Transcriptome Analysis of Two Flax Varieties at Different Developmental Stages Reveals Significant Differential Expression of Genes Related to Stem Fiber Development

Abstract

Flax stem bast fiber, a natural raw material used to make textiles, possesses poor heat and dye resistance, excessive stiffness and low elasticity. To improve fiber quality and quantity, flax fiber development-related differentially expressed genes (DEGs) were identified using RNA-seq of middle stems of Agatha and White Flower varieties during the rapid growth period and mature green stage. There were 300 and 486 DEGs at two developmental stages between the two varieties, respectively. Comparisons of DEGs between developmental stages yielded 2504 DEGs for Agatha and 2986 DEGs for White Flower. Of these, 710 and 1182 DEGs were solely expressed in Agatha and White Flower, respectively. For both varieties, the plant circadian rhythm pathway yielded most DEGs, highlighting circadian rhythm regulation was important during flax fiber development. Notably, 59 transcription factors were uniquely expressed in Agatha, 73 in White Flower and 94 in both varieties. Expression of 15 cellulose synthase A genes in both varieties varied significantly between developmental stages. Expression patterns of eight DEGs measured using qRT-PCR confirmed RNA-seq results. Thus, several interesting genes described here warrant future molecular mechanistic studies to learn their roles in fiber formation toward improving flax fiber quality through molecular breeding. Abbreviations: 4CL: 4-coumarate-CoA ligase; AP2-EREBP: apetala2/ethylene-responsive element binding protein; ARR-B: arabidopsis response regulator-B; bHLH: basic helix-loop-helix; bZIP: basic region/leucine zipper motif; CAD: cinnamyl alcohol dehydrogenase; CCoAOMT: caffeoyl CoA O-methyltransferase; CesA: cellulose synthase A; COMT: catechol-o-methyl transferase; CPP: cysteine-rich polycomb-like protein; CSL: cellulase synthase-like; DEGs: differentially expressed genes; DeTFs: differentially expressed transcription factors; FHA: forkhead-associated domain; GDP: guanosine diphosphate; GTP: guanosine triohosphte; GO: gene ontology; HSF: heat shock transcription factor; KEGG: kyoto encyclopedia of genes and genomes; LOB: lateral organboundaries; Lus: linum usitatissimum; MGS: mature green stage; mTERF: mitochondrial transcription termination factor; MYB: v-myb avian myeloblastosis viral oncogene homolog; NAC: nam, ataf1-2 and cuc2; NCBI: national center for biotechnology information; OFP: ovate family proteins; PLATZ: plant A/T rich sequence-and zinc-binding protein; qRT-PCR: quantitative RT-PCR; QC: quality control; RGP: rapid growth period; SBP: squmosa promoter binding protein; SNP: single nucleotide polymorphisms; SRA: short read archive; TAZ: tafazzin; TCP: tb1, cyc and pcfs; TFs: transcription factors.

Keywords

• flax
• fiber
• differentially expressed genes
• transcriptome
• qrt-pcr
• stem