Dharminder Bhatia

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.

Yield-Enhancing Heterotic QTL Transferred from Wild Species to Cultivated Rice Oryza sativa L

Utilization of “hidden genes” from wild species has emerged as a novel option for enrichment of genetic diversity for productivity traits. In rice we have generated more than 2000 lines having introgression from ‘A’ genome-donor wild species of rice in the genetic background of popular varieties PR114 and Pusa44 were developed. Out of these, based on agronomic acceptability, 318 lines were used for developing rice hybrids to assess the effect of introgressions in heterozygous state. These introgression lines and their recurrent parents, possessing fertility restoration ability for wild abortive (WA) cytoplasm, were crossed with cytoplasmic male sterile (CMS) line PMS17A to develop hybrids. Hybrids developed from recurrent parents were used as checks to compare the performance of 318 hybrids developed by hybridizing alien introgression lines with PMS17A. Seventeen hybrids expressed a significant increase in yield and its component traits over check hybrids. These 17 hybrids were re-evaluated in large-size replicated plots. Of these, four hybrids, viz., ILH299, ILH326, ILH867 and ILH901, having introgressions from O. rufipogon and two hybrids (ILH921 and ILH951) having introgressions from O. nivara showed significant heterosis over parental introgression line, recurrent parents and check hybrids for grain yield-related traits. Alien introgressions were detected in the lines taken as male parents for developing six superior hybrids, using a set of 100 polymorphic simple sequence repeat (SSR) markers. Percent introgression showed a range of 2.24 from in O. nivara to 7.66 from O. rufipogon. The introgressed regions and their putative association with yield components in hybrids is reported and discussed.

Genetics and Genomics of Bacterial Blight Resistance in Rice

Rice is an important food crop for half the world’s population and has been in cultivation for over 10,000 years. During the last few decades, rice has evolved intricate relationships with associated pathogens and pests, bacterial blight (BB) being one of the most important among them. Utilization of resistant varieties with agricultural management practices is a more effective way to control BB. Of the 42 different resistance (R) genes identified to confer BB resistance, 9 have been isolated and cloned, whereas a few of the avirulence genes and a large number of candidate pathogenicity genes have been isolated from Xanthomonas oryzae pv. oryzae. The complete genome sequences of two different rice subspecies japonica and indica and three different races of BB pathogen are available. Therefore, the interaction between rice-Xoo could be deciphered and pave a way to study the molecular aspects of bacterial pathogenesis and host counter measures like innate immunity and R gene–mediated immunity. Although several of the type III effectors of Xoo have been characterized and the host targets of a few of them identified, a relatively large number of candidate effectors remain to be studied and their functional analysis may provide key for developing broad spectrum and durable resistance to BB.

Advances in Breeding for Resistance to Hoppers in Rice

Rice productivity is hampered by a number of diseases and insects. Among the insects, hoppers including planthoppers and leafhoppers are typical phloem-sap feeders, which are very serious and damaging insect pests of rice in Asia. Many chemicals have been recommended for the control of planthoppers, but due to their feeding habit at the base of the plant, the farmers are unable to notice and effectively control these pests. Exploiting host plant resistance to hoppers and incorporating resistant genes in commercial cultivars are an alternative, economical and environment-friendly approach. To date, approximately 70 resistance genes against hoppers have been identified, and most of these genes have been tagged with molecular markers. Recently six genes for resistance to brown planthopper (BPH) in different lines have been cloned using map-based cloning. Based on molecular analysis of cloned genes, it appears that there is considerable similarity in the plant response to BPH infestation and fungal/bacterial pathogen attack. Marker-assisted selection (MAS) and pyramiding of genes for resistance to BPH and green rice leafhopper (GRH) have shown higher level and wide spectrum of resistance than their monogenic lines. In addition, transgenic approaches including RNAi have targeted various plant lectins and volatile compounds to generate resistance to hoppers. In context of changing climate, the major challenge for plant breeders is to breed varieties while taking care of changing populations of planthoppers and biotype development. Future research priorities should concentrate on high-throughput screening of germplasm for field resistance to planthoppers, identifying and transferring new genes for resistance from different sources to broaden the gene pool of rice and identifying durable combination of genes for marker-assisted pyramiding.

Heterotic response of genomic regions derived from Oryza rufipogon and O. nivara in improving grain morphology and quality of indica rice (Oryza sativa L.)

Limited backcrossing was followed to introgress useful variability, needed for improving grain morphology and milling traits, from wild Oryza species into two indica cultivars PR114 and Pusa44.These alien introgressions lines (ILs), having similar grain quality parameters to the recurrent parent, were used for developing rice hybrids to assess the effect of these introgressions in the heterozygous state and to assess their grain quality parameters, as most of the hybrids commercialized in the tropics have inferior grain quality. These ILs and their recurrent parents, possessing fertility restoration ability for wide abortive cytoplasm, were crossed with CMS line PMS 17A to generate introgressions line hybrids (ILHs). Hybrids developed from recurrent parents were used as a check to compare the performance of ILHs. Based on yield and phenotypic acceptability, six ILHs having enriched genome of O. rufipogon and O. nivara were selected and analyzed for grain quality traits. All six hybrids observed significant improvement in milled rice recovery (up to 10%), head rice recovery (up to 25%) over ILs and check hybrids. Introgressions were analyzed using polymorphic SSR markers. The majority of O. rufipogon and O.nivara alleles identified in the study seems to be effective across recipient genotypes and could be used effectively in quality breeding programs.

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.

Access and Benefit Sharing on the Use of Indigenous Traditional Knowledge

Knowledge, innovations and practices that are generated in a unique, tradition-based context from indigenous peoples is termed as traditional knowledge that forms an integral part of indigenous peoples’ social, cultural and spiritual values. Access to various biological resources, fair and equitable sharing of benefits from the use of these resources and TK has become an important agenda after the CBD came into force. The debates are still going on the requirement for institutional mechanisms to regulate the access and benefit-sharing agreements, defining ownership of biological resources and their associated TK. With the advent in recent technologies, TK associated with natural biological resources and their economic and scientific importance has attracted a wide range of private sector stakeholders for their utilization. In the past, TK has often been accessed without the consent of the owners of TK and without sharing the benefits arising out of its utilization. Various measures for the protection of TK, through either adapted intellectual property rights or sui generis systems, are in vain as long as the holders of TK and the specific context in which TK has been generated, transmitted and preserved do not enjoy appropriate protection through the recognition of indigenous peoples’ rights. Indigenous rights can gain strength from progress made and legal standards set in international level elaborating measures for the protection of TK and vice versa. This chapter explores and reports the various negotiations on an international regime on access and benefit sharing in the framework of the Convention on Biological Diversity that provides a forum to push indigenous peoples’ right to their TK.