Oryza Sativa L

Direct and indirect economic loss in the agricultural sector due to drought is huge. With the advent of molecular-marker technology, research on drought resistance in crop plants has shifted from physiological descriptions of the phenomenon to genetic dissection of the mechanisms involved. Here, we report a comprehensive study of mapping the drought resistance components (osmotic adjustment and root traits) in a doubled-haploid rice (Oryza sativa L.) population of 154 lines. A genetic linkage map consisting of 315 DNA markers was constructed. A total of 41 quantitative trait loci (QTLs) were identified for osmotic adjustment and root traits, and individually explained 8–38% of the phenotypic variance. A region on chromosome 4 harbored major QTLs for several root traits. Consistent QTLs for drought responses across genetic backgrounds were detected and should be useful for marker-assisted selection towards the incorporation of a trait of interest into an elite line. Comparative mapping identified three conserved genomic regions associated with various physiological responses to drought in several grass species. These results suggest that these regions conferring drought adaptation have been conserved across grass species during genome evolution and might be directly applied across species for the improvement of drought resistance in cereal crops.

ABSTRACT Rice (Oryza sativa L) is an important cereal for one-third of the world’s population. Its productivity is continually threatened by a series of biotic and abiotic stresses. There is thus an urgent need to broaden the gene pool of rice for developing varieties with high yield and resistance to several stresses. Wild species of Oryza are a reservoir of genes for tolerance to various biotic and abiotic stresses and also possess yield-enhancing loci. Morphological, cytological, and molecular divergence studies have been used to identify ten genome types in 22 Oryza species. Interspecific hybrids and alien introgression lines have been produced. Genes for resistance to grassy stunt virus, tungro virus, brown planthopper, bacterial blight, blast, tolerance to soil toxicity, and cytoplasmic male sterility have been transferred from wild species and varieties released. Many of the genes/QTL introgressed from wild species have been tagged with DNA markers. Xa21, a gene for bacterial blight resistance has been pyramided along with other genes through MAS and 12 varieties/hybrids released. Molecular analysis has shown limited introgression of short segments from distant genomes. Parental genomes and alien chromosomes segments have been characterized using genomic in situ hybridization. BAC libraries from different wild species have been established. BAC end sequence, physical framework of different genomes of Oryza, and alignment with the rice reference genome have provided valuable information on evolutionary mechanisms and on genome organization, structural rearrangements, repeats, transposable elements, SSR, miRNA, and single nucleotide variation. Long terminal repeated (LTR)-retrotransposons are considered as the predominant class of repeat elements that increase the genome size in some species. Introgression of genes with broad spectrum of resistance to stresses, yield-enhancing loci/QTLs, and identification of genes controlling homoeologous pairing to introgress wild species genes from distant genomes need to be explored. BAC libraries and CSSL of wild relatives are important genetic resource for functional genomics and for mapping and cloning of agronomically important genes/QTLs harbored in wild species of Oryza. With the advances in tissue culture techniques, molecular markers, and genomics, the scope for utilization of wild species in genetic enhancement of rice seems more promising than before.

In Latin America early weed competition is a constraint upon upland rice production, leading to intensive herbicide use. Breeding for rice competitiveness may help reduce the need for herbicides. Two consecutive screenhouse pot experiments were conducted with 13 upland cultivars grown alone or in mixtures with Brachana brizantha to identify plant characteristics for early rice competitiveness which could serve as selection criteria. Rice growth reduction from B. brizantha competition was evident in all cultivars by 30 d.a.e., and the traits most related to cultivar competitiveness were: total above‐ground plant biomass > leaf weight > stem weight > leaf area. Plant height and tillering were least affected by competition. Rice and B. brizantha partially avoided competition since the competing canopies did not fully intercept the incoming light. Traits measured in monoculture did not correlate well with the competition‐induced growth reductions. In breeding for competitiveness, selection according to the above traits should be conducted on rice growing in competition, rather than in monoculture. A measure of plant biomass or leaf area at 30 d.a.e. appears to provide the most convenient estimates of early interference.

