Background: High yielding rice varieties are usually low in grain iron (Fe) and zinc (Zn) content. These two micronutrients are involved in many enzymatic activities, lack of which cause many disorders in human body. Bio-fortification is a cheaper and easier way to improve the content of these nutrients in rice grain.Results: A population panel was prepared representing all the phenotypic classes for grain Fe-Zn content from 485 germplasm lines. The panel was studied for genetic diversity, population structure and association mapping of grain Fe-Zn content in the milled rice. The population showed linkage disequilibrium showing deviation of Hardy-Weinberg’s expectation for Fe-Zn content in rice. Population structure at K = 3 categorized the panel population into distinct sub-populations corroborating with their grain Fe-Zn content. STRUCTURE analysis revealed a common primary ancestor for each sub-population. Novel quantitative trait loci (QTLs) namelyqFe3.3andqFe7.3for grain Fe andqZn2.2,qZn8.3andqZn12.3for Zn content were detected using association mapping. Four QTLs, namelyqFe3.3,qFe7.3,qFe8.1andqFe12.2for grain Fe content were detected to be co-localized withqZn3.1,qZn7,qZn8.3andqZn12.3QTLs controlling grain Zn content, respectively. Additionally, some Fe-Zn controlling QTLs were co-localized with the yield component QTLs,qTBGW,OsSPL14andqPN. The QTLsqFe1.1,qFe3.1,qFe5.1, qFe7.1, qFe8.1, qZn6, qZn7 and gRMm9–1for grain Fe-Zn content reported in earlier studies were validated in this study.Conclusion: Novel QTLs,qFe3.3andqFe7.3for grain Fe andqZn2.2,qZn8.3andqZn12.3for Zn content were detected for these two traits. Four Fe-Zn controlling QTLs and few yield component QTLs were detected to be co-localized. The QTLs,qFe1.1,qFe3.1,qFe5.1, qFe7.1, qFe8.1, qFe3.3, qFe7.3, qZn6, qZn7, qZn2.2, qZn8.3andqZn12.3will be useful for biofortification of the micronutrients. Simultaneous enhancement of Fe-Zn content may be possible with yield component traits in rice.

Bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae is a major biotic constraint on obtaining higher grain yields in rice. Marker-assisted backcross breeding (MABB) was performed by the pyramiding of Xa4, xa5, xa13 and Xa21 resistance genes in the popular variety, Ranidhan. A foreground selection in BC₁F₁, BC₂F₁, and BC₃F₁ progenies detected all the target genes in 12, 7 and 16 progenies by using the closely linked markers from a population size of 446, 410, and 530, respectively. The BB-positive progenies carrying the target genes with a maximal similarity to the recipient parent was backcrossed in each backcross generation. A total of 1784 BC₃F₂ seeds were obtained from the best BC₃F₁ progeny. The screening of the BC₃F₂ progenies for the four target genes resulted in eight plants carrying all the four target genes. A bioassay of the pyramided lines conferred very high levels of resistance to the predominant isolates of bacterial blight disease. In addition, these pyramided lines were similar to Ranidhan in 16 morpho-quality traits, namely, plant height, filled grains/panicle, panicles/plant, grain length, grain breadth, grain weight, milling, head rice recovery, kernel length after cooking, water uptake, the volume expansion ratio, gel consistency, alkali-spreading value, and the amylose content.

Ranidhan is a popular late-maturing rice variety of Odisha state, India. The farmers of the state suffer heavy loss in years with flash floods as the variety is sensitive to submergence. Bacterial blight (BB) disease is a major yield-limiting factor, and the variety is susceptible to the disease. BB resistance genes Xa21, xa13, and xa5, along with the Sub1 QTL, for submergence stress tolerance were transferred into the variety using marker-assisted backcross breeding approach. Foreground selection using direct and closely linked markers detected the progenies carrying all four target genes in the BC₁F₁, BC₂F₁, and BC₃F₁ generations, and the positive progenies carrying these genes with maximum similarity to the recipient parent, Ranidhan, were backcrossed into each segregating generation. Foreground selection in the BC₁F₁ generation progenies detected all target genes in 11 progenies. The progeny carrying all target genes and similar to the recipient parent in terms of phenotype was backcrossed, and a total of 321 BC₂F₁ seeds were produced. Ten progenies carried all target genes/QTL in the BC₂F₁ generation. Screening of the BC₃F₁ progenies using markers detected 12 plants carrying the target genes. A total of 1270 BC₃F₂ seeds were obtained from the best BC₃F₁ progeny. Foreground selection in the BC₃F₂ progenies detected four plants carrying the target genes in the homozygous condition. The bioassay of the pyramided lines conferred very high levels of resistance to the predominant isolates of bacterial blight pathogen. These BB pyramided lines were submergence-tolerant and similar to Ranidhan in 13 agro-morphologic and grain quality traits; hence, they are likely to be adopted by farmers.

