Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity

BMC Genomics

Research Article

Subodh Srivastava¹  Niranjan Baisakh²  Venkata Ramanarao Mangu²  Renesh Bedre²  Luis Eduardo Sanchez³ 

[1] Department of Genetics and Biochemistry, Clemson University, 29634, Clemson, SC, USA;School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, 70803, Baton Rouge, LA, USA;School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, 70803, Baton Rouge, LA, USA;Current address: Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Km 30.5 Via Perimetral, Guayaquil, Ecuador;

关键词: Gene expression;    GS-FLX;    Salinity;    Spartina alterniflora;    Transcriptome;   

DOI  :  10.1186/s12864-016-3017-3

 received in 2015-12-23, accepted in 2016-08-13,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundSoil salinity affects growth and yield of crop plants. Plants respond to salinity by physiological and biochemical adjustments through a coordinated regulation and expression of a cascade of genes. Recently, halophytes have attracted attention of the biologists to understand their salt adaptation mechanisms. Spartina alterniflora (smooth cordgrass) is a Louisiana native monocot halophyte that can withstand salinity up to double the strength of sea water. To dissect the molecular mechanisms underlying its salinity adaptation, leaf and root transcriptome of S. alterniflora was sequenced using 454/GS-FLX.ResultsAltogether, 770,690 high quality reads with an average length 324-bp were assembled de novo into 73,131 contigs (average 577-bp long) with 5.9X sequence coverage. Most unigenes (95 %) annotated to proteins with known functions, and had more than 90 % similarity to rice genes. About 28 % unigenes were considered specific to S. alterniflora. Digital expression profiles revealed significant enrichment (P < 0.01) of transporters, vacuolar proton pump members and transcription factors under salt stress, which suggested the role of ion homeostasis and transcriptional regulation in the salinity adaptation of this grass. Also, 10,805 SSRs markers from 9457 unigenes were generated and validated through genetic diversity analysis among 13 accessions of S. alterniflora.ConclusionsThe present study explores the transcriptome of S. alterniflora to understand the gene regulation under salt stress in halophytes. The sequenced transcriptome (control and salt-regulated) of S. alterniflora provides a platform for further gene finding studies in grasses. This study and our previously published studies suggested that S. alterniflora is a rich reservoir of salt tolerance genes that can be used to develop salt tolerant cereal crops, especially rice, a major food crop of global importance.

【 授权许可】

CC BY   
© The Author(s). 2016