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Chuanqing Sun - One of the best experts on this subject based on the ideXlab platform.

  • integrated rna sequencing and qtl mapping to identify candidate genes from Oryza Rufipogon associated with salt tolerance at the seedling stage
    Frontiers in Plant Science, 2017
    Co-Authors: Shanshan Wang, Chuanqing Sun, Lubin Tan, Meng Cao, Weikang Chen, Jie Zhao, Fengxia Liu
    Abstract:

    Soil salinity is a common abiotic stress affecting crop productivity. To identify favorable alleles from wild rice (Oryza Rufipogon Griff.) that enhance salinity tolerance of rice (O. sativa L.), a set of introgression lines were developed. The introgression lines were derived from an O. Rufipogon accession collected from Chaling (Hunan Province, China) as the donor, and a widely-grown O. sativa indica cultivar 93-11 as the recipient. Through evaluating the salt tolerance of 285 introgression lines at the seedling stage, a total of 10 quantitative trait loci (QTLs) related to salt tolerance were identified on chromosomes 1, 5, 7 and 9–12, with individual QTLs explaining 2–8% of phenotypic variance. The O. Rufipogon-derived alleles at four QTLs improved salt tolerance in the 93-11 background. At the same time, a salt-tolerant introgression line, 9L136, was identified and characterized. Compared with the recipient parent 93-11, a total of 1,391 differentially expressed genes (DEGs) were detected specifically in 9L136 between salt stress and normal condition through genome-wide expression analysis. Of these, four DEGs located in the QTL regions carried by 9L136, suggesting that the four genes might be candidates associated with salt tolerance. Both the highly salt-tolerant introgression lines and the favorable O. Rufipogon-derived QTLs identified in the present study will provide new genetic resources for improving the resistance of cultivated rice against salinity stress using molecular breeding strategies in the future.

  • identification of quantitative trait loci associated with salt tolerance at seedling stage from Oryza Rufipogon
    Journal of Genetics and Genomics, 2011
    Co-Authors: Lei Tian, Hongwei Cai, Lubin Tan, Fengxia Liu, Chuanqing Sun
    Abstract:

    Soil salinity is one of the major abiotic stresses affecting plant growth and crop production. In the present study, salt tolerance at rice seedling stage was evaluated using 87 introgression lines (ILs), which were derived from a cross between an elite indica cultivar Teqing and an accession of common wild rice (Oryza Rufipogon Griff.). Substantial variation was observed for four traits including salt tolerance score (STS), relative root dry weight (RRW), relative shoot dry weight (RSW) and relative total dry weight (RTW). STS was significantly positively correlated with all other three traits. A total of 15 putative quantitative trait loci (QTLs) associated with these four traits were detected using single-point analysis, which were located on chromosomes 1, 2, 3, 6, 7, 9 and 10 with 8%-26% explaining the phenotypic variance. The O. Rufipogon-derived alleles at 13 QTLs (86.7%) could improve the salt tolerance in the Teqing background. Four QTL clusters affecting RRW, RSW and RTW were found on chromosomes 6, 7, 9 and 10, respectively. Among these four QTL clusters, a major cluster including three QTLs (qRRW10, qRSW10 and qRTW10) was found near the maker RM271 on the long arm of chromosome 10, and the O. Rufipogon-derived alleles at these three loci increased RRW, RSW and RTW with additive effects of 22.7%, 17.3% and 18.5%, respectively, while the phenotypic variance explained by these three individual QTLs for the three traits varied from 19% to 26%. In addition, several salt tolerant ILs were selected and could be used for identifying and utilizing favorable salt tolerant genes from common wild rice and used in the salt tolerant rice breeding program.

  • identification of heterotic loci associated with yield related traits in chinese common wild rice Oryza Rufipogon griff
    Plant Science, 2011
    Co-Authors: Xiaojin Luo, Xiangkun Wang, Feng Tian, Xiaoyun Xin, Xiaojun Zha, Xianxin Dong, Jinshui Yang, Chuanqing Sun
    Abstract:

    Abstract Many rice breeding programs have currently reached yield plateaus as a result of limited genetic variability in parental strains. Dongxiang common wild rice (Oryza Rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and serves as an important gene pool for the genetic improvement of rice cultivars. In this study, heterotic loci (HLs) associated with six yield-related traits were identified in wild and cultivated rice and investigated using a set of 265 introgression lines (ILs) of O. Rufipogon Griff. in the background of the Indica high-yielding cultivar Guichao 2 (O. sativa L.). Forty-two HLs were detected by a single point analysis of mid-parent heterosis values from test cross F1 offspring, and 30 (71.5%) of these HLs showed significantly positive effects, consistent with the superiority shown by the F1 test cross population in the six yield-related traits under study. Genetic mapping of hsp11, a locus responsible for the number of spikelets per panicle, confirmed the utility of these HLs. The results indicate that favorable HLs capable of improving agronomic traits are available. The identification of HLs between wild rice and cultivated rice could lead to a new strategy for the application of heterosis in rice breeding.

