A marker-assisted backcross approach for developing submergence-tolerant rice cultivars

Submergence stress regularly affects 15 million hectares or more of rainfed lowland rice areas in South and Southeast Asia. A major QTL on chromosome 9, Sub1, has provided the opportunity to apply marker assisted backcrossing (MAB) to develop submergence tolerant versions of rice cultivars that are widely grown in the region. In the present study, molecular markers that were tightly linked with Sub1, flanking Sub1, and unlinked to Sub1 were used to apply foreground, recombinant, and background selection, respectively, in backcrosses between a submergence-tolerant donor and the widely grown recurrent parent Swarna. By the BC2F2 generation a submergence tolerant plant was identified that possessed Swarna type simple sequence repeat (SSR) alleles on all fragments analyzed except the tip segment of rice chromosome 9 that possessed the Sub1 locus. A BC3F2 double recombinant plant was identified that was homozygous for all Swarna type alleles except for an approximately 2.3-3.4 Mb region surrounding the Sub1 locus. The results showed that the mega variety Swarna could be efficiently converted to a submergence tolerant variety in three backcross generations, involving a time of two to three years. Polymorphic markers for foreground and recombinant selection were identified for four other mega varieties to develop a wider range of submergence tolerant varieties to meet the needs of farmers in the flood-prone regions. This approach demonstrates the effective use of marker assisted selection for a major QTL in a molecular breeding program

Submergence risks and farmers' preferences: Implications for breeding Sub1 rice in Southeast Asia

Rice (Oryza sativa L.) provides a life support system to millions of resource-poor farmers in rainfed environments; however, yields are very low because of various biotic and abiotic stresses. Submergence caused by typhoons and floods is one of the major reasons for production losses. Because of the complexity of these ecosystems, the breeding framework necessitates adequate feedback and a more in-depth understanding of the ecological and socioeconomic conditions in these flood-prone areas. Within this purview, this study validated the performance in farmers' fields of lines with the SUB1 gene that confers tolerance of submergence for up to two weeks. The SUB1 gene was incorporated through marker-assisted backcrossing, MABC. The evaluation was conducted through participatory approaches to gain understanding of the risks as well as farmers' preferences for these varieties. A baseline survey of 658 farm households accomplished during 2008, focus group discussions, key informant interviews, and adaptability trials were conducted, with focus on farmers commonly affected by submergence in four Southeast Asian countries: the Philippines, Lao PDR, Indonesia, and Southern Viet Nam. The study further examined farmers' criteria in evaluating new varieties through the participatory varietal selection (PVS) process. Results showed that varying conditions of submergence can influence farmers' criteria and preferences for rice cultivars. 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' duration and >100 cm depth can cause damage ranging from 40% to 77%. Major findings of PVS trials and preference analysis indicated that farmers prefer rice cultivars that are tolerant of submergence, have early to medium maturity relative to their commonly grown varieties, are resistant to pests and diseases, and are resistant to lodging, among other traits. To enhance adoption, male and female farmers should be involved in the evaluation process. The results of this study can contribute to enhancing breeding programs to develop appropriate varieties that reduce production losses, improve income, and ultimately reduce poverty incidence in submergence-prone areas.Submergence-tolerant rice Participatory varietal selection Farmers' preferences SUB1 gene Sub1 rice Submergence risks