The Evolutionary Basis of Naturally Diverse Rice Leaves Anatomy

Rice contains genetically and ecologically diverse wild and cultivated species that show a wide variation in plant and leaf architecture. A systematic characterization of leaf anatomy is essential in understanding the dynamics behind such diversity. Therefore, leaf anatomies of 24 Oryza species spanning 11 genetically diverse rice genomes were studied in both lateral and longitudinal directions and possible evolutionary trends were examined. A significant inter-species variation in mesophyll cells, bundle sheath cells, and vein structure was observed, suggesting precise genetic control over these major rice leaf anatomical traits. Cellular dimensions, measured along three growth axes, were further combined proportionately to construct three-dimensional (3D) leaf anatomy models to compare the relative size and orientation of the major cell types present in a fully expanded leaf. A reconstruction of the ancestral leaf state revealed that the following are the major characteristics of recently evolved rice species: fewer veins, larger and laterally elongated mesophyll cells, with an increase in total mesophyll area and in bundle sheath cell number. A huge diversity in leaf anatomy within wild and domesticated rice species has been portrayed in this study, on an evolutionary context, predicting a two-pronged evolutionary pathway leading to the ‘sativa leaf type’ that we see today in domesticated species

Genetic analysis of resistance to green leafhopper, Nephotettix virescens (Distant), in IR rice varieties

The genetics of resistance to green leafhopper (GLH), Nephotettix virescens (Distant), in 22 IRRI-bred rice varieties was studied. These varieties were crossed with a susceptible (S) variety, Taichung Native-1 (TN1), and reaction to green leafhopper of F1 hybrids, F2 populations, and F3 lines was studied. Results revealed that single recessive (R) genes govern resistance in IR32, IR38, IR40, IR44, and IR46, while single dominant genes convey resistance in the remaining varieties. Allele tests with known genes for resistance revealed that dominant genes in IR5, IR20, IR30, and IR45 are allelic to Glh3. On the other hand, IR34, IR50, IR52, IR54, IR56, IR58, IR60, and IR65 have Glh9. The dominant genes in IR24, IR26, IR29, IR43, and IR48 and the recessive genes in IR32, IR38, IR40, IR44, and IR46 segregate independently from Glh1, Glh2, and Glh3. The allelic relationships of these genes with other known genes for resistance to GLH are not known

Breeding rice for resistance to tungro virus at IRRI

Tungro, one of the most serious diseases of rice, is transmitted by the green leafhopper (Nephotettix virescens) (GLH). The rice tungro spherical virus (RTSV) and rice tungro bacilliform virus (RTBV) cause this disease. Several sources of resistance to RTSV have been identified. However, resistance to RTBV is lacking, although some cultivars such as Buliman Putih, Utri Merah, ARC 11154, and the wild species O. longistaminata and O. rufipogon, have shown tolerance to RTBV. Mass screening in the screenhouse and field screening in hot spots have been used in screening breeding materials. Enzyme linked immunosorbent assay (ELISA) has further allowed the detection of individual virus strains in infected plants. A number of advanced breeding lines developed through backcrossing with elite recurrent rice parents have been evaluated in India, Indonesia, and the Philippines. Promising lines have been identified and some of the agronomically superior lines resistant to tungro have been released as varieties. IR20, IR26, and IR30 were the first tungro resistant cultivars released by IRRI followed by IR28, IR29, IR34, IR36, IR38, and IR40 during the 1970s. Some GLH resistant cultivars such as IR54, IR56, IR60, and IR62 were released in the 1980s followed by PSBRc4, PSBRc10, PSBRc18, and PSBRc28 during the 1990s. Recently, five tungro resistant lines showing resistance to RTSV were released as cultivars in Indonesia and the Philippines. Utri Merah, Balimau Putih, Habiganj DW8, and O. rufipogon served as donors of resistance

Nuclear genome differentiation in Asian cultivated rice as revealed by RFLP analysis