  • analysis of qtls for yield related traits in yuanjiang common wild rice Oryza Rufipogon griff
    Journal of Genetics and Genomics, 2010
    Co-Authors: Lubin Tan, Peijiang Zhang, Yongcai Fu, Qiang Fu, Zuofeng Zhu, Xinchun Zhan, Hongwei Cai, Chuanqing Sun
    Abstract:

    Using an accession of common wild rice (Oryza Rufipogon Griff.) collected from Yuanjiang County, Yunnan Province, China, as the donor and an elite cultivar 93-11, widely used in two-line indica hybrid rice production in China, as the recurrent parent, an advanced backcross populations were developed. Through genotyping of 187 SSR markers and investigation of six yield-related traits of two generations (BC4F2 and BC4F4), a total of 26 QTLs were detected by employing single point analysis and interval mapping in both generations. Of the 26 QTLs, the alleles of 10 (38.5%) QTLs originating from O. Rufipogon had shown a beneficial effect for yield-related traits in the 93-11 genetic background. In addition, five QTLs controlling yield and its components were newly identified, indicating that there are potentially novel alleles in Yuanjiang common wild rice. Three regions underling significant QTLs for several yield-related traits were detected on chromosome 1, 7 and 12. The QTL clusters were founded and corresponding agronomic traits of those QTLs showed highly significant correlation, suggesting the pleiotropism or tight linkage. Fine-mapping and cloning of these yield-related QTLs from wild rice would be helpful to elucidating molecular mechanism of rice domestication and rice breeding in the future.

  • mapping quantitative trait loci influencing panicle related traits from chinese common wild rice Oryza Rufipogon using introgression lines
    Plant Breeding, 2009
    Co-Authors: Xiaojin Luo, Feng Tian, Jingmin Yang, Chuanqing Sun
    Abstract:

    Panicle-related traits are important agronomic traits which directly associated with grain yield. In this study, we investigated quantitative trait loci (QTLs) associated with panicle-related traits using a set of 265 introgression lines (ILs) of common wild rice (Oryza Rufipogon Griff.) in the background of Indica high-yielding cultivar Guichao 2 (O. sativa L.). A total of 39 QTLs associated with panicle-related traits including panicle length (PL), primary branch number (PBN), secondary branch number (SBN), spikelet number per panicle (SPP) and spikelet density (SD), were detected in the ILs with single-point analysis. The alleles of 20 QTLs derived from wild rice showed positive effects, and some QTLs, such as, QPl1b for PL, QPbn8 for PBN, QSd4 and QSd11b for SD and QSpp4 for SPP showed larger positive effects, providing good candidates and useful information for marker-aided improvement of yield potential of rice. Most of the QTLs controlling SPP, SBN and SD were located in cluster or closely linked on chromosomes, and the directions of their additive effects were consistent, which explained the genetic basis of significant correlations between their phenotypic characters.

Xiangkun Wang - One of the best experts on this subject based on the ideXlab platform.

  • identification of heterotic loci associated with yield related traits in chinese common wild rice Oryza Rufipogon griff
    Plant Science, 2011
    Co-Authors: Xiaojin Luo, Xiangkun Wang, Feng Tian, Xiaoyun Xin, Xiaojun Zha, Xianxin Dong, Jinshui Yang, Chuanqing Sun
    Abstract:

    Abstract Many rice breeding programs have currently reached yield plateaus as a result of limited genetic variability in parental strains. Dongxiang common wild rice (Oryza Rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and serves as an important gene pool for the genetic improvement of rice cultivars. In this study, heterotic loci (HLs) associated with six yield-related traits were identified in wild and cultivated rice and investigated using a set of 265 introgression lines (ILs) of O. Rufipogon Griff. in the background of the Indica high-yielding cultivar Guichao 2 (O. sativa L.). Forty-two HLs were detected by a single point analysis of mid-parent heterosis values from test cross F1 offspring, and 30 (71.5%) of these HLs showed significantly positive effects, consistent with the superiority shown by the F1 test cross population in the six yield-related traits under study. Genetic mapping of hsp11, a locus responsible for the number of spikelets per panicle, confirmed the utility of these HLs. The results indicate that favorable HLs capable of improving agronomic traits are available. The identification of HLs between wild rice and cultivated rice could lead to a new strategy for the application of heterosis in rice breeding.

