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

Abstract

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 BC₄F₈ 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.

Figure 1

Volcano plot showing gene expression differences in (a) flag leaf and (b) panicles of test hybrid IR79156A/IL50-13 with P-values and intensity ratios as log-scaled axes. Significant differences at p < 0.05 with >1-fold and <1 fold intensity ratios are shown. Blue: Fold <= −1 & p-value >0.05, Yellow: Fold >= 1 & p-value > 0.05, Green: Fold <= −1 & p-value <0.05, Red: Fold >= 1 & p-value <0.05. (c) Venn diagrams of up-regulated genes (d) down-regulated genes in flag leaf and panicle of test hybrid in comparison with control hybrid.

Figure 2

Gene Ontology enrichment analysis of differentially expressed genes by WEGO (Web Gene Ontology Annotation Plot -http://wego.genomics.org.cn/cgi-bin/wego/index.pl). The P-value is below the significance level of p < 0.05. Percentage of enrichment is also shown (a) flag leaf (b) panicle.

Figure 3

Phenyl propanoid biosynthesis pathway in rice. The green squares represent down-regulation and red squares represent up-regulation in test hybrid (a) flag leaf (b) panicle.

Figure 4

Schematic representation of the ubiquitination reaction involving a HECT-type E3. The green squares represent down-regulation and red squares represent up-regulation in test hybrid (a) flag leaf (b) panicle.