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1.
Preserving many kinds of rice resources and rich variations, Guizhou Province is one of the districts with the highest genetic diversity of cultivated rice (Oryza sativa L.) in China. In the current research, genetic diversity and structure of 537 accessions of cultivated rice from Guizhou were studied using 36 microsetellite markers and 39 phenotypic characters. The results showed that the model-based genetic structure was the same as genetic-distance-based one using SSRs but somewhat different from the documented classification (mainly based on phenotype) of two subspecies. The accessions being classified into indica by phenotype but japonica by genetic structure were much more than that being classified into japonica by phenotype but indica by genetic structure. Like Ding Ying's taxonomic system of cultivated rice, the subspecific differentiation was the most distinct differentiation within cultivated rice. But the differentiation within indica or japonica population was different: japonica presented clearer differentiation between soil-watery ecotypes than indica, and indica presented clearer differentiation between seasonal ecotypes than japonica. Cultivated rices in Guizhou revealed high genetic diversity at both DNA and phenotypic levels. Possessing the highest genetic diversity and all the necessary conditions as a center of genetic diversity, region Southwestern of Guizhou was suggested as the center of genetic diversity of O. sativa L. from Guizhou.  相似文献   

2.
An efficient molecular method for the accurate and efficient identification of indica and japonica rice was created based on the polymorphisms of insertion/deletion (InDel) DNA fragments obtained from the basic local alignment search tool (BLAST) to the entire genomic sequences of indica (93-11) and japonica rice (Nipponbare). The 45 InDel loci were validated experimentally by the polymerase chain reaction (PCR) and polyacrylamide gel electrophoresis (PAGE) in 44 typical indica and japonica rice varieties, including 93-11 and Nipponbare. A neutrality test of the data matrix generated from electrophoretic banding patterns of various InDel loci indicated that 34 InDel loci were strongly associated with the differentiation of indica and japonica rice. More extensive analyses involving cultivated rice varieties from 11 Asian countries, and 12 wild Oryza species with various origins confirmed that indica and japonica characteristics could accurately be determined via calculating the average frequency of indica- or japonica-specific alleles on different InDel loci across the rice genome. This method was named as the “InDel molecular index” that combines molecular and statistical methods in determining the indica and japonica characteristics of rice varieties. Compared with the traditional methods based essentially on morphology, the InDel molecular index provides a very accurate, rapid, simple, and efficient method for identifying indica and japonica rice. In addition, the InDel index can be used to determine indica or japonica characteristics of wild Oryza species, which largely extends the utility of this method. The InDel molecular index provides a new tool for the effective selection of appropriate indica or japonica rice germplasm in rice breeding. It also offers a novel model for the study of the origin, evolution, and genetic differentiation of indica and japonica rice adapted to various environmental changes.  相似文献   

3.
The pedigrees of three sequenced rice cultivars were analyzed to show that a majority of the genetic composition of 'Nipponbare' originates from japonica cultivars while the minority originates from indica cultivars. In contrast, '93-11' is derived mainly from indica cultivars with a smaller contribution from japonica cultivars. All ancestors of 'Guang lu ai 4' appeared to be indica lines. A set of molecular markers (46 InDels and 53 SSRs) polymorphic between 'Nipponbare' and '93-11' were examined in 46 typical indica and 47 typical japonica cultivars selected from 443 accessions according to Cheng's index. All cultivars were divided into indica and japonica groups without overlapping when clustered by Cheng's index, InDels and SSRs. Much higher InDel and SSR diversity between groups than within groups implies that the marker polymorphisms between 'Nipponbare' and '93-11' represent a large proportion of inter-subspecific diversity. About 85% of indica cultivars and more than 90% of japonica cultivars were confirmed to have the same PCR banding patterns as '93-11' and 'Nipponbare', respectively. Some polymorphic loci between 'Nipponbare' and '93-11' cannot be validated in other indica and japonica cultivars, either as subspecies-specific but not predominant alleles, or alleles not specific between the two groups. It was concluded that molecular markers developed from sequence polymorphism between 'Nipponbare' and '93-11' often represent inter-subspecific diversity, although some exceptions were sensitive to either particular marker loci or particular cultivars.  相似文献   

