Jagjeet Singh Lore

A novel bacterial blight resistance gene from Oryza nivara mapped to 38 kb region on chromosome 4L and transferred to Oryza sativa L.

Bacterial blight (BB) of rice caused by Xanthomonas oryzae pv oryzae (Xoo) is one of the major constraints to productivity in South-East Asia. The strategy of using major genes, singly or in combination, continues to be the most effective approach for BB management. Currently, more than two dozen genes have been designated but not all the known genes are effective against all the prevalent pathotypes. The challenge, therefore, is to continue to expand the gene pool of effective and potentially durable resistance genes. Wild species constitute an important reservoir of the resistance genes including BB. An accession of Oryza nivara (IRGC 81825) was found to be resistant to all the seven Xoo pathotypes prevalent in northern states of India. Inheritance and mapping of resistance in O. nivara was studied by using F2, BC2F2, BC3F1 and BC3F2 progenies of the cross involving Oryza sativa cv PR114 and the O. nivara acc. 81825 using the most virulent Xoo pathotype. Genetic analysis of the segregating progenies revealed that the BB resistance in O. nivara was conditioned by a single dominant gene. Bulked segregant analysis (BSA) of F2 population using 191 polymorphic SSR markers identified a approximately 35 centiMorgans (cM) chromosomal region on 4L, bracketed by RM317 and RM562, to be associated with BB resistance. Screening of BC3F1 and BC2F2 progenies and their genotyping with more than 30 polymorphic SSR markers in the region, covering Bacterial artificial chromosome (BAC) clone OSJNBb0085C12, led to mapping of the resistance gene between the STS markers based on annotated genes LOC_Os04g53060 and LOC_Os04g53120, which is approximately 38.4 kb. Since none of the known Xa genes, which are mapped on chromosome 4L, are effective against the Xoo pathotypes tested, the BB resistance gene identified and transferred from O. nivara is novel and is tentatively designated as Xa30(t). Homozygous resistant BC3F3 progenies with smallest introgression region have been identified.

Quantification of the Components of Resistance to Rice Sheath Blight Using a Detached Tiller Test Under Controlled Conditions

Resistance of rice (Oryza sativa) to sheath blight, caused by Rhizoctonia solani, is quantitative and involves two mechanisms: physiological resistance and disease escape. The epidemiological concept of components of resistance was applied using a detached tiller method under controlled conditions, to specifically address physiological resistance to sheath blight in rice. A sclerotium was inserted below the leaf collar of individual rice tillers maintained in tubes filled with water. Different variables were measured after incubation: number of lesions, lesion length, vertical sheath colonization, presence or absence of dark margin at the edge of lesions, and survival duration of the leaf blade. Several rice varieties reported to have different levels of susceptibility to sheath blight were assessed, together with varieties that are cultivated over large areas. Although numerical differences between rice varieties were observed for all disease variables, only the number of lesions significantly differed among varieties tested in this study. The varieties Pecos and IR64 had the consistently lowest and highest disease intensities, respectively. This methodology may allow the detection of sources of resistance that specifically involve defense mechanisms. When combined with field assessment, this methodology should also enable to quantitatively assess the relative role of both mechanisms of resistance to sheath blight.

Mapping of bacterial blight resistance gene xa8 in rice (Oryza sativa L.)

Bacterial blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the major diseases causing yield losses in rice worldwide. Development and deployment of resistant rice cultivars and pyramiding two or more resistance genes into elite varieties is the only strategy available to combat the disease. The BB resistance gene, xa8 conferred complete resistance to only one pathotype and partial resistance against two pathotypes at seedling stage while complete resistance against five of the seven pathotypes prevalent in Punjab at adult plant stage. The gene was earlier mapped on rice chromosome 7 at 19.9 cM genetic distance from SSR marker, RM214 using a recombinant inbred line (RIL) population generated from the cross between PR106 and IRBB8. However, due to the paucity of markers in that region, the gap could not be narrowed. With the availability of new SSR markers in that region, the gene was placed between two consecutive SSR markers, RM21044 and RM21045 at 7.0 and 9.9 cM respectively. Analysis of the 9.5 kb DNA sequence harboring the xa8 gene revealed the presence of three intact genes, which codes for putative expressed proteins viz., Zinc finger A20 and AN1 domain-containing protein (LOC_Os07g07400), Oxidoreductase, 2OG-Fe oxygenase family protein (LOC_Os07g07410) and Gibberellin 20 oxidase 1-B protein (LOC_Os07g07420). All the three genes are involved in plant response to various stresses and could be the possible candidate genes for xa8.

