Stage Specific Comparative Transcriptomic Analysis To Reveal Gene Networks Regulating Iron And Zinc Content In Pearl Millet [Pennisetum glaucum (L.) R. Br.]

Abstract

Pearl millet is an important staple food crop of poor people which is rich in micronutrients like iron and zinc and amenable for focused breeding for these micronutrients along with high yield. Transcriptome sequencing using ION S5 Next Generation Sequencer generated 43.5 million sequence reads resulting in 83,721 transcripts with N50 of 597 bp and 84.35% of transcripts matched with the pearl millet genome assembly. The genotypes having high Fe and Zn showed differential gene expression during different stages. Of which, 155 were up-regulated and 251were down-regulated while during flowering stage and milking stage 349 and 378 transcripts were differentially expressed, respectively. Gene annotation and GO term showed the presence of transcripts involved in metabolic activities associated with uptake and transport of iron and zinc. In the present study, the 83,721 transcripts were also examined for identification of SSRs. A total of 4,327 SSRs were identified with dominance of tri-nucleotide SSRs in comparison to di-nucleotide SSRs. These EST-SSRs can be used in molecular breeding, genetic diversity analysis and determination of heterozygosity of the allelic loci. Information generated will help in gaining insights into iron and zinc metabolism and develop genotypes with high yield, grain iron and zinc content.

Genome-wide association study and expression of candidate genes for Fe and Zn concentration in sorghum grains

“…However, there is no specific information on how cytochrome P450 gene is involved in Fe and Zn uptake. Satyavathi et al 106 identified a cytochrome P450 superfamily protein involved in element transport, iron, and zinc binding, and found out that it was present in the genotypes with high Fe and Zn contents. A study on rice biofortification with zinc and selenium found that the expression pattern of a Cytochrome P450 (CYP) gene followed the mineral accumulation in flag leaves 107 .…”

Genetic and genomic interventions in crop biofortification: Examples in millets

“…In a recent study, transcriptome profiling of stage-specific spikes of pearl millet genotypes contrasting for grain Fe and Zn content was performed to identify candidate genes expressed in developing spikes and those associated with the variation in Fe and Zn levels (Satyavathi et al, 2022). Here, 155 and 251 transcripts were found to be up-and downregulated, respectively, in the genotypes showing high Fe and Zn content, whereas 349 and 378 transcripts were differentially expressed during the flowering and milking stages of development, respectively.…”

“…Here, 155 and 251 transcripts were found to be up-and downregulated, respectively, in the genotypes showing high Fe and Zn content, whereas 349 and 378 transcripts were differentially expressed during the flowering and milking stages of development, respectively. Gene Ontology analysis revealed that the genes involved in metabolic activities were primarily associated with uptake and transport of Zn and Fe in pearl millet (Satyavathi et al, 2022). Since finger millet grains contain higher levels of calcium content, RNA-seq of spike tissues of two finger millet genotypes contrasting for calcium content (GP-45, high calcium content; GP-1, low calcium content) was performed (Singh et al, 2014).…”

Gene coexpression analysis identifies genes associated with chlorophyll content and relative water content in pearl millet

“…Pearl millet is a staple crop of arid and semi-arid tropics and is known for its unique ability to tolerate abiotic stress. Various studies used a genomic approach to identify genes and pathways related to abiotic stress in pearl millet (20)(21)(22)(23)(24)(25). But none of the studies performed a coexpression analysis to discover genes that regulate abiotic stress-related traits.…”