Transcriptome Analysis of Pennisetum glaucum (L.) R. Br. Provides Insight Into Heat Stress Responses

Albert Maibam; Showkat Ahmad Lone; Sunil Ningombam; Kishor Gaikwad; S V Amitha Mithra; Madan Pal Singh; Sumer Pal Singh; Monika Dalal; Jasdeep Chatrath Padaria

doi:10.3389/fgene.2022.884106

Transcriptome Analysis of Pennisetum glaucum (L.) R. Br. Provides Insight Into Heat Stress Responses

Front Genet. 2022 Jun 2:13:884106. doi: 10.3389/fgene.2022.884106. eCollection 2022.

Authors

Affiliations

¹ PG School, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India.
² Indian Council of Agricultural Research -National Institute for Plant Biotechnology, New Delhi, India.
³ Division of Plant Physiology, Indian Council of Agricultural Research -Indian Agricultural Research Institute, New Delhi, India.
⁴ Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India.

Abstract

Pennisetum glaucum (L.) R. Br., being widely grown in dry and hot weather, frequently encounters heat stress at various stages of growth. The crop, due to its inherent capacity, efficiently overcomes such stress during vegetative stages. However, the same is not always the case with the terminal (flowering through grain filling) stages of growth, where recovery from stress is more challenging. However, certain pearl millet genotypes such as 841-B are known to overcome heat stress even at the terminal growth stages. Therefore, we performed RNA sequencing of two contrasting genotypes of pearl millet (841-B and PPMI-69) subjected to heat stress (42°C for 6 h) at flowering stages. Over 274 million high quality reads with an average length of 150 nt were generated, which were assembled into 47,310 unigenes having an average length of 1,254 nucleotides, N50 length of 1853 nucleotides, and GC content of 53.11%. Blastx resulted in the annotation of 35,628 unigenes, and functional classification showed 15,950 unigenes designated to 51 Gene Ontology terms. A total of 13,786 unigenes were allocated to 23 Clusters of Orthologous Groups, and 4,255 unigenes were distributed to 132 functional Kyoto Encyclopedia of Genes and Genomes database pathways. A total of 12,976 simple sequence repeats and 305,759 SNPs were identified in the transcriptome data. Out of 2,301 differentially expressed genes, 10 potential candidate genes were selected based on log2 fold change and adjusted p value parameters for their differential gene expression by qRT-PCR. We were able to identify differentially expressed genes unique to either of the two genotypes, and also, some DEGs common to both the genotypes were enriched. The differential expression patterns suggested that 841-B 6 h has better ability to maintain homeostasis during heat stress as compared to PPMI-69 6 h. The sequencing data generated in this study, like the SSRs and SNPs, shall serve as an important resource for the development of genetic markers, and the differentially expressed heat responsive genes shall be used for the development of transgenic crops.

Keywords: Pennisetum glaucum (L.) R. Br.; RNA sequencing (RNAseq); SNPs (single-nucleotide polymorphisms); SSRs (simple sequence repeats); flag leaf; heat stress (HS).