Genome-Wide Association Study in Rice Revealed a Novel Gene in Determining Plant Height and Stem Development, by Encoding a WRKY Transcription Factor.

Semi-dwarfism is a main agronomic trait in crop breeding. In this study, we performed genome-wide association study (GWAS) and identified a new quantitative trait nucleotide (QTN) for rice shoot length. The peak QTN (C/T) was located in the first coding region of a group III WRKY transcription factor OsWRKY21 (LOC_Os01g60640). Interestingly, further haplotype analysis showed that C/T difference only existed in the indica group but not in the japonica group, resulting in significant differences in plant height among the different indica rice varieties. OsWRKY21 was expressed in embryo, radicle, shoots, leaves, and stems. Most notably, overexpressing OsWRKY21 resulted in the semi-dwarf phenotype, early heading date and short internodes compared to the wild type, while the knockout mutant plants by CRISPR/Cas9 technology yielded the opposite. The overexpressing lines exhibited the decreased length of the cells near sclerenchyma epidermis, accompanied with the lower levels of indole-3-acetic acid (IAA) and gibberellin 3 (GA3), but increased levels of the abscisic acid (ABA) and salicylic acid (SA) in the internodes at heading stage. Moreover, the semi-dwarf phenotype could be fully rescued by exogenous GA3 application at seedling stage. The RNA-seq and qRT-PCR analysis confirmed the differential expression levels of genes in development and the stress responses in rice, including GA metabolism (GA20ox2, GA2ox6, and YABY1) and cell wall biosynthesis (CesA4, 7, and 9) and regulation (MYB103L). These data suggest the essential role of OsWRKY21 in regulation of internode elongation and plant height in rice.

Genetic analysis and fine mapping of the gall midge resistance gene Gm5 in rice (Oryza sativa L.).

KEY MESSAGE: The rice gall midge resistance gene, Gm5, confers remarkable antibiosis and is located in the same region on chromosome 12 in three different rice varieties. Fine mapping narrowed this region to a 49-kb segment and identified two candidate genes showing remarkable response to GM infestation. The Asian rice gall midge (GM; Orseolia oryzae; Diptera: Cecidomyiidae) invades rice shoots and forms galls, adversely affecting plant growth and yield production. Thus, the development of resistant varieties through the identification, mapping, and application of GM resistance genes is considered the most efficient strategy for managing this insect. Here, a GM resistance survey of F2 populations derived from intercrosses between resistant rice varieties 'ARC5984,' '570011,' and 'ARC5833' indicated that the resistance gene Gm5 was located on the same chromosomal region in the three varieties. For the initial mapping, three independent F2 mapping populations were developed for the three resistant varieties, and the Gm5 gene was consistently mapped to the same chromosomal region near marker 12M22.6. Fine mapping, which was conducted using the BC1F2 and BC2F2 populations derived from the 9311/ARC5984 cross, narrowed the Gm5 gene region to a 49-kb segment flanked by the markers Z57 and Z64. In the final mapped region, we detected 10 candidate genes, of which six were analyzed for their relative expression. Consequently, two of these genes, Os12g36830 and Os12g36880, showed significantly higher expression in GM-resistant plants than in GM-susceptible plants at 24 and 72 h after GM infestation. Finally, the PCR amplification of markers 12M22.5 and 12M22.6 yielded clear single bands, and these markers were effectively applied for the marker-assisted selection (MAS) of the Gm5 gene. With the developed MAS markers, the fine mapping of this resistance gene will facilitate its map-based cloning and incorporation into insect-resistant rice varieties through breeding.

Hanseniaspora uvarum prolongs shelf life of strawberry via volatile production.

Gray mold caused by Botrytis cinerea led to severe postharvest losses for strawberry industry. In recent years, some studies have shown that postharvest diseases of strawberry can be controlled by using bacterial, fungal and yeast strains. The yeast strain Hanseniaspora uvarum was shown as an effective antagonist against B. cinerea growth. Here, we further investigated the volatile organic compounds (VOCs) production of H. uvarum and how this could impact on postharvest gray mold control of strawberry. A total of 28 VOCs were detected by GC-MS in the headspace of H. uvarum and strawberry with/without B. cinerea (SI and RSI ≥800). Among these VOCs, 15 VOCs were detected in both conditions, 4 VOCs were H. uvarum and strawberry without B. cinerea and the other 9 VOCs were only detected when B. cinerea was inoculated. Two VOCs, ethyl acetate and 1,3,5,7-cyclooctatetraene, enhanced by inoculation of B. cinerea. In in vitro assay, H. uvarum significantly inhibited mycelial growth and spore germination of B. cinerea via VOCs production. Moreover, in vivo assay showed that H. uvarum reduced B. cinerea infection of strawberry and maintained fruit appearance, firmness and total soluble solids via VOCs production. Collectively, our results showed that H. uvarum VOCs significantly controlled postharvest gray mold of strawberry and prolonged the storage time and shelf life.

The Divergent Roles of the Rice bcl-2 Associated Athanogene (BAG) Genes in Plant Development and Environmental Responses.

