Hypoxic metabolism in wild rice (Zizania palustris): enzyme induction and metabolite production

Alcohol dehydrogenase (ADH, EC 1. 1. 1. 1), lactate dehydrogenase (LDH, EC 1. 1. 1. 27) and alanine aminotransferase (AlaAT, EC 2. 6. 1. 2) activity in wild rice ( Zizania palustris L.) root tissue increased after 4 days of exposure to hypoxic stress. The activities of ADH and AlaAT also increased in leaf tissue under these same conditions, whereas LDH activity did not. Isozyme banding patterns indicate that wild rice has at least two functional Adh genes, only one of which is hypoxically induced in root and leaf tissue. The isozyme profile of LDH also indicates the presence of two functional Ldh genes in wild rice. Two bands of AlaAT activity are visible on native electrophoretic gels of root and leaf tissue. Neither of these bands appears to increase in activity in hypoxic samples, even though spectrophotometric assays indicate an increase in AlaAT activity. Ethanol accumulation was the highest of all the metabolites measured. Alanine and malate also accumulated under hypoxic conditions but only to about one-fifth the level of ethanol. Succinate, aspartate and lactate showed no observable changes throughout the induction period. These results show that wild rice differs from domesticated rice ( Oryza sativa L.) in its metabolic responses to anaerobic stress. The possible role of these responses in conferring flood tolerance is discussed.     

The effect of sediment chemistry on the successful establishment of wild rice (Zizania palustris L.) in northern Saskatchewan water bodies

Sediment chemistry of productive and non-productive wild rice sites was measured over 3 consecutive growing seasons Although productive sites differed from non-productive sites in terms of pH, N and potential N mineralization, redox potential was considered to be the major factor which distinguished these site classes. Productivity of wild rice in commercial stands could not be consistently correlated to sediment nutrients. However, growth appeared to be restricted in strongly reduced sediments and sediment Eh is considered to be a rapid, accurate method of estimating site potential. Good growth is expected if Eh is above –150 mB while poor growth is expected when Eh drops below –200 mV. Eh values of sediment samples changed as storage time increased. It is therefore recommended that Eh is recorded on-site.     

Genome assembly and annotation of Arabidopsis halleri,a model for heavy metal hyperaccumulation and evolutionary ecology

The self‐incompatible species Arabidopsis halleri is a close relative of the self‐compatible model plant Arabidopsis thaliana. The broad European and Asian distribution and heavy metal hyperaccumulation ability make A. halleri a useful model for ecological genomics studies. We used long‐insert mate‐pair libraries to improve the genome assembly of the A. halleri ssp. gemmifera Tada mine genotype (W302) collected from a site with high contamination by heavy metals in Japan. After five rounds of forced selfing, heterozygosity was reduced to 0.04%, which facilitated subsequent genome assembly. Our assembly now covers 196 Mb or 78% of the estimated genome size and achieved scaffold N50 length of 712 kb. To validate assembly and annotation, we used synteny of A. halleri Tada mine with a previously published high‐quality reference assembly of a closely related species, Arabidopsis lyrata. Further validation of the assembly quality comes from synteny and phylogenetic analysis of the HEAVY METAL ATPASE4 (HMA4) and METAL TOLERANCE PROTEIN1 (MTP1) regions using published sequences from European A. halleri for comparison. Three tandemly duplicated copies of HMA4, key gene involved in cadmium and zinc hyperaccumulation, were assembled on a single scaffold. The assembly will enhance the genomewide studies of A. halleri as well as the allopolyploid Arabidopsis kamchatica derived from A. lyrata and A. halleri.     

Genome assembly and annotation of a Drosophila simulans strain from Madagascar

Drosophila simulans is a close relative of the genetic model D. melanogaster. Its worldwide distribution in combination with the absence of segregating chromosomal inversions makes this species an increasingly attractive model to study the molecular signatures of adaptation in natural and experimental populations. In an effort to improve the genomic resources for D. simulans, we assembled and annotated the genome of a strain originating from Madagascar (M252), the ancestral range of D. simulans. The comparison of the M252 genome to other available D. simulans assemblies confirmed its high quality, but also highlighted genomic regions that are difficult to assemble with NGS data. The annotation of M252 provides a clear improvement with alternative splicing for 52% of the multiple‐exon genes, UTRs for 70% of the genes, 225 novel genes and 781 pseudogenes being reported. We anticipate that the M252 genome will be a valuable resource for many research questions.     