  • genetic structure of Oryza Rufipogon griff in china
    Heredity, 2008
    Co-Authors: Meixing Wang, Hongliang Zhang, Dongling Zhang, Zhilan Fan, Dajian Pan, Y S Cao, Z E Qiu, Qingwen Yang, Xiangkun Wang
    Abstract:

    Oryza Rufipogon Griff. (common wild rice; CWR) is the ancestor of Asian cultivated rice (Oryza sativa L.). Investigation of the genetic structure and diversity of CWR in China will provide information about the origin of cultivated rice and the grain quality and yield. In this study, we used 36 simple sequence repeat (SSR) markers to assay 889 accessions, which were highly representative of whole germplasm in China. The analysis revealed a hierarchical genetic structure within CWR. First, CWR has diverged into two ecotypic populations, a south subtropical population (SSP) and a middle subtropical population (MSP), probably owing to natural selection by the different climates. The distribution of specific alleles and haplotypes indicated that Chinese CWR had both indica-like and japonica-like variations; the SSP was an indica-like type, whereas the MSP was more japonica-like. The SSP and MSP further diverged into five (HN, GD-GX1, GX2, FJ and YN) and two (JX-HuN1 and HuN2) geographical populations, respectively. The genetic data suggest the isolation by distance, although water systems also appear to play an important role in the formation of homogenous populations, and occasionally landscape was also involved. The population GD-GX1, which grew widely in Guangdong and Guangxi provinces, was the largest geographical population in China. It had a high level of genetic diversity (GD) and the closest genetic relationship with other inferred populations. The population HN, with the smallest SSR molecular weights and the highest level of GD, may be the most ancestral population.

  • development of Oryza Rufipogon and o sativa introgression lines and assessment for yield related quantitative trait loci
    Journal of Integrative Plant Biology, 2007
    Co-Authors: Lubin Tan, Zuofeng Zhu, Fengxia Liu, Xiangkun Wang, Wei Xue, Guijuan Wang
    Abstract:

    Introgression lines population was effectively used in mapping quantitative trait loci (QTLs), identifying favorable genes, discovering hidden genetic variation, evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research. In this study, an advanced backcross and consecutive selfing strategy was used to develop introgression lines (ILs), which derived from an accession of Oryza Rufipogon Griff. collected from Yuanjiang County, Yunnan Province of China, as the donor, and an elite indica cultivar Teqing (O. sativa L.), as the recipient. Introgression segments from O. Rufipogon were screened using 179 polymorphic simple sequence repeats (SSR) markers in the genome of each IL. Introgressed segments carried by the introgression lines population contained 120 ILs covering the whole O. Rufipogon genome. The mean number of homozygous O. Rufipogon segments per introgression line was about 3.88. The average length of introgressed segments was approximate 25.5 cM, and about 20.8% of these segments had sizes less than 10 cM. The genome of each IL harbored the chromosomal fragments of O. Rufipogon ranging from 0.54% to 23.7%, with an overall average of 5.79%. At each locus, the ratio of substitution of O. Rufipogon alleles had a range of 1.67-9.33, with an average of 5.50. A wide range of alterations in morphological and yield-related traits were also found in the introgression lines population. Using single-point analysis, a total of 37 putative QTLs for yield and yield components were detected at two sites with 7%-20% explaining the phenotypic variance. Nineteen QTLs (51.4%) were detected at both sites, and the alleles from O. Rufipogon at fifteen loci (40.5%) improved the yield and yield components in the Teging background. These O. Rufipogon -O. sativa introgression lines will serve as genetic materials for identifying and using favorable genes from common wild rice.

  • fine mapping of a quantitative trait locus for grain number per panicle from wild rice Oryza Rufipogon griff
    Theoretical and Applied Genetics, 2006
    Co-Authors: Feng Tian, Lubin Tan, Yongcai Fu, Zuofeng Zhu, Xiangkun Wang, Boshen Zhang, Chuanqing Sun
    Abstract:

