Meta-QTL analysis identified stable quantitative trait loci (QTLs) and associated resistance gene analogues in rice

Abstract

Disease resistant rice varieties are mandatory for sustainable rice production to ensure the global food supply. This study aimed to identify meta-QTLs associated with the disease resistance and candidate R-genes. A consensus map was constructed by merging 9 QTL mapping studies, 115 QTLs and 943 markers. The consensus map was 1554.71 cm in length with a 1.65 cm-1 average marker density. Totally, 24 meta-QTLs were projected on the consensus chromosome maps except on chromosomes 5, 6, and 10. Larger effect meta-QTLs (R2 ≥ 25 to 56 %) were reported on chromosomes 1, 2, 3, 4, 8, and 11. Three or more meta-QTLs were predicted on 1, 2, 7, 8, and 9 chromosomes. More than 62 % of the meta-QTLs were contributed by 3 or more mapping studies. Furthermore, 6 of the putative meta-QTLs collocated with 11 meta-QTLs from previous studies, and 23 resistance loci that are used in existing resistance breeding programs indicating robust expression. Nine meta-QTLs were associated with blast (BL) resistance whereas 14 were associated with both BL and sheath blight (SHB) resistance. Candidate gene mining identified 79 disease resistance gene analogues (RGAs) of which 74 % were complete putative R genes. Nine of the meta-QTLs predicted clusters of RGAs. Out of these, expression of LOC_Os11g12340 was cross-validated using publicly available expression data in tissues infected with M. oryzae, indicating a functional role of this gene in the disease cycle. The outcome clearly exposed genomic abundance of R-genes and their potential functional redundancy. Further, these findings provide potential resources for rice breeding for disease resistance.