Abscisic acid and oxidative stress implications in overall ferritin synthesis by African rice (Oryza glaberrima Steud.) seedlings exposed to short term iron toxicity

Iron toxicity occurs under flooded conditions such as those prevailing in lowland rice fields and is due to an excess of ferrous ions. Ferritin is a multimeric protein responsible for Fe sequestration and storage, playing a key role in Fe homeostasis. Our aim was to study the modalities of overall ferritin synthesis in different organs of young seedlings from the African rice species (Oryza glaberrima) in relation to the putative involvement of abscisic acid (ABA) and oxidative stress in signalling processes. Seedlings from a moderately resistant to iron toxicity cultivar were grown in hydroponic culture for 2 weeks and treated with 500 mg l^?1 Fe²⁺ in the presence or in the absence of 200?µM ABA, 50?µM methylviologen or 50?µM fluridone. Iron treatment increased iron and malondialdehyde concentration in all organs as well as ABA in roots and laminae. Although ferritin protein was detected in controls plants, iron treatment strongly reinforced its accumulation in sheaths and laminae after 24 h and 72 h. Ferritin mRNA was induced as early as 24 h after the beginning of the Fe-treatment in sheaths and, to a higher extent, in laminae. In the absence of iron treatment, exogenous ABA increased ferritin mRNA in laminae only but did not lead to further ferritin accumulation. Unexpectedly, it decreased ferritin mRNA levels in the sheaths of iron-treated plants and may thus have a dual influence depending on the considered organ. The inhibitor of ABA synthesis fluridone reduced endogenous ABA but did not compromise ferritin gene expression or ferritin synthesis, whatever the iron dose. Methyviologen application induced obvious oxidative damages but reduced ferritin synthesis. It is suggested that the signalling pathway leading to ferritin synthesis in the semi-aquatic African rice species may involve other components than those reported for typical terrestrial plants.     

Evolutionary implications of substitution patterns in prolamin genes of Oryza glaberrima (African rice, Poaceae) and related species

Patterns of sequence variation of nuclear genes encoding 10-kDa and 16-kDa prolamin seed storage proteins were examined in Oryza glaberrima (African rice, Poaceae) and O. barthii and compared to available sequences for the genus to assess potential application of these gene families in evolutionary studies. Sequence variation among species in 10-kDa genes was very low. In contrast, the 16-kDa genes have undergone rapid evolution, displaying a larger number of length and point mutations that in some cases result in frame shift or produce truncated protein or pseudogenes. The proportion of nonsynonymous substitution is high in both genes. Although nonsynonymous mutations did not alter the overall profile of the protein, pronounced shifts in proportions of some amino acids were evident and could have systematic application. The data provide support for a proposed direct evolution of the Asian (O. sativa) and African rice from O. rufipogon and O. barthii, respectively. Patterns of amino acid frequencies of the 10-kDa genes show the distinctness of O. rufipogon and O. longistaminata from the other species. The study underscores the potential application of the prolamin genes as markers from the nuclear genome for evolutionary studies in grasses at different taxonomic levels.     

GC-biased gene conversion and selection affect GC content in the Oryza genus (rice)

Base composition varies among and within eukaryote genomes. Although mutational bias and selection have initially been invoked, more recently GC-biased gene conversion (gBGC) has been proposed to play a central role in shaping nucleotide landscapes, especially in yeast, mammals, and birds. gBGC is a kind of meiotic drive in favor of G and C alleles, associated with recombination. Previous studies have also suggested that gBGC could be at work in grass genomes. However, these studies were carried on third codon positions that can undergo selection on codon usage. As most preferred codons end in G or C in grasses, gBGC and selection can be confounded. Here we investigated further the forces that might drive GC content evolution in the rice genus using both coding and noncoding sequences. We found that recombination rates correlate positively with equilibrium GC content and that selfing species (Oryza sativa and O. glaberrima) have significantly lower equilibrium GC content compared with more outcrossing species. As recombination is less efficient in selfing species, these results suggest that recombination drives GC content. We also detected a positive relationship between expression levels and GC content in third codon positions, suggesting that selection favors codons ending with G or C bases. However, the correlation between GC content and recombination cannot be explained by selection on codon usage alone as it was also observed in noncoding positions. Finally, analyses of polymorphism data ruled out the hypothesis that genomic variation in GC content is due to mutational processes. Our results suggest that both gBGC and selection on codon usage affect GC content in the Oryza genus and likely in other grass species.     

