Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL

Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs over gene families, biosynthetic pathways or certain traits represent functional gene-clusters of genes of the same gene ontology (GO). Gene-clusters containing genes of different GO have not been elaborated, except in silico as coexpressed genes within QTLs. Here we demonstrate the requirement of multiple intra-QTL genes for the full impact of QTL qDTY(12.1) on rice yield under drought. Multiple evidences are presented for the need of the transcription factor ‘no apical meristem’ (OsNAM(12.1)) and its co-localized target genes of separate GO categories for qDTY(12.1) function, raising a regulon-like model of genetic architecture. The molecular underpinnings of qDTY(12.1) support its effectiveness in further improving a drought tolerant genotype and for its validity in multiple genotypes/ecosystems/environments. Resolving the combinatorial value of OsNAM(12.1) with individual intra-QTL genes notwithstanding, identification and analyses of qDTY(12.1)has fast-tracked rice improvement towards food security.