Impairment in a member of AP2/ERF and F-box family protein enhances complete panicle exsertion, an economically important trait in rice.

Complete panicle exsertion (CPE) is an economically important quantitative trait that contributes to grain yield in rice. We deployed an integrated approach for understanding the molecular mechanism of CPE using a stable EMS mutant line, CPE-109 of Samba Mahsuri (SM) exhibiting CPE. Two consistent genomic regions have been identified for CPE through QTL mapping [qCPE-4 (28.24-31.22 Mb) and qCPE-12 (2.30-3.18 Mb)] and QTL-sequencing [Chr-4 (31.21-33.69 Mb) and Chr-12 (0.12-3.15 Mb)]. Two non-synonymous SNPs, viz; KASP 12-12 (T→C; Chr12:1269983) in Os12g0126300; AP2/ERF transcription factor and KASP 12-16 (G→A; Chr12:1515198) in Os12g0131400; F-box domain-containing protein explained 81.05 and 59.61% phenotypic variance respectively and exhibited strong co-segregation with CPE in F2 mapping populations, advanced generation lines and CPE exhibiting SM mutants through KASP assays. The downregulation of these genes in CPE-109 compared to SM was observed in transcriptome sequencing of flag leaves which was validated through qRT-PCR. We propose that the abrogation of Os12g0126300 and Os12g0131400 in CPE-109 combinatorially influences the downregulation of ethylene biosynthetic genes viz. ACC synthase, ethylene-responsive factor-2, and up-regulation of gibberellic acid synthetic genes viz. ent-kaurene synthase and two cytokinin biosynthesis genes viz. cytokinin-O-glucosyltransferase 2, carboxy-lyase which result in complete panicle exsertion.

Multiomics-assisted characterization of rice-Yellow Stem Borer interaction provides genomic and mechanistic insights into stem borer resistance in rice.

KEY MESSAGE: By deploying a multi-omics approach, we unraveled the mechanisms that might help rice to combat Yellow Stem Borer infestation, thus providing insights and scope for developing YSB resistant rice varieties. Yellow Stem Borer (YSB), Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae), is a major pest of rice, that can lead to 20-60% loss in rice production. Effective management of YSB infestation is challenged by the non-availability of adequate sources of resistance and poor understanding of resistance mechanisms, thus necessitating studies for generating resources to breed YSB resistant rice and to understand rice-YSB interaction. In this study, by using bulk-segregant analysis in combination with next-generation sequencing, Quantitative Trait Loci (QTL) intervals in five rice chromosomes were mapped that could be associated with YSB resistance at the vegetative phase in a resistant rice line named SM92. Further, multiple SNP markers that showed significant association with YSB resistance in rice chromosomes 1, 5, 10, and 12 were developed. RNA-sequencing of the susceptible and resistant lines revealed several genes present in the candidate QTL intervals to be differentially regulated upon YSB infestation. Comparative transcriptome analysis revealed a putative candidate gene that was predicted to encode an alpha-amylase inhibitor. Analysis of the transcriptome and metabolite profiles further revealed a possible link between phenylpropanoid metabolism and YSB resistance. Taken together, our study provides deeper insights into rice-YSB interaction and enhances the understanding of YSB resistance mechanism. Importantly, a promising breeding line and markers for YSB resistance have been developed that can potentially aid in marker-assisted breeding of YSB resistance among elite rice cultivars.