Multiple Small-Effect Alleles of Indica Origin Enhance High Iron-Associated Stress Tolerance in Rice Under Field Conditions in West Africa

Abstract

Understanding the genetics of field-based tolerance to high iron-associated (HIA) stress in rice can accelerate the development of new varieties with enhanced yield performance in West African lowland ecosystems. To date, few field-based studies have been undertaken to rigorously evaluate rice yield performance under HIA stress conditions. In this study, two NERICA × O. sativa bi-parental rice populations and one O.sativa diversity panel consisting of 296 rice accessions were evaluated for grain yield and leaf bronzing symptoms over multiple years in four West African HIA stress and control sites. Mapping of these traits identified a large number of QTLs and single nucleotide polymorphisms (SNPs) associated with stress tolerance in the field. Favorable alleles associated with tolerance to high levels of iron in anaerobic rice soils were rare and almost exclusively derived from the indica subpopulation, including the most favorable alleles identified in NERICA varieties. These findings highlight the complex genetic architecture underlying rice response to HIA stress and suggest that a recurrent selection program focusing on an expanded indica genepool could be productively used in combination with genomic selection to increase the efficiency of selection in breeding programs designed to enhance tolerance to this prevalent abiotic stress in West Africa.

Below-ground plant-soil interactions affecting adaptations of rice to iron toxicity

“…Sikirou et al (2018) evaluated more than 2000 O. glaberrima accessions in the Africa Rice Center gene bank at multiple Fe toxic hotspots across West Africa, and identified highly tolerant accessions such as TOG 7250-A, TOG 14367, TOG 7206 and TOG 6218-B. Melandri et al (2021) confirmed the tolerance of some of these accessions. This suggests transferring genes/alleles conferring Fe toxicity tolerance from O. glaberrima to high yielding O. sativa varieties as a promising breeding strategy.…”

“…6 implications for rice breeding 6 .1 Tolerance within the Oryza gene pool Numerous studies have screened sets of varieties or larger germplasm collections in attempts to identify donors for Fe toxicity, typically employing one of two main screening strategies. They may have been conducted in the field in Fe toxic hotspots, evaluating grain yield in addition to biomass and leaf symptoms (Melandri et al, 2021;Pawar et al 2021;Sikirou et al 2018), or they were designed as rapid screens in nutrient solution to which excess Fe had been added at high concentrations for short periods of time (Dufey et al 2015;Matthus et al 2015). From these and other studies it can be concluded that ample genetic variation for tolerance to Fe toxicity exists within theO.…”

“…The indigenous African rice O. glaberrima , domesticated from its wild ancestor O. barthii about 3500 years ago (Heuer et al, 2003), includes accessions tolerant of a wide range of abiotic stresses, including Fe toxicity (Linares et al, 2002;Melandri et al, 2021;Sié et al, 2012;Sikirou et al, 2018). Sikirou et al (2018) evaluated more than 2000 O. glaberrima accessions in the Africa Rice Center gene bank at multiple Fe toxic hotspots across West Africa, and identified highly tolerant accessions such as TOG 7250-A, TOG 14367, TOG 7206 and TOG 6218-B.…”

“…Where such environmental variation reduces the reliability of phenotyping, marker assisted selection rather than conventional phenotypic selection should be the breeding method of choice. Markers associated with aspects of Fe toxicity tolerance exist, identified through genome-wide associations studies (GWAS) (Matthus et al 2015;Pawar et al 2021;Melandri et al, 2021) or through bi-parental QTL mapping populations (Dufey et al 2015;Rasheed et al, 2020 and references therein). To our knowledge none of these studies identified loci with large enough effects to be utilized in applied breeding.…”

“…Hence yield losses are only weakly correlated with above-ground symptoms, though these are widely used for screening (Sikirou et al 2015). Most work on tolerance mechanisms has been done in hydroponics, far removed from field reality, and there has been limited progress with the genetics of tolerance and gene mapping (Dufey et al, 2015;Matthus et al, 2015;Melandri et al, 2021;Pawar et al, 2021;Sikirou et al, 2018). There is a need for an integrated approach to understand the mechanisms and genetics of Fe toxicity tolerance, taking account of the complex below-ground plant-soil interactions.…”