Knowledge Resource Center for Ecological Environment in Arid Area
DOI | 10.1186/s12863-017-0584-5 |
An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench) | |
Woldesemayat, Adugna Abdi1,2; Van Heusden, Peter1; Ndimba, Bongani K.; Christoffels, Alan1 | |
通讯作者 | Woldesemayat, Adugna Abdi |
来源期刊 | BMC GENETICS
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ISSN | 1471-2156 |
出版年 | 2017 |
卷号 | 18 |
英文摘要 | Background: Drought is the most disastrous abiotic stress that severely affects agricultural productivity worldwide. Understanding the biological basis of drought-regulated traits, requires identification and an in-depth characterization of genetic determinants using model organisms and high-throughput technologies. However, studies on drought tolerance have generally been limited to traditional candidate gene approach that targets only a single gene in a pathway that is related to a trait. In this study, we used sorghum, one of the model crops that is well adapted to arid regions, to mine genes and define determinants for drought tolerance using drought expression libraries and RNA-seq data. Results: We provide an integrated and comparative in silico candidate gene identification, characterization and annotation approach, with an emphasis on genes playing a prominent role in conferring drought tolerance in sorghum. A total of 470 non-redundant functionally annotated drought responsive genes (DRGs) were identified using experimental data from drought responses by employing pairwise sequence similarity searches, pathway and interpro-domain analysis, expression profiling and orthology relation. Comparison of the genomic locations between these genes and sorghum quantitative trait loci (QTLs) showed that 40% of these genes were co-localized with QTLs known for drought tolerance. The genome reannotation conducted using the Program to Assemble Spliced Alignment (PASA), resulted in 9.6% of existing single gene models being updated. In addition, 210 putative novel genes were identified using AUGUSTUS and PASA based analysis on expression dataset. Among these, 50% were single exonic, 69.5% represented drought responsive and 5.7% were complete gene structure models. Analysis of biochemical metabolism revealed 14 metabolic pathways that are related to drought tolerance and also had a strong biological network, among categories of genes involved. Identification of these pathways, signifies the interplay of biochemical reactions that make up the metabolic network, constituting fundamental interface for sorghum defence mechanism against drought stress. Conclusions: This study suggests untapped natural variability in sorghum that could be used for developing drought tolerance. The data presented here, may be regarded as an initial reference point in functional and comparative genomics in the Gramineae family. |
英文关键词 | Candidate gene identification Drought tolerance Functional genomics Integrated in silico approach Genome annotation Sorghum bicolor (L.) Moench |
类型 | Article |
语种 | 英语 |
国家 | South Africa |
收录类别 | SCI-E |
WOS记录号 | WOS:000418687300001 |
WOS关键词 | ABIOTIC STRESS ; GENOME ; QTL ; ARABIDOPSIS ; EXPRESSION ; EVOLUTION ; ALIGNMENT ; DATABASE ; DOMAIN ; DIVERSIFICATION |
WOS类目 | Genetics & Heredity |
WOS研究方向 | Genetics & Heredity |
资源类型 | 期刊论文 |
条目标识符 | http://119.78.100.177/qdio/handle/2XILL650/197911 |
作者单位 | 1.Univ Western Cape, South African Med Res Council, Bioinformat Unit, South African Natl Bioinformat Inst, Private Bag X17, ZA-7535 Bellville, South Africa; 2.Univ South Africa, Dept Life & Consumer Sci, Coll Agr & Environm Sci, UNISA Sci Campus, ZA-1710 Johannesburg, Florida, South Africa |
推荐引用方式 GB/T 7714 | Woldesemayat, Adugna Abdi,Van Heusden, Peter,Ndimba, Bongani K.,et al. An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench)[J],2017,18. |
APA | Woldesemayat, Adugna Abdi,Van Heusden, Peter,Ndimba, Bongani K.,&Christoffels, Alan.(2017).An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench).BMC GENETICS,18. |
MLA | Woldesemayat, Adugna Abdi,et al."An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench)".BMC GENETICS 18(2017). |
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