**7.1 Conventional breeding approaches**

The conventional breeding approaches, including the pedigree method, backcrossing, recurrent selection, and mutation breeding, have been widely used in developing blast-resistant varieties in rice [182]. The pedigree method of breeding is the most commonly used breeding method for improving pest and disease resistance in rice. The pedigree method is the quick method employed to develop the resistance for one or more pests or diseases governed by major R genes. Backcross breeding improves an agronomically superior and high-yielding elite variety for resistance against insect pests and disease-causing pathogens. The major advantage of backcross breeding is avoiding the undesired genes from the donor parent due to linkage drag [183]. Backcross breeding has been used in South and Southeast Asia to improve blast resistance of several rice varieties including, KDML 105, Basmati, and Manawthukha [184]. With the advantages of shorter breeding cycles, control of genetic gains, and developing a broad range of genetic diversity in breeding lines, the recurrent selection breeding method is another choice of conventional breeding method to improve disease resistance in rice [185]. Mutation breeding is the method of choice when all the alleles available in the germplasm are exhausted, and there is a need to develop novel alleles. Mutation breeding has been effectively used to complement the other conventional methods of breeding. Although there are no breakthroughs achieved using mutation breeding, several examples of the use of this method exist that include the development of blast-resistant varieties RD6, KDML 105, Ratna, and R917 [186, 187]. However, the major limitation of the mutation breeding is the low efficiency, generation of recessive alleles, tracking of the mutated gene, and exposure of the personnel for mutagenic agents.

Further, associated markers have been effectively used to tag the mutated gene and follow them up in the subsequent generations [188]. The blast resistance genes that have been deployed in different rice varieties to address the incidence of the blast pathogen by using the above-mentioned conventional breeding methods include Pib, Pita, Pia, Pi1, Pikh, Pi2(t), and Pi4(t) [130]. Despite several rice varieties with high yield and grain quality in the previous few decades, the conventional breeding methods suffer several limitations, including high cost, labor-intensive, more time consuming, less reliability, difficulties in the appropriate genotypic selection, and linkage drag. Therefore, these limitations have necessitated the development of modern molecular breeding methods, which have overcome the limitations of conventional breeding methods.

#### **7.2 Marker-based breeding methods**

The main problem of traditional breeding methods is the selection of a genotype based on the phenotype. For instance, in disease resistance breeding, the resistant genotype is selected on their manifestation of resistance to the disease. However, a particular genotype without any R gene may be selected as resistant in the absence of a minimum level of disease pressure. Therefore, molecular markers associated with specific R genes have been widely employed to make the selection procedure more reliable, effective, and less time-consuming. Modern sequencing technologies have led to the identification of a large number of different DNA markers such as

simple sequence repeats (SSRs), single-nucleotide polymorphisms (SNPs), small insertions/deletions (InDels), amplified fragment length polymorphisms (AFLPs), random amplified polymorphic DNAs (RAPDs), restriction fragment length polymorphisms (RFLPs) associated with blast resistance genes that are effectively used in the selection of a genotype during handling of segregating generations [163, 179].

A panel of 80 released varieties from National Rice Research Institute, Cuttack, India, was genotyped with 36 molecular markers that were linked to 36 different blast resistance genes, to investigate the varietal genetic diversity and molecular markertrait association with blast resistance. The cluster analysis and population structure categorized the 80 National Rice Research Institute released varieties (NRVs) into three major genetic groups. The principal co-ordinate analysis displays the distribution of resistant and moderately resistant NRVs into different groups. Analysis of molecular variance result demonstrated maximum (97%) diversity within populations and minimum (3%) diversity between populations. Among tested markers, two markers (RM7364 and pi21\_79-3) corresponding to the blast resistance genes (*Pi56(t)* and *pi21*) were significantly associated and explained a phenotypic variance of 4.9 to 5.1% with the blast resistance [189]. In another research article, molecular analysis of variance of landraces originated from nine diverse rice ecologies of India showed maximum (93%) diversity within the population and least (7%) between populations. Five markers like K3957, Pikh, Pi2–i, RM212and RM302 were strongly associated with blast disease with the phenotypic variance of 1.4% to 7.6% [190].

#### *7.2.1 Marker Assisted Selection (MAS)*

In MAS, the resistant phenotype of a variety is selected based on the presence of an R gene linked or R gene-based molecular marker. This selection method is more dependable and time-saving, does not require proper disease favoring environmental conditions, and selects the resistant genotypes even in the absence of the pathogen or disease. Hence, many present-day breeders are resorting to MAS in the developing blast-resistant varieties [163, 179, 191]. A set of well-characterized PCR-based markers such as SSR markers linked to blast R genes have been established currently used in the MAS programs worldwide. Similar to the rice breeders in the rest of the world, Indian rice breeders working on the improvement of blast resistance are not left behind in the use of MAS. The pioneering work of MAS in rice blast improvement began with Hittalmani *et al*. in 2000 [192]. Since then, several rice breeders in India have efficiently used MAS to incorporate different blast resistance genes, resulting in blast-resistant varieties. In China, rice lines were recently bred for blast resistance with four broad-spectrum resistance genes viz., *Pi9*, *Pi47*, *Pi48*, and *Pi49* [193]. A list of blast resistance breeding programs in rice using MAS in India is furnished in **Table 2**.

#### *7.2.2 Marker-Assisted Backcross Breeding (MABB)*

Like MAS, the MABB is also dependent upon DNA markers such as SSRs or SNPs. However, the main difference between the MAS and MABB lies in the type of the parent variety in which the improvement is sought and in recurrent parent genome recovery. While the MAS is used to introduce the blast resistance gene into any genotype, the MABB is employed to improve blast resistance in otherwise highyielding elite varieties or genotypes. Therefore, the end product of the MABB is the same as the original rice variety except with improved blast resistance. Further, the ill effects of the unwanted genes from the donor are avoided by using a set of polymorphic markers for the recovery of the recurrent parent genome. Hence, MABB involves two stages of selection: foreground selection using markers linked

#### *Rice Blast Disease in India: Present Status and Future Challenges DOI: http://dx.doi.org/10.5772/intechopen.98847*

to blast resistance genes and background selection using polymorphic markers spread randomly throughout the rice genome. It is reported that short-grained landrace *Mushk Budji* was crossed to a triple-gene donor line, DHMAS 70Q 164-1b, and followed through marker-assisted foreground and background selection in first and second backcross generations that helped to incorporate blast resistance genes *Pi54, Pi1* and *Pita*. Marker-assisted background selection was carried out using 78 SSR and STS markers [194]. Several elite varieties such as MTU1010, IR-64, and Swarna have been improved for their blast resistance in India. A list of all other rice varieties improved for blast resistance in India following MABB is listed in **Table 2**.
