Jiankun Xie

Genetic diversity associated with conservation of endangered Dongxiang wild rice (Oryza rufipogon)

The wild progenitor species (Oryza rufipogon) of Asian cultivated rice (O. sativa L.) is located in Dongxiang county, China which is considered its the northernmost range worldwide. Nine ex situ and three in situ populations of the Dongxiang wild rice (DXWR) and four groups of modern cultivars were genotyped using 21 SSR markers for study of population structure, conservation efficiency and genetic relationship. We demonstrated that the ex situ conservation of the DXWR failed to maintain the genetic identity and reduced genetic diversity. Therefore, in situ conservation is absolutely necessary to maintain the genetic identity, diversity and heterozygosity. Also, in situ conservation is urgently needed because natural populations in DXWR have decreased from nine to three at present due to farming activity and urban expansion. In DXWR, the three surviving in situ populations had greater expected heterozygosity than any cultivated rice, and were genetically closer to japonica than either the male-sterile maintainer or restorer lines, or indica. Japonica has the lowest genetic diversity of cultivated rice. As a result, DXWR is a rich gene pool and is especially valuable for genetic improvement of japonica rice because these O. rufipogon accessions are most closely related to the japonica as compared to O. rufipogon collected anywhere else in the world.

Transcriptome Analysis of Salt Stress Responsiveness in the Seedlings of Dongxiang Wild Rice (Oryza rufipogon Griff.)

Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.), and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. The analysis results for the sequencing data showed that 6,867 transcripts were differentially expressed in the leaves (2,216 up-regulated and 4,651 down-regulated) and 4,988 transcripts in the roots (3,105 up-regulated and 1,883 down-regulated). Among these differentially expressed genes, the detection of many transcription factor genes demonstrated that multiple regulatory pathways were involved in salt stress tolerance. In addition, the differentially expressed genes were compared with the previous RNA-Seq analysis of salt-stress responses in cultivated rice Nipponbare, indicating the possible specific molecular mechanisms of salt-stress responses for Dongxiang wild rice. A large number of the salt-inducible genes identified in this study were co-localized onto fine-mapped salt-tolerance-related quantitative trait loci, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for salt-stress tolerance in rice.

Genome-wide identification of conserved microRNA and their response to drought stress in Dongxiang wild rice (Oryza rufipogon Griff.).

ObjectivesTo identify drought stress-responsive conserved microRNA (miRNA) from Dongxiang wild rice (Oryza rufipogon Griff., DXWR) on a genome-wide scale, high-throughput sequencing technology was used to sequence libraries of DXWR samples, treated with and without drought stress.Results505 conserved miRNAs corresponding to 215 families were identified. 17 were significantly down-regulated and 16 were up-regulated under drought stress. Stem-loop qRT-PCR revealed the same expression patterns as high-throughput sequencing, suggesting the accuracy of the sequencing result was high. Potential target genes of the drought-responsive miRNA were predicted to be involved in diverse biological processes. Furthermore, 16 miRNA families were first identified to be involved in drought stress response from plants.ConclusionThese results present a comprehensive view of the conserved miRNA and their expression patterns under drought stress for DXWR, which will provide valuable information and sequence resources for future basis studies.

Genome-wide analysis of Dongxiang wild rice ( Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication

BackgroundIt is widely accepted that cultivated rice (Oryza sativa L.) was domesticated from common wild rice (Oryza rufipogon Griff.). Compared to other studies which concentrate on rice origin, this study is to genetically elucidate the substantially phenotypic and physiological changes from wild rice to cultivated rice at the whole genome level.ResultsInstead of comparing two assembled genomes, this study directly compared the Dongxiang wild rice (DXWR) Illumina sequencing reads with the Nipponbare (O. sativa) complete genome without assembly of the DXWR genome. Based on the results from the comparative genomics analysis, structural variations (SVs) between DXWR and Nipponbare were determined to locate deleted genes which could have been acquired by Nipponbare during rice domestication. To overcome the limit of the SV detection, the DXWR transcriptome was also sequenced and compared with the Nipponbare transcriptome to discover the genes which could have been lost in DXWR during domestication. Both 1591 Nipponbare-acquired genes and 206 DXWR-lost transcripts were further analyzed using annotations from multiple sources. The NGS data are available in the NCBI SRA database with ID SRP070627.ConclusionsThese results help better understanding the domestication from wild rice to cultivated rice at the whole genome level and provide a genomic data resource for rice genetic research or breeding. One finding confirmed transposable elements contribute greatly to the genome evolution from wild rice to cultivated rice. Another finding suggested the photophosphorylation and oxidative phosphorylation system in cultivated rice could have adapted to environmental changes simultaneously during domestication.