4.
Great heterosis exists in the inter-subspecific crossesbetween indica and japonica rice cultivars[1,2] and the ex-ploitation of this heterosis has long been considered as apromising method to further increase rice yield potential[3].Previous studies indicated that there were large differencesbetween the two subspecies with respect to morphology,isozyme, polymorphism of molecular markers and DNAstructure due to long time genetic differentiation[4,5]. Thosedifferences were identified to be clos…  相似文献   

5.
Hybrid sterility is a major form of postzygotic reproductive isolation and frequently occurs in hybrids between divergent populations, such as the indica and japonica subspecies of Asian cultivated rice (Oryza sativa L.). It has been a major barrier for utilization of the strong heterosis expressed in hybrids between indica and japonica. A large number of loci for rice inter-subspecific hybrid sterility have been identified by genetic analysis. Cytological studies revealed that male and female gamete abortions and reduced affinity between the uniting gametes all occurred in indica-japonica hybrids, suggesting the complexity of the causes for inter-subspecific hybrid sterility. Two genes conditioning embryo-sac and pollen sterility respectively in indica-japonica hybrids have been cloned recently, providing opportunities for molecular characterization of the indica-japonica hybrid sterility and wide-compatibility. Future studies should aim at cloning more genes for indica-japonica hybrid sterility, characterizing the underlying molecular mechanism, and utilization of the findings for the development of inter-subspecific hybrids to increase rice productivity.  相似文献   

6.
We have used the polymerase chain reaction to analyze variation in the size of 5S ribosomal gene spacer sequence. Eighty accessions, including 65 cultivated rice and 15 wild rice, were analyzed. Among them seven size classes of 5S DNA spacer were observed. Classification asindica orjaponica on the basis of 5S DNA spacer patterns generally agrees with classification based on morphological studies, indicating that the length polymorphism of 5S DNA spacer could be used as a molecular marker for taxonomic and phylogenetic analysis. Supported by the National Natural Science Fundation of China Yi Qingming: born in Apr. 1938, Professor  相似文献   

7.
We have used the polymerase chain reaction to analyze variation in the size of 5S ribosomal gene spacer sequence. Eighty accessions, including 65 cultivated rice and 15 wild rice, were analyzed. Among them seven size classes of 5S DNA spacer were observed. Classification asindica orjaponica on the basis of 5S DNA spacer patterns generally agrees with classification based on morphological studies, indicating that the length polymorphism of 5S DNA spacer could be used as a molecular marker for taxonomic and phylogenetic analysis. Supported by the National Natural Science Fundation of China Yi Qingming: born in Apr. 1938, Professor  相似文献   

8.
The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a “whole genome shotgun” approach, we have produced a draft rice genome sequence ofOryza sativa ssp.indica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from anindica variant cultivar93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEMBLER, a custom-designed software package used for the initial assembly, were verified rigorously by comparisons against finished BAC clone sequences from bothindica andjapanica strains, available from the public databases. Over all, 96.3% of full-length cDNAs, 96.4% of STS, STR, RFLP markers, 94.0% of ESTs and 94.9% unigene clusters were identified from the draft sequence. Our preliminary analysis on the data set shows that our rice draft sequence is consistent with the comman standard accepted by the genome sequencing community. The unconditional release of the draft to the public also undoubtedly provides a fundamental resource to the international scientific communities to facilitate genomic and genetic studies on rice biology. These authors contributed equally to this work.  相似文献   

