Genome-wide analyses of late pollen-preferred genes conserved in various rice cultivars and functional identification of a gene involved in the key processes of late pollen development

Abstract

BackgroundUnderstanding late pollen development, including the maturation and pollination process, is a key component in maintaining crop yields. Transcriptome data obtained through microarray or RNA-seq technologies can provide useful insight into those developmental processes. Six series of microarray data from a public transcriptome database, the Gene Expression Omnibus of the National Center for Biotechnology Information, are related to anther and pollen development.ResultsWe performed a systematic and functional study across the rice genome of genes that are preferentially expressed in the late stages of pollen development, including maturation and germination. By comparing the transcriptomes of sporophytes and male gametes over time, we identified 627 late pollen-preferred genes that are conserved among japonica and indica rice cultivars. Functional classification analysis with a MapMan tool kit revealed a significant association between cell wall organization/metabolism and mature pollen grains. Comparative analysis of rice and Arabidopsis demonstrated that genes involved in cell wall modifications and the metabolism of major carbohydrates are unique to rice. We used the GUS reporter system to monitor the expression of eight of those genes. In addition, we evaluated the significance of our candidate genes, using T-DNA insertional mutant population and the CRISPR/Cas9 system. Mutants from T-DNA insertion and CRISPR/Cas9 systems of a rice gene encoding glycerophosphoryl diester phosphodiesterase are defective in their male gamete transfer.ConclusionThrough the global analyses of the late pollen-preferred genes from rice, we found several biological features of these genes. First, biological process related to cell wall organization and modification is over-represented in these genes to support rapid tube growth. Second, comparative analysis of late pollen preferred genes between rice and Arabidopsis provide a significant insight on the evolutional disparateness in cell wall biogenesis and storage reserves of pollen. In addition, these candidates might be useful targets for future examinations of late pollen development, and will be a valuable resource for accelerating the understanding of molecular mechanisms for pollen maturation and germination processes in rice.Electronic supplementary materialThe online version of this article (10.1186/s12284-018-0219-0) contains supplementary material, which is available to authorized users.

Genome-wide analysis of RopGEF gene family to identify genes contributing to pollen tube growth in rice (Oryza sativa)

“…To identify the pollen-preferred genes of rice, we examined a publicly available Affymetrix rice microarray data [31]. Expression patterns conserved between indica and japonica rice varieties at various developmental stages of anthers and pollen, and anatomical meta-expression data from our established database, Rice Anther Pollen Expression Database (RAPED) (http://ricephylogenomicskhu.org/RAPED/home.php), were analyzed.…”

“…These native pollen-preferred OsRopGEFs were generally not expressed in other tissues, similar to meta-expression profiles using microarray data. Especially in rice, gene expression profiles of mature and germinated pollen were highly correlated [31]. Therefore, these four genes may play key roles in pollen tube growth and other processes that occur after pollen maturation.…”

“…We used a publicly available rice Affymetrix microarray data set prepared from diverse tissues include anthers and pollen from the NCBI GEO [51] to identify latepollen-preferred genes (GSE21494, GSE109811, [31]). To examine these data, we used the Affy package encoded by R language to normalize the signal intensity and then transformed them into log 2 values.…”

Transcriptional trajectories of anther development provide candidates for engineering male fertility in sorghum

“…Pollen wall comprises an outer exine made of sporopollenin, and an inner intine which is composed of cellulose, pectin, and hemicellulose. Cellulose synthase (CESA) and synthase like (CSL) genes in Arabidopsis have been shown to play important roles in pollen wall development and tube growth 61,65,66 . CESA7 ortholog, Sobic.001G224300 and eight cellulose synthase-like genes belonging to CSLD, CSLE, CSLF, and CSLH subfamilies exhibit group 6 pattern.…”

Genome-wide analysis of RopGEF gene family to identify genes contributing to pollen tube growth in rice (Oryza sativa)

“…Especially in rice, gene expression profiles of mature and germinated pollen were highly correlated [31]. Therefore, these four genes may play key roles in pollen tube growth and other processes that occur after pollen maturation.…”