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.

Vegetative to reproductive phase transition in phototropic plants is an important developmental process and is sequentially mediated by the expression of micro-RNA MIR172. To obtain insight into the evolution, adaptation, and function of MIR172 in photophilic rice and its wild relatives, we analyzed the genescape of a 100 kb segment harboring MIR172 homologs from 11 genomes. The expression analysis of MIR172 revealed its incremental accumulation from the 2-leaf to 10-leaf stage, with maximum expression coinciding with the flag-leaf stage in rice. Nonetheless, the microsynteny analysis of MIR172s revealed collinearity within the genus Oryza, but a loss of synteny was observed in (i) MIR172A in O. barthii (AA) and O. glaberima (AA); (ii) MIR172B in O. brachyantha (FF); and (iii) MIR172C in O. punctata (BB). Phylogenetic analysis of precursor sequences/region of MIR172 revealed a distinct tri-modal clade of evolution. The genomic information generated in this investigation through comparative analysis of MIRNA, suggests mature MIR172s to have evolved in a disruptive and conservative mode amongst all Oryza species with a common origin of descent. Further, the phylogenomic delineation provided an insight into the adaptation and molecular evolution of MIR172 to changing environmental conditions (biotic and abiotic) of phototropic rice through natural selection and the opportunity to harness untapped genomic regions from rice wild relatives (RWR).

Seed vigor is the key performance parameter of good quality seed. A panel was prepared by shortlisting genotypes from all the phenotypic groups representing seedling growth parameters from a total of 278 germplasm lines. A wide variation was observed for the traits in the population. The panel was classified into four genetic structure groups. Fixation indices indicated the existence of linkage disequilibrium in the population. A moderate to high level of diversity parameters was assessed using 143 SSR markers. Principal component, coordinate, neighbor-joining tree and cluster analyses showed subpopulations with a fair degree of correspondence with the growth parameters. Marker–trait association analysis detected eight novel QTLs, namely qAGR4.1, qAGR6.1, qAGR6.2 and qAGR8.1 for absolute growth rate (AGR); qRSG6.1, qRSG7.1 and qRSG8.1 for relative shoot growth (RSG); and qRGR11.1 for relative growth rate (RGR), as analyzed by GLM and MLM. The reported QTL for germination rate (GR), qGR4-1, was validated in this population. Additionally, QTLs present on chromosome 6 controlling RSG and AGR at 221 cM and RSG and AGR on chromosome 8 at 27 cM were detected as genetic hotspots for the parameters. The QTLs identified in the study will be useful for improvement of the seed vigor trait in rice.

A set of ninety six land races including a few popular upland rice varieties were assessed to study inter-relationship of drought and yield related traits. Number of ear bearing tillers/m2, panicle weight and fertility percentage correlated significantly with grain yield/ha and the latter two component traits have very high inter se significant positive correlation under drought stress. Bold kernel type was shown to have significant positive association with grain fertility percentage. Plant height and seed yield under drought stress was negatively associated with leaf rolling score which in turn had inverse relationship with flowering and maturity duration. Thus, drought tolerance in upland rice varieties could be assessed in terms of improved grain filling and such characteristic feature may be associated with genotypes having intermediate plant height, moderate flowering and maturity duration.