1. Molecular Marker Application to Incorporate Salinity Tolerance to West Africa Rice Varieties Isaac Kofi Bimpong 1, Baboucarr Manneh 1, Bathe Diop 1 and Glenn B. Gregorio 2 1 Africa Rice Centre, Sahel station, B.P 96, Saint Louis, Senegal, 2 International Rice Research Institute (IRRI), DAPO Box 7777, Manila, Philippines Salinity is a serious constraint for rice production in West Africa. Molecular markers are now routinely being used to identify and transfer useful genes/QTLs for salinity tolerance. One of the major QTL (Saltol) derived from the salt-tolerant Indian landrace Pokkali, has been mapped on chromosome 1.The QTL for salt tolerance (SKC1), maintains K + homoeostasis in the salt- tolerant cultivars under salt stress, and the SKC1 gene encodes a member of HKT-type transporters. Fine-mapping of the Saltol QTL and the development of indel markers based on candidate genes in this region is being pursued at IRRI. Marker-assisted backcrossing (MABC) has been used to transfer the Saltol QTL into popular varieties such as IR64, BR28, and BR11. A diverse set of germplasm including the NERICAs (New Rice for Africa), collection from Cassamance regions in Senegal and Gambia are being characterized for physiological traits underlying salinity tolerance to identify new sources of tolerance for use as donors in breeding and identification of novel QTLs. Besides, MABC is currently being used to introgress Saltol into few varieties popular in West Africa. The long term goal is to identify and combine genes/QTLs controlling different physiological mechanisms to achieve a higher level of salt tolerance in high yielding West African rice varieties. Objectives  To use MABC approach to introgress Saltol into several African varieties that will subsequently be deployed for commercial cultivation  Identify new source of suitable donors of major QTLs/genes other than Saltol  Identify new salt tolerance breeding lines using the participatory varietal selection (PVS) approach MABC to introgress Saltol in African Varieties Conclusions Materials and methods Evaluation of physiological traits for salt tolerance A total of 348 germplasm comprising of NERICAs, O. glaberrimas and O. sativas were evaluated for salinity tolerance under controlled conditions. Salt stress was imposed 5 d after germination by adding NaCl to an EC of 12 dS m -1 in Yoshida nutrient solution. IR29 (sensitive) and FL 478 (highly tolerant) were used as checks. Entries were scored based on visual symptoms using IRRI’s Standard evaluation system (SES) scores. New Germplasm Tolerant to Salinity Results African variety/FL478 African variety // BC 1 F 1 Selected BC 1 F 1 BC 1 F 1 BC 2 F 1 Selected BC 2 F 1 African variety / BC 2 F 1 African variety / BC 3 F 2 X BC 3 F 1 Selected BC 3 F 1 BC 3 F 1 Recipient varieties: –IR64, Sahel 108, Sahel 201, BG90-2, Kogoni 91-1, Bouake189, Rassi, NERICA L-19, ITA212 Donors: –Pokkali, FL478 (salt tolerance) Routine use of MAB to transfer Saltol : using flanking SSRs: 11-13 Mb on chrom1 –Foreground (36 markers) –& recombinant markers used for selection after each cross –SSRs for background selection (179 markers) VarietyTolerance to Salinity Country of Origin Jarmissa5Gambia Many Fingo3Gambia Camaro5Gambia Condeh Mano5Gambia Madina Koyo5Senegal Gold Coast Fingo3Gambia Nafisatu5Gambia FL 478 (Tolerant Ck)4IRRI IR 29 (Sensitive Ck)9IRRI  8 Salt tolerant landraces from 188 identified from hydroponic and field screening  Molecular analysis show 5 of 8 appear to have different genes from Saltol  4 out of 104 accession of O. glaberrima; (TOG7230, RAM26, RAM121) tolerant Cross combinationMapping popn used Lines with Saltol identified Seeds produced with Saltol background Rassi x FL478BC2F17 out of 29BC2F2 & BC3F1 Rassi x FL478BC3F25 out of 23BC3F3 & BC4F2 Sahel 108 x POKKALI BC2F16 out of 37BC2F2 & BC3F1 Current status of MABC Saltol (control) qNa+S V-1-1 QSst2 qNa+/ K+SV- 2.2 qNa+L V-3.1 Trait based QTL QPh4chrm6 qNa+/ K+ SV 8-1 QSds8 qDWS- 9/ qSTR- 9 chrm 10 Name RM 10843 RM 572 RM 208 RM 145 RM 563 RM 551 RM 273 RM 336 RM 281 RM 38 RM 215 RM 311 Jarmissa Camaro n.a Codeh mano n.a Madina koyo Gold coast fingo n.a RAM121 TOG6224 TOG7230 NERICA L9 NERICA L23 n..a. NERICA L24 n.a NERICA L27 HASAWI n.a Pokkali FL478 n.a  To genotype for Saltol (10 markers used;  3 each at the upper & lower flanking region  4 Saltol specific markers  Background genotyping using 151 polymorphic markers Comparison of 15 major QTL/genes published as tolerant to salinity other than Saltol with identified tolerant germplasm Blue = tolerance in germplasm is different from the already identified & published QTLs/gene. Yellow = alleles is similar to the already identified & published QTLs/gene n.a= not clear or poor amplification  New source of tolerance have been identified in both O. sativa & O. glaberrima  Saltol gene/QTL have been introgressed into the background of 3 African mega varieties  More than 5 breeding & mapping populations at different stages have been developed  10 salt tolerant lines/varieties identified by NARs after 2 season of PVS Allelic diversity for Saltol QTL with 34 lowland NERICAs Genotype Mean salt injury at EC 12 dSm -1 NERICA-L93 NERICA-L233 NERICA_L245 NERICA_L273 FL 478(Tolerant check)5 IR 29 (Sensitive check)9  4 Nericas-L9, -L23, -L24 & L27: tolerant & different genes from Saltol GambiaMaliSenegal 1WAR 1 WAS 201-B-2 IR 66946-3R-178-1-1 2IR 1907-3R-2-1-2-B IR 59418-7-B-27-3 IR 72593-B-3-2-1-2-B 3IR 63275-B-1-1-1-3-3-2 WAS 202-B-1 IR 59418-7B-21-3 4WAS 73-B-B-84-2 WAS 197-B-8-2 IR 1829-3R-89-1-1 5 CT6163-8-9-5-2-M-134M IR 76393-2B-7-1-13-1 6WAS 73-B-B-231-4 & WAS 236 PVS for Salt Tolerant in 3 countries  After 2 phases of PVS 4-6 promising lines have been selected by farmers  Selected lines being validated in final round of PVS  Main selection criteria :Earliness, plant height, tillering ability, panicle length and weight, resitance to birds,