Xu J.,Yangzhou University |
Zhao Q.,CAS Shanghai Institutes for Biological Sciences |
Du P.,Yangzhou University |
Xu C.,Yangzhou University |
And 7 more authors.
BMC Genomics | Year: 2010
Background: Genetic populations provide the basis for a wide range of genetic and genomic studies and have been widely used in genetic mapping, gene discovery and genomics-assisted breeding. Chromosome segment substitution lines (CSSLs) are the most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs), for the analysis of complex traits in plant molecular genetics.Results: In this study, a wide population consisting of 128 CSSLs was developed, derived from the crossing and back-crossing of two sequenced rice cultivars: 9311, an elite indica cultivar as the recipient and Nipponbare, a japonica cultivar as the donor. First, a physical map of the 128 CSSLs was constructed on the basis of estimates of the lengths and locations of the substituted chromosome segments using 254 PCR-based molecular markers. From this map, the total size of the 142 substituted segments in the population was 882.2 Mb, was 2.37 times that of the rice genome. Second, every CSSL underwent high-throughput genotyping by whole-genome re-sequencing with a 0.13× genome sequence, and an ultrahigh-quality physical map was constructed. This sequencing-based physical map indicated that 117 new segments were detected; almost all were shorter than 3 Mb and were not apparent in the molecular marker map. Furthermore, relative to the molecular marker-based map, the sequencing-based map yielded more precise recombination breakpoint determination and greater accuracy of the lengths of the substituted segments, and provided more accurate background information. Third, using the 128 CSSLs combined with the bin-map converted from the sequencing-based physical map, a multiple linear regression QTL analysis mapped nine QTLs, which explained 89.50% of the phenotypic variance for culm length. A large-effect QTL was located in a 791,655 bp region that contained the rice 'green revolution' gene.Conclusions: The present results demonstrated that high throughput genotyped CSSLs combine the advantages of an ultrahigh-quality physical map with high mapping accuracy, thus being of great potential value for gene discovery and genetic mapping. These CSSLs may provide powerful tools for future whole genome large-scale gene discovery in rice and offer foundations enabling the development of superior rice varieties. © 2010 Xu et al; licensee BioMed Central Ltd.
Comparative proteomics analysis of superior and inferior spikelets in hybrid rice during grain filling and response of inferior spikelets to drought stress using isobaric tags for relative and absolute quantification
Dong M.,Suzhou Academy of Agricultural Science |
Dong M.,Yangzhou University |
Gu J.,Suzhou Academy of Agricultural Science |
Gu J.,Yangzhou University |
And 7 more authors.
Journal of Proteomics | Year: 2014
The biological functions of the differentially abundant proteins between superior and inferior spikelet grains were investigated based on the isobaric tags for relative and absolute quantification to further clarify the mechanism of rice grain filling at the proteomic level, as well as the response of inferior spikelets to drought dress (-. 20. kPa or -. 40. kPa). Compared with superior spikelets, inferior ones had lower sink strength due to the lower sink activities (lower abundances of ADP-glucose pyrophosphorylase, granule-bound starch synthase, starch branching enzyme and pullulanase) and smaller sink sizes (lower abundances of structural proteins). The slower and later grain filling resulted from the weaker decomposition and conversion of photoassimilate and the slower cell division. Moderate drought stress (-. 20. kPa) promoted the grain filling of inferior spikelets through regulating the proteins associated with photoassimilate supply and conversion. These proteins may be important targets for rice breeding programs that raise the rice yield under drought condition. The findings offer new insights into rice grain-filling and provide theoretical evidences for better quality control and scientific improvement of super rice in practice. Biological significance: Rice cultivars with large panicles do not always guarantee high yield and grain quality probably due to the slow grain filling and many unfilled grains of inferior spikelets. In general, earlier-flowering superior spikelets, which are usually located on apical primary branches, fill faster and produce larger and heavier grains. In contrast, later-flowering inferior spikelets located on proximal secondary branches are either sterile or fill slowly and poorly, and the differences are more significant in large panicle rice or super rice. The increase of rice yield has been limited by the unsatisfactory grain filling of inferior spikelets, and the inferior spikelets are more prone to environmental factors during grain filling. Thus, we herein investigated the biological functions of differently abundant proteins between superior and inferior spikelet grains by using iTRAQ to unravel the mechanism of rice grain filling and the response of inferior spikelets to drought stress at proteomic level. This study offers new insights into rice grain-filling and provides valuable evidences for better quality control and scientific improvement of super rice in practice. © 2014 Elsevier B.V.