    SIL040, an introgression line (IL) developed by introgressing chromosomal segments from an accession of Oryza Rufipogon into an indica cultivar Guichao 2, showed significantly less grains per panicle than the recurrent parent Guichao 2. Quantitative trait locus (QTL) analysis in F2 and F3 generations derived from the cross between SIL040 and Guichao 2 revealed that gpa7, a QTL located on the short arm of chromosome 7, was responsible of this variation. Alleles from O. Rufipogon decreased grains per panicle. To fine mapping of gpa7, a high-resolution map with 1,966 F2 plants derived from the cross between SIL040 and Guichao 2 using markers flanking gpa7 was constructed, and detailed quantitative evaluation of the structure of main panicle of each of F3 families derived from recombinants screened was performed. By two-step substitution mapping, gpa7 was finally narrowed down to a 35-kb region that contains five predicted genes in cultivated rice. The fact that QTLs for five panicle traits (length of panicle, primary branches per panicle, secondary branches per panicle, grains on primary branches and grains on secondary branches) were all mapped in the same interval as that for gpa7 suggested that this locus was associated with panicle structure, showing pleiotropic effects. The characterizing of panicle structure of IL SIL040 further revealed that, during the domestication from common wild allele to cultivated rice one at gpa7, not only the number of branches and grains per panicle increased significantly, more importantly, but also the ratio of secondary branches per panicle to total branches per panicle and the ratio of grains on secondary branches per panicle to total grains per panicle increased significantly. All these results reinforced the idea that gpa7 might play an important role in the regulation of grain number per panicle and the ratio of secondary branches per panicle during the domestication of rice panicle.

  • construction of introgression lines carrying wild rice Oryza Rufipogon griff segments in cultivated rice Oryza sativa l background and characterization of introgressed segments associated with yield related traits
    Theoretical and Applied Genetics, 2006
    Co-Authors: Feng Tian, Yongcai Fu, Qiang Fu, Zuofeng Zhu, Xiangkun Wang, De Jun Li, Chuanqing Sun
    Abstract:

    Introgression lines (ILs) are useful tools for precise mapping of quantitative trait loci (QTLs) and the evaluation of gene action or interaction in theoretical studies. A set of 159 ILs carrying variant introgressed segments from Chinese common wild rice (Oryza Rufipogon Griff.), collected from Dongxiang county, Jiangxi Province, in the background of Indica cultivar (Oryza sativa L.), Guichao 2, was developed using 126 polymorphic simple sequence repeats (SSR) loci. The 159 ILs represented 67.5% of the genome of O. Rufipogon. All the ILs have the proportions of the recurrent parent ranging from 92.4 to 99.9%, with an average of 97.4%. The average proportion of the donor genome for the BC4F4 population was about 2.2%. The mean numbers of homozygous and heterozygous donor segments were 2 (ranging 0–8) and 1 (ranging 0–7), respectively, and the majority of these segments had sizes less than 10 cM. QTL analysis was conducted based on evaluation of yield-related traits of the 159 ILs at two sites, in Beijing and Hainan. For 6 out of 17 QTLs identified at two sites corresponding to three traits (panicles per plant, grains per panicle and filled grains per plant, respectively), the QTLs derived from O. Rufipogon were usually associated with an improvement of the target trait, although the overall phenotypic characters of O. Rufipogon were inferior to that of the recurrent parent. Of the 17 QTLs, 5 specific QTLs strongly associated with more than one trait were observed. Further analysis of the high-yielding and low-yielding ILs revealed that the high-yielding ILs contained relatively less introgressed segments than the low-yielding ILs, and that the yield increase or decrease was mainly due to the number of grain. On the other hand, low-yielding ILs contained more negative QTLs or disharmonious interactions between QTLs which masked trait-enchancing QTLs. These ILs will be useful in identifying the traits of yield, tolerance to low temperature and drought stress, and detecting favorable genes of common wild rice.

Lizhi Gao - One of the best experts on this subject based on the ideXlab platform.

  • genome wide analysis of wrky genes and their response to salt stress in the wild progenitor of asian cultivated rice Oryza Rufipogon
    Frontiers in Genetics, 2020
    Co-Authors: Lizhi Gao, Hong Nan, Yanglei Lin
    Abstract:

    WRKY gene family is widespread in plants, which is of significance in determining plant development and stress response. Although WRKY transcription factors have been widely characterized in many plants, a genome-wide analysis of the WRKY gene family is still lacking in Oryza Rufipogon. In this study, we identified 101 O. Rufipogon WRKY (OrWRKY) transcription factors, which were further classified into eight subgroups. Phylogenetic analysis showed that OrWRKY transcription factors were supported by highly conserved motifs and gene structures. Chromosomal distribution of OrWRKYs indicated that most genes were dispersed on all twelve chromosomes, especially enriched on Chromosome 1. Syntenic analysis revealed that 69 (68.3%) genes were derived from either segmental (49) or tandem duplication events (20), suggesting a essential role of segmental duplications. We characterized a total of 39 orthologous gene pairs between O. sativa ssp. japonica WRKY (OsjWRKY) and OrWRKY. We then performed quantitative real-time polymerase chain reaction (qPCR) experiments to validate tissue-specific and differential expression of the OrWRKYs. We also investigated corresponsive expression of the OrWRKYs in response to salt stresses in leaves and roots. This study gains a new insight on the evolution of the OrWRKYs and will help further functional characterization of candidate genes towards wild rice germplasm exploration for rice genetic improvement.

