Sheath Blight Resistance In Rice Research Articles

Association Mapping and Resistant Alleles Analysis for Sheath Blight Resistance in Rice

To identify and map sheath blight(ShB) resistance loci in rice, we carried out association analysis of 456 rice accessions using 144 genome-wide markers based on GLM(Q), MLM(Q+K), and MLM(PCA+K) models of TASSEL software. The phenotyping were assayed at the seedling stage with a micro-chamber screening method. The results showed that thirteen markers were significantly associated with ShB resistance detected by using at least two models, which explained from 1.84% to 8.42% of the phenotypic variance. In addition, ten of the identified resistant loci were either quite near or within the interval of previously identified QTLs. RM1036, RM5371, and RM7585 were novel resistant loci that had not been previously reported. The resistant allele 150 of RM7585 showed the largest negative effect to ShB rating, allele 129 of RM5371 existed in 259(56.8%) of 456 rice accessions, and 82 of RM1036 existed in 26(5.7%) rice accessions. The number of putative resistant alleles presented in rice was highly and significantly correlated with the decrease of ShB rating. The resistant alleles identified in this study are readily available and can be exploited for marker-assisted selection.

Mapping and validation of QTLs for rice sheath blight resistance

Sheath blight, caused by Rhizoctonia solani, is one of the most serious diseases of rice. Among 33 rice accessions, mainly from National Institute of Agrobiological Sciences (NIAS) Core Collection, we found three landraces from the Himalayas—Jarjan, Nepal 555 and Nepal 8—with resistance to sheath blight in 3 years’ field testing. Backcrossed inbred lines (BILs) derived from a cross between Jarjan and the leading Japanese cultivar Koshihikari were used in QTL analyses. Since later-heading lines show fewer lesions, we used only earlier-heading BILs to avoid association with heading date. We detected eight QTLs; the Jarjan allele of three of these increased resistance. Only one QTL, on chromosome 9 (between markers Nag08KK18184 and Nag08KK18871), was detected in all 3 years. Chromosome segment substitution lines (CSSLs) carrying it showed resistance in field tests. Thirty F2 lines derived from a cross between Koshihikari and one CSSL supported the QTL.

Allelic analysis of sheath blight resistance with association mapping in rice.

Sheath blight (ShB) caused by the soil-borne pathogen Rhizoctonia solani is one of the most devastating diseases in rice world-wide. Global attention has focused on examining individual mapping populations for quantitative trait loci (QTLs) for ShB resistance, but to date no study has taken advantage of association mapping to examine hundreds of lines for potentially novel QTLs. Our objective was to identify ShB QTLs via association mapping in rice using 217 sub-core entries from the USDA rice core collection, which were phenotyped with a micro-chamber screening method and genotyped with 155 genome-wide markers. Structure analysis divided the mapping panel into five groups, and model comparison revealed that PCA5 with genomic control was the best model for association mapping of ShB. Ten marker loci on seven chromosomes were significantly associated with response to the ShB pathogen. Among multiple alleles in each identified loci, the allele contributing the greatest effect to ShB resistance was named the putative resistant allele. Among 217 entries, entry GSOR 310389 contained the most putative resistant alleles, eight out of ten. The number of putative resistant alleles presented in an entry was highly and significantly correlated with the decrease of ShB rating (r = −0.535) or the increase of ShB resistance. Majority of the resistant entries that contained a large number of the putative resistant alleles belonged to indica, which is consistent with a general observation that most ShB resistant accessions are of indica origin. These findings demonstrate the potential to improve breeding efficiency by using marker-assisted selection to pyramid putative resistant alleles from various loci in a cultivar for enhanced ShB resistance in rice.

Phenotypic gain from introgression of two QTL, qSB9-2 and qSB12-1, for rice sheath blight resistance

