Adam Puteh

Blast resistance in rice: a review of conventional breeding to molecular approaches

Blast disease caused by the fungal pathogen Magnaporthe oryzae is the most severe diseases of rice. Using classical plant breeding techniques, breeders have developed a number of blast resistant cultivars adapted to different rice growing regions worldwide. However, the rice industry remains threatened by blast disease due to the instability of blast fungus. Recent advances in rice genomics provide additional tools for plant breeders to improve rice production systems that would be environmentally friendly. This article outlines the application of conventional breeding, tissue culture and DNA-based markers that are used for accelerating the development of blast resistant rice cultivars. The best way for controlling the disease is to incorporate both qualitative and quantitative genes in resistant variety. Through conventional and molecular breeding many blast-resistant varieties have been developed. Conventional breeding for disease resistance is tedious, time consuming and mostly dependent on environment as compare to molecular breeding particularly marker assisted selection, which is easier, highly efficient and precise. For effective management of blast disease, breeding work should be focused on utilizing the broad spectrum of resistance genes and pyramiding genes and quantitative trait loci. Marker assisted selection provides potential solution to some of the problems that conventional breeding cannot resolve. In recent years, blast resistant genes have introgressed into Luhui 17, G46B, Zhenshan 97B, Jin 23B, CO39, IR50, Pusa1602 and Pusa1603 lines through marker assisted selection. Introduction of exotic genes for resistance induced the occurrence of new races of blast fungus, therefore breeding work should be concentrated in local resistance genes. This review focuses on the conventional breeding to the latest molecular progress in blast disease resistance in rice. This update information will be helpful guidance for rice breeders to develop durable blast resistant rice variety through marker assisted selection.

A Review of Microsatellite Markers and Their Applications in Rice Breeding Programs to Improve Blast Disease Resistance

Over the last few decades, the use of molecular markers has played an increasing role in rice breeding and genetics. Of the different types of molecular markers, microsatellites have been utilized most extensively, because they can be readily amplified by PCR and the large amount of allelic variation at each locus. Microsatellites are also known as simple sequence repeats (SSR), and they are typically composed of 1–6 nucleotide repeats. These markers are abundant, distributed throughout the genome and are highly polymorphic compared with other genetic markers, as well as being species-specific and co-dominant. For these reasons, they have become increasingly important genetic markers in rice breeding programs. The evolution of new biotypes of pests and diseases as well as the pressures of climate change pose serious challenges to rice breeders, who would like to increase rice production by introducing resistance to multiple biotic and abiotic stresses. Recent advances in rice genomics have now made it possible to identify and map a number of genes through linkage to existing DNA markers. Among the more noteworthy examples of genes that have been tightly linked to molecular markers in rice are those that confer resistance or tolerance to blast. Therefore, in combination with conventional breeding approaches, marker-assisted selection (MAS) can be used to monitor the presence or lack of these genes in breeding populations. For example, marker-assisted backcross breeding has been used to integrate important genes with significant biological effects into a number of commonly grown rice varieties. The use of cost-effective, finely mapped microsatellite markers and MAS strategies should provide opportunities for breeders to develop high-yield, blast resistance rice cultivars. The aim of this review is to summarize the current knowledge concerning the linkage of microsatellite markers to rice blast resistance genes, as well as to explore the use of MAS in rice breeding programs aimed at improving blast resistance in this species. We also discuss the various advantages, disadvantages and uses of microsatellite markers relative to other molecular marker types.

Seeding method and rate influence on weed suppression in aerobic rice

-2 (SR400); and two weed control levels were established as weedy (W) and weed free (F) in a factorial RCBD with four replications. Twenty (20) weed species comprising eleven broadleaved, five grasses and four sedges were identified. Broadleaved weeds contributed more than 50% of the total dry matter. Weed density and dry weight decreased gradually with increased seeding rate, but were independent of methods. REW produced significantly higher grain yield compared with CBS. Among the seeding rates, SR300 produced the highest grain yield followed by SR200 and SR400. Weed free treatment performed better with a yield advantage of 23% over weedy treatment. Weed inflicted relative yield loss did not vary due to seeding methods or rates. Therefore, increasing seeding rate up to 300 seeds m -2 may be

Genetic Diversity and Differentiation of Colletotrichum spp. Isolates Associated with Leguminosae Using Multigene Loci, RAPD and ISSR