Genetic Diversity and Genetic Changes in the Introgression Lines Derived from Oryza sativa L. Mating with O. rufipogon Griff.

The objectives of the present study were to estimate genetic diversity and genetic changes of introgression lines (ILs) which derived from cultivated rice (Oryza sativa L. cv. Xieqingzao B, XB) mating with common wild rice (O. rufipogon Griff., CWR). The genetic data of 239 ILs were based on a total of 131 polymorphic microsatellite (SSR) markers distributed across the 12 chromosomes of rice. On average, these ILs possessed 77.1 and 14.31% homozygous bands from XB and CWR, respectively. Most of the ILs were clustered together with XB individual, which was revealed by principal coordinate analysis (PCA) and the program STRUCTURE analysis. The result from PCA demonstrated that some intermediate genotypes between XB and CWR were also found. Moreover, there were some genomic sequence changes including parental bands elimination and novel bands emergence in the ILs. The average Neis gene diversity (He) was 0.296, which was higher than that of cultivated rice. It suggested that interspecific hybridization and gene introgression could broaden the base of genetic variation and lay an important foundation for rice genetic improvement. These different genotypic ILs would provide a better experimental system for understanding the evolution of rice species and the mechanism of alien gene introgression.

Transcriptome analysis of phosphorus stress responsiveness in the seedlings of Dongxiang wild rice ( Oryza rufipogon Griff.)

BackgroundLow phosphorus availability is a major factor restricting rice growth. Dongxiang wild rice (Oryza rufipogon Griff.) has many useful genes lacking in cultivated rice, including stress resistance to phosphorus deficiency, cold, salt and drought, which is considered to be a precious germplasm resource for rice breeding. However, the molecular mechanism of regulation of phosphorus deficiency tolerance is not clear.ResultsIn this study, cDNA libraries were constructed from the leaf and root tissues of phosphorus stressed and untreated Dongxiang wild rice seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in phosphorus stress response. The results indicated that 1184 transcripts were differentially expressed in the leaves (323 up-regulated and 861 down-regulated) and 986 transcripts were differentially expressed in the roots (756 up-regulated and 230 down-regulated). 43 genes were up-regulated both in leaves and roots, 38 genes were up-regulated in roots but down-regulated in leaves, and only 2 genes were down-regulated in roots but up-regulated in leaves. Among these differentially expressed genes, the detection of many transcription factors and functional genes demonstrated that multiple regulatory pathways were involved in phosphorus deficiency tolerance. Meanwhile, the differentially expressed genes were also annotated with gene ontology terms and key pathways via functional classification and Kyoto Encyclopedia of Gene and Genomes pathway mapping, respectively. A set of the most important candidate genes was then identified by combining the differentially expressed genes found in the present study with previously identified phosphorus deficiency tolerance quantitative trait loci.ConclusionThe present work provides abundant genomic information for functional dissection of the phosphorus deficiency resistance of Dongxiang wild rice, which will be help to understand the biological regulatory mechanisms of phosphorus deficiency tolerance in Dongxiang wild rice.

Linkage map construction and QTL mapping for cold tolerance in Oryza rufipogon Griff. at early seedling stage

Abstract Cold stress is one of the major restraints for rice production. Cold tolerance is controlled by complex genetic factor. In this study, a backcross inbred lines (BILs) population derived from an inter-specific cross ( Oryza sativa L.× O. rufipogon Griff.) was used for genetic linkage map construction and quantitative trait locus (QTL) mapping. A linkage map consisting of 153 markers was constructed, spanning 1 596.8 cM with an average distance of 11.32 cM between the adjacent markers. Phenotypic evaluation of the parents and BILs under (6±1)°C cold stress revealed that the ability of cold tolerance in BILs at early seedling obeyed a skewed normal and continuous distribution. Fifteen QTLs on chromosomes 6, 7, 8, 11, and 12 were identified using survival percent (SP) and non death percent (NDP) as indicators of cold tolerance, which could explain 5.99 to 40.07% of the phenotypic variance, of which the LOD values ranged from 3.04 to 11.32. Four QTLs on chromosomes 3, 5 and 7 were detected using leaf conductivity (LC) and root conductivity (RC) as indicators of cold tolerance, ranging from 19.54 to 33.53% for the phenotypic variance explained and 2.54 to 6.12 for the LOD values. These results suggested that there might be multi major QTLs in O. rufipogon and some useful genes for cold tolerance have been transferred into cultivated rice, which would be helpful for cloning and utilizing the cold tolerance-responsive genes from wild rice.