F2:3 families from crosses between three rice indica introgression lines and their common japonica recurrent parent were used to evaluate two quantitative trait loci (QTL) for sheath blight (SB) resistance. Three selected TeQing-into-Lemont backcross introgression lines (TILs) were more resistant than their susceptible parent (Lemont) in inoculated field plots, and were molecularly verified to contain TeQing alleles at qSB9-2 and/or qSB12-1. F2 individuals homozygous for qSB9-2 and qSB12-1 provided F2:3 families that fit four genotypic classes: containing the resistant TeQing allele for qSB9-2TQ alone, qSB12-1TQ alone, both qSB9-2TQ and qSB12-1TQ, and neither SB QTL introgression. By comparing the SB resistance of these four genotypic classes in micro-chamber evaluations and inoculated field plots, the phenotypic values of the QTL were measured. Under both study conditions, disease resistance ranked qSB9-2 + qSB12-1 > qSB9-2 > qSB12-1 > no QTL, with both qSB9-2 and qSB12-1 acting as dominant resistance genes. In micro-chamber studies, qSB9-2TQ reduced disease an average of 1.0 disease index units and qSB12-1TQ by 0.7 using a scale of 0–9. Field effects of qSB9-2TQ and qB12-1TQ were less pronounced, with average phenotypic gains of 0.5 and 0.2 units, respectively. TIL:642 proved to contain qSB9-2TQ in an introgression so small it was tagged by just RM205 on the tip of chromosome 9. These studies verify that the indica introgression of qSB9-2TQ or qSB12-1TQ can measurably improve resistance to sheath blight disease in a highly susceptible tropical japonica cultivar, and fine-mapped the qSB9-2 locus. Markers presently verified as linked to these QTL can support marker-assisted breeding to improve disease resistance.

Advances in Mapping Loci Conferring Resistance to Rice Sheath Blight and Mining Rhizoctonia solani Resistant Resources

Sheath blight (SB) caused by Rhizoctonia solani is one of the three major diseases of rice, and now has become the most severe disease causing rice yield loss in China. Breeding and use of varieties resistant to SB is crucial in controlling the disease, but the advances achieved have been limited due to the lack of highly SB-resistant rice germplasm. Genetic analysis revealed that the SB resistance in rice was a typical quantitative trait controlled by multi-genes. Although many QTLs conferring resistance to SB have been identified in recent years, most of the QTLs only showed small effects and few of them have been evaluated for utilization potential. Many R. solani-resistant resources have been found in wild rice species, microorganisms and other plant species. It is already known that the SB-resistance could be improved in transgenic rice plants by genetic transformation. This paper reviewed the genetic mapping of loci associated with resistance to rice SB, the evaluation of the potential of resistance QTLs, and the resistant resources found in various organisms besides rice. To develop SB-resistant rice varieties, it is important to develop and explore new resistant rice germplasms, fine map and evaluate resistance QTLs, and also to pay attention to various bio-resources showing resistance to R. solani.

Identification of major quantitative trait loci qSBR11-1 for sheath blight resistance in rice

Sheath blight caused by Rhizoctonia solani Kuhn is one of the important diseases of rice, resulting in heavy yield loss in rice every year. No rice line resistant to sheath blight has been identified till date. However, in some rice lines a high degree of resistance to R. solani has been observed. An indica rice line, Tetep, is a well documented source of durable and broad spectrum resistance to rice blast as well as quantitative resistance to sheath blight. The present study identified genetic loci for quantitative resistance to sheath blight in rice line Tetep. A mapping population consisting of 127 recombinant inbred lines derived from a cross between rice cultivars HP2216 (susceptible) and Tetep (resistant to sheath blight) was evaluated for sheath blight resistance and other agronomic traits for 4 years across three locations. Based on sheath blight phenotypes and genetic map with 126 evenly distributed molecular markers, a quantitative trait loci (QTLs) contributing to sheath blight resistance was identified on long arm of chromosome 11. Two QTL mapping approaches i.e., single marker analysis and composite interval mapping in multi environments were used to identify QTLs for sheath blight resistance and agronomical traits. The QTL qSBR11-1 for sheath blight resistance was identified between the marker interval RM1233 (26.45 Mb) to sbq33 (28.35 Mb) on chromosome 11. This region was further narrowed down to marker interval K39516 to sbq33 (~0.85 Mb) and a total of 154 genes were predicted including 11 tandem repeats of chitinase genes which may be responsible for sheath blight resistance in rice line Tetep. A set of 96 varieties and a F2 population were used for validation of markers linked to the QTL region. The results indicate that there is very high genetic variation among varieties at this locus, which can serve as a starting point for allele mining of sheath blight resistance.

Field and greenhouse inoculation methods for assessment of sheath blight resistance in rice

Field and greenhouse inoculation methods were compared to determine the genetic variation for resistance to Rhizoctonia solani in 38 somaclones of rice cultivar Metica-1. Rice plants in pots were inoculated with isolate 4F1 at the age of sixty four days, with 2.0 g of the fungal culture, multiplied on rice grain and hull medium and placed on the soil surface around the plant. The differences among somaclones in relation to lesion height were significant and varied from 6.5 to 15.5 cm. In the field trial of artificial inoculation with fungal culture, 52 days after planting, the lesion height varied from 6.2 to 17.7 cm. The correlation between disease severity in the greenhouse and the field was positive and highly significant (r=0.44; P< 0.01), indicating the greenhouse inoculation as a safe method for screening germplasm for sheath blight resistance.