In Latin America early weed competition is a constraint upon upland rice production, leading to intensive herbicide use. Breeding for rice competitiveness may help reduce the need for herbicides. Two consecutive screenhouse pot experiments were conducted with 13 upland cultivars grown alone or in mixtures with Brachana brizantha to identify plant characteristics for early rice competitiveness which could serve as selection criteria. Rice growth reduction from B. brizantha competition was evident in all cultivars by 30 d.a.e., and the traits most related to cultivar competitiveness were: total above‐ground plant biomass > leaf weight > stem weight > leaf area. Plant height and tillering were least affected by competition. Rice and B. brizantha partially avoided competition since the competing canopies did not fully intercept the incoming light. Traits measured in monoculture did not correlate well with the competition‐induced growth reductions. In breeding for competitiveness, selection according to the above traits should be conducted on rice growing in competition, rather than in monoculture. A measure of plant biomass or leaf area at 30 d.a.e. appears to provide the most convenient estimates of early interference.

Water-deficit stress is detrimental for rice growth, development, and yield. Transcriptome analysis of 1-week-old rice (Oryza sativa L. var. IR64) seedling under water-deficit stress condition using Affymetrix 57 K GeneChip® has revealed 1,563 and 1,746 genes to be up- and downregulated, respectively. In an effort to amalgamate data across laboratories, we identified 5,611 differentially expressing genes under varying extrinsic water-deficit stress conditions in six vegetative and one reproductive stage of development in rice. Transcription factors (TFs) involved in ABA-dependent and ABA-independent pathways have been found to be upregulated during water-deficit stress. Members of zinc-finger TFs namely, C2H2, C2C2, C3H, LIM, PHD, WRKY, ZF-HD, and ZIM, along with TF families like GeBP, jumonji, MBF1 and ULT express differentially under water-deficit conditions. NAC (NAM, ATAF and CUC) TF family emerges to be a potential key regulator of multiple abiotic stresses. Among the 12 TF genes that are co-upregulated under water-deficit, salt and cold stress conditions, five belong to the NAC TF family. We identified water-deficit stress-responsive genes encoding key enzymes involved in biosynthesis of osmoprotectants like polyols and sugars; amino acid and quaternary ammonium compounds; cell wall loosening and structural components; cholesterol and very long chain fatty acid; cytokinin and secondary metabolites. Comparison of genes responsive to water-deficit stress conditions with genes preferentially expressed during panicle and seed development revealed a significant overlap of transcriptome alteration and pathways.

The genetic relationship among three cytoplasmic male sterility (CMS) systems, consisting of WA, Dissi, and Gambiaca, was studied. The results showed that the maintainers of one CMS system can also maintain sterility in other cytoplasmic backgrounds. The F1 plants derived from crosses involving A and R lines of the respective cytoplasm and their cross-combination with other CMS systems showed similar pollen and spikelet fertility values, indicating that similar biological processes govern fertility restoration in these three CMS systems. The results from an inheritance study showed that the pollen fertility restoration in all three CMS systems was governed by two independent and dominant genes with classical duplicate gene action. Three F2 populations, generated from the crosses between the parents of good-performing rice hybrids, that possess WA, Dissi, and Gambiaca CMS cytoplasm, were used to map the Rf genes. For the WA-CMS system, Rf3 was located at a distance of 2.8 cM from RM490 on chromosome 1 and Rf4 was located at 1.6 cM from RM1108 on chromosome 10. For the Dissi-CMS system, Rf3 was located on chromosome 1 at 1.9 cM from RM7466 and Rf4 on chromosome 10 was located at 2.3 cM from RM6100. The effect of Rf3 on pollen fertility appeared to be stronger than the effect of Rf4. In the Gambiaca-CMS system, only one major locus was mapped on chromosome 1 at 2.1 cM from RM576. These studies have led to the development of marker-assisted selection (MAS) for selecting putative restorer lines, new approaches to alloplasmic line breeding, and the transfer of Rf genes into adapted cultivars through a backcrossing program in an active hybrid rice breeding program.

Crop husbandry practices such as plant density and irrigation regimes significantly affect the rice (Oryza sativa L.) crop at initial growth and development and ultimately grain yield. The objective of this study was to characterize the effects of increasing plant density and irrigation ...

Jasmonic acid (JA) has been shown to be a signaling compound which elicits the production of secondary metabolites including phytoalexins in plants. It has been shown that the phytoalexin production is elicited by exogenously applied JA in rice leaves. We now show that this phytoalexin production by exogenously applied JA is significantly counteracted by cytokinins, kinetin and zeatin. Kinetin and zeatin also inhibit the induction of naringenin-7-O-methyltransferase (a key enzyme in rice phytoalexin production) by JA. A natural free radical scavenger, ascorbic acid (AsA) shows both counteractive and enhancing effects on JA-inducible phytoalexin production, depending on its concentration. This effect of AsA suggests that active oxygen species (AOS) may play important roles in phytoalexin production by JA in rice leaves.

