Molecular Marker Application to Incorporate Salinity Tolerance to West Africa Rice Varieties

1. African variety // African variety/FL478 BC1F1 Selected BC1F1 / BC1F1 African variety BC2F1 Selected BC2F1 BC2F1 / African variety BC3F1 Selected BC3F1 BC3F1 X BC3F2 Molecular Marker Application to Incorporate Salinity Tolerance to West Africa Rice Varieties Isaac Kofi Bimpong1, Baboucarr Manneh1, Bathe Diop1 and Glenn B. Gregorio2 1Africa Rice Centre, Sahel station, B.P 96, Saint Louis, Senegal, 2 International Rice Research Institute (IRRI), DAPO Box 7777, Manila, Philippines • 4 Nericas-L9, -L23, -L24 & L27: tolerant & different genes from Saltol 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 Allelic diversity for Saltol QTL with 34 lowland NERICAs • 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 Comparison of 15 major QTL/genes published as tolerant to salinity other than Saltol with identified tolerant germplasm 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. MABC to introgress Saltol in African Varieties • 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) 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 PVS for Salt Tolerant in 3 countries Results Current status of MABC • 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 • After 2 phases of PVS 4-6 promisinglines have been selected by farmers • Selected linesbeingvalidated in final round of PVS • Main selectioncriteria :Earliness, plant height, tilleringability, paniclelength and weight, resitance to birds, Conclusions 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 New Germplasm Tolerant to Salinity • 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