Ramya Ranjan Mishra

Marker-Assisted Breeding for Stress Resistance in Crop Plants

Molecular markers have extensively been used for tagging and mapping of genes and QTLs conferring resistance to biotic and abiotic stresses. These tools have also been used for screening of germplasms, fingerprinting, and marker-assisted breeding in crop systems. This chapter presents an overview on the basic concepts of molecular mapping and marker-assisted breeding and its most widely used applications in crop improvement programs, viz., marker-assisted backcross breeding, gene introgression, gene pyramiding, and marker-assisted selection at an early generation, with emphasis on stress-related traits and examples from several crops. We have also discussed some quantitative aspects of marker-based introgression, backcross breeding, and gene pyramiding programs. We have also added a note on breeding by design and genomic selection as tools for future breeding endeavors aiming at introgression of stress resistance into high-yielding cultivars. Harnessing the full potential of marker-aided breeding for improvement of stress resistance in crop systems will require a multidisciplinary approach and integrated knowledge of the molecular and physiological processes influencing the stress-related traits. Hence, marker-aided breeding for stress resistance in the post-genomic era poses great challenge for molecular breeders to realize the target objectives.

Estimation of genetic diversity among 34 genotypes in the genus Cajanus with contrasting host response to the pod borer and its allied pests

The genetic divergence among 34 genotypes belonging to 12 species of genus Cajanus were carried out using plant pest interaction and DNA marker analysis. Principal component analysis based on average percentage of pod damage caused by pod borer, plume moth, and blue butterfly in the field conditions, and growth of their larva and pupa on an artificial diet in vitro dispersed these genotypes into four coordinates evincing high genetic divergence as expected. DNA marker analysis using 11 pairs of SSR and nine ISSR primers showed higher polymorphism at the species level, and these primers exhibited variation with regard to average band informativeness, resolving power, and PIC value. No single primer was able to distinguish between all the 34 genotypes of Cajanus but nine species specific amplified fragments were generated by five ISSR primers. The pairwise Jaccard’s similarity coefficient and Nei’s genetic distance values revealed a higher level of inter-specific genetic variation in the genus Cajanus. The clustering of genotypes based on Jaccard’s similarity coefficient vis-a-vis Nei’s genetic distance agreed with the sectional classification of the genus Cajanus. Seven cultivars of C. cajan and the genotypes of their wild progenitor C. cajanifolius remained in one cluster, whereas accessions of C. platycarpus and C. scarabaeoides were out grouped. The rest of the genotypes belonging to nine species of Cajanus formed another cluster. The principal coordinate analysis also supported this clustering pattern. Moreover, these findings have good many implications for future breeding endeavors aimed at the introgression of pod borer resistance alleles.

Genetic linkage mapping of loci conferring resistance to Blue butterfly (Lampides boeticus L.) and Plume moth (Exelastis atomosa Wals.) on chromosome 2 (CcLG02) in Pigeonpea

Abstract Inheritance of host resistance to blue butterfly (PBB1) and plume moth (PPM1) in interspecific mapping populations (F2, F3 and BC1) derived from a cross involving Cajanus cajan (cv. ICP-26) × Cajanus scarabaeoides (acc. ICPW-94) appeared to be under monogenic control either by a single major gene or a cluster of tightly linked genes. Bulked segregant analysis using 237 [85 simple sequence repeats (SSR), 143 random amplified polymorphic DNA (RAPD) and nine inter simple sequence repeats (ISSR)] parental polymorphic primers led to the identification of 43 markers that distinguished the resistant and susceptible bulks alike to parents, and which were also segregating among F2 progenies. Linkage analysis of these markers along with interaction phenotype score for both traits generated a linkage group consisting of 11 markers (two SSR, seven RAPD and two ISSR) and two trait loci (PBB1 and PPM1). This linkage group distributed over 133.9 cM with an average marker interval of 10.3 cM. The PBB1 and PPM1 loci were linked to each other by 11.2 cM (rf 0.110), and were flanked by ISSR marker UBC8722000 (15.9 cM), and RAPD marker OPA09910 (15.3 cM), respectively. On the basis of sequence homology of linked marker OPA09910 these two loci were assigned to chromosome 2 (CcLG02). Composite interval mapping led to the detection of two major quantitative trait loci (qPBB2.1 and qPPM2.1) controlling blue butterfly and plume moth resistance, respectively and the quantitative trait locus peaks coinciding with PBB1 and PPM1 loci on the map.