Wang X.-Z.,Yangzhou University |
Wang X.-Z.,Service Center for Efficient |
Wang A.-L.,Yangzhou University |
Wang S.-H.,Lixiahe Region Agricultural Research Institute of Jiangsu |
And 5 more authors.
Journal of Ecology and Rural Environment | Year: 2011
Influence on the properties of turf-bed and growth of creeping bentgrass based on cow-manure-vermicompost as the basic materials were studied to determine the feasibility and effectiveness of cow-manure-vermicompost as substrate modifier of the turf-bed. The results show that pH value of the turf-bed decreased with an increasing addition of vermicompost while conductivity(σ) value remarkably increased. Conductivity value in 100 g • kg-1 vermicompost treatment was about 16 times of that in CK. But after the turf establishment stage, conductivity values decreased to the level close to that of CK. Compared with addition of 40 g • kg-1 peat, the addition of 40, 60, 80 and 100 g • kg-1 vermicompost can significantly shorten the time of the formation process of the lawn, considerably increase the regeneration speed, and remarkably improve the chlorophyll content and the clipping content. The growth of grass in vermicompost treatments was better than that in peat treatment. During actual performance, it should be considered that the growth of grass may be too fast at the later stage due to the higher content of phosphorus in vermicompost.
Yang G.,Yangzhou University |
Zuo Q.,Yangzhou University |
Liu R.,Yangzhou University |
Yin C.,Yangzhou University |
And 3 more authors.
Journal of Plant Nutrition | Year: 2016
Phosphorus (P) is one of nutrients essential for plant growth. The differences in P content, accumulation, and distribution among 98 rapeseed (Brassica napus) varieties with different P use efficiency for grain production (PUEg) were studied. The results showed that there were highly significant differences in P contents of the whole plant and various organs among different rapeseed varieties. Furthermore, PUEg had significantly negative correlations with P accumulations in whole plant, stems, shells, and seeds. The correlation analysis showed that the correlation coefficient of PUEg and P distribution ratio in stems was smaller, and it was significantly negatively correlated in shells, while it showed highly positive correlations in seeds. It indicated that P content in rapeseed plant stems and shells appeared to be transported into seeds to increase P distribution in seedpods at the late maturity stage, which could help improve PUEg. © 2016 Taylor & Francis Group, LLC.
Dong M.-H.,Suzhou Academy of Agriculture science |
Dong M.-H.,Yangzhou University |
Gu J.-R.,Suzhou Academy of Agriculture science |
Chen P.-F.,Suzhou Academy of Agriculture science |
And 2 more authors.
Zhiwu Shengli Xuebao/Plant Physiology Journal | Year: 2013
To investigate the changes of abscisic acid (ABA) content in grains at different spikelet positions of rice and explore their relations with grain-filling rates, two super rice genotypes, 'Yangliangyou 6' (indica rice) and 'Wuyunjin 24' (japonica rice) were field-grown. The changes of ABA content in each group of spikelets at middle part on a panicle during grain filling were determined. Meanwhile, to test and verify the hypothesis that ABA is involved in mediating the postanthesis development of the different categories of spikelets, low concentration (75.7 μmol·L-1) of ABA was sprayed on the two genotypes at early grain-filling stage. The results showed that earlier-flowered spikelets exerted dominance over later-flowered ones in grain-filling rate and grain weight. There was no difference between the two genotypes. Later-flowered spikelets contained higher concentration of soluble sugars than the earlier-flowered ones at early grain-filling stage, indicating that carbohydrate supply may not be a limiting factor to the development of inferior spikelets. Similar to grainfilling rate, earlier-flowered spikelets contained a higher ABA content than later-flowered ones. The grain-filling rate was significantly and positively correlated with ABA content. Application of low concentration of ABA at early grain-filling stage significantly increased grain weight of those later-flowered grains on the proximal secondary branch and the same branch. The results indicate that low ABA content in inferior spikelets results in their poor grain filling, and a higher ABA content in rice spikelets is required to maintain a faster grain-filling rate. Above all, the results suggest that the promotion of ABA content in grains at earlier grain-filling stage could enhance the transformation efficiency of sucrose to starch, and eventually accelerate grain filling.
Xu J.,Yangzhou University |
Wang B.,Lixiahe Region Agricultural Research Institute of Jiangsu |
Wu Y.,Yangzhou University |
Du P.,Yangzhou University |
And 5 more authors.