  • lowered diversity and increased inbreeding depression within peripheral populations of wild rice Oryza Rufipogon
    PLOS ONE, 2016
    Co-Authors: Lizhi Gao, Chengwen Gao
    Abstract:

    Background The distribution of genetic variability from the interior towards the periphery of a species’ range is of great interest to evolutionary biologists. Although it has been long presumed that population genetic variation should decrease as a species’ range is approached, results of empirical investigations still remain ambiguous. Knowledge regarding patterns of genetic variability as well as affected factors is particularly not conclusive in plants. Methodology/Principal Findings To determine genetic divergence in peripheral populations of the wild rice Oryza Rufipogon Griff. from China, genetic diversity and population structure were studied in five northern & northeastern peripheral and 16 central populations using six microsatellite loci. We found that populations resided at peripheries of the species possessed markedly decreased microsatellite diversity than those located in its center. Population size was observed to be positively correlated with microsatellite diversity. Moreover, there are significantly positive correlations between levels of microsatellite diversity and distances from the northern and northeastern periphery of this species. To investigate genetic structure and heterozygosity variation between generations of O. Rufipogon, a total of 2382 progeny seeds from 186 maternal families were further assayed from three peripheral and central populations, respectively. Peripheral populations exhibited significantly lower levels of heterozygosities than central populations for both seed and maternal generations. In comparisons with maternal samples, significantly low observed heterozygosity (HO) and high heterozygote deficit within populations (FIS) values were detected in seed samples from both peripheral and central populations. Significantly lower observed heterozygosity (HO) and higher FIS values were further observed in peripheral populations than those in central populations for seed samples. The results indicate an excess of homozygotes and thus high inbreeding depression in peripheral populations. Conclusions/Significance Our results together suggest that historical contraction of geographical range, demographic changes, and environmental conditions near the northern and northeastern margins of O. Rufipogon favor inbreeding and possibly selfing, leading to the rapidly decreased effective population size. Genetic drift, reduced gene flow, and possible local selection, consequently lead to lowered gene diversity, accelerated genetic divergence and increased inbreeding depression found in peripheral populations of O. Rufipogon. Given these characteristics observed, northern and northeastern peripheral populations deserve relatively different conservation strategies for either germplasm sampling of ex situ conservation or setting in situ reserves for the adaptation to possible environmental changes and the future germplasm utilization of wild rice.

  • population structure and conservation genetics of wild rice Oryza Rufipogon poaceae a region wide perspective from microsatellite variation
    Molecular Ecology, 2004
    Co-Authors: Lizhi Gao
    Abstract:

    Oryza Rufipogon Griff. is the most agriculturally important but seriously endangered wild rice species. To better estimate how genetic structure can be used to obtained a conservation perspective of the species, genetic variability at six polymorphic microsatellite DNA loci was examined. High levels of genetic variability were detected at six loci in 1245 individuals of 47 natural populations covering most of the species' range in China (overall RS = 3.0740, HO = 0.2290, HS = 0.6700). Partitioning of genetic variability (FST = 0.246) showed that most microsatellite variation was distributed within populations. Significant departures from Hardy-Weinberg expectations and very strong linkage disequilibrium indicate a high degree of inbreeding in the species and severe subdivision within populations. A mean Nm value of 0.7662 suggested a limited gene flow among the assayed populations. Our study suggests that conservation and restoration genetics should focus in particular on the maintenance of historically significant processes such as high levels of outbreeding and gene flow and large effective population size in the species.

  • assessment of population genetic structure in common wild rice Oryza Rufipogon griff using microsatellite and allozyme markers
    Theoretical and Applied Genetics, 2002
    Co-Authors: Lizhi Gao, Barbara A Schaal, Chi Zhang, J Z Jia, Y S Dong
    Abstract:

    The genetic structure of five natural populations of common wild rice Oryza Rufipogon Griff. from China, was investigated with 21 microsatellite loci and compared to estimates of genetic diversity and genetic differentiation detected by 22 allozyme loci. Microsatellite loci, as expected, have much higher levels of genetic diversity (mean values of A = 3.1, P = 73.3%, Ho = 0.358 and He = 0.345) than allozyme loci (mean values of A = 1.2, P = 12.7%, Ho = 0.020 and He = 0.030). Genetic differentiation detected by microsatellite loci (FST = 0.468, mean I = 0.472) was higher than that for allozyme loci (FST =0.388, mean I = 0.976). However, microsatellite markers showed less deviation from Hardy-Weinberg expectation (Wright's inbreeding coefficient FIS = –0.069) than do allozymes (FIS = 0.337). These results suggest that microsatellite markers are powerful high-resolution tools for the accurate assessment of important parameters in population biology and conservation genetics of O. Rufipogon, and offer advantages over allozyme markers.

