Identification and molecular characterization of tissue-preferred rice genes and their upstream regularly sequences on a genome-wide level

Genome-wide analysis of polymorphisms identified domestication-associated long low-diversity region carrying important rice grain size/weight quantitative trait loci

Rice grain size and weight are major determinants of grain quality and yield and so have been under rigorous selection since domestication. However, the genetic basis for contrasting grain size/weight trait among Indian germplasms and their association with domestication-driven evolution is not well understood. In this study, two long (LGG) and two short grain (SGG) genotypes were resequenced. LGG (LGR and PB 1121) differentiated from SGG (Sonasal and Bindli) by 504 439 single nucleotide polymorphisms (SNPs) and 78 166 insertion-and-deletion polymorphisms. The LRK gene cluster was different and a truncation mutation in the LRK8 kinase domain was associated with LGG. Phylogeny with 3000 diverse rice accessions revealed that the four sequenced genotypes belonged to the japonica group and were at the edge of the clades indicating them to be the potential source of genetic diversity available in Indian rice germplasm. Six SNPs were significantly associated with grain size/weight and the top four of these could be validated in mapping a population, suggesting this study as a valuable resource for high-throughput genotyping. A contiguous long low-diversity region (LDR) of approximately 6 Mb carrying a major grain weight quantitative trait loci (harbouring OsTOR gene) was identified on Chromosome 5. This LDR was identified as an evolutionary important site with significant positive selection and multiple selection sweeps, and showed association with many domestication-related traits, including grain size/weight. The aus population retained more allelic variations in the LDR than the japonica and indica populations, suggesting it to be one of the divergence loci. All the data and analyses can be accessed from the RiceSzWtBase database.

Choice of the Promoter for Tissue and Developmental Stage-Specific Gene Expression

Transgenic technologies belong to important tools of reverse genetics and biotechnology in plants. Targeted genetic modifications can reveal functions of genes of interest, change metabolic and regulatory pathways, or result in accumulation of valuable proteins or metabolites. However, to be efficient in targeted genetic modification, the chimeric gene construct should be designed properly. In particular, the promoters used to control transgene expression need to be carefully chosen. Most promoters in widely used vectors belong to strong and constitutively expressed variants. However, in many cases transgene expression has to be restricted to certain tissue, stage of development, or response to some internal or external stimuli. In turn, a large variety of tissue-specific promoters have been studied and information on their characteristics may be recovered from the literature. An appropriate promoter may be selected and used in genetic construct to optimize the transgene transcription pattern. We have previously designed the TGP database (TransGene Promoters, http://wwwmgs.bionet.nsc.ru/mgs/dbases/tgp/home.html ) collecting information from the publications in this field. Here we review the wide range of noncanonical tissue-specific and developmentally regulated promoters that might be used for transgene expression control.

OsPKS1 is required for sexine layer formation, which shows functional conservation between rice and Arabidopsis

The sporopollenin precursors, as a general constituent of sexine, are synthesized in the tapetum and deposited on the pollen surface after transportation and processing. The polyketide synthase condenses the acyl-CoA into a hydroxyalkyl α-pyrone, which is predicted to be a component of the sporopollenin precursors. In this study, we found that the rice POLYKETIDE SYNTHASE 1 (OsPKS1) was the orthologue of Arabidopsis POLYKETIDE SYNTHASE A/LESS ADHESIVE POLLEN 6 (PKSA/LAP6) through sequence alignment. The OsPKS1 knockout mutants obtained by Crispr-Cas9-mediated editing exhibited a complete male sterile phenotype. Cytological observations revealed that abnormal bacula deposition and ubisch body structures for sexine formation led to pollen rupture in ospks1. The expression analysis showed that the OsPKS1 was highly expressed in tapetal cells and anther locules from stage 9 to stage 11 during anther development in rice. Subcellular localization demonstrated that the OsPKS1 protein was preferentially localized to the ER. The genomic sequence of OsPKS1 driven by the PKSA/LAP6 promoter restored the sexine pattern of Arabidopsis pksa/lap6. These results indicated that OsPKS1 is required for sexine layer formation in rice and functionally conserved in the sporopollenin synthesis pathway.

Identification and analysis of the stigma and embryo sac-preferential/specific genes in rice pistils

BACKGROUND

In rice, the pistil is the female reproductive organ, and it consists of two stigmas and an ovary. The stigma is capable of receiving pollen grains and guiding pollen tube growth. The ovary holds the embryo sac, which is fertilized with male gametes to produce seed. However, little is known about the gene function and regulatory networks during these processes in rice.

RESULTS

Here, using the RNA-Seq technique, we identified 3531 stigma-preferential genes and 703 stigma-specific genes within the rice pistils, and we verified 13 stigma-specific genes via qRT-PCR and in situ hybridization. The GO analysis showed that the transport-, localization-, membrane-, communication-, and pollination-related genes were significantly enriched in the stigma. Additionally, to identify the embryo sac-preferential/specific genes within the pistils, we compared a wild-type ovary with a mutant dst (defective stigma) ovary and found that 385 genes were down-regulated in dst. Among these genes, 122 exhibited an ovary-specific expression pattern and are thought to be embryo sac-preferential/specific genes within the pistils. Most of them were preferentially expressed, while 14 of them were specifically expressed in the pistil. Moreover, the rice homologs of some Arabidopsis embryo sac-specific genes, which played essential roles during sexual reproduction, were down-regulated in dst. Additionally, we identified 102 novel protein-coding genes, and 6 of them exhibited differences between the stigma and ovary in rice as determined using RT-PCR.

CONCLUSIONS

According to these rice ovary comparisons, numerous genes were preferentially or specifically expressed in the stigma, suggesting that they were involved in stigma development or pollination. The GO analysis indicated that a dry rice stigma might primarily perform its function through the cell membrane, which was different from the wet stigma of other species. Moreover, many embryo sac-preferential/specific genes within the pistils were identified and may be expressed in female rice gametophytes, implying that these genes might participate in the process of female gametophyte specialization and fertilization. Therefore, we provide the gene information for investigating the gene function and regulatory networks during female gametophyte development and fertilization. In addition, these novel genes are valuable for the supplementation and perfection of the existing transcriptome in rice, which provides an effective method of detecting novel rice genes.