Transcriptome profiling of developmental leaf senescence in sorghum (Sorghum bicolor)

Abstract

This piece of the submission is being sent via mail. Leaf senescence is essential for the nutrient economy of crops and is executed by so-called senescence-associated genes (SAGs). Here we explored the monocot C model crop Sorghum bicolor for a holistic picture of SAG profiles by RNA-seq. Leaf samples were collected at four stages during developmental senescence, and in total, 3396 SAGs were identified, predominantly enriched in GO categories of metabolic processes and catalytic activities. These genes were enriched in 13 KEGG pathways, wherein flavonoid and phenylpropanoid biosynthesis and phenylalanine metabolism were overrepresented. Seven regions on Chromosomes 1, 4, 5 and 7 contained SAG 'hotspots' of duplicated genes or members of cupin superfamily involved in manganese ion binding and nutrient reservoir activity. Forty-eight expression clusters were identified, and the candidate orthologues of the known important senescence transcription factors such as ORE1, EIN3 and WRKY53 showed "SAG" expression patterns, implicating their possible roles in regulating sorghum leaf senescence. Comparison of developmental senescence with salt- and dark- induced senescence allowed for the identification of 507 common SAGs, 1996 developmental specific SAGs as well as 176 potential markers for monitoring senescence in sorghum. Taken together, these data provide valuable resources for comparative genomics analyses of leaf senescence and potential targets for the manipulation of genetic improvement of Sorghum bicolor.

Integrated Genome-Scale Analysis Identifies Novel Genes and Networks Underlying Senescence in Maize

“…We have performed transcriptomic analysis of leaf and internode tissues in the maize B73 inbred line undergoing premature senescence induced by lack of seed sink and identified genes involved in source-sink-regulated senescence (Sekhon et al, 2012). Differentially expressed (DE) genes during senescence have also been identified in sorghum (Johnson et al, 2015;Wu et al, 2016), wheat (Gregersen and Holm, 2007), and rice (Ma et al, 2005). While these studies provide general insights into global senescence-related transcriptome, identification of the underlying causal genes is difficult due to a large number of DE candidates.…”

Global transcriptome analysis of the maize (Zea mays L.) inbred line 08LF during leaf senescence initiated by pollination-prevention

“…An in-house Perl script was employed to remove paired-end reads that consisted of >5% ambiguous residues (Ns), in addition to those showing >10% bases and with a Phred quality score of <20 [ 17 ]. DEGs identification was performed as described elsewhere [ 31 ].…”

“…In recent years, several senescence-associated genes ( SAGs ) have been identified in various species at the transcriptional level [ 5 , 8 , 15 – 17 ]. Early senescence has been induced in the inbred maize line B73 by preventing pollination [ 18 ].…”

Global transcriptome analysis of alfalfa reveals six key biological processes of senescent leaves

“…NGS technologies are very powerful tools for RNA-seq and genomic studies because they are high throughput, and the read length and error rate can be determined (Metzker, 2010;Ozsolak & Milos, 2011). Several studies have used RNA-seq to investigate leaf senescence in plants such as Medicago truncatula, Arabidopsis, Sorghum bicolor, Gossypium hirsutum, Panicum virgatum, and maize (Buchanan-Wollaston et al, 2005;De Michele et al, 2009;Li et al, 2010;Lin et al, 2015;Palmer et al, 2015;Wu et al, 2016). Alfalfa is allogamous and autotetraploid that result in genetic background complexity (Gherardi et al, 1998).…”