Evaluation of different fungicides against rice blast disease was carried out during kharif 2007, at Rice Research Institute, Kala Shah Kaku. A highly susceptible rice variety Basmati C-622 was planted in Randomized Complete Block Design and the application of various fungicides viz Rabicide 30WP, Nativo SC, Thiovit 80 WP, Cuproxit 345 SC, Score 250 EC, Filia 525 SC, Armure, Tilt 250 EC, and WSH004 were made with dose rates of 3 g/liter H2O, 0.8 gm/liter H2O, 10 gm/liter of H2O, 3 ml/liter of H2O, 1.25 ml/liter of H2O, 3 ml/liter H2O, 1.2 ml/liter H2O, 0.8 ml/liter of H2O and 10 ml/liter of H2O. All the fungicides proved to be affective in the management of rice blast disease but Rabicide, Nativo and Score proved effective in all the three weeks in reducing the disease percentage more in 3 rd week with 11.46%, 12.15% and 12.85%.. The control of disease in case of neck blast was shown by Rabcide, Score and Nativo with 12.81%, 14.24% and 17.01% disease respectively. WHS004 was proved ...

Aluminum toxicity is the main factor limiting the productivity of crop plants in acid soils, particularly in the tropics and subtropics. In this study, a doubled-haploid population derived from the rice (Oryza sativa L.) breeding lines CT9993 and IR62266 was used to map genes controlling Al tolerance. A genetic linkage map consisting of 280 DNA markers (RFLP, AFLP and SSR) was constructed to determine the position and nature of quantitative trait loci (QTLs) affecting Al tolerance. Three characters – control root length (CRL), Al-stressed root length (SRL) and root length ratio (RR) – were evaluated for the DH lines and the parents at the seedling stage in nutrient solution. A total of 20 QTLs controlling root growth under Al stress and control conditions were detected and distributed over 10 of the 12 rice chromosomes, reflecting multigenic control of these traits. The two QTLs of largest effect, qALRR-1-1 and qALRR-8 for root length ratio (a measurement of Al tolerance) were localized on chromosomes 1 and 8, respectively. Three other QTLs in addition to qALRR-8 were apparently unique in the CT9993 × IR62266 mapping population, which may explain the high level of Al tolerance in CT9993. Comparative mapping identified a conserved genomic region on chromosome 1 associated with Al tolerance across three rice genetic backgrounds. This region provides an important starting point for isolating genes responsible for different mechanisms of aluminum tolerance and understanding the genetic nature of this trait in rice and other cereals.

In the valley land of North-East Hill (NEH) ecosystems of India, about 70% area under rice (Oryza sativa L.) is transplanted. Physiological attributes and yield performance of aerobic rice over conventional flood-irrigated rice need to be assessed while promoting water saving technology. A field experiment was conducted at the experimental farm, ICAR Research Complex for NEH Region, Umiam (950 m msl), Meghalaya during rainy seasons of 2006 and 2007 under aerobic and flooded conditions with aerobic rice variety collected from IRRI, Philippines. Some important high-yielding varieties (HYVs) recommended for the region were also included in the study. The objectives of this study were (i) to evaluate the influence of frequent mid-season drainage as a measure of water saving technique besides inducing the pre-conditioning effect on genotypes to withstand water stress during the subsequent growth period of crop ontogeny, (ii) to compare crop performance between aerobic and flooded rice management practices, and (iii) to identify attributes responsible for the yield gap between aerobic and flooded rice. The results revealed that the yield difference between aerobic (average yield, 1.67 t/ha) and flooded rice (average yield, 2.31 t/ha) ranged from 18.4 to 37.8% (P < 0.05) depending on varieties, highest difference being observed with rice hybrid DRRH 1. Cultivation of rice under aerobic condition resulted in 27.5% yield reduction over flooded rice. Among the yield components assessed, sink size (spikelets per panicle) contributed more to the yield and is considered to be most important factor responsible for yield gap between aerobic and flooded rice. The study suggests that, variety Sahsarang 1 with its moderate values of photosynthesis rate, transpiration rate and water use efficiency (WUE) along with higher grain yield seems to be better choice for both stress (aerobic) as well as normal (flooded) condition. Aerobic rice varieties with minimum yield gap compared to flooded rice is the key for success of aerobic rice cultivation.