Upland rice production is limited by the low phosphorus (P) availability of many highly weathered tropical soils and P deficiency is likely to become increasingly limiting in future drier climates because P mobility decreases sharply with soil moisture. Good seedling root development will be crucial to cope with the combined effects of low P and water availability. Upland rice genebank accession DJ123 was used as a donor for P efficiency and root vigor traits in a cross with inefficient local variety Nerica4 and a set of backcross lines were used to characterize the seedling stage response of upland rice to low P availability and to identify associated QTL in field trials in Japan and Madagascar. Ten QTL were detected for crown root number, root, shoot and total dry weight per plant in a highly P deficient field in Japan using the BC1F3 generation. Of these, qPef9 on chromosome 9 affected multiple traits, increasing root number, root weight and total biomass, whereas a neighboring QTL on chromosome 9 (qPef9-2) increased shoot biomass. Field trials with derived BC1F5 lines in a low-P field in Madagascar confirmed a highly influential region on chromosome 9. However, qPef9-2 appeared more influential than qPef9, as the shoot and root biomass contrast between lines carrying DJ123 or Nerica4 alleles at qPef9-2 was +23.8% and +13.5% compared to +19.2% and +14.4% at qPef9. This advantage increased further during the growing season, leading to 46% higher shoot biomass at the late vegetative stage. Results suggest an introgression between 8.0 and 12.9 Mb on chromosome 9 from P efficient donor DJ123 can improve plant performance under P-limited conditions. The QTL identified here have practical relevance because they were confirmed in the target genetic background of the local variety Nerica4 and can therefore be applied directly to improve its performance.

Key message Despite phenotyping the training set under unfavorable conditions on smallholder farms in Madagascar, we were able to successfully apply genomic prediction to select donors among gene bank accessions. Abstract Poor soil fertility and low fertilizer application rates are main reasons for the large yield gap observed for rice produced in sub-Saharan Africa. Traditional varieties that are preserved in gene banks were shown to possess traits and alleles that would improve the performance of modern variety under such low-input conditions. How to accelerate the utilization of gene bank resources in crop improvement is an unresolved question and here our objective was to test whether genomic prediction could aid in the selection of promising donors. A subset of the 3,024 sequenced accessions from the IRRI rice gene bank was phenotyped for yield and agronomic traits for two years in unfertilized farmers’ fields in Madagascar, and based on these data, a genomic prediction model was developed. This model was applied to predict the performance of the entire set of 3024 accessions, and the top predicted performers were sent to Madagascar for confirmatory trials. The prediction accuracies ranged from 0.10 to 0.30 for grain yield, from 0.25 to 0.63 for straw biomass, to 0.71 for heading date. Two accessions have subsequently been utilized as donors in rice breeding programs in Madagascar. Despite having conducted phenotypic evaluations under challenging conditions on smallholder farms, our results are encouraging as the prediction accuracy realized in on-farm experiments was in the range of accuracies achieved in on-station studies. Thus, we could provide clear empirical evidence on the value of genomic selection in identifying suitable genetic resources for crop improvement, if genotypic data are available.

Rice (Oryza sativa L.) is a staple food of Madagascar, where per capita rice consumption is among the highest worldwide. Rice in Madagascar is mainly grown on smallholder farms on soils with low fertility and in the absence of external inputs such as mineral fertilizers. Consequently, rice productivity remains low and the gap between rice production and consumption is widening at the national level. This study evaluates genetic resources imported from the IRRI rice gene bank to identify potential donors and loci associated with low soil fertility tolerance (LFT) that could be utilized in improving rice yield under local cultivation conditions. Accessions were grown on-farm without fertilizer inputs in the central highlands of Madagascar. A Genome-wide association study (GWAS) identified quantitative trait loci (QTL) for total panicle weight per plant, straw weight, total plant biomass, heading date and plant height. We detected loci at locations of known major genes for heading date (hd1) and plant height (sd1), confirming the validity of GWAS procedures. Two QTLs for total panicle weight were detected on chromosomes 5 (qLFT5) and 11 (qLFT11) and superior panicle weight was conferred by minor alleles. Further phenotyping under P and N deficiency suggested qLFT11 to be related to preferential resource allocation to root growth under nutrient deficiency. A donor (IRIS 313–11949) carrying both minor advantageous alleles was identified and crossed to a local variety (X265) lacking these alleles to initiate variety development through a combination of marker-assisted selection with selection on-farm in the target environment rather than on-station as typically practiced.

A corrigendum on QTL mapping for early root and shoot vigor of upland rice (Oryza sativa L.) under P deficient field conditions in Japan and Madagascar