Mapping QTLs for tolerance to salt stress at the early seedling stage in rice (Oryza sativa L.) using a newly identified donor \u2018Madina Koyo\u2019

Nana Kofi Abaka Amoah,Baboucarr Manneh,Richard Akromah,Isaac Kofi Bimpong,Ibnou Dieng,Alex Wireko Kena

doi:10.1007/s10681-020-02689-5

Abstract

Salt stress is a menace to rice production and a threat to food security worldwide. We evaluated 308 F4 families from Sahel 317/Madina Koyo for tolerance to salt stress at the early seedling stage. To better understand genomic regions controlling tolerance in the population, we genotyped the progenies and the two parents using single nucleotide polymorphism (SNP) markers and regressed the genotypic data on their phenotype to detect QTLs. An average reduction of 63.4% was observed for all fitness-related traits among the F4 families. A total of 46 progenies recorded an average salt injury score (SIS) between 1–3 and were rated as tolerant to salt stress at the early seedling stage. A high-density genetic map was constructed for the 12 rice chromosomes using 3698 SNP markers. Multiple interval mapping identified 13 QTLs for SIS, shoot length, shoot dry weight and root length on chromosomes 2, 3, 4, 6, 7, 10 and 12, with trait increasing alleles coming from both parents. Two (qSDW2 and qRL2.2) and three (qSL2, qRL2.1 and qSIS2) QTLs at different regions on chromosome 2 and another two on chromosome 7 (qSDW7 and qSL7) were tightly linked. These QTLs could facilitate breeding for salt tolerance at the early seedling stage as direct selection for one, would mean indirectly selecting for the other. Fine mapping of these novel QTLs in a different genetic background is necessary to confirm their stability and usefulness in breeding for tolerance to salinity in rice.

Highlights

Salt stress is a major constraint in the production of rice, considerably reducing grain yield while156 Page 2 of 23 rendering vast majority of arable lands unproductive
An average reduction of 63.4% was observed for all fitness-related traits among the F4 families
Through a hydroponic protocol developed by Gregorio et al (1997), it is possible to efficiently evaluate larger number of progenies for tolerance to salt stress at the early seedling stage under homogenous conditions in a relatively shorter period based on visual salt injury score (SIS)

Summary

Introduction

Salt stress is a major constraint in the production of rice, considerably reducing grain yield while156 Page 2 of 23 rendering vast majority of arable lands unproductive. Salt stress is a major constraint in the production of rice, considerably reducing grain yield while. Salt stress is most problematic when it occurs at the early seedling stage and/or the reproductive growth stages. Though it is the reproductive stage salt stress that causes direct yield loss, early seedling stage salt stress is important as it dictates the actual crop stand grain yield. Through a hydroponic protocol developed by Gregorio et al (1997), it is possible to efficiently evaluate larger number of progenies for tolerance to salt stress at the early seedling stage under homogenous conditions in a relatively shorter period based on visual salt injury score (SIS)

Methods

Results

Discussion

Conclusion