Because it is rich in antioxidant compounds, the staple food of rice provides many health benefits. Four antioxidant traits in rice grain, viz., catalase, CUPRAC, DPPH, FRAP and peroxidase, were mapped in a representative panel population containing 117 germplasm lines using 131 SSR markers through association mapping. Donor lines rich in multiple antioxidant properties were identified from the mapping population. The population was classified into three genetic groups and each group showed reasonable correspondence with the antioxidant traits. The presence of linkage disequilibrium in the population was confirmed from the estimated Fst values. A strong positive correlation of DPPH was established with TPC, FRAP and CUPRAC. A moderate to high mean gene diversity was observed in the panel population. Eleven significant marker-trait associations for antioxidant traits were mapped, namely, qACD2.1, qACD11.1 and qACD12.2 for DPPH; qCAT8.1 and qCAT11.1 for catalase; qFRAP11.1, qFRAP12.1 and qFRAP12.2 for FRAP; and qCUPRAC3.1, qCUPRAC11.1 and qCUPRA12.1 regulating CUPRAC. Co-localization of the QTLs for qACD11.1, qFRAP11.1 and qCUPRAC11.1 were detected, which may act as antioxidant hotspots regulating DPPH, FRAP and CUPRAC activities, respectively, while qACD12.2 and qFRAP12.1 remained close on the chromosome 12. These detected QTLs will be useful in antioxidant improvement programs in rice.

Reproductive stage drought stress is an important factor for yield reduction in rice. Genetic mapping of drought responsive QTLs will help to develop cultivars suitable for drought prone environments through marker-assisted breeding. QTLs linked to morpho-physiological traits under drought stress were mapped by evaluating 190 F ₇ recombinant inbred lines (RIL). Significant variations were observed for eleven morpho-physiological traits involved during the stress. Bulked segregant analysis (BSA) strategy was adopted for genotyping the RIL population. A total of 401 SSR primers were tested for parental polymorphism of which 77 were polymorphic. Inclusive composite interval mapping detected a total of five consistent QTLs controlling leaf rolling ( qLR _{9 .1} ), leaf drying ( qLD _{9 .1} ), harvest index ( qHI _{9 .1} ), spikelet fertility ( qSF _{9 .1} ) and relative water content ( qRWC _{9 .1} ) under reproductive stage drought stress. Another two non-allelic QTLs controlling leaf rolling ( qLR _{8 .1} ) and leaf drying ( qLD _{12 .1} ) were linked in a single year. QTL controlling leaf rolling, qLR8.1 was validated in this mapping population and useful in marker-assisted breeding (MAB) programs. Out of these five consistent QTLs, four ( qLR _{9 .1} , qLD _{9 .1} , qHI _{9 .1} and qRWC _{9 .1} ) were detected to be novel QTLs and useful for MAB for reproductive stage drought tolerance in rice.

Reeta is a popular late-maturing high-yielding rice variety recommended for cultivation in the eastern Indian states. The cultivar is highly sensitive to submergence stress. Phosphorus deficiency is an additional constraint for realizing high yield. The quantitative trait loci (QTLs), Sub1, for submergence and Pup1 for low phosphorus stress tolerance along with narrow-grained trait, GW5 were introgressed into the variety from the donor parent, Swarna-Sub1 through marker-assisted breeding. In addition, phenotypic selections for higher panicle weight, grain number, and spikelet fertility were performed in each segregating generation. Foreground selection detected the 3 target QTLs in 9, 8 and 7 progenies in the BC₁F₁, BC₂F₁, and BC₃F₁ generation, respectively. Recurrent parent’s genome recovery was analyzed using 168 SSR polymorphic markers. The foreground analysis in 452 BC₃F₂ progenies showed five pyramided lines in homozygous condition for the target QTLs. No donor fragment drag was noticed in the Sub1 and GW5 QTLs carrier while a segmentwas observed in the Pup1 carrier chromosome. The developed lines were higher yielding, had submergence, and had low phosphorus stress-tolerance alongwith similar to the recipient parent in the studied morpho-quality traits. A promising pyramided line is released in the name of Reeta-Panidhan (CR Dhan 413) for the flood-prone areas of Odisha state.