranjith Kumar Bakku |
| collection | DOAJ |
| description | Higher temperature conditions during the final stages of rice seed development (seed filling and maturation) are known to cause damage to both rice yield and rice kernel quality. The western and central parts of Japan especially have seen record high temperatures during the past decade, resulting in the decrease of rice kernel quality. In this study, we looked at the rice harvested from a town in the central Kanto-plains (Japan) in 2010. The daytime temperatures were above the critical limits ranging from 34 to 38 °C at the final stages of seed development and maturity allowing us to investigate high-temperature effects in the actual field condition. Three sets of dry mature rice seeds (commercial), each with specific quality standards, were obtained from Japan Agriculture (JA Zen-Noh) branch in Ami-town of Ibaraki Prefecture in September 2010: grade 1 (top quality, labeled as Y1), grade 2 (medium quality, labeled as Y2), and grade 3 (out-of-grade or low quality, labeled as Y3). The research objective was to examine particular alterations in genome-wide gene expression in grade 2 (Y2) and grade 3 (Y3) seeds compared to grade 1 (Y1). We followed the high-temperature spike using a high-throughput omics-approach DNA microarray (Agilent 4 × 44 K rice oligo DNA chip) in conjunction with MapMan bioinformatics analysis. As expected, rice seed quality analysis revealed low quality in Y3 > Y2 over Y1 in taste, amylose, protein, and fatty acid degree, but not in water content. Differentially expressed gene (DEG) analysis from the transcriptomic profiling data revealed that there are more than one hundred upregulated (124 and 373) and downregulated (106 and 129) genes in Y2 (grade 2 rice seed) and Y3 (grade 3 rice seed), respectively. Bioinformatic analysis of DEGs selected as highly regulated differentially expressed (HRDE) genes revealed changes in function of genes related to metabolism, defense/stress response, fatty acid biosynthesis, and hormones. This research provides, for the first time, the seed transcriptome profile for the classified low grades (grade 2, and out-of-grade; i.e., grade 3) of rice under high-temperature stress condition. |
| first_indexed | 2024-03-10T19:43:09Z |
| format | Article |
| id | doaj.art-bb258e7d1b22473aa5b3deb0ac661aee |
| institution | Directory Open Access Journal |
| issn | 2073-4433 |
| language | English |
| last_indexed | 2024-03-10T19:43:09Z |
| publishDate | 2020-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Atmosphere |
| spelling | doaj.art-bb258e7d1b22473aa5b3deb0ac661aee2023-11-20T01:07:00ZengMDPI AGAtmosphere2073-44332020-05-0111552810.3390/atmos11050528Transcriptomics of Mature Rice (<i>Oryza Sativa</i> L. Koshihikari) Seed under Hot Conditions by DNA Microarray AnalysesRanjith Kumar Bakku0Randeep Rakwal1Junko Shibato2Kyoungwon Cho3Soshi Kikuchi4Masami Yonekura5Abhijit Sarkar6Seiji Shioda7Ganesh Kumar Agrawal8Faculty of Engineering Information and Systems, Department of Computer Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, JapanFaculty of Health and Sport Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8574, JapanResearch Laboratory for Biotechnology and Biochemistry (RLABB), PO Box 13265, Kathmandu 44600, NepalDepartment of Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, KoreaGenetic Resources Center, National Agriculture and Food Research Organization, Kannondai, Tsukuba, Ibaraki 305-8602, JapanLaboratory of Molecular Food Functionality, College of Agriculture, Ibaraki University, Ami, Ibaraki 300-0393, JapanLaboratory of Applied Stress Biology, Department of Botany, University of Gour Banga, Malda 732103, West Bengal, IndiaGlobal Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 4-41 Ebara 2-chome, Shinagawa, Tokyo 142-8501, JapanGlobal Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 4-41 Ebara 2-chome, Shinagawa, Tokyo 142-8501, JapanHigher temperature conditions during the final stages of rice seed development (seed filling and maturation) are known to cause damage to both rice yield and rice kernel quality. The western and central parts of Japan especially have seen record high temperatures during the past decade, resulting in the decrease of rice kernel quality. In this study, we looked at the rice