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 and excels all other cereals due to its unique features of resilience to adverse climatic conditions. It is rich in micronutrients like iron and zinc and amenable for focused breeding for these micronutrients along with high yield. Hence, this is a key to alleviate malnutrition and ensure nutritional security. This study was conducted to identify and validate candidate genes governing grain iron and zinc content enabling the desired modifications in the genotypes. 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 iron and zinc showed differential gene expression during different stages. Of which, 155 were up-regulated and 251 were 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. Information generated will help in gaining insights into iron and zinc metabolism and develop genotypes with high yield, grain iron and zinc content.

A Genome-Wide Association Study Identifying Single-Nucleotide Polymorphisms for Iron and Zinc Biofortification in a Worldwide Barley Collection

“…They are involved in several functions related to metal transport, ion binding, and remobilization of Fe and Zn into grains. For example, candidate genes such as the cytochrome P450 superfamily participate in element transport [ 12 ]. Other proteins expressed in low Fe and Zn conditions, including acyl-ACP thioesterase and ribosomal protein, respectively, were identified in this study, [ 13 , 14 ] ( Supplement Tables S2 and S3 ).…”

“…On the other hand, we have identified important candidate genes for SNPs ( p < 0.001). They correspond to genes such as the cytochrome P450 superfamily protein, which is involved in element transport, iron and zinc binding, and is found in genotypes with a higher Fe and Zn content [ 12 ]. This study identified serine/threonine-protein kinase, which is an ATP and protein binder [ 21 ].…”

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 [ 21 , 22 , 23 , 24 , 25 , 26 ]. However, none of the studies performed coexpression analysis to discover genes that regulate abiotic-stress-related traits.…”

Comparative transcriptome profiling of high and low grain-iron containing Indian barnyard millet (Echinochloa frumentacea L.) genotypes during different stages of grain development

“…In the present investigation, we have tried to identify the genes responsible for the accumulation of Fe in the grains of barnyard millet. These genes include ABC Transporter family proteins, Calcium-dependent kinase family, Ferritin, Metal ion binding, Iron-sulfur cluster binding, Cytochrome family, Zinc nger transcription factor family, Ferredoxin-NADP reductase type 1 family, Putative laccase, Multicopper oxidase family and Terpene synthase 27,28,29 . However, the stage of spike development is also for maximum accumulation of Fe in the grains.…”