Effects of drought stress on global gene expression profile in leaf and root samples of Dongxiang wild rice (Oryza rufipogon)

Drought is a serious constraint to rice production throughout the world, and although Dongxiang wild rice (Oryza rufipogon, DXWR) possesses a high degree of drought resistance, the underlying mechanisms of this trait remains unclear. In the present study, cDNA libraries were constructed from the leaf and root tissues of drought-stressed and untreated DXWR seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in drought-stress response. The results indicated that 11231 transcripts were differentially expressed in the leaves (4040 up-regulated and 7191 down-regulated) and 7025 transcripts were differentially expressed in the roots (3097 up-regulated and 3928 down-regulated). Among these differentially expressed genes (DEGs), the detection of many transcriptional factors and functional genes demonstrated that multiple regulatory pathways were involved in drought resistance. Meanwhile, the DEGs were also annotated with gene ontology (GO) terms and key pathways via functional classification and Kyoto Encyclopedia of Gene and Genomes (KEGG) pathway mapping, respectively. A set of the most interesting candidate genes was then identified by combining the DEGs with previously identified drought-resistant quantitative trait loci (QTL). The present work provides abundant genomic information for functional dissection of the drought resistance of DXWR, and findings will further help the current understanding of the biological regulatory mechanisms of drought resistance in plants and facilitate the breeding of new drought-resistant rice cultivars.

Mapping QTLs for Fertility Restoration of Different Cytoplasmic Male Sterility Types in Rice Using Two Oryza sativa ×O. rufipogon Backcross Inbred Line Populations

Hybrid rice breeding using cytoplasmic male sterility/fertility restoration (CMS/Rf) systems plays an important role in ensuring global food security. Two backcross inbred line (BIL) populations derived from either Xieqingzao B (XB)//XB/Dongxiang wild rice (DWR) (XXD) or XB//DWR/XB (XDX) were used to detect quantitative trait loci (QTLs) for fertility restoration of Dwarf wild abortive- (DA-), Indonesia Paddy- (ID-), and DWR-type CMS in rice. Lines with ID- and DA-type CMS were testcrossed with both the XXD- and XDX-BILs, while the line with DWR-type CMS was testcrossed with the XDX-BILs only. A total of 16 QTLs for fertility restoration of CMS systems were identified, including three for DWR-type CMS, six for DA-type CMS, and seven for ID-type CMS. All of the additive alleles in the QTLs were derived from Oryza rufipogon. Eleven QTLs were clustered in five chromosomal regions, indicating that common Rf loci restored different CMS systems, and the favorable O. rufipogon alleles could be used to develop restorer lines for various CMS types by marker-assisted selection.

Identification of novel insertion–deletion markers for Dongxiang wild rice (Oryza rufipogon Griff.) using high-throughput sequencing technology

Common wild rice (Oryza rufipogon Griff.) is considered to be the ancestor of cultivated rice (Oryza sativa L.) (Ishii et al. 2011). During the domestication process from wild rice to cultivated rice, many genes of the wild rice were filtered either by drift or naturally and human selection or both, resulting in a significant reduction of genetic diversity in the cultivated rice gene pool (Brar and Khush 2003). An accession of wild rice collected from Dongxiang, Jiangxi province of China, originates in the northern most habitats (28◦14’N), among all the common wild rice populations discovered in China and even in the world (Chen et al. 2008). Dongxiang wild rice (DXWR) has many elite genes of valuable agronomic traits, including strong cold resistance (Liu et al. 2003), drought resistance (Zhang et al. 2006, 2014), and high grain yield (Tian et al. 2006). Basically, DXWR contains fertility restorer genes that makes F1 plants fertile when crossed with cultivated male sterile rice lines which is the key for hybrid rice (Chen et al. 2008; Zhang et al. 2011). Therefore, DXWR is considered as an important genetic resource for rice breeding. There are difficulties in transferring desirable genes from wild rice to cultivated rice using traditional breeding method (Sabu et al. 2009). The major problem is to get rid of the unfavourable genes because most agriculturally desirable genes are present in very low frequencies and are always linked to unfavourable genes in wild rice (Moncada et al. 2001). Molecular-marker-assisted selection (MAS) could help to break the linkage, thus becoming an increasingly important approach for complementing traditional breeding selection methods (Kujur et al. 2013). Establishing molecular markers