Genomic Regions and Molecular Markers Associated with Deeper Rooting to Improve Grain Yield in Aerobic Rice (Oryza sativa L.) Production Systems

A greater proportion of deep roots could ensure water uptake at depth and is considered a key trait for aerobic adaptation. However, the study of genomic regions and molecular markers related to deep rooting is limited especially for aerobic rice production. This study utilised 705 genotypes composed of recombinant inbred lines and predominantly diverse japonica sets to identify and validate genomic regions associated with the proportion of deep roots below 20 cm (DR20). Six quantitative trait loci (QTL) for DR20 were identified under well-watered aerobic conditions, explaining 5.3-23.7% of the phenotypic variance and introgression of the favourable alleles resulted in 10-21.6% deeper roots. Simultaneous development of high throughput molecular markers and QTL validation demonstrated the effect of four (qADR1, qADR9, qADR10, and qADR11) out of six QTL increasing DR20 up to 29.4% across genetic backgrounds. The four QTL also conferred a mean grain yield advantage of 1.46 t/ha. This study reports for the first time validated genomic regions and high throughput molecular markers associated with deeper rooting and improved grain yield in rice under aerobic conditions. These tools may accelerate the development of rice adapted to aerobic production systems and ultimately enhance sustainable rice production in areas with limited water availability.