Annotation of Secretariat and Hydrus, two DJ cluster phages isolated on Gordonia rubripertincta.

Secretariat and Hydrus are phages grouped into the DJ cluster that were isolated on Gordonia rubripertincta NRRL B-16540. The phages have 75% nucleotide identity and share 73% gene content. Secretariat has a genome with 84 predicted genes, while Hydrus has 91 predicted genes and can also infect Gordonia terrae 3612.

Isolation and Annotation of Azira, a CT Cluster Phage That Infects Gordonia rubripertincta.

Azira is a CT cluster actinobacteriophage that infects Gordonia rubripertincta NRRL B-16540. The genome contains 67 predicted protein coding genes, of which 31 have a putative function. Azira has a lysis cassette encoding two endolysins and three transmembrane proteins. Azira contains four genes predicted to encode enzymes involved in thymine synthesis.

Development of genetic markers linked to straighthead resistance through fine mapping in rice (Oryza sativa L.).

Straighthead, a physiological disorder characterized by sterile florets and distorted spikelets, causes significant yield losses in rice, and occurs in many countries. The current control method of draining paddies early in the season stresses plants, is costly, and wastes water. Development of resistant cultivar is regarded as the most efficient way for its control. We mapped a QTL for straighthead resistance using two recombinant inbred line (RIL) F(9) populations that were phenotyped over two years using monosodium methanearsonate (MSMA) to induce the symptoms. One population of 170 RILs was genotyped with 136 SSRs and the other population of 91 RILs was genotyped with 159 SSRs. A major QTL qSH-8 was identified in an overlapping region in both populations, and explained 46% of total variation in one and 67% in another population for straighthead resistance. qSH-8 was fine mapped from 1.0 Mbp to 340 kb using 7 SSR markers and further mapped to 290 kb in a population between RM22573 and InDel 27 using 4 InDel markers. SSR AP3858-1 and InDel 11 were within the fine mapped region, and co-segregated with straighthead resistance in both RIL populations, as well as in a collection of diverse global accessions. These results demonstrate that AP3858-1 and InDel 11 can be used for marker-assisted selection (MAS) for straighthead resistant cultivars, which is especially important because there is no effective way to directly evaluate straighthead resistance.

Divergence between sympatric rice- and maize-infecting populations of Rhizoctonia solani AG-1 IA from Latin America.

ABSTRACT The basidiomycetous fungus Rhizoctonia solani anastomosis group (AG)-1 IA is a major pathogen in Latin America causing sheath blight (SB) of rice. Particularly in Venezuela, the fungus also causes banded leaf and sheath blight (BLSB) on maize, which is considered an emerging disease problem where maize replaced traditional rice-cropping areas or is now planted in adjacent fields. Our goals in this study were to elucidate (i) the effects of host specialization on gene flow between sympatric and allopatric rice and maize-infecting fungal populations and (ii) the reproductive mode of the fungus, looking for evidence of recombination. In total, 375 isolates of R. solani AG1 IA sampled from three sympatric rice and maize fields in Venezuela (Portuguesa State) and two allopatric rice fields from Colombia (Meta State) and Panama (Chiriquí State) were genotyped using 10 microsatellite loci. Allopatric populations from Venezuela, Colombia, and Panama were significantly differentiated (Phi(ST) of 0.16 to 0.34). Partitioning of the genetic diversity indicated differentiation between sympatric populations from different host species, with 17% of the total genetic variation distributed between hosts while only 3 to 6% was distributed geographically among the sympatric Venezuelan fields. We detected symmetrical historical migration between the rice- and the maize-infecting populations from Venezuela. Rice- and maize-derived isolates were able to infect both rice and maize but were more aggressive on their original hosts, consistent with host specialization. Because the maize- and rice-infecting populations are still cross-pathogenic, we postulate that the genetic differentiation was relatively recent and mediated via a host shift. An isolation with migration analysis indicated that the maize-infecting population diverged from the rice-infecting population between 40 and 240 years ago. Our findings also suggest that maize-infecting populations have a mainly recombining reproductive system whereas the rice-infecting populations have a mixed reproductive system in Latin America.

Mapping quantitative trait Loci responsible for resistance to sheath blight in rice.

Rice sheath blight (ShB), caused by the soilborne pathogen Rhizoctonia solani, annually causes severe losses in yield and quality in many rice production areas worldwide. Jasmine 85 is an indica cultivar that has proven to have a high level of resistance to this pathogen. The objective of this study was to determine the ability of controlled environment inoculation assays to detect ShB resistance quantitative trait loci (QTLs) in a cross derived from the susceptible cv. Lemont and the resistant cv. Jasmine 85. The disease reactions of 250 F(5) recombinant inbred lines (RILs) were measured on the seedlings inoculated using microchamber and mist-chamber assays under greenhouse conditions. In total, 10 ShB-QTLs were identified on chromosomes 1, 2, 3, 5, 6, and 9 using these two methods. The microchamber method identified four of five new ShB-QTLs, one on each of chromosomes 1, 3, 5, and 6. Both microchamber and mist-chamber methods identified two ShB-QTLs, qShB1 and qShB9-2. Four of the ShB-QTLs or ShB-QTL regions identified on chromosomes 2, 3, and 9 were previously reported in the literature. The major ShB-QTL qShB9-2, which cosegregated with simple sequence repeat (SSR) marker RM245 on chromosome 9, contributed to 24.3 and 27.2% of total phenotypic variation in ShB using microchamber and mistchamber assays, respectively. qShB9-2, a plant-stage-independent QTL, was also verified in nine haplotypes of 10 resistant Lemont/Jasmine 85 RILs using haplotype analysis. These results suggest that multiple ShB-QTLs are involved in ShB resistance and that microchamber and mist-chamber methods are effective for detecting plant-stage-independent QTLs. Furthermore, two SSR markers, RM215 and RM245, are robust markers and can be used in marker-assisted breeding programs to improve ShB resistance.