Confirming QTLs and Finding Additional Loci Conditioning Sheath Blight Resistance in Rice Using Recombinant Inbred Lines

One method for confirming the existence of quantitative trait loci (QTLs) is to identify loci of similar location and effect in multiple populations and/or environments. The literature contains two prior publications reporting the location of QTLs affecting resistance to sheath blight (SB) disease in rice (Oryza sativa L.), but lack of agreement between QTLs in the studies left all 12 unconfirmed, limiting the potential of marker‐assisted selection of this trait with worldwide importance. The earlier linkage analyses were imprecise due to heterozygosity, segregation, and limited plot size and replication. We evaluated a replicated set of pure‐breeding recombinant inbred lines (RILs) to increase reliability of the quantitative disease data and in turn improve accuracy of the QTL mapping. The RILs were F2:10 descendants from an early‐generation ‘Lemont’ × ‘Teqing’ population wherein SB resistance QTLs (SB‐QTLs) were first identified. The present study confirmed the location and effect of six SB‐QTLs, confirmed the existence but not the specific location of another, and identified eight new loci. Three of the confirmed QTLs were also found to be independent from undesirable plant height and maturity effects. This research demonstrated the importance of using replicated phenotypic data for reliably establishing the identity and effect of putative QTLs for complex traits such as SB resistance. Further marker development to facilitate marker‐assisted selection of these three SB‐QTLs is warranted.

Advances in rice breeding, genetics and genomics

Summary Plant breeders are responsible for impressive gains incrop productivity. More than 50% of the increasedworld food output over the past 50 years could be at-tributed to improved varieties. Recent advances inmolecular biology, such as engineering disease andinsect resistance genes, will augment work by plantbreeders and provide traits that previously did not ex-ist in the germplasm, for example, sheath blight re-sistance in rice (Lin et al. 1995). Population growthis continuing at more than 2% annually in many de-veloping rice growing countries. To feed this grow-ing population, the growth rate of rice productionneeds to be accelerated. Innovative breeding methodsand the emerging tools of molecular and genome bi-ology must supplement the conventional breedingmethods in achieving the future rice breeding goals.Biotechnological tools accelerate rice breeding andbroaden the rice gene pool. Transformation usingalien genes from bacteria, fungi, protozoan, insects,animals and plant species allow breeders to accom-347

Mapping quantitative trait loci controlling sheath blight resistance in two rice cultivars (Oryza sativa L.)

Rice sheath blight, caused by Rhizoctonia solani Kuhn, is one of the three major diseases of rice. The present study was conducted with an F2 clonal population of Jasmine 85/Lemont. The F2 population, including 128 clonal families, was inoculated by short toothpicks incubated with a strain, RH-9 of the fungus. Based on field disease evaluations in 2 years and a genetic map with 118 evenly distributed molecular markers, we identified six quantitative trait loci (QTLs) contributing to sheath blight resistance. These QTLs, qSB-2, qSB-3, qSB-7, qSB-9-1, qSB-9-2 and qSB-11, were located on chromosomes 2, 3, 7, 9 and 11, respectively. The respective alleles of qSB-2, qSB-3, qSB-7, and qSB-9-2 from Jasmine 85 could explain 21.2%, 26.5%, 22.2% and 10.1% of the total phenotypic variation, respectively; while the alleles of qSB-9-1 and qSB-11 from Lemont could explain 9.8% and 31.2% of the total phenotypic variation. Of these qSB-2 and qSB-11 could be detected in both years, while remaining loci were detected only in a single year. Furthermore, four QTLs (qHD-2, qHD-3, qHD-5 and qHD-7) controlling heading date and three QTLs (qPH-3, qPH-4 and qPH-11) controlling plant height were also identified. Though rice sheath blight resistance may be influenced by morphological traits, such as heading date and plant height, in the present study most detected resistance loci were not linked to the loci for heading date or plant height.

Testing for Sheath Blight Resistance in Rice

Testing for Sheath Blight Resistance in Rice

Evaluation for Sheath Blight Resistance in Rice

Evaluation for Sheath Blight Resistance in Rice