Accessing genes in the tertiary gene pool of rice by direct introduction of total DNA fromZizania palustris (wild rice)

Transfer of useful genes from wild relatives of crop plants has relied upon successful conventional crossing or the availability of the cloned gene. Co-bombardment of rice callus with total genomic DNA from wild rice (Zizania palustris) and a plasmid containing a gene confirming hygromycin resistance allowed recovery under selection of transgenic plants with grain characteristics from wild rice. Amplified Fragment Length Polymorphism (AFLP) analysis suggested that a significant amount of DNA fromZizania was introduced by this procedure. One plant had 16 of a possible 122Zizania specific AFLP markers detected with the primers used. This approach may have potential for introgression of genes from wild relatives in other cases where highly efficient transformation methods are available.     

Variation in the nucleotide sequence of a prolamin gene family in wild rice

Variation in the DNA sequence of the 10 kDa prolamin gene family within the wild rice species Oryza rufipogon was probed using the direct sequencing of PCR-amplified genes. A comparison of the nucleotide and deduced amino-acid sequences of eight Asian strains of O. rufipogon and one strain of the related African species O. longistaminata is presented.     

Identification and fine mapping of a new bacterial blight resistance gene,Xa43(t), in Zhangpu wild rice (Oryza rufipogon)

• Bacterial blight (BB) is currently considered one of the most serious rice diseases and is caused by Xanthomonas oryzae pv. oryzae (Xoo). Numerous studies have shown that breeding resistant rice varieties is one of the most effective methods to prevent BB, and it is important to identify and isolate more BB resistance (R) genes from different rice resources.
• Using a map-based approach, we identified a new QTL/gene, Xa43(t), from ZhangPu wild rice, which was highly resistant to the BB isolate PX099. We performed bulked segregant analysis combined with candidate gene prediction to identify the candidate gene.
• The Xa43(t) gene was narrowed down to a 29-kb region containing four putative genes. More importantly, the candidate gene Xa43(t) did not affect the main agronomic traits of rice. We also identified a widely applicable molecular marker, namely Inde1-18, which co-segregates with the Xa43(t) gene.
• The Xa43(t) gene is a new broad-spectrum BB resistance gene without identified alleles and has good application prospects for rice disease resistance breeding.

     

Sex ratio bias in the F1 adult progeny of African rice gall midge, Orseolia oryzivora H. and G. (Dipt., Cecidomyiidae)

Abstract:  Against the background of conflicting reports of variable sex ratio distribution in different populations of the African rice gall midge (AfRGM), Orseolia oryzivora Harris and Gagne, the number and sex ratios of F₁ adult progeny produced per female from wild and screen house populations were investigated in the screen house at 27 ± 3°C, 60–70% relative humidity and 12 : 12 h (light : dark) photoperiod. Results indicated the occurrence of a single sex-biased ratio in all the F₁ adult progeny produced per female of this pest. Regardless of the source, whether from wild or screen house population, each mated female AfRGM produced a full complement of either sex only but never both. The difference between the number of eggs laid and F₁ adult progeny that emerged per female from wild and screen house populations was not significant (P > 0.05), indicating consistency in the occurrence of this phenomenon among AfRGM populations. The reason for this could not be ascertained in this study but AfRGM eggs must be fertilized for development and eclosion to occur. No F₂ adults emerged when a cohort of emergents from the same female were allowed to re-infest susceptible seedlings, indicating absence of parthenogenesis.     

Structure,evolution and expression of a second subfamily of protein phosphatase 2A catalytic subunit genes in the rice plant (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Protein phosphatase 2A (PP2A) is one of the major serine/threonine protein phosphatases in the cell and plays a variety of regulatory roles in metabolism and signal transduction. Previously, we described the structure and expression of two genes encoding PP2A catalytic subunits (PP2Ac)—OsPP2A-1 and OsPP2A-3—in the rice plant (Yu et al. 2003). Here, we report the isolation and characterisation of a second structurally distinguishable PP2Ac subfamily comprised of three additional isogenes, OsPP2A-2, OsPP2A-4 (each containing ten introns) and OsPP2A-5 (which contains nine introns). Northern blot analysis demonstrated that the three isogenes are ubiquitously expressed in all rice tissues during plant development, and differentially expressed in response to high salinity and the combined stresses of drought and heat. Phylogenetic analyses indicated that the two PP2Ac subfamilies are descended from two ancient lineages, which derived from gene duplications that occurred after the monocotyledon–dicotyledon split. In the second subfamily, it is proposed that two duplication events were involved; in which, the initial duplication of a ten-intron primordial gene yielded OsPP2A-2 and the progenitor of OsPP2A-4 and OsPP2A-5. The OsPP2A-4/OsPP2A-5 progenitor, in turn, underwent a second duplication event, resulting in the present day OsPP2A-4 and OsPP2A-5. It is proposed that loss of the 5′-most intron from OsPP2A-5 occurred after these two duplication events.