Re-envisioning QTL dynamics in rice: Interaction of the drought-mediated yield penalty QTL qDTY12.1 with its genetic background
Kaur, Pushpinder Pal
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Breeding to improve the drought tolerance of rice with respect to yield retention under drought have been underway for quite some time now. The discovery of large-effect QTL (qDTY) and their introgression into elite genetic backgrounds is on-going. Recurrent backcross introgression has been the typical method by which breeders have been seeking to introgress beneficial traits while maintaining as high a percentage of the recipient parent’s genomic landscape as intact as possible. The result of the recurrent backcrossing has been the complete loss of qDTY function. Against this backdrop, this study sought to redefine QTL dynamics post-introgression. The objective of this study was to investigate qDTY12.1 function and possible interactions with the genetic landscape of the recurrent genetic background. Transcriptomic analysis showed that in siblings of a cross between cv. IR64 and Way Rarem/Vandana, the two sibling backcrossed introgression lines (BILs, i.e., LPB and HPB) had very divergent drought phenotypes and showed inherited patterns of gene expression from the donor of qDTY12.1, Way Rarem. These inherited patterns were seen at the transcription factor, whole transcriptome, and stress-related gene level. Notably, the inherited patterns were located outside the qDTY12.1 boundary region. More importantly, this study uncovered a genetic network whose founder was a locus within qDTY12.1, a gene annotated as ‘Decussate’. The genetic circuit that emerged was functionally related to many yield related traits and it showed constitutive expression during the transition from vegetative to reproductive stage (i.e., early booting) and further enhanced by stress thus making the drought tolerant introgression line (LPB) more stress-prepared. The importance of the Decussate gene to yield was validated in Arabidopsis thaliana with the use of mutants whose Decussate ortholog was knocked-out by T-DNA insertion. Together the results of this study demonstrate that upon introgression, dynamic interactions occurred between the qDTY12.1 and the recurrent genomic landscape within which it is operating and that these interactions are unique, even though they contain qDTY12.1. It is then proposed that the unique alliances necessary for the full potential of qDTY12.1 genes for the maintenance of grain yield under drought are the results of very specific interactions between qDTY12.1 and other genes or alleles in the recurrent genetic background. These interactions center around a genetic circuit, whose founder is the Decussate gene encoded by qDTY12.1.