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Light intensity is a crucial environmental factor that affects photosynthesis and ultimately, grain yield in rice. However, no gene or marker directly associated with improved performance under low-light intensity under field conditions has been identified till date. With an aim of identifying genes and markers associated with improved performance (measured in terms of better yields) under low-light intensity, an integrated field screening, in silico and wet lab validation analysis was performed. Field-based screening of a diverse set of 110 genotypes led to the identification of two physiological and three morphological parameters critical for low-light tolerance in rice. In silico analysis using information available in public databases led to the identification of a set of 90 potential candidate genes which were narrowed to thirteen genic targets for possible marker-trait association. Marker-trait association on the panel of 48 diverse rice genotypes varying in their response to low-light intensity led to the identification of six markers [HvSSR02-44 (biological yield), HvSSR02-52 (spikelet fertility), HvSSR02-54 (grain yield), HvSSR06-56 (spikelet fertility), HvSSR06-69 (spikelet fertility; biological yield), HvSSR09-45 (spikelet fertility)] lying on chromosomes 2, 6 and 9 showing significant association (R > 0.1) for traits like grain yield/plant, biological yield and spikelet fertility under low light. Eight rice genes [including member of BBX (B-box) family] lying within 10 kb distance of these identified markers already reported for their role in response to stress or change in plant architecture in rice were also identified. The eight rice genotypes, five traits, eight genes and six markers identified in the current study will help in devising strategies to increase yield under low light intensity and pave way for future application in marker-assisted breeding.

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Genetically modified crops are the most auspicious development of scientists of today. Rice being the staple food crop globally, it is needed to give immense importance for its improvement. Development of rice varieties tolerant to pests and diseases will ensure safety to farmers against the harmful effects of chemicals used as insecticides and fungicides. Certain abiotic factors like drought, cold, heat, salinity, which hinders the growth of rice can be battled by developing GM rice carrying genes that impact tolerance to these factors. Moreover, increased production and utilization of golden rice would provide the required nutrients especially for the poor to meet their nutritional requirements. But commercialization of GM crops is still an issue as people are yet to accept them globally. Finally, the future prospect of GM rice will flourish unless it is met by some loop holes.

Low light intensity stress is a critical abiotic stress that reduces rice yield and quality. Present study has been carried out with a set of hill rice germplasm under ambient light and low light condition. Results related to principal components analysis (PCA) revealed that grain yield, plant height and pollen viability are the most informative components accounted for 63.95 % variance among the genotypes studied under low light condition. The three main traits contributing to PCA was. IRCTN 91 -84, IRCTN 91-94 and RCPL 1-9C were found to be the most tolerant genotype to low light intensity under this study.