Pyramiding salt tolerant QTLs of rice landrace Horkuch using fluorescence-based marker (KASP) enhances tolerance of commercial varieties

Abstract Introduction: Pyramiding salt-tolerant QTLs using SNP markers could be a useful approach to address the threat of salinity intrusion caused by climate change. Horkuch, a landrace endemic to the coastal regions of Bangladesh, has multiple salt-tolerant loci previously identified in RILs of reciprocal crosses between Horkuch and IR29 rice. Salt-tolerant QTLs of Horkuch found in two RILs, I-14 and I-71, were novel QTLs related to root length in chromosome 2, Potassium ion concentration located in chromosome 3, and the variant Horkuch-specific Saltol allele on chromosome 1. Methodology: These three QTLs were introduced together into each of the Bangladeshi commercial high-yielding cultivars BD63, and BD74 and moderately salt-tolerant cultivar BD67 for the first time by crossing and repeated backcrossing. The fluorescence marker-based KASP method was used for precisely introducing these three QTLs in the background of the BRRI cultivars. Eight markers tightly linked to the QTLs and eight recombinant markers at two ends of the QTLs were used for the target loci. Background selection was done using 78 SNP markers. Results: Recovery of 64.7–90% of the recipient genome was achieved by the BC 2 F 2 generation. BC 2 F 3 progenies carrying all three QTLs exhibited significantly enhanced root length, improved K + homeostasis, and robust salinity tolerance in laboratory assays. They also exhibited improved tolerance and yield traits compared to their respective high-yielding parents in field trials in the coastal saline region. This work has the potential to produce suitable breeding lines for the ever-increasing soil salinity in the coastal region of Bangladesh.