Rapid Determination of Rice Cultivar Responses to the Sheath Blight Pathogen Rhizoctonia solani Using a Micro-Chamber Screening Method.

An accurate greenhouse screening method has not been developed previously to identify host response to sheath blight disease caused by Rhizoctonia solani Kühn that causes significant economic losses in rice yield worldwide. The unavailability of a robust screening system in the greenhouse has made it difficult to quantify disease reactions to R. solani, and has hampered studies on the genetics of resistance and plant breeding efforts to improve resistance. In an effort to develop a standardized laboratory micro-chamber screening method to quantify resistance to R. solani in rice, five rice cultivars, representing a wide range of observed disease reactions under field conditions, were examined in a blind inoculation test at three locations (Arkansas, Texas, and Colombia). Rice seedlings were inoculated at the three- to four-leaf stage with potato dextrose agar plugs containing mycelium and then covered with a 2- or 3-liter transparent plastic bottle for maintaining high humidity after inoculation. Two cultivars, Jasmine 85 and Lemont, that consistently have shown the highest and lowest levels of resistance, respectively, in previous field and greenhouse studies, were used as standards. Concurrent field experiments in Arkansas and Texas also were performed to compare the greenhouse disease ratings with those observed under field conditions. Overall, the relative disease ratings of the seven test cultivars were consistent between test locations and with field evaluations. Thus, the micro-chamber screening method can be used as an effective approach to accurately quantify resistance to the sheath blight pathogen under controlled greenhouse conditions and should help expedite the selection process to improve resistance to this important pathogen.

Effects of Silicon and Fungicides on the Control of Leaf and Neck Blast in Upland Rice.

Silicon (Si) has been shown to suppress diseases of rice such as blast when applied to Si-deficient soils. In 1995 and 1996, Si was applied at 1,000 kg ha-1 to at two locations in eastern Colombia to determine if Si combined with reduced rates of fungicide could be used to manage leaf and neck blast effectively in upland rice. Two applications of edifenphos and three applications of tricyclazole were made at 0, 10, 25, or 100% of their labeled rates after amendment of soil with Si. At both locations, Si alone and Si combined with edifenphos reduced leaf blast severity by 22 to 75% when compared with nonamended, untreated controls, and suppression of leaf blast by Si alone was equal to or better than the full rate of edifenphos alone. Si alone suppressed neck blast as effectively or better than the full rate tricyclazole when severity was low; however, when severity was higher, a 10% rate of tricyclazole was needed in addition to Si. No differences in yield were observed between Si without fungicides and fungicides (full rate) without Si. Applications of Si made in 1995 had significant residual activity in terms of disease control and yield in 1996. The application of Si to Si-deficient soils may permit the use of reduced rates of fungicide to manage leaf and neck blast in upland rice.

The influence of silicon on components of resistance to blast in susceptible, partially resistant, and resistant cultivars of rice.

ABSTRACT The application of silicon (Si) fertilizers reduces the severity of blast, caused by Magnaporthe grisea, in irrigated and upland rice; however, little research has been conducted to examine the epidemiological and etiological components of this reduction. Four cultivars of rice with differential susceptibilities to race IB-49 of M. grisea were fertilized with three rates of a calcium silicate fertilizer and inoculated with the pathogen to test the effects of Si on the following components of resistance to blast: incubation period, latent period, infection efficiency, lesion size, rate of lesion expansion, sporulation per lesion, and diseased leaf area. For each cultivar, the incubation period was lengthened by increased rates of Si, and the numbers of sporulating lesions, lesion size, rate of lesion expansion, diseased leaf area, and number of spores per lesion were reduced. Lesion size and sporulation per lesion were lowered by 30 to 45%, and the number of sporulating lesions per leaf and diseased leaf area were significantly reduced at the highest rate of Si. The net effect of Si on these components of resistance is an overall reduction in the production of conidia on plants infected with M. grisea, thereby slowing the epidemic rate of blast.

Effect of Silicon Rate and Host Resistance on Blast, Scald, and Yield of Upland Rice.

Blast-resistant, partially resistant, and susceptible cultivars of rice were planted in soil amended with Si at 0, 500, or 1,000 kg/ha at two locations in eastern Colombia to assess differential responses to leaf blast, neck blast, and leaf scald, and to examine the quantity and quality of grains harvested. Leaf and neck blast on partially resistant and susceptible cultivars were reduced by Si as the rate of Si was increased. Depending on the location, the level of severity of leaf and neck blast on partially resistant cultivars, when fertilized with Si at 500 or 1,000 kg/ha, was lowered to that of resistant cultivars without Si. At both locations, yields were increased by as much as 42%, depending on the cultivar, by Si applied at 1,000 kg/ha. In general, high rates of Si reduced the number of broken grains harvested. Grain discoloration, regardless of cultivar or location, was reduced by as much as 70% at the high rate of Si. The application of Si to complement host resistance to blast and scald appears to be an effective strategy for disease management in rice and provides the added benefit of improving the quantity and quality of rice yields.