9.
Amylose content in rice endosperm is one of the key determinants of rice eating and cooking quality, and the poor quality ofindica hybrid rice is closely related to the high amylose level in rice grains. In order to improve the grain quality of theindica hybrid rice by genetic engineering, an antisense fragment of ricewaxy gene, driven by the 5′-franking sequences of the ricewaxy gene, was successfully introduced into three major parent lines ofindica hybrid rice, all contain a high amylose level in the grains, viaAgrobacterium, and more than 100 hygromycinresistant plants were regenerated. The analysis of PCR amplification and Southern blots indicated that the T-DNA containing the antisensewaxy gene had been integrated into the genome of transgenic rice plants. Most of the primary transgenic rice plants grew normally, and the mature seeds from these transgenic plants were performed for analysis of the amylose content. The results showed that the amylose content in the endosperm of some grains was reduced and the lowest reached 7.02% in one homozygous transgenic line, 72.4% lower than that of the wild type. The influence of the altered amylose content on the gelatinization temperature and gel consistency was also observed in several homozygous transgenic rice plants. The two authors contributed equally to this work.  相似文献   

10.
A doubled haploid population, derived from anther culture of F1 hybrid between a typicalindica cv. and ajaponica cv. has been used to investigate the seedling cold tolerance (SCT) in growth cabinet. By dynamically analyzing every day’s survival percentages of the parents and DH lines under 7-d cold plus 9-d normal temperature condition, the quantitative trait loci (QTLs) for SCT have been mapped based on a molecular linkage map constructed from this population. The results show that two parents had significant differences in SCT and the segregation of SCT in DH lines was basically a continuous distribution with most serious injury on the 6th d of the cold treatment. A total of 4 QTLs for SCT have been identified on chromosomes 1, 2, 3 and 4 respectively. The additive effects of qSCT-1, qSCT-2 and qSCT-3 have been contributed by thejaponica cv JX17, but that of qSCT-4 has been contributed by theindica cv ZYQ8. The mechanism of SCT seems complicated since the above 4 QTLs detected at different stages during the treatment. Further study on the genotypes for these SCT QTLs in the DH lines shows transgressive segregation. It is demonstrated that the lines with stronger SCT over JXI7 have 3–4 loci for SCT. Integration of these QTLs into an appropriate variety may lead to a successful rice breeding program for cold tolerance.  相似文献   

11.
Relationships between D1 protein, xanthophyll cycle and subspecific difference of photodamage-resistant capacity have been studied inO. japonica rice varieties 02428 and 029 (photoinhibition-tolerance) andO. indica rice varieties 3037 and Palghar (photoinhibition-sensitivity) and their reciprocal cross F1 hybrids after photoinhibitory treatment. It was shown that PS II photochemical efficiency (F v /F m) decreased, and xanthophyll cycle from violaxanthin (V), via anaxanthin (A), to zeaxanthin (Z) was enhanced and non-photochemical quenching (qN) increased accordingly in SM-pretreated leaves of rice when the synthesis of D1 protein was inhibited, and that there was a decrease inqN and, as a result, more loss of D1 protein and a big decrease inF v/F m in DTT-pretreated leaves when xanthophyll cycle was inhibited.O. japonica subspecies had a higher maintaining capacity of D1 protein and a decrease ofF v/F m in a more narrow range, and exhibited more resistance against photodamage, as compared withO. indica subspecies. The above physiological indexes in reciprocal cross F1 hybrids, though between the values of their parents, were closer to maternal lines than to paternal lines. Experimental results support the concept that the turnover capacity for D1 protein is an important physiological basis of photoinhibition-tolerance, and will provide the physiological basis for selection of the photoinhibition-tolerant parents and develop a new approach to breed hybrids with high photosynthetic efficiency.  相似文献   

