Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background

doi:10.1186/1471-2164-13-461

	Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background
	Zhang, Fan 1,2; Huang, Liyu 1,2; Wang, Wensheng 1,2; Zhao, Xiuqin 1,2; Zhu, Linghua 1,2; Fu, Binying 1,2; Li, Zhikang 1,2,3
刊名	BMC GENOMICS
	2012
卷号	13 页码:-
关键词	Rice Cold tolerance Transcriptome Introgression line
ISSN号	1471-2164
DOI	10.1186/1471-2164-13-461
通讯作者	Zhang, Fan
英文摘要	Background: Rice in tropical and sub-tropical areas is often subjected to cold stress at the seedling stage, resulting in poor growth and yield loss. Although japonica rice is generally more cold tolerant (CT) than indica rice, there are several favorable alleles for CT exist in indica that can be used to enhance CT in rice with a japonica background. Genome-wide gene expression profiling is an efficient way to decipher the molecular genetic mechanisms of CT enhancement and to provide valuable information for CT improvement in rice molecular breeding. In this study, the transcriptome of the CT introgression line (IL) K354 and its recurrent parent C418 under cold stress were comparatively analyzed to explore the possible CT enhancement mechanisms of K354.Results: A total of 3184 differentially expressed genes (DEGs), including 195 transcription factors, were identified in both lines under cold stress. About half of these DEGs were commonly regulated and involved in major cold responsive pathways associated with OsDREB1 and OsMyb4 regulons. K354-specific cold-induced genes were functionally related to stimulus response, cellular cell wall organization, and microtubule-based movement processes that may contribute to increase CT. A set of genes encoding membrane fluidity and defensive proteins were highly enriched only in K354, suggesting that they contribute to the inherent CT of K354. Candidate gene prediction based on introgressed regions in K354 revealed genotype-dependent CT enhancement mechanisms, associated with Sir2, OsFAD7, OsWAK112d, and programmed cell death (PCD) related genes, present in CT IL K354 but absent in its recurrent parent C418. In K354, a number of DEGs were co-localized onto introgressed segments associated with CT QTLs, providing a basis for gene cloning and elucidation of molecular mechanisms responsible for CT in rice.Conclusions: Genome-wide gene expression analysis revealed that genotype-specific cold induced genes and genes with higher basal expression in the CT genotype contribute jointly to CT improvement. The molecular genetic pathways of cold stress tolerance uncovered in this study, as well as the DEGs co-localized with CT-related QTLs, will serve as useful resources for further functional dissection of the molecular mechanisms of cold stress response in rice.
学科主题	Biotechnology & Applied Microbiology ; Genetics & Heredity ; BIOTECHNOLOGY & APPLIED MICROBIOLOGY ; GENETICS & HEREDITY
语种	英语
出版者	BIOMED CENTRAL LTD
WOS记录号	WOS:000312736400001
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/5133]
专题	作物科学研究所_分子生物学系
作者单位	1.Chinese Acad Agr Sci, Inst Crop Sci, Natl Key Facil Crop Gene Resources & Genet Improv, Beijing 100081, Peoples R China 2.Chinese Acad Agr Sci, Shenzhen Inst Breeding & Innovat, Shenzhen 518083, Peoples R China 3.Int Rice Res Inst, Manila, Philippines
推荐引用方式 GB/T 7714	Zhang, Fan,Huang, Liyu,Wang, Wensheng,et al. Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background[J]. BMC GENOMICS,2012,13:-.
APA	Zhang, Fan.,Huang, Liyu.,Wang, Wensheng.,Zhao, Xiuqin.,Zhu, Linghua.,...&Li, Zhikang.(2012).Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background.BMC GENOMICS,13,-.
MLA	Zhang, Fan,et al."Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background".BMC GENOMICS 13(2012):-.