Leaf Blade Dimensions of Rice (Oryza sativa L. and Oryza glaberrima Steud.). Relationships between Tillers and the Main Stem

The effects of genotype and environment on the leaf area indexof rice are well documented, but the rules governing leaf areadistribution among main stem and tillers are less well understood.This study investigated the ontogenetic patterns of leaf bladearea and dimensions on the main stem and tillers of three ricecultivars, IAC47, Javaé (Oryza sativa L.) and CG14 (O.glaberrima Steud.) grown in pots without competition among plants.No differences in phyllochron were observed among culms, butleaves on tillers appeared 0.5 to 0.8 phyllochrons earlier thanthe genealogically corresponding leaves on the main stem (systemof Katayama). Cohorts were thus not fully synchronized. Allculms produced their largest leaves soon after panicle initiation(PI), despite differences in tiller age. Leaves that appearedsubsequently were smaller owing to reduced length but not width,which remained constant. Three different hypothetical rulesgoverning the behaviour of culms were tested: (1) tillers behaveas clones of the main stem; (2) cohorts behave uniformly, and(3) behaviour is determined by leaf position (sum of genealogicalleaf and tiller indices). The results were best explained byhypotheses (2) and (3), with leaf blade width and length showingmarkedly different patterns. Copyright 2001 Annals of BotanyCompany Phenology, phyllochron, leaf area, leaf position, leaf cohorts, summed leaf position, leaf blade length and width     

Fine mapping of a gene responsible for pollen semi-sterility in hybrids between Oryza sativa L. and O. glaberrima Steud

Asian cultivated rice (Oryza sativa L.) and African cultivated rice (Oryza glaberrima Steud.) are the two main cultivated rice species in the world, with strong heterosis in their F1 hybrids. However, hybrid sterility is a major barrier, although significant heterosis has been observed. In this study, an F1 pollen semi-sterility locus, S19, was identified on rice chromosome 3 by using near-isogenic lines derived from repeated backcross and marker-assisted selection. The typical pollen semi-sterility was observed in F1 hybrids between S19-NIL and Dianjingyou 1. Cytological study of pollen developmental stages indicated that pollen abortion occurred at the late binucleate stage because of a starch accumulation obstacle in some pollen grains. Molecular analysis revealed that the semi-sterility was caused by the abortion of most male gametophytes carrying the S19 allele from the japonica variety Dianjingyou 1. In a population of 12,780 F2 plants derived from S19-NIL/Dianjingyou 1, the S19 locus was fine-mapped to a chromosomal region of 54 kb based on BAC clones of cv. Nipponbare. Interestingly, an addition of a DNA fragment of about 89 kb to the 54-kb region was found in S19-NIL based on BAC clones of O. glaberrima. Gene prediction analysis identified 12 open reading frames (ORF) based on the region of Dianjingyou 1, while 32 ORFs were predicted in S19-NIL. Map-based cloning of this gene will help us to understand the underlying mechanism of hybrid sterility between the two cultivated rice species.     

Robustness and Strategies of Adaptation among Farmer Varieties of African Rice (Oryza glaberrima) and Asian Rice (Oryza sativa) across West Africa

This study offers evidence of the robustness of farmer rice varieties (Oryza glaberrima and O. sativa) in West Africa. Our experiments in five West African countries showed that farmer varieties were tolerant of sub-optimal conditions, but employed a range of strategies to cope with stress. Varieties belonging to the species Oryza glaberrima – solely the product of farmer agency – were the most successful in adapting to a range of adverse conditions. Some of the farmer selections from within the indica and japonica subspecies of O. sativa also performed well in a range of conditions, but other farmer selections from within these two subspecies were mainly limited to more specific niches. The results contradict the rather common belief that farmer varieties are only of local value. Farmer varieties should be considered by breeding programmes and used (alongside improved varieties) in dissemination projects for rural food security.     