  • allozyme variation and conservation genetics of common wild rice Oryza Rufipogon griff in yunnan china
    Euphytica, 2002
    Co-Authors: Lizhi Gao, Deyuan Hong, Rushun Lin, Guoda Tao
    Abstract:

    In order to reveal levels and distribution of genetic variation within Oryza Rufipogon Griff. of Yunnan, China, where one of the centers of genetic diversity for Asian cultivated rice O. sativa L. is located, allozyme variation encoded by 22 loci was electrophoretically analyzed in 149 individuals of all three existing populations as well as five from other regions (Guangxi, Hainan and Jiangxi provinces) of China. As compared to the level of genetic diversity (the mean A = 1.2, P = 24.1%, Ho = 0.045 and He = 0.079) for the populations from other regions, a rather low genetic diversity (the mean A = 1.1, P = 7.6%, Ho = 0.007 and He = 0.011) was found in Yunnan, which may originate from marginal nature of these populations, recent reduction of populations and consequent drift. The result suggests that the current center of genetic diversity for O. Rufipogon fail to agree with that for cultivated rice in China. The genetic differentiation for all the eight populations(FST = 0.254) was slightly lower than that for three populations from Yunnan (FST = 0.302), indicating a fairly high genetic differentiation in the region. Finally, a conservation plan for sampling/preserving fewer populations but more individuals from each population for the species was given, and an appropriate strategy for conserving the three surviving populations from Yunnan was proposed.

Barbara A Schaal - One of the best experts on this subject based on the ideXlab platform.

  • life history traits and geographical divergence in wild rice Oryza Rufipogon gene pool in indochina peninsula region
    Annals of Applied Biology, 2016
    Co-Authors: Tonapha Pusadee, Sansanee Jamjod, Benjavan Rerkasem, Barbara A Schaal
    Abstract:

    Indochina Peninsula is the primary centre of diversity of rice and lies partly in the centre of origin of cultivated rice (Oryza sativa) where the wild ancestor (Oryza Rufipogon) is still abundant. The wild gene pool is potentially endangered by urbanisation and the expansion of agriculture, and by introgression hybridisation with locally cultivated rice varieties. To determine genetic diversity and structure of the wild rice of the region we genotyped nearly 1000 individuals using 20 microsatellite loci. We found ecological differentiation in 48 populations, distinguishable by their life-history traits and the country of origin. Geographical divergence was suggested by isolation of the perennial Myanmar populations from those of Cambodia, Laos and Thailand. The annual types would be most likely to have lost genetic variation because of genetic drift and inbreeding. The growing of cultivated and wild rice together, however, gives ample opportunities for hybridisation, which already shows signs of genetic mixing, and will ultimately lead to replacement of the original wild rice gene pool. For conservation we suggest that wild rice should be conserved ex situ in order to prevent introgression from cultivated rice, along with in situ conservation in individual countries for the recurrent evolutionary process through local adaptation, but with sufficient isolation from cultivated rice fields to preserve genetic integrity of the wild populations.

  • association between the geographic distribution during the last glacial maximum of asian wild rice Oryza Rufipogon poaceae and its current genetic variation
    American Journal of Botany, 2012
    Co-Authors: Pu Huang, Barbara A Schaal
    Abstract:

    Premise of the study The combination of traditional population genetic studies and species distribution modeling (SDM) provides many new insights in detecting phylogeographic signals. In Asian wild rice (Oryza Rufipogon), the progenitor of cultivated Asian rice, geographical subdivision has been documented in many genetic studies although the root cause of this subdivision remains unknown. Surprisingly, environmental factors associated with the spatial and temporal distribution of O. Rufipogon have rarely been examined. The aim of this study is to understand the historical distribution of O. Rufipogon and its relationship to the current geographical pattern of genetic variation. Methods We used SDM to examine the present, past, and future distribution of O. Rufipogon. The estimated distribution during the Last Glacial Maximum was then compared with genetic data from our previous work. Key results The predicted paleodistribution of O. Rufipogon at the Last Glacial Maximum was separated into disconnected east and west ranges. This past distribution is consistent with the current geographic pattern of genetic variation, with two genetic groups that intergrade. Annual precipitation is the single factor that contributes most to SDM estimates. SDM predictions for 2080 indicate a general trend of increasing probability of presence and range expansion. Conclusions (1) The historically disjunct distribution potentially contributes to the current genetic subdivision of O. Rufipogon. (2) Water availability is an important factor that limits the distribution of O. Rufipogon. (3) Global warming is a lesser threat than other human-mediated factors to the conservation of this endangered species.

