Genetic Improvement of Rice for Bacterial Blight Resistance:Present Status and Future Prospects

The production and productivity of rice has been challenged due to biotic and abiotic factors.Bacterial blight(BB)disease,caused by Xanthomonas oryzae pv.oryzae,is one of the important biotic stress factors,which reduces rice production by 20%-50%.The deployment of host plant resistance is the most preferred strategy for management of BB disease,and breeding disease resistant varieties remains a very economical and effective option.However,it is difficult to develop rice varieties with durable broad-spectrum resistance against BB using conventional approaches alone.Modern biotechnological tools,particularly the deployment of molecular markers,have facilitated the cloning,characterization and introgression of BB resistance genes into elite varieties.At least 46 BB resistance genes have been identified and mapped from diverse sources till date.Among these,11 genes have been cloned and characterized.Marker-assisted breeding remains the most efficient approach to improve BB resistance by introducing two or more resistance genes into target varieties.Among the identified genes,xa5,xa13 and Xa21 are being widely used in marker-assisted breeding and more than 70 rice varieties or hybrid rice parental lines have been improved for their BB resistance alone or in combination with genes/QTLs conferring tolerance to other stress.We review the developments related to identification and utilization of various resistance genes to develop BB resistant rice varieties through marker-assisted breeding.

Marker-Assisted Pyramiding of Genes Conferring ResistanceAgainst Bacterial Blight and Blast Diseases into Indian RiceVariety MTU1010

Two major bacterial blight （BB） resistance genes （Xa21 and xa13） and a major gene for blastresistance （Pi54） were introgressed into an Indian rice variety MTU1010 through marker-assistedbackcross breeding. Improved Samba Mahsuri （possessing Xa21 and xa13） and NLR145 （possessingPi54） were used as donor parents. Marker-assisted backcrossing was continued till BC2 generationwherein PCR based functional markers specific for the resistance genes were used for foregroundselection and a set of parental polymorphic microsatellite markers were used for background selectionat each stage of backcrossing. Selected BC2F1 plants from both crosses, having the highest recoveriesof MTU1010 genome （90% and 92%, respectively）, were intercrossed to obtain intercross F1 （ICF1） plants,which were then selfed to generate 880 ICF2 plants possessing different combinations of the BB andblast resistance genes. Among the ICF2 plants, seven triple homozygous plants （xa13xa13Xa21Xa21Pi54Pi54）with recurrent parent genome recovery ranging from 82% to 92% were identified. All the seven ICF2plants showed high resistance against the bacterial blight disease with a lesion lengths of only 0.53–2.28 cm, 1%–5% disease leaf areas and disease scoring values of ‘1’ or ‘3’. The seven ICF2 plants wereselfed to generate ICF3, which were then screened for blast resistance, and all were observed to behighly resistant to the diseases. Several ICF3 lines possessing high level of resistance against BB andblast, coupled with yield, grain quality and plant type on par with MTU1010 were identified and advanced forfurther selection and evaluation.

A Single-Tube, Functional Marker-Based Multiplex PCR Assay for Simultaneous Detection of Major Bacterial Blight Resistance Genes Xa21, xa13 and xa5 in Rice

In marker-assisted breeding for bacterial blight(BB) resistance in rice, three major resistance genes, viz., Xa21, xa13 and xa5, are routinely deployed either singly or in combinations. As efficient and functional markers are yet to be developed for xa13 and xa5, we have developed simple PCR-based functional markers for both the genes. For xa13, we designed a functional PCR-based marker, xa13-prom targeting the In Del polymorphism in the promoter of candidate gene Os8N3 located on chromosome 8 of rice. With respect to xa5, a multiplex-PCR based functional marker system, named xa5 FM, consisting of two sets of primer pairs targeting the 2-bp functional nucleotide polymorphism in the exon II of the gene TFIIA5(candidate for xa5), has been developed. Both xa13-prom and xa5 FM can differentiate the resistant and susceptible alleles for xa13 and xa5, respectively, in a co-dominant fashion. Using these two functional markers along with the already reported functional PCR-based marker for Xa21(p TA248), we designed a single-tube multiplex PCR based assay for simultaneous detection of all the three major resistance genes and demonstrated the utility of the multiplex marker system in a segregating population.