Bcl-2-associated athanogene (BAG), a group of proteins evolutionarily conserved and functioned as co-chaperones in plants and animals, is involved in various cell activities and diverse physiological processes. However, the biological functions of this gene family in rice are largely unknown. In this study, we identified a total of six BAG members in rice. These genes were classified into two groups, OsBAG1, -2, -3, and -4 are in group I with a conserved ubiquitin-like structure and OsBAG5 and -6 are in group Ⅱ with a calmodulin-binding domain, in addition to a common BAG domain. The BAG genes exhibited diverse expression patterns, with OsBAG4 showing the highest expression level, followed by OsBAG1 and OsBAG3, and OsBAG6 preferentially expressed in the panicle, endosperm, and calli. The co-expression analysis and the hierarchical cluster analysis indicated that the OsBAG1 and OsBAG3 were co-expressed with primary cell wall-biosynthesizing genes, OsBAG4 was co-expressed with phytohormone and transcriptional factors, and OsBAG6 was co-expressed with disease and shock-associated genes. ß-glucuronidase (GUS) staining further indicated that OsBAG3 is mainly involved in primary young tissues under both primary and secondary growth. In addition, the expression of the BAG genes under brown planthopper (BPH) feeding, N, P, and K deficiency, heat, drought and plant hormones treatments was investigated. Our results clearly showed that OsBAGs are multifunctional molecules as inferred by their protein structures, subcellular localizations, and expression profiles. BAGs in group I are mainly involved in plant development, whereas BAGs in group II are reactive in gene regulations and stress responses. Our results provide a solid basis for the further elucidation of the biological functions of plant BAG genes.

High-resolution mapping and breeding application of a novel brown planthopper resistance gene derived from wild rice (Oryza. rufipogon Griff).

BACKGROUND: The brown planthopper (Nilaparvata lugens Stål; BPH), one of the most destructive pests of rice, has proven to be a substantial threat, conferring enormous production losses in Asia and becoming a difficult challenge to manipulate and control under field conditions. The continuous use of insecticides promotes the resurgence of BPH, which results in resistant varieties adapting through the upgrading of new BPH biotypes. To overcome resistance acquired by BPH against resistance varieties, different forms of novel resistant gene fusions act as functional domains for breeding to enhance insect resistance. RESULTS: The current study reports on the novel BPH resistance gene Bph36 derived from two introgression lines (RBPH16 and RBPH17) developed from wild rice GX2183 which was previously reported to be resistant to BPH. Using two F2 crossing populations (Kangwenqizhan × RBPH16 and Huanghuazhan × RBPH17) in a bulked segregant analysis (BSA) for identification of resistant genes and QTL analysis, two QTLs for BPH resistance were generated on the long and short arms of chromosome 4, which was further confirmed by developing BC1F2:3 populations by backcrossing via marker assisted selection (MAS) approach. One BPH resistance locus on the short arm of chromosome 4 was mapped to a 38-kb interval flanked by InDel markers S13 and X48, and then was named Bph36, whereas another locus on the long arm of chromosome 4 was also detected in an interval flanked by RM16766 and RM17033, which was the same as that of Bph27. An evaluation analysis based on four parameters (BPH host selection, honeydew weight, BPH survival rate and BPH population growth rate) shows that Bph36 conferred high levels antibiosis and antixenosis to BPH. Moreover, Bph36 pyramided with Bph3, Bph27, and Bph29 through MAS into elite cultivars 9311 and MH511 (harbored Xa23), creating different background breeding lines that also exhibited strong resistance to BPH in the seedling or tillering stage. CONCLUSION: Bph36 can be utilized in BPH resistance breeding programs to develop high resistant rice lines and the high-resolution fine mapping will facilitate further map-based cloning and marker-assisted gene pyramiding of resistant gene. MAS exploited to pyramid with Bph3, Bph27, Bph29, and Xa23 was confirmed the effectiveness for BPH resistance breeding in rice and provided insights into the molecular mechanism of defense to control this devastating insect.

Biomimetic matrix fabricated by LMP-1 gene-transduced MC3T3-E1 cells for bone regeneration.

Bone healing is regulated by multiple microenvironmental signals provided by the extracellular matrix (ECM). This study aimed to mimic the native osteoinductive microenvironment by developing an ECM using gene-transduced cells. The LIM mineralization protein-1 (LMP-1) gene was transferred to murine pre-osteoblast cells (MC3T3-E1) using lentiviral vectors. Western blotting assay indicated that the MC3T3-E1 cells expressed an increased level of bone morphologic protein-2, -4 and -7 (BMP-2, -4 and -7) after LMP-1 gene transduction. The transduced cells were then seeded into calcined bovine bone scaffolds and cultured for 7, 14, and 21 days to construct ECMs on the scaffolds. The ECM-scaffold composites were then decellularized using the freeze-drying method. Scaffolds without ECM deposition were used as controls. The composites and controls were implanted into critical-sized bone defects created in the distal femurs of New Zealand rabbits. Twelve weeks after the surgery, both microcomputed tomography and histologic results indicated that the 7-day-cell-modified ECM-scaffold composites induced bone regeneration with significantly larger volume, trabecular thickness and connectivity than the controls. However, the 14- and 21-day-cell-modified ECM-scaffold composites triggered sustained inflammation response even at 12 weeks after the surgery and showed less bone ingrowth and integration than their 7-day-cell-modified counterparts. In conclusion, these results highlight the viable gene transfer techniques for manipulating cells in a constructed microenvironment of ECM for bone regeneration. However, the unresolved inflammation relating to the duration of ECM modification needs to be considered.