Genome-wide association mapping of salinity tolerance in rice (Oryza sativa)

Salinity tolerance in rice is highly desirable to sustain production in areas rendered saline due to various reasons. It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS). Here, we implemented GWAS to identify loci controlling salinity tolerance in rice. A custom-designed array based on 6,000 single nucleotide polymorphisms (SNPs) in as many stress-responsive genes, distributed at an average physical interval of <100 kb on 12 rice chromosomes, was used to genotype 220 rice accessions using Infinium high-throughput assay. Genetic association was analysed with 12 different traits recorded on these accessions under field conditions at reproductive stage. We identified 20 SNPs (loci) significantly associated with Na⁺/K⁺ ratio, and 44 SNPs with other traits observed under stress condition. The loci identified for various salinity indices through GWAS explained 5–18% of the phenotypic variance. The region harbouring Saltol, a major quantitative trait loci (QTLs) on chromosome 1 in rice, which is known to control salinity tolerance at seedling stage, was detected as a major association with Na⁺/K⁺ ratio measured at reproductive stage in our study. In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7. The current association mapping panel contained mostly indica accessions that can serve as source of novel salt tolerance genes and alleles. The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice.     

Mechanism of salt tolerance in wild rice (Oryza coarctata Roxb)

Summary Oryza coarctata, a highly salt-resistant wild rice species, is commonly found on the banks of coastal rivers in India. This species can also withstand saline water (20 to 40 dSm⁻¹ E.C) submergence for quite a long period. It was revealed thatO. coarctata has some special unicellular salt hairs (trichomes) on the adaxial surface of the leaves, by which they efficiently maintain a low concentration of toxic salts in the plant tissue. Sodium and chloride were the dominant ions in the excreted material but they also excrete potassium, magnesium and calcium. With the increase in soil salinity sodium, magnesium and chloride excretion increased.O. coarctata maintained the optimum mineral concentration in its tissues. Maximum accumulation of potassium was observed in the leaves. With the increase in salt stress total biomass production and osmotic potential increased over control but there was no change in the moisture percentage of leaves.     

A novel repetitive DNA sequence in the genus Oryza

Summary Repetitive DNA sequences in the genus Oryza (rice) represent a large fraction of the nuclear DNA. The isolation and characterization of major repetitive DNA sequences will lead to a better understanding of rice genome organization and evolution. Here we report the characterization of a novel repetitive sequence, CC-1, from the CC genome. This repetitive sequence is present as long tandem arrays with a repeat unit 194 bp in length in the CC-diploid genome but 172 bp in length in the BBCC and CCDD tetraploid genomes. This repetitive sequence is also present, though at lower copy numbers, in the AA and BB genomes, but is absent in the EE and FF genomes. Hybridization experiments revealed considerable differences both in copy numbers and in restriction fragment patterns of CC-1 both between and within rice species. The results support the hypothesis that the CC genome is more closely related to the AA genome than to the BB genome, and most distantly related to the EE and FF genomes.     