Genetic diversity and differentiation of 50 Colletotrichum spp. isolates from legume crops studied through multigene loci, RAPD and ISSR analysis. DNA sequence comparisons by six genes (ITS, ACT, Tub2, CHS-1, GAPDH, and HIS3) verified species identity of C. truncatum, C. dematium and C. gloeosporiodes and identity C. capsici as a synonym of C. truncatum. Based on the matrix distance analysis of multigene sequences, the Colletotrichum species showed diverse degrees of intera and interspecific divergence (0.0 to 1.4%) and (15.5–19.9), respectively. A multilocus molecular phylogenetic analysis clustered Colletotrichum spp. isolates into 3 well-defined clades, representing three distinct species; C. truncatum, C. dematium and C. gloeosporioides. The ISSR and RAPD and cluster analysis exhibited a high degree of variability among different isolates and permitted the grouping of isolates of Colletotrichum spp. into three distinct clusters. Distinct populations of Colletotrichum spp. isolates were genetically in accordance with host specificity and inconsistent with geographical origins. The large population of C. truncatum showed greater amounts of genetic diversity than smaller populations of C. dematium and C. gloeosporioides species. Results of ISSR and RAPD markers were congruent, but the effective maker ratio and the number of private alleles were greater in ISSR markers.

Critical Period of Weed Control in Aerobic Rice

Critical period of weed control is the foundation of integrated weed management and, hence, can be considered the first step to design weed control strategy. To determine critical period of weed control of aerobic rice, field trials were conducted during 2010/2011 at Universiti Putra Malaysia. A quantitative series of treatments comprising two components, (a) increasing duration of weed interference and (b) increasing length of weed-free period, were imposed. Critical period was determined through Logistic and Gompertz equations. Critical period varied between seasons; in main season, it started earlier and lasted longer, as compared to off-season. The onset of the critical period was found relatively stable between seasons, while the end was more variable. Critical period was determined as 7–49 days after seeding in off-season and 7–53 days in main season to achieve 95% of weed-free yield, and 23–40 days in off-season and 21–43 days in main season to achieve 90% of weed-free yield. Since 5% yield loss level is not practical from economic view point, a 10% yield loss may be considered excellent from economic view point. Therefore, aerobic rice should be kept weed-free during 21–43 days for better yield and higher economic return.

Integration of agronomic practices with herbicides for sustainable weed management in aerobic rice

Till now, herbicide seems to be a cost effective tool from an agronomic view point to control weeds. But long term efficacy and sustainability issues are the driving forces behind the reconsideration of herbicide dependent weed management strategy in rice. This demands reappearance of physical and cultural management options combined with judicious herbicide application in a more comprehensive and integrated way. Keeping those in mind, some agronomic tools along with different manual weeding and herbicides combinations were evaluated for their weed control efficacy in rice under aerobic soil conditions. Combination of competitive variety, higher seeding rate, and seed priming resulted in more competitive cropping system in favor of rice, which was reflected in lower weed pressure, higher weed control efficiency, and better yield. Most of the herbicides exhibited excellent weed control efficiency. Treatments comprising only herbicides required less cost involvement but produced higher net benefit. On the contrary, treatments comprising both herbicide and manual weeding required high cost involvement and thus produced lower net benefit. Therefore, adoption of competitive rice variety, higher seed rate, and seed priming along with spraying different early-postemergence herbicides in rotation at 10 days after seeding (DAS) followed by a manual weeding at 30 DAS may be recommended from sustainability view point.

Alleviation of Water Stress Effects on MR220 Rice by Application of Periodical Water Stress and Potassium Fertilization

The use of periodical water stress and potassium fertilization may enhance rice tolerance to drought stress and improve the crop’s instantaneous water use efficiency without much yield reduction. This study was conducted to assess the effects of different periodical water stress combined with potassium fertilization regimes on growth, yield, leaf gas exchanges and biochemical changes in rice grown in pots and compare them with standard local rice grower practices. Five treatments including (1) standard local grower’s practice (control, 80CF = 80 kg K2O/ha + control flooding); (2) 120PW15 = 120 kg K2O/ha + periodical water stress for 15 days; (3) 120DS15V = 120 kg K2O/ha + drought stress for 15 days during the vegetative stage; (4) 120DS25V = 120 kg K2O/ha + drought stress for 25 days and (5) 120DS15R = 120 kg K2O/ha + drought stress for 15 days during the reproductive stage, were evaluated in this experiment. Control and 120PW15 treatments were stopped at 100 DAS, and continuously saturated conditions were applied until harvest. It was found that rice under 120PW15 treatment showed tolerance to drought stress evidenced by increased water use efficiency, peroxidase (POX), catalase (CAT) and proline levels, maximum efficiency of photosystem II (fv/fm) and lower minimal fluorescence (fo), compared to other treatments. Path coefficient analysis revealed that most of parameters contribute directly rather than indirectly to rice yield. In this experiment, there were four factors that are directly involved with rice yield: grain soluble sugar, photosynthesis, water use efficiency and total chlorophyll content. The residual factors affecting rice yield are observed to be quite low in the experiment (0.350), confirming that rice yield was mostly influenced by the parameters measured during the study.