  • phylogeography of asian wild rice Oryza Rufipogon a genome wide view
    Molecular Ecology, 2012
    Co-Authors: Pu Huang, Scott A. Jackson, Jeanmaire Molina, Jonathan M Flowers, Samara Rubinstein, Michael D Purugganan, Barbara A Schaal
    Abstract:

    Asian wild rice (Oryza Rufipogon) that ranges widely across the eastern and southern part of Asia is recognized as the direct ancestor of cultivated Asian rice (O. sativa). Studies of the geographic structure of O. Rufipogon, based on chloroplast and low-copy nuclear markers, reveal a possible phylogeographic signal of subdivision in O. Rufipogon. However, this signal of geographic differentiation is not consistently observed among different markers and studies, with often conflicting results. To more precisely characterize the phylogeography of O. Rufipogon populations, a genome-wide survey of unlinked markers, intensively sampled from across the entire range of O. Rufipogon is critical. In this study, we surveyed sequence variation at 42 genome-wide sequence tagged sites (STS) in 108 O. Rufipogon accessions from throughout the native range of the species. Using Bayesian clustering, principal component analysis and AMOVA ,w e conclude that there are two genetically distinct O. Rufipogon groups, Ruf-I and Ruf-II. The two groups exhibit a clinal variation pattern generally from north-east to south-west. Different from many earlier studies, Ruf-I, which is found mainly in China and the Indochinese Peninsula, shows genetic similarity with one major cultivated rice variety, O. satvia indica, whereas Ruf-II, mainly from South Asia and the Indochinese Peninsula, is not found to be closely related to cultivated rice varieties. The other major cultivated rice variety, O. sativa japonica, is not found to be similar to either O. Rufipogon groups. Our results support the hypothesis of a single origin of the domesticated O. sativa in China. The possible role of palaeoclimate, introgression and migration–drift balance in creating this clinal variation pattern is also discussed.

  • Phylogeography of Asian wild rice, Oryza Rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa.
    Proceedings of the National Academy of Sciences of the United States of America, 2006
    Co-Authors: Jason P Londo, Kuo-hsiang Hung, Yu-chung Chiang, Tzen Yuh Chiang, Barbara A Schaal
    Abstract:

    Cultivated rice, Oryza sativa L., represents the world's most important staple food crop, feeding more than half of the human population. Despite this essential role in world agriculture, the history of cultivated rice's domestication from its wild ancestor, Oryza Rufipogon, remains unclear. In this study, DNA sequence variation in three gene regions is examined in a phylogeographic approach to investigate the domestication of cultivated rice. Results indicate that India and Indochina may represent the ancestral center of diversity for O. Rufipogon. Additionally, the data suggest that cultivated rice was domesticated at least twice from different O. Rufipogon populations and that the products of these two independent domestication events are the two major rice varieties, Oryza sativa indica and Oryza sativa japonica. Based on this geographical analysis, O. sativa indica was domesticated within a region south of the Himalaya mountain range, likely eastern India, Myanmar, and Thailand, whereas O. sativa japonica was domesticated from wild rice in southern China.

  • assessment of population genetic structure in common wild rice Oryza Rufipogon griff using microsatellite and allozyme markers
    Theoretical and Applied Genetics, 2002
    Co-Authors: Lizhi Gao, Barbara A Schaal, Chi Zhang, J Z Jia, Y S Dong
    Abstract:

    The genetic structure of five natural populations of common wild rice Oryza Rufipogon Griff. from China, was investigated with 21 microsatellite loci and compared to estimates of genetic diversity and genetic differentiation detected by 22 allozyme loci. Microsatellite loci, as expected, have much higher levels of genetic diversity (mean values of A = 3.1, P = 73.3%, Ho = 0.358 and He = 0.345) than allozyme loci (mean values of A = 1.2, P = 12.7%, Ho = 0.020 and He = 0.030). Genetic differentiation detected by microsatellite loci (FST = 0.468, mean I = 0.472) was higher than that for allozyme loci (FST =0.388, mean I = 0.976). However, microsatellite markers showed less deviation from Hardy-Weinberg expectation (Wright's inbreeding coefficient FIS = –0.069) than do allozymes (FIS = 0.337). These results suggest that microsatellite markers are powerful high-resolution tools for the accurate assessment of important parameters in population biology and conservation genetics of O. Rufipogon, and offer advantages over allozyme markers.

