Haitao Zhu

Characterization of Epistatic Interaction of QTLs LH8 and EH3 Controlling Heading Date in Rice

Heading date is a critical trait for adaptation of rice to different cultivation areas and cropping seasons. We evaluated the heading dates of 1,123 chromosome segments substitution lines (CSSLs) in the genetic background of an elite rice variety Huajingxian74 (HJX74). A CSSL with the substituted segments from Zihui100 exhibited late heading under both natural long-day (NLD) and natural short-day (NSD) conditions, and the late heading phenotype was controlled by two novel epistatic loci on chromosome 8 and chromosome 3, respectively, termed LH8 and EH3. The function of EH3 was dependent on the LH8 genotype through epistatic interaction between EH3Zihui100 and LH8Zihui100 alleles. Genetic and molecular characterization revealed LH8 encodes a CCAAT-box-binding transcription factor with Heading date1 (Hd1)-binding activity and may delay flowering by repressing the expression of Early heading date1 (Ehd1). Our work provides a solid foundation for further study on gene interaction in heading date and has application in breeding rice with greater adaptability.

Allelic differentiations and effects of the Rf3 and Rf4 genes on fertility restoration in rice with wild abortive cytoplasmic male sterility

To reveal the allelic differentiations at the two genes for fertility restoration (Rf) on chromosomes 1 (Rf3) and 10 (Rf4), 15 chromosome single segment substitution lines (SSSLs) with the Rf3 locus and 18 SSSLs with the Rf4 locus were crossed with Bobai A (BbA), a cytoplasmic male sterility line with wild abortive type of cytoplasm (WA-CMS), respectively. Based on the pollen and seed fertility of the F1 hybrids, the Rf3 and Rf4 genes were each classified into four alleles, namely Rf3-1, Rf3-2, Rf3-3, and Rf3-4 for Rf3, and Rf4-1, Rf4-2, Rf4-3, and Rf4-4 for Rf4. Out of the 33 SSSLs, an SSSL W23-19-06-06-11 carrying the genotype Rf3-4Rf3-4/Rf4-4Rf4-4 possessed the strongest restoring ability for BbA. To determine the genetic effects of Rf3 and Rf4 for WA-CMS, one BC3F2 population possessing the genetic background of W23-19-06-06-11 was generated from the cross between W23-19-06-06-11 and BbA by backcrossing and marker-assisted selection. In the BC3F2 population, the plants carrying the Rf3Rf3/Rf4Rf4, Rf3Rf3/rf4rf4, and rf3rf3/Rf4Rf4 genotypes were selected and their phenotyping for pollen and spikelet fertility were evaluated. The result showed that under the genetic background of SSSL W23-19-06-06-11, the effect of Rf4 appeared to be slightly larger than that of Rf3 and their effects were additive for WA-CMS system. These studies will lead to the transfer of Rf genes into adapted cultivars through marker-assisted selection in active hybrid rice breeding programs.

Overcoming inter-subspecific hybrid sterility in rice by developing indica -compatible japonica lines

Rice (Oryza sativa L.) is an important staple crop. The exploitation of the great heterosis that exists in the inter-subspecific crosses between the indica and japonica rice has long been considered as a promising way to increase the yield potential. However, the male and female sterility frequently occurred in the inter-subspecific hybrids hampered the utilization of the heterosis. Here we report that the inter-subspecific hybrid sterility in rice is mainly affected by the genes at Sb, Sc, Sd and Se loci for F1 male sterility and the gene at S5 locus for F1 female sterility. The indica-compatible japonica lines (ICJLs) developed by pyramiding the indica allele (S-i) at Sb, Sc, Sd and Se loci and the neutral allele (S-n) at S5 locus in japonica genetic background through marker-assisted selection are compatible with indica rice in pollen fertility and in spikelet fertility. These results showed a great promise of overcoming the inter-subspecific hybrid sterility and exploiting the heterosis by developing ICJLs.

Knockout of the VPS22 component of the ESCRT-II complex in rice ( Oryza sativa L.) causes chalky endosperm and early seedling lethality

In both yeast and mammals, the major constituent of the endosomal sorting complex required for transport-II (ESCRT-II) is the VPS22/EAP30 protein, which plays an important role in ubiquitin-mediated degradation of membrane proteins through the multivesicular body pathway. However, the functions of ESCRT-II subunits in plants are largely unknown. In this work, we report the genetic analysis and phenotypic characterization of mutants in OsVPS22 gene, which encodes a functional VPS22 homolog in rice. On the basis of a collection of T-DNA lines, we identified a T-DNA insertion mutant, which showed abnormal segregation ratios; we then found that the T-DNA insertion is located within the sixth intron of the OsVPS22 gene. Compared with the wild type, this vps22 mutant exhibited seedling lethality and severe reduction in shoot and root growth. In addition, the vps22 mutant had a chalky endosperm in the grain. In summary, our data suggest that OsVPS22 may be required for seedling viability and grain filling in rice, thus providing a valuable resource for further exploration of the functions of the ESCRTing machinery in plants.

