American Journal of Plant Sciences, 2012, 3, 528-536 http://dx.doi.org/10.4236/ajps.2012.34063 Published Online April 2012 (http://www.SciRP.org/journal/ajps) Application of Marker Assisted Backcrossing to Introgress the Submergence Tolerance QTL SUB1 into the Vietnam Elite Rice Variety-AS996 Luu M. Cuc 1* , Luu T. N. Huyen 1 , Pham T. M. Hien 1 , Vu T. T. Hang 1 , Nguyen Q. Dam 1 , Pham T. Mui 2 , Vu D. Quang 1 , Abdelbagi M. Ismail 3 , Le H. Ham 1 1 Agricultural Genetics Institute, Tu Liem, Vietnam; 2 Cuu Long River Delta Rice Research Institute, Tan Thanh, Vietnam; 3 International Rice Research Institute, Metro Manila, Philippine. Email: * cucchi04@gmail.com, LHHAM@agi.ac.vn Received December 20 th , 2011; revised January 19 th , 2012; accepted February 20 th , 2012 ABSTRACT The result of the study contributes to enhancing and sustaining future livelihoods and food security in Vietnam vis-a-vis climate change. An innovative strategy based on marker-assisted backcrossing (MABC) was used to transform popular rice variety AS996 into the one can tolerate submergence while maintaining its original characteristics preferred by farmers and consumers. The submergence tolerance QTL SUB1 counts for up to 70% of the submergence tolerant and provides a marked improvement of submergence tolerance in all genetic backgrounds and environments tested so far. Parental diversity was carried out with 460 markers. Of which, 53 polymorphic markers were used for assessment on BC1F1, BC2F1 and BC3F1 generations. The best BC1F1 plant was P422 with highest recipient allele was 87.5%, while the additional chosen plants were P412, P428, P215 and P39 (81% - 84%). All these plants were used to develop BC2F1 generation. The six BC2F1 plants were used to develop BC3F1 and BC2F2 were the plants number P422-11 and P422-14 having 93.75% recipient alleles and P422-12, P422-3, P39-17, P39-25 having 92.25% recipient alleles. Total of 445 BC3F1 plants were confirmed the introgresion of SUB1 using ART5 and SC3. After three generations of backcrossing, application of MABC resulted in the best BC3F1 individual P422-14-177 with 100% of recipient alleles based on the number of 53 markers used with only the introgression size of SUB1 was 0.3 Mb between ART5 and SC3. Phenotyping was carried out on BC3F1 and BC2F2 of the selected lines. The survival ratio of these selected lines and IR64SUB1 were the same. It convinced the successfully introgress SUB1 into AS996 rice variety. The breeding line BC4F1 having 100% genetic background of donor variety is ready for develop new submergence tolerant rice variety ASS996-SUB1 to cope with climate change. Keywords: AS996-SUB1; Climate Change; Marker-Assisted Backcrossing (MABC); Rice; Submergence 1. Introduction Vietnam is among the five countries hardest hit by cli- mate change. The frequency of natural disasters like ty- phoon, flooding etc… are increasing annually. Submer- gence caused by flash-flooding is one of the most serious impacts to the agricultural productions of the country. In Vietnam, rice is the number one agricultural product, not only for second largest exporter but also accounts for 90% of national food production. Of the 4.5 million ha rice area, more than one million ha is affected by flood- ing, remains for at least one to two weeks in many parts of the country. Depending on the timing of flood with respect to growth stage, shorter duration and shallow flashfloods can result in less than 10% production losses while deeper and stagnant water with two weeks’ dura- tion and >100 cm in depth can cause damage ranging from 40% to 77% [1]. Traditional varieties adapted to the submergence prone environments are low yielding due to their low tillering ability, long droopy leaves, suscepti- bility to lodging and poor grain quality. Development of submergence tolerant varieties is generally considered as the most effective entry point for improving productivity of rice varieties damaged from typhoon and flash flood, and it is also the cheapest option for farmers. Mackill (2006) proposed that adoption of a completely new vari- ety could take considerable time, whereas the chances of rapid adoption of popular varieties converted through marker assisted backcrossing (MABC) were relatively higher [2]. MABC is a precise and effective method to introgress * Corresponding author. Copyright © 2012 SciRes. AJPS