J Xie - One of the best experts on this subject based on the ideXlab platform.

  • genome wide development of lncrna derived ssr markers for dongxiang wild rice Oryza Rufipogon griff
    bioRxiv, 2021
    Co-Authors: Wanling Yang, J Xie, Yuanwei Fan, Yong Chen, Gumu Ding, Hu Liu, Fantao Zhang
    Abstract:

    Dongxiang wild rice (Oryza Rufipogon Griff., DXWR) is the northernmost distributed common wild rice found in the world. It contains a large number of agronomically valuable genes, which makes it a natural gene pool for rice breeding. Molecular markers, especially simple repeat sequence (SSR) markers, play important roles in crop breeding. Although a large number of SSR markers have been developed, most of them are derived from the genome coding sequences, rarely from non-coding sequences. Meanwhile, long non-coding RNAs (lncRNAs), which are derived from the transcription of non-coding sequences, play vital roles in plant growth, development and stress responses. In this study, 1878 SSR loci were detected from the lncRNA sequences of DXWR, and 1258 lncRNA-derived-SSR markers were developed on the genome-wide scale. To verify the validity and applicability of these markers, 72 pairs of primers were randomly selected to test 44 rice materials. The results showed that 42 (58.33%) pairs of primers have abundant polymorphism among these rice materials; the polymorphism information content (PIC) values ranged from 0.04 to 0.87 with an average of 0.50; the genetic diversity index of SSR loci varied from 0.04 to 0.88 with an average of 0.56; and the number of alleles per marker ranged from 2 to 11 with an average of 4.36. Thus, we concluded that these lncRNA-derived-SSR markers are a very useful source for future basic and applied research, including genetic diversity analysis, QTL mapping, and molecular breeding programs, to make good use of the elite lncRNA genes from DXWR.

  • transcriptome analysis of phosphorus stress responsiveness in the seedlings of dongxiang wild rice Oryza Rufipogon griff
    Biological Research, 2018
    Co-Authors: Qianwen Deng, Yi Zhou, Fantao Zhang, Xiangdong Luo, Yaling Chen, J Xie
    Abstract:

    Low 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. In 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. The 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.

  • rapid mapping of candidate genes for cold tolerance in Oryza Rufipogon griff by qtl seq of seedlings
    Journal of Integrative Agriculture, 2018
    Co-Authors: Xiangdong Luo, Fantao Zhang, Jian Liu, Jun Zhao, Liangfang Dai, Yaling Chen, Ling Zhang, H U Biaolin, J Xie
    Abstract:

    Abstract Cold stress is a major problem in rice production. To rapidly identify genes for cold tolerance in Dongxiang wild rice (DWR, Oryza Rufipogon Griff.), sequencing-based bulked segregant analysis of QTL-seq method was used to resequence the extremely resistant (R) and susceptible (S) bulks of a backcross inbred lines (BILs) population (derived from Oryza sativa×O. Rufipogon) and their parents. Single nucleotide polymorphisms (SNP)-index graphs and corresponding ρ(SNP-index) graphs (at 99 and 95% confidence levels) for R- and S-bulks detected a total of 2 609 candidate SNPs, including 58 candidate cold-tolerance genes. Quantitative real-time PCR analysis revealed that 5 out of the 58 candidate genes had significant differences in expression between O. sativa and O. Rufipogon. Structural variation and functional annotations of the 5 candidate genes were also analyzed, and allowed us to identify 2 insertion-deletion (InDel) markers (12-7 and 12-16) that were linked with candidate genes on chromosome 12 in DWR. These results are helpful for cloning and using cold tolerance genes from common wild rice in cultivated rice.

  • Transcriptome analysis of phosphorus stress responsiveness in the seedlings of Dongxiang wild rice (Oryza Rufipogon Griff.)
    'Springer Science and Business Media LLC', 2018
    Co-Authors: Qianwen Deng, Yi Zhou, Fantao Zhang, Xiangdong Luo, Yaling Chen, J Xie
    Abstract:

    Abstract Background Low 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. Results In 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. Conclusion The 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

  • effects of drought stress on global gene expression profile in leaf and root samples of dongxiang wild rice Oryza Rufipogon
    Bioscience Reports, 2017
    Co-Authors: Fantao Zhang, Yi Zhou, Xiangdong Luo, Meng Zhang, J Xie
    Abstract:

    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.