title: Genome-wide identification and analysis of rice genes preferentially expressed in pollen at an early developmental stage.
abstract: Microspore production using endogenous developmental programs has not been well studied. The main limitation is the difficulty in identifying genes preferentially expressed in pollen grains at early stages. To overcome this limitation, we collected transcriptome data from anthers and microspore/pollen and performed meta-expression analysis. Subsequently, we identified 410 genes showing preferential expression patterns in early developing pollen samples of both japonica and indica cultivars. The expression patterns of these genes are distinguishable from genes showing pollen mother cell or tapetum-preferred expression patterns. Gene Ontology enrichment and MapMan analyses indicated that microspores in rice are closely linked with protein degradation, nucleotide metabolism, and DNA biosynthesis and regulation, while the pollen mother cell or tapetum are strongly associated with cell wall metabolism, lipid metabolism, secondary metabolism, and RNA biosynthesis and regulation. We also generated transgenic lines under the control of the promoters of eight microspore-preferred genes and confirmed the preferred expression patterns in plants using the GUS reporting system. Furthermore, cis-regulatory element analysis revealed that pollen specific elements such as POLLEN1LELAT52, and 5659BOXLELAT5659 were commonly identified in the promoter regions of eight rice genes with more frequency than estimation. Our study will provide new sights on early pollen development in rice, a model crop plant.
authors.affiliation: School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea.
authors.forename: Tien Dung
authors.initials: TD
authors.lastname: Nguyen
authors.affiliation: Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea.
authors.forename: Sunok
authors.initials: S
authors.lastname: Moon
authors.affiliation: Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea.
authors.forename: Van Ngoc Tuyet
authors.initials: VN
authors.lastname: Nguyen
authors.affiliation: Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea.
authors.forename: Yunsil
authors.initials: Y
authors.lastname: Gho
authors.affiliation: Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea.
authors.forename: Anil Kumar Nalini
authors.initials: AK
authors.lastname: Chandran
authors.affiliation: Department of Molecular Biology, Sejong University, Seoul, 143-747, Republic of Korea.
authors.forename: Moon-Soo
authors.initials: MS
authors.lastname: Soh
authors.affiliation: School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea.
authors.forename: Jong Tae
authors.initials: JT
authors.lastname: Song
authors.affiliation: Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea.
authors.forename: Gynheung
authors.initials: G
authors.lastname: An
authors.affiliation: School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea.
authors.forename: Sung Aeong
authors.initials: SA
authors.lastname: Oh
authors.affiliation: School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea. psk@knu.ac.kr.
authors.forename: Soon Ki
authors.initials: SK
authors.lastname: Park
authors.affiliation: Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea. khjung2010@khu.ac.kr.
authors.forename: Ki-Hong
authors.initials: KH
authors.lastname: Jung
mesh_terms: D018507:Gene Expression Regulation, Developmental / Q000235:genetics / Q000502:physiology; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D012275:Oryza / Q000235:genetics / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D011058:Pollen / Q000235:genetics / Q000378:metabolism*; D011401:Promoter Regions, Genetic / Q000235:genetics
chemical_list: D010940:Plant Proteins
keywords: GUS reporter system; Microspore-preferred genes; Rice; cis-Regulatory element