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RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress.
BMC Genomics. 2015 Aug 04; 16:575.BG

Abstract

BACKGROUND

Soil salinity is one of the most significant abiotic stresses affecting plant shoots and roots growth. The adjustment of root architecture to spatio-temporal heterogeneity in salinity is particularly critical for plant growth and survival. Bermudagrass (Cynodon dactylon) is a widely used turf and forage perennial grass with a high degree of salinity tolerance. Salinity appears to stimulate the growth of roots and decrease their mortality in tolerant bermudagrass. To estimate a broad spectrum of genes related to root elongation affected by salt stress and the molecular mechanisms that control the positive response of root architecture to salinity, we analyzed the transcriptome of bermudagrass root tips in response to salinity.

RESULTS

RNA-sequencing was performed in root tips of two bermudagrass genotypes contrasting in salt tolerance. A total of 237,850,130 high quality clean reads were generated and 250,359 transcripts were assembled with an average length of 1115 bp. Totally, 103,324 unigenes obtained with 53,765 unigenes (52 %) successfully annotated in databases. Bioinformatics analysis indicated that major transcription factor (TF) families linked to stress responses and growth regulation (MYB, bHLH, WRKY) were differentially expressed in root tips of bermudagrass under salinity. In addition, genes related to cell wall loosening and stiffening (xyloglucan endotransglucosylase/hydrolases, peroxidases) were identified.

CONCLUSIONS

RNA-seq analysis identified candidate genes encoding TFs involved in the regulation of lignin synthesis, reactive oxygen species (ROS) homeostasis controlled by peroxidases, and the regulation of phytohormone signaling that promote cell wall loosening and therefore root growth under salinity.

Authors+Show Affiliations

Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, PR China. hulx@wbgcas.cn.Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, PR China. lihuiying@wbgcas.cn.Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, PR China. chenliang888@wbgcas.cn.Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, PR China. yanhonglou1985@163.com.Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, PR China. amomboerick@yahoo.com.Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, PR China. jfu@wbgcas.cn.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

26238595

Citation

Hu, Longxing, et al. "RNA-seq for Gene Identification and Transcript Profiling in Relation to Root Growth of Bermudagrass (Cynodon Dactylon) Under Salinity Stress." BMC Genomics, vol. 16, 2015, p. 575.
Hu L, Li H, Chen L, et al. RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress. BMC Genomics. 2015;16:575.
Hu, L., Li, H., Chen, L., Lou, Y., Amombo, E., & Fu, J. (2015). RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress. BMC Genomics, 16, 575. https://doi.org/10.1186/s12864-015-1799-3
Hu L, et al. RNA-seq for Gene Identification and Transcript Profiling in Relation to Root Growth of Bermudagrass (Cynodon Dactylon) Under Salinity Stress. BMC Genomics. 2015 Aug 4;16:575. PubMed PMID: 26238595.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress. AU - Hu,Longxing, AU - Li,Huiying, AU - Chen,Liang, AU - Lou,Yanhong, AU - Amombo,Erick, AU - Fu,Jinmin, Y1 - 2015/08/04/ PY - 2014/12/28/received PY - 2015/07/27/accepted PY - 2015/8/5/entrez PY - 2015/8/5/pubmed PY - 2016/5/25/medline SP - 575 EP - 575 JF - BMC genomics JO - BMC Genomics VL - 16 N2 - BACKGROUND: Soil salinity is one of the most significant abiotic stresses affecting plant shoots and roots growth. The adjustment of root architecture to spatio-temporal heterogeneity in salinity is particularly critical for plant growth and survival. Bermudagrass (Cynodon dactylon) is a widely used turf and forage perennial grass with a high degree of salinity tolerance. Salinity appears to stimulate the growth of roots and decrease their mortality in tolerant bermudagrass. To estimate a broad spectrum of genes related to root elongation affected by salt stress and the molecular mechanisms that control the positive response of root architecture to salinity, we analyzed the transcriptome of bermudagrass root tips in response to salinity. RESULTS: RNA-sequencing was performed in root tips of two bermudagrass genotypes contrasting in salt tolerance. A total of 237,850,130 high quality clean reads were generated and 250,359 transcripts were assembled with an average length of 1115 bp. Totally, 103,324 unigenes obtained with 53,765 unigenes (52 %) successfully annotated in databases. Bioinformatics analysis indicated that major transcription factor (TF) families linked to stress responses and growth regulation (MYB, bHLH, WRKY) were differentially expressed in root tips of bermudagrass under salinity. In addition, genes related to cell wall loosening and stiffening (xyloglucan endotransglucosylase/hydrolases, peroxidases) were identified. CONCLUSIONS: RNA-seq analysis identified candidate genes encoding TFs involved in the regulation of lignin synthesis, reactive oxygen species (ROS) homeostasis controlled by peroxidases, and the regulation of phytohormone signaling that promote cell wall loosening and therefore root growth under salinity. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/26238595/RNA_seq_for_gene_identification_and_transcript_profiling_in_relation_to_root_growth_of_bermudagrass__Cynodon_dactylon__under_salinity_stress_ DB - PRIME DP - Unbound Medicine ER -