Climate change is termed as variation in statistical distribution of weather patterns(temperature variations, rainfall, light intensity etc.) when that change persists for aprolonged duration. Erratic fluctuations in rainfall and other types of precipitation will be oneof the most perilous aspects determining the overall sway of climate change scenario. It isalso predicted that some regions will be prone to extreme drought while already wet regionswill be wetter due to extreme rainfalls causing flooding. World population is increasing tremendously and so is the case with food demand. Rice isbasic food item of nearly 50% of the world population. This demand necessitates a significantenhancement of rice production even in marginal-farmlands of the world.Summermonsoonrains damage rice crops drastically every year in terms of yield and grain quality (DMC,2002). Out of total area under rice, more than 1.6 million hectares have been affected byexcessive rains and floods (MNFSR, 2014). In Pakistan, approximately 70% rice farms areprone to seasonal flooding. Rice crop, may be the only crop which can effectively be grownin flood prone ecosystems (Sarkar and Bhattacharjee, 2011). These floods are sometimes sodamaging that rice farmers in some parts of the country lose their entire rice crop.Accordingto annual flood reports of Pakistan,Punjab’s paddy production had suffered an estimated lossof 217 thousand tons due to seasonal floods during 2014-15 and as a result overall nationalpaddy production remained below the target of previous year. According to Toojinda et al.,(2003),flooding is a serious constraint to rice cropand its survival in rainfed lowland anddeep-water areas.Recently, extreme weather conditions and unpredicted heavy rains due todrastic climatic changes in Pakistan, have resulted increased extent of submergence duringrice season. Major rice-damaged districts are Hafizabad, Jhang, Gujranwala and Chiniot thatare major rice growing areas of Pakistan. The experts say that the situation may becomeworse as climate change progresses.Flash floods, in which muddy water recedes in three toseven days, prohibit the sunlight to reach plants resulting in termination of photosynthesis,food making process in plants. Low oxygen level in deep floods also causes submerged plants to suffocate without oxygen. This rapid decline in the oxygen (~10,000-fold less) during prolonged submergence in accompanied by drastic lessening in cellular O2levels andan energy crisis, becomes severe under absence of photosynthesis (Bailey-Serres and Voesenek, 2008; Licausi and Perata, 2009). All this results in severe damages to rice crop interms of yield loss as well as quality deterioration. Therefore, submergence tolerance has become an important breeding objective in order toreduce yield losses (Kawano et al., 2009; Mackill, 1986; Mohanty and Chaudhary,1986).Recently, in Pakistan, all the rice cultivars being cultivated are much sensitive toflooding and anaerobic water-logged situation. With the new developments, it has becomepossible to cope with such flooded and water-logged situation by incorporating genes such asSUBMERGENCE 1 (SUB1), a robust quantitative trait locus from a submergence tolerantFR13A landrace, into local high yielding cultivars using Marker-assisted Breeding (MAB).Although, rice (Oryza sativa L.) is considered a flood-tolerant crop, its level of tolerancediffers significantly and only limited cultivars show tolerance to prolonged submergence,most of them with SUB1 QTL (Niroula et al., 2012). SUB1 is a variable polygenic locus thatencodes two to three ethylene responsive factors (ERF) DNA binding proteins (Juliaet al,2010). However, the response of this SUB1 QTL differs with the genotypes and otherenvironmental factors (Sarkar and Bhattacharjee, 2011). In order to study these responses, anexperiment was organized to screen that included 115 rice genotypes with SUB1 QTL fromInternational Rice Research Institute (IRRI), Philippines along with six local high yieldingrice cultivars being cultivated in Pakistan.