Error reduction in promoted confidence factor of a rule using improved fuzzy rule promotion technique

Abstract A dynamic fuzzy rule promotion approach for the promotion of a confidence factor of a rule for every successful session in diagnosis of a disease in crops by using the specific rules, has already been proposed in literature. This technique has the limitation that an error in the initial estimation of weights reduces linearly after every session the rule is being used. In this paper an improved approach has been proposed using the square root of sum of squares of frequencies, which are spread around the mean true value to reduce the error around a mean value. A rule set for the diseases and their symptoms for the paddy plant has been provided to make comparison between the previous and the improved approach. It has been shown that the improved approach decreases the error in uncertainty of estimation of weight for rules after every successful session. It has also been proposed that the improved approach must be applied in agricultural information dissemination system.

A strain of an emerging Indian pathotype of Xanthomonas oryzae pv. oryzae defeats the rice bacterial blight resistance gene xa13 without inducing a clade III SWEET gene and is nearly identical to a recent Thai isolate

The rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) injects transcription activator-like effectors (TALEs) that bind and activate host ‘susceptibility’ (S) genes important for disease. Clade III SWEET genes are major S genes for bacterial blight. The resistance genes xa5, which reduces TALE activity generally, and xa13, a SWEET11 allele not recognized by the cognate TALE, have been effectively deployed. However, strains that defeat both resistance genes individually were recently reported in India and Thailand. To gain insight into the mechanism(s), we completely sequenced the genome of one such strain from each country and examined the encoded TALEs. Strikingly, the two strains are clones, sharing nearly identical TALE repertoires, including a TALE known to activate SWEET11 strongly enough to be effective even when diminished by xa5. We next investigated SWEET gene induction by the Indian strain. The Indian strain induced no clade III SWEET in plants harbouring xa13, indicating a pathogen adaptation that relieves dependence on these genes for susceptibility. The findings open a door to mechanistic understanding of the role SWEET genes play in susceptibility and illustrate the importance of complete genome sequence-based monitoring of Xoo populations in developing varieties with effective disease resistance.

Induction of useful variability for pericarp colour and bacterial blight resistance in rice (Oryza sativa L.) cv. PAU 201 through EMS based mutagenesis

PAU 201, a high yielding variety of rice released by Punjab Agricultural University in 2007, was withdrawn from cultivation in the year 2010 mainly due to its red coloured pericarp. It also became susceptible to a new pathotype (PbXo-8) of bacterial blight (BB) pathogen. To improve these specific defects, PAU 201 was mutagenized with ethyl methane sulphonate in different concentrations of 0.6, 0.8 and 1.0% in water (v/v). A total of 841 M1 single panicles were harvested and advanced to M4 generation following selfing and selection for white pericarp colour in each generation. A set of promising 68 M4 progenies was also screened for BB resistance and one putative mutant possessing white pericarp colour as well as BB resistance (designated as RYT 3207) was identified. On further evaluation, RYT 3207 was found to be resistant to all the ten pathotypes of BB pathogen prevalent in the Punjab state and it yielded at par with the PAU 201 in multi-location trials during 2011 to 2013. Molecular marker analysis showed presence of xa13 locus in RYT 3207. The acquired resistance to all the ten pathotypes in RYT 3207, compared to nine pathotypes in PAU 201, could be due to modified function of xa13 gene. The new genotype RYT 3207 is a mutagenized version of the high yielding rice cultivar PAU 201 possessing white pericarp and enhanced resistance to bacterial blight.