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

Haritha Guttikonda,Rajeshwari Ramanan,Sarla Neelamraju,Shashi Rekha Thummala,Satendra K Mangrauthia,Surekha Agarwal

doi:10.1038/s41598-020-60922-6

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.

Highlights

Rice (Oryza sativa) is an important food crop providing 20% of daily calories to more than 50 percent of global population
The transcriptome of flag leaf of test hybrid was compared with that of control hybrid to know the effect of O. rufipogon introgressions in the hybrid
The analysis revealed that the differentially expressed genes (DEGs) involved in major metabolic pathways such as carbohydrate metabolism, phenyl propanoid pathway, ubiquitin - dependent degradation and jasmonic acid pathways play a key role in contributing to grain yield in test hybrid

Summary

Introduction

Rice (Oryza sativa) is an important food crop providing 20% of daily calories to more than 50 percent of global population. The whole-genome oligonucleotide microarray of flag leaves in three super-hybrid rice combinations LY2163 (SE21s x MH63), LY2186 (SE21s x MH86) and LYP9 (PA64s x 93-11) and their respective parental lines at flowering and grain filling stages showed that DEGs in all three super-hybrid combinations were significantly enriched in carbon fixation pathway, starch and sucrose metabolic pathway and flavonoid biosynthesis pathway[24]. In addition the test hybrid IR79156A × IL50-13 [IET 24441 (DRRH 102)] was tested in multilocation trials of All India Coordinated Rice Improvement Program (AICRIP) in 2014 It gave mean grain yield of 2.2 t/ha and showed 14% yield advantage over the best salinity check variety CSR10 and 24% over the yield check variety Jaya and was promoted to advanced variety trial 1 - Coastal Saline Tolerant Variety Trial (AVT 1 -CSTVT)[29].

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