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In this study, we compared genome-wide transcriptome profile of two rice hybrids, one with (test hybrid IR79156A/IL50-13) and the other without (control hybrid IR79156A/KMR3)  O. rufipogon  introgressions to identify candidate genes related to grain yield in the test hybrid. IL50-13 (Chinsurah Nona2 IET21943) the male parent (restorer) used in the test hybrid, is an elite BC 4 F 8  introgression line of KMR3 with  O. rufipogon  introgressions. We identified 2798 differentially expressed genes (DEGs) in flag leaf and 3706 DEGs in panicle. Overall, 78 DEGs were within the major yield QTL  qyld2.1  and 25 within minor QTL  qyld8.2 . The DEGs were significantly ( p  < 0.05) enriched in starch synthesis, phenyl propanoid pathway, ubiquitin degradation and phytohormone related pathways in test hybrid compared to control hybrid. Sequence analysis of 136 DEGs from KMR3 and IL50-13 revealed 19 DEGs with SNP/InDel variations. Of the 19 DEGs only 6 showed both SNP and InDel variations in exon regions. Of these, two DEGs within  qyld2.1 ,  Phenylalanine ammonia- lyase  (PAL) (Os02t0626400-01,  OsPAL2 ) showed 184 SNPs and 11 InDel variations and  Similar to phenylalanine ammonia- lyase  (Os02t0627100-01,  OsPAL4 ) showed 205 SNPs and 13 InDel variations. Both PAL genes within  qyld2.1  and derived from  O. rufipogon  are high priority candidate genes for increasing grain yield in rice.

Genome-wide transcriptome profile of rice hybrids with and without Oryza rufipogon introgression reveals candidate genes for yield