Efficacy, phytotoxicity and economics of different herbicides in aerobic rice

Abstract Aerobic rice is a potential water-wise rice production system, but high weed infestation has threatened its sustainability, which demands an efficient and cost-effective weed management technique. Eight commercial herbicide products were applied singly or as tank-mix or in sequence to evaluate their efficacy, rice selectivity and cost-effectiveness in aerobic rice. The study was conducted under field conditions in Malaysia during 2010/2011 following a randomized complete block design. Most of the herbicide treatments provided excellent weed control, and produced much higher net benefit than weedy or weed-free check. None of the herbicides caused significant phytotoxicity to rice plants. Among the herbicide treatments, sequential application of Cyhalofop-butyl+Bensulfuron at early growth stage followed by Bentazon/MCPA at mid growth stage provided the highest weed control efficiency, productivity and net benefit. Application of Bispyribac-sodium at early growth stage followed by Bentazon/MCPA at mid growth stage performed very close to the above-mentioned treatments. Sequential application of Pretilachlor/safener just after seeding followed by Propanil/Thiobencarb at early growth stage also provided satisfactory results in terms of efficacy and economic return. Since manual weeding was not economic, herbicide rotation using the above chemicals may be recommended for effective weed management in aerobic rice.

Influence of municipal wastewater on rice seed germination, seedling performance, nutrient uptake, and chlorophyll content

The sand medium experiment was conducted in the laboratory with the aim of evaluating the suitability of municipal wastewater (treated and untreated) at different concentrations (0, 2.5, 5, 10, 25, 50, and 100%) for irrigation purposes on seed germination, seedling performance, nutrient uptake, and chlorophyll content of rice (MR220). The utilization of municipal wastewater for irrigation purposes has developed an important way to exploit the nutrients it contains. The study indicated a significant (P < 0.05) difference between untreated and treated municipal wastewater for seedling length (SL), root volume (RV), root surface area (RSA), seedling vigor index (SVI), and root: shoot ratio (R : S) while no significant different was observed between untreated and treated municipal wastewater for germination percentage (GP) and percentage phytotoxicity (PPT). The municipal wastewaters had stimulatory effect on the rice seeds at lower wastewater concentrations (< 25%) while inhibitory effect was observed at higher wastewater concentrations (> 50%). N, P, K, Ca, Mg, Zn, Fe, Cu, and Mn were high in the untreated municipal wastewater compare to treated municipal wastewater. Seedlings irrigated with untreated municipal wastewater have high seed germination, seedling performance with high nutrient uptake compare to treated municipal wastewater. The municipal wastewaters showed inhibitory effect on chlorophyll content. The inhibition effect was observed at > 50% concentration of both untreated and treated municipal wastewater while promoting effects were observed at lower (< 25%) concentration. The rice MR220 variety showed better growth resistance, tolerance, and adaptability to wastewater. This can be due to its excellent genetic makeup and capacity to sustain the toxicity. Conclusively, municipal wastewater could be recommended as a good source of water and nutrient for seed germination and seedling performance.

Recurrent parent genome recovery analysis in a marker-assisted backcrossing program of rice (Oryza sativa L.).

Backcross breeding is the most commonly used method for incorporating a blast resistance gene into a rice cultivar. Linkage between the resistance gene and undesirable units can persist for many generations of backcrossing. Marker-assisted backcrossing (MABC) along with marker-assisted selection (MAS) contributes immensely to overcome the main limitation of the conventional breeding and accelerates recurrent parent genome (RPG) recovery. The MABC approach was employed to incorporate (a) blast resistance gene(s) from the donor parent Pongsu Seribu 1, the blast-resistant local variety in Malaysia, into the genetic background of MR219, a popular high-yielding rice variety that is blast susceptible, to develop a blast-resistant MR219 improved variety. In this perspective, the recurrent parent genome recovery was analyzed in early generations of backcrossing using simple sequence repeat (SSR) markers. Out of 375 SSR markers, 70 markers were found polymorphic between the parents, and these markers were used to evaluate the plants in subsequent generations. Background analysis revealed that the extent of RPG recovery ranged from 75.40% to 91.3% and from 80.40% to 96.70% in BC1F1 and BC2F1 generations, respectively. In this study, the recurrent parent genome content in the selected BC2F2 lines ranged from 92.7% to 97.7%. The average proportion of the recurrent parent in the selected improved line was 95.98%. MAS allowed identification of the plants that are more similar to the recurrent parent for the loci evaluated in backcross generations. The application of MAS with the MABC breeding program accelerated the recovery of the RP genome, reducing the number of generations and the time for incorporating resistance against rice blast.