RFLP analysis was carried out to clarify the nuclear genome differentiation in Asian rice varieties of Oryza sativa. Based on the restriction fragment patterns with two endonucleases, EcoRI and HindIII, using 12 single-copy rice DNA probes, 93 types of nuclear genome were found among 112 local varieties from 17 Asian countries. In a dendrogram showing genetic relationships among nuclear genome types, they were mainly divided into eight groups, A, B1, B2, C1, C2, D1, D2 and E. These results were compared with previous isozyme analysis and RFLP analysis on chloroplast genome using the same varieties. Classification on isozyme analysis matches well with that on nuclear genome, indicating synchronous differentiation of isozyme constitutions and nuclear genomes in Asian varieties. Considering the correspondence between them, nuclear genomes were grouped into Indica (A, B1 and B2), intermediate (C1, C2 and D1) and Japonica (D2 and E) types. From the comparison of chloroplast with nucleus for genome differentiation, two major chloroplast genomes (types 1 and 3) were found in the varieties with several nuclear genome types. However, Japonica group with D2 and E nuclear genomes has only type 1 chloroplast genome, whereas Indica and intermediate groups contain both two major chloroplast genomes. Especially, type 3 chloroplast genome which was not found in Japonica group is dominant type in Indica varieties. The results indicate the differentiation of nuclear genome has partially synchronized with that of chloroplast genome

RDA derived Oryza minuta-specific clones to probe genomic conservation across Oryza and introgression into rice (O. sativa L.)

International audienceMolecular markers have been successfully used in rice breeding however available markers based on Oryza sativa sequences are not efficient to monitor alien introgression from distant genomes of Oryza. We developed O. minuta (2n = 48, BBCC)-specific clones comprising of 105 clones (266-715 bp) from the initial library composed of 1,920 clones against O. sativa by representational difference analysis (RDA), a subtractive cloning method and validated through Southern blot hybridization. Chromosomal location of O. minuta-specific clones was identified by hybridization with the genomic DNA of eight monosomic alien additional lines (MAALs). The 37 clones were located either on chromosomes 6, 7, or 12. Different hybridization patterns between O. minuta-specific clones and wild species such as O. punctata, O. officinalis, O. rhizomatis, O. australiensis, and O. ridleyi were observed indicating conservation of the O. minuta fragments across Oryza spp. A highly repetitive clone, OmSC45 hybridized with O. minuta and O. australiensis (EE), and was found in 6,500 and 9,000 copies, respectively, suggesting an independent and exponential amplification of the fragment in both species during the evolution of Oryza. Hybridization of 105 O. minuta specific clones with BB- and CC-genome wild Oryza species resulted in the identification of 4 BB-genome-specific and 14 CC-genome-specific clones. OmSC45 was identified as a fragment of RIRE1, an LTR-retrotransposon. Furthermore this clone was introgressed from O. minuta into the advanced breeding lines of O. sativa

Genetic erosion over time of rice landrace agrobiodiversity

Changes in global biodiversity at the genetic level have proved difficult to determine for most organisms because of lack of standardized, repeated or historical data; this hampers the attempts to meet the convention on biological diversity (CBD) 2010 targets of reducing loss of genetic diversity, particularly of crop species. For rice, where germplasm and genetic data have been collected throughout South and Southeast Asia over many decades, contrary to popular opinion, we have been unable to detect a significant reduction of available genetic diversity in our study material. This absence of a decline may be viewed positively; over the 33-year timescale of our study, genetic diversity amongst landraces grown in traditional agricultural systems was still sufficiently abundant to be collected for ex situ conservation. However, if significant genetic erosion does take place in the future as a result of accelerating global warming and/or major changes in land use or agricultural practices, will it be catastrophic or gradual, and how will it be detected? We have shown a strong link between numbers of landraces collected (and therefore extant) and genetic diversity; hence, we have a clear indicator to detect loss of genetic diversity in the future. Our findings lend considerable support for ex situ conservation of germplasm; the more than substantial genetic resources already in genebanks are now safe. On the other hand, it is the germplasm growing in farmers' fields, continually adapting genetically to changing environmental conditions and evolving novel genetic forms, whose future has been much less certain but can now be effectively monitored using our criteria