harvested from a town in the central Kanto-plains (Japan) in 2010. The daytime temperatures were above the critical limits ranging from 34 to 38 °C at the final stages of seed development and maturity allowing us to investigate high-temperature effects in the actual field condition. Three sets of dry mature rice seeds (commercial), each with specific quality standards, were obtained from Japan Agriculture (JA Zen-Noh) branch in Ami-town of Ibaraki Prefecture in September 2010: grade 1 (top quality, labeled as Y1), grade 2 (medium quality, labeled as Y2), and grade 3 (out-of-grade or low quality, labeled as Y3). The research objective was to examine particular alterations in genome-wide gene expression in grade 2 (Y2) and grade 3 (Y3) seeds compared to grade 1 (Y1). We followed the high-temperature spike using a high-throughput omics-approach DNA microarray (Agilent 4 × 44 K rice oligo DNA chip) in conjunction with MapMan bioinformatics analysis. As expected, rice seed quality analysis revealed low quality in Y3 > Y2 over Y1 in taste, amylose, protein, and fatty acid degree, but not in water content. Differentially expressed gene (DEG) analysis from the transcriptomic profiling data revealed that there are more than one hundred upregulated (124 and 373) and downregulated (106 and 129) genes in Y2 (grade 2 rice seed) and Y3 (grade 3 rice seed), respectively. Bioinformatic analysis of DEGs selected as highly regulated differentially expressed (HRDE) genes revealed changes in function of genes related to metabolism, defense/stress response, fatty acid biosynthesis, and hormones. This research provides, for the first time, the seed transcriptome profile for the classified low grades (grade 2, and out-of-grade; i.e., grade 3) of rice under high-temperature stress condition.https://www.mdpi.com/2073-4433/11/5/528riceheat stresswhole genome DNA microarrayyield lossMapMan analysisHRDE |
| spellingShingle | Ranjith Kumar Bakku Randeep Rakwal Junko Shibato Kyoungwon Cho Soshi Kikuchi Masami Yonekura Abhijit Sarkar Seiji Shioda Ganesh Kumar Agrawal Transcriptomics of Mature Rice (<i>Oryza Sativa</i> L. Koshihikari) Seed under Hot Conditions by DNA Microarray Analyses Atmosphere rice heat stress whole genome DNA microarray yield loss MapMan analysis HRDE |
| title | Transcriptomics of Mature Rice (<i>Oryza Sativa</i> L. Koshihikari) Seed under Hot Conditions by DNA Microarray Analyses |
| title_full | Transcriptomics of Mature Rice (<i>Oryza Sativa</i> L. Koshihikari) Seed under Hot Conditions by DNA Microarray Analyses |
| title_fullStr | Transcriptomics of Mature Rice (<i>Oryza Sativa</i> L. Koshihikari) Seed under Hot Conditions by DNA Microarray Analyses |
| title_full_unstemmed | Transcriptomics of Mature Rice (<i>Oryza Sativa</i> L. Koshihikari) Seed under Hot Conditions by DNA Microarray Analyses |
| title_short | Transcriptomics of Mature Rice (<i>Oryza Sativa</i> L. Koshihikari) Seed under Hot Conditions by DNA Microarray Analyses |
| title_sort | transcriptomics of mature rice i oryza sativa i l koshihikari seed under hot conditions by dna microarray analyses |
| topic | rice heat stress whole genome DNA microarray yield loss MapMan analysis HRDE |
| url | https://www.mdpi.com/2073-4433/11/5/528 |
| work_keys_str_mv | AT ranjithkumarbakku transcriptomicsofmaturericeioryzasativailkoshihikariseedunderhotconditionsbydnamicroarrayanalyses AT randeeprakwal transcriptomicsofmaturericeioryzasativailkoshihikariseedunderhotconditionsbydnamicroarrayanalyses AT junkoshibato transcriptomicsofmaturericeioryzasativailkoshihikariseedunderhotconditionsbydnamicroarrayanalyses AT kyoungwoncho transcriptomicsofmaturericeioryzasativailkoshihikariseedunderhotconditionsbydnamicroarrayanalyses AT soshikikuchi transcriptomicsofmaturericeioryzasativailkoshihikariseedunderhotconditionsbydnamicroarrayanalyses AT masamiyonekura transcriptomicsofmaturericeioryzasativailkoshihikariseedunderhotconditionsbydnamicroarrayanalyses AT abhijitsarkar transcriptomicsofmaturericeioryzasativailkoshihikariseedunderhotconditionsbydnamicroarrayanalyses AT seijishioda transcriptomicsofmaturericeioryzasativailkoshihikariseedunderhotconditionsbydnamicroarrayanalyses AT ganeshkumaragrawal transcriptomicsofmaturericeioryzasativailkoshihikariseedunderhotconditionsbydnamicroarrayanalyses |