Theoretical and Applied Genetics | Year: 2011
Photoperiod-thermo-sensitive genic male sterile (PTGMS) rice exhibits a number of desirable traits for hybrid rice production. The cloning genes responsible for PTGMS and those elucidating male sterility mechanisms and reversibility to fertility would be of great significance to provide a foundation to develop new male sterile lines. Guangzhan63S, a PTGMS line, is one of the most widely used indica two-line hybrid rice breeding systems in China. In this study, genetic analysis based on F2 and BC1F2 populations derived from a cross between Guangzhan63S and 1587, determined a single recessive gene controls male sterility in Guangzhan63S. Molecular marker techniques combined with bulked-segregant analysis (BSA) were used and located the target gene (named ptgms2-1) between two SSR markers RM12521 and RM12823. Fine mapping of the ptgms2-1 locus was conducted with 45 new Insertion-Deletion (InDel) markers developed between the RM12521 and RM12823 region, using 634 sterile individuals from F2 and BC1F2 populations. Ptgms2-1 was further mapped to a 50.4 kb DNA fragment between two InDel markers, S2-40 and S2-44, with genetic distances of 0.08 and 0.16 cM, respectively, which cosegregated with S2-43 located on the AP004039 BAC clone. Ten genes were identified in this region based on annotation results from the RiceGAAS system. A nuclear ribonuclease Z gene was identified as the candidate for the ptgms2-1 gene. This result will facilitate cloning the ptgms2-1 gene. The tightly linked markers for the ptgms2-1 gene locus will further provide a useful tool for marker-assisted selection of this gene in rice breeding programs. © Springer-Verlag 2010.
Yang G.,Yangzhou University |
Zuo Q.-S.,Yangzhou University |
Tang Y.,Yangzhou University |
Shi J.-F.,Yangzhou University |
And 2 more authors.
Bulgarian Journal of Agricultural Science | Year: 2010
By using rapeseed (Brassia napus L.) cultivars with different seed yields, we measured the organ dry weight and phosphorus content, and then used cluster analysis (average linkage method) to classify different cultivars' yields, and further investigated different cultivars' phosphorus accumulation and allocation. Our study showed that, different cultivars' yields have distinct change and can be divided into six types according to clustering dendrogram. Different cultivars' yields are significantly different. Both phosphorus absorption total volume and phosphorus utilization efficiency for grain production (PUEg) for different types are significantly different. When yield increases, different types' phosphorus absorption total volume and PUEg values are increased significantly. The accumulation and allocation ratio of phosphorus in seeds from High-yield cultivars are significantly higher than those from low-yield cultivars. The implication is, if we'd like to increase rapeseed's PUEg, the priority method is to select high PUEg cultivars, and the second choice is to employ appropriate planting strategies so that more phosphorus can be transported to seeds from stems and leafs.
Cloning of genome-specific repetitive DNA sequences in wild rice (O. rufipogon Griff.), and the development of Ty3-gypsy retrotransposon-based SSAP marker for distinguishing rice (O. sativa L.) indica and japonica subspecies
Xiao N.,Yangzhou University |
Xiao N.,Lixiahe Region Agricultural Research Institute of Jiangsu |
Sun G.,Saint Mary's University, Halifax |
Hong Y.,Yangzhou University |
And 4 more authors.
Genetic Resources and Crop Evolution | Year: 2011
In the rice genome, insertions and eliminations of transposable elements have generated numerous transposon insertion polymorphisms (TIPs). Common wild rice (O. rufipogon Griff.), the ancestor of Asian cultivated rice (O. sativa L.), carries abundant genetic variations. To find subspecies-specific (SS) markers that can distinguish O. sativa ssp. indica and ssp. japonica, some long terminal repeat (LTR) sequences (sc1-14) of AA genome-specific RIRE retrotransposon were isolated from O. rufipogon genome. Sequences sc1 and sc12 were successfully utilized to develop the SS marker system based on retrotransposon inserted position polymorphisms. Twenty-two SS markers (ssi1-9, ssj1-13) were developed, where ssi1-9 are the indica-specific types, and ssj1-13 the japonica-specific types. The average accuracy of these markers in distinguishing the two subspecies is over 85%. SS marker ssj-10 can distinguish the two subspecies at 100% accuracy. Principal component analysis (PCA) showed that these markers could successfully distinguish indica from japonica varieties, regardless of their geographical origin. © 2011 Springer Science+Business Media B.V.