Analysis of QTLs on heading date based on single segment substitution lines in rice ( Oryza Sativa L.)

Single segment substitution lines (SSSLs) have been confirmed to be powerful tools to perform quantitative trait locus (QTL) analysis. This study illuminated the process and methods of QTL analysis with SSSLs on heading date (HD) in rice. QTL identification under two cropping seasons revealed 98 of 202 SSSLs associated with HD. A total of 22 QTLs were positioned in relative narrow regions on chromosomes by mrMLM.GUI software. QTL qHd3-1 was precisely positioned at 4.4 cM on chromosome 3 by a secondary F2 population. Through SSSL pyramiding, double segment substitution lines were constructed and used to analyze epistatic interactions of digenic loci. Epistatic effects for three pairs of QTLs were estimated, indicating the interactions of QTL qHd3-1 with other QTLs detected and the role to enhance the expression of early ripening or restraining of late flowering QTLs. Additionally, analysis of QTL in different environments provided information about the stability of HD QTLs. This type of research points out the way to excavate favorable genes for design breeding.

Genome-wide transcriptome profiling provides insights into panicle development of rice (Oryza sativa L.).

Panicle architecture is an important component of agronomic trait in rice, which is also a key ingredient that could influence yield and quality of rice. In the panicle growth and development process, there are a series of complicated molecular and cellular events which are regulated by many interlinking genes. In this study, to explore the potential mechanism and identify genes and pathways involved in the formation of rice panicle, we compared the transcriptional profile of rice panicles (NIL-GW8 and NIL-gw8Amol) at three different stages of panicle development: In5 (formation of higher-order branches), In6 (differentiation of glumes) and In7 (differentiation of floral organs). A range of 40.5 to 54.1 million clean reads was aligned to 31,209 genes in our RNA-Seq analysis. In addition, we investigated transcriptomic changes between the two rice lines during different stages. A total of 726, 1121 and 2584 differentially expressed genes (DEGs) were identified at stages 1, 2 and 3, respectively. Based on an impact analysis of the DEGs, we hypothesize that MADS-box gene family, cytochrome P450 (CYP) and pentatricopeptide repeat (PPR) protein and various transcription factors may be involved in regulation of panicle development. Further, we also explored the functional properties of DEGs by gene ontology analysis, and the results showed that different numbers of DEGs genes were associated with 53 GO groups. In KEGG pathway enrichment analysis, many DEGs related to biosynthesis of secondary metabolites and plant hormone signal transduction, suggesting their important roles during panicle development. This study provides the first examination of changes in gene expression between different panicle development stages in rice. Our results of transcriptomic characterization provide important information to elucidate the complex molecular and cellular events about the panicle formation in rice or other cereal crops. Also, the findings will be helpful for the further identification of the genes related to panicle development.

ER-localized adenine nucleotide transporter ER-ANT1: an integrator of energy and stress signaling in rice

Most environmental perturbations have a direct or indirect deleterious impact on photosynthesis, and, in consequence, the overall energy status of the cell. Despite our increased understanding of convergent energy and stress signals, the connections between photosynthesis, energy and stress signals through putative common nodes are still unclear. Here we identified an endoplasmic reticulum (ER)-localized adenine nucleotide transporter1 (ER-ANT1), whose deficiency causes seedling lethality in air but viable under high CO2, exhibiting the typical photorespiratory phenotype. Metabolic analysis suggested that depletion of ER-ANT1 resulted in circadian rhythm disorders in sucrose synthesis and induced sucrose signaling pathways, indicating that the ER is involved in the regulation of vital energy metabolism in plants. In addition, the defect of ER-ANT1 triggers ER stress and activates the unfolded protein response in plant cells, suggesting ER stress and photorespiration are closely linked. These findings provide an important evidence for a key role of ER-localized ER-ANT1 in convergent energy and stress signals in rice. Our findings support the idea that ATP is a central signal involved in the plant response to a variety of stresses.