云南景洪直立型普通野生稻抗稻瘟病Pi-ta+等位基因的克隆与分析

用PCR法从景洪直立紫杆普通野生稻中克隆了抗稻瘟病基因Pi-ta⁺ 的4 672 bp序列, 该序列包含完整的编码框、内含子和终止密码子下游的331 bp。所克隆的直立型紫杆普通野生稻Pi-ta基因序列的编码区与已报道的日本栽培稻社糯(Yashiro-mochi)和元江普通野生稻相应序列间的同源性分别为99.86%和98.78%。与社糯的Pi-ta基因相比, 其编码区有4个核苷酸的差异并导致3个氨基酸残基的改变, 而内含子区域有6个核苷酸差异。对该序列进一步分析发现, 其推导的氨基酸残基的918位为丙氨酸, 属于稀有的抗稻瘟病的Pi-ta⁺ 等位基因。景洪直立型普通野生稻Pi-ta⁺ 基因因其编码序列和推导的氨基酸序列与社糯有所不同, 推测其抗病能力大小和抗菌谱可能与社糯的Pi-ta基因不同。直立型普通野生稻中Pi-ta⁺ 等位基因的克隆为进一步利用该基因改良栽培稻抗病能力提供了前期物质基础。     

Inheritance of tolerance to rice tungro bacilliform virus (RTBV) in rice (Oryza sativa L.)

Summary From a large number of rice varieties tested, no variety was identified as resistant to tungro bacilliform virus (RTBV). Only in Utri Merah was the RTBV multiplication restrictive, whereas other varieties such as Kataribhog and Pankhari 203 were identified as tolerant. These varieties were crossed with a susceptible variety. TN1, to study the inheritance of restrictive multiplication and tolerance to RTBV. After 3 weeks of inoculation with RTBV, F₁; F₂, and F₃ progenies were assessed by enzyme-linked immunosorbent assay (ELISA). The RTBV concentration in all F₁ populations was intermediate between parents. The frequency distribution of F₂ seedlings with various levels of RTBV concentration indicated that the RTBV tolerance is controlled by multiple genes. The RTBV concentrations in F₁ and F₂ progenies from the Utri Merah x TN1 cross revealed that restrictive multiplication of RTBV in Utri Merah is a polygenic character. The continuous variation observed in F₂ populations from crosses between tolerant varieties and Utri merah indicated no allelic relationships between tolerant and restrictive multiplication traits.Part of PhD thesis submitted by senior author to University of Kebangsaan Malaysia, Bangi     

水稻线粒体丝氨酸羟甲基转移酶基因的电子克隆

采用基于EST的电子克隆方法得到了一段长1611bp的cDNA序列,以此为信息探针搜索HTGs数据库,找到一个与之高度匹配的基因组DNA序列——OSJNBa0057G07克隆。用FGENESH分析该克隆中的联配区域得到一个包含14个外显子和13个内含子的基因。该基因位于水稻第3染色体物理图谱的136．0～137．6cM区域。推导的ORF编码498个氨基酸,经BLASTP搜索SWISS-PROT数据库和蛋白序列的亚细胞定位显示,该基因编码水稻的线粒体丝氨酸羟甲基转移酶(mSHMT)。该基因受到EST序列的完全支持,其中不乏来自盐胁迫、稻瘟病菌侵染等逆境处理的EST序列,推测该基因与水稻对逆境的应答反应有关。     

Differentiation in wild-type allele of the sd1 locus concerning culm length between indica and japonica subspecies of Oryza sativa (rice)

A dwarfing gene (allele) sd1-d has been intensively utilized to develop short-culm indica varieties in southeast Asia up to now. Before the first sd1-d-carrying variety IR8 was released, rice researchers had recognized the general tendency that culm length is higher in indica varieties than in temperate-japonica ones. Inter-subspecific difference of the tall (wild-type) allele SD1 at the sd1 locus was examined on the common genetic background, using five isogenic lines developed by substituting sd1-d of the recurrent parent IR36 by SD1s of two indica varieties, two temperate-japonica varieties and one tropical-japonica variety. The two indica -donor isogenic lines had longer culms than the three japonica-donor isogenic lines consistently in two different environmental conditions. Moreover, nonsynonymous single-nucleotide polymorphism between the two subspecies was detected at two sites in Exon 1 and Exon 3 of the sd1 locus. It is demonstrated that the inter-subspecific differentiation of SD1 contributes height difference between indica and japonica. The indica-originating and japonica-originating alleles at the sd1 locus were designated as SD1-in(t) and SD1-ja(t), respectively.