12.
A rice male-sterile mutant OsMS-L of japonica cultivar 9522 background, was obtained in M4 population treated with ^60Co γ-Ray. Genetic analysis indicated that the male.sterile phenotype was controlled by a single recessive gene. Results of tissue section showed that at microspore stage, OsMS-L tapetum was retarded. Then tapetal calls expanded and microspores degenerated. No matured pollens were observed in OsMS-L anther locus. To map OsMS-L locus, an F2 population was constructed from the cross between the OsMS-L (japonica) and LongTeFu B(indica). Firstly, the OsMS-L locus was roughly mapped between two SSR markers, RM109 and RM7562 on chromosome 2. And then eleven polymorphic markers were developed for further fine fine-mapping. At last the OsMS-L locus was mapped between the two lnDel markers, Lhsl0 and Lhs6 with genetic distance of 0.4 cM, respectively. The region was delimited to 133 kb. All these results were useful for further cloning and functional analysis of OsMS-L.  相似文献   

13.
Quantitative trait locus (QTLs) mapping for rapid visco analyser (RVA) profile parameters has been carried out by using a double haploid (DH) population derhred from a cross betweenindica variety Zhai-Ye-Qing 8 andjaponica variety Jing-Xi 17 and its genetic linkage map. The results indicate that the segregation of the RVA profiles is continually distributed among the DH lines, and some DH lines show transgressive segregation for all the parameters. A major QTL,Waxy (Wx) gene on chromosome 6 which controls the amylose synthesis, has been detected significantly for 5 traits: hot paste viscosity (HPV), cool paste viscosity (CPV), breakdown viscosity (BDV), consistency viscoslty (CSV) and setback viscoslty (SBV). Therefore, the RVA profile parameters are mainly controlled byWx gene. Other 3 and 2 QTLs have also been identified for BDV and SBV, respectively, and two of them share the same region on chromosomes 1 and 5. However, the peak viscosity (PKV) is controlled by a minor QTL on chromosome 12, qPKV-12.  相似文献   

14.
Studies showed that elevated [CO2] would improve photosynthetic rates and enhance yields of rice;however,few studies have focused on the response of rice lodging,which is a major cause of cereal yield loss and quality reduction,under elevated [CO2].In this study,we examined the effects of elevated [CO2] on stem and root lodging using 4 rice cultivars(86Y8,japonica hybrid;LYP9,2-line indica hybrid;variety 9311,type of indica inbred rice,and SY63,3-line indica hybrid) grown under two [CO2] levels:400 and 680 μmol mol-1.Our results indicated that under elevated [CO2],the stem-lodging risk(SLR) of 9311 decreased,while in SY63 the SLR increased,86Y8 and LYP9 were not significantly affected;the risk of root lodging was reduced for all cultivars,because root biomass(instead of root number) and bending strength were increased significantly,and then the increase of anti-lodging ability is far higher than that of self-weight mass moment for all cultivars.These findings suggested that higher [CO2] can enhance the risk of stem-lodging for cultivars with strong-[CO2]-responses,but may not aggravate the root lodging for all rice cultivars.  相似文献   

15.
Rice (Oryza sativa) was first domesticated in the lower and middle Yangtze regions of China, and rice remains have been found in many Chinese archaeological sites. Until now, only phenotypic archeobotanical evidence, such as the spikelet bases of ancient grains, has been used to speculate on the domestication process and domestication rate of rice. In this study, we sequenced 4 genomic segments from rice remains in Tianluoshan, a site of the local Hemudu Neolithic culture in the low Yangtze and two other archaeological sites (??2400 and 1200 BC, respectively). We compared our sequences with those of the current domesticated and wild rice (O. rufipogon) populations. At least two genotypes were found in the remains from each site, suggesting a heterozygotic state of the rice seeds. One ancient genotype was not found in the current domesticated population and might have been lost. The rice remains belonged to the japonica group, and most if not all were japonica-type, suggesting that the remains might be at an early stage of indica-japonica divergence or an indica-japonica mixture. We also identified sequences with significant similarity to those from species of Sapindales, Zygophyllales, and Brassicales, which is consistent with the identification of other plant remains in the Tianluoshan site and the common rice field weeds such as mustards in southern China.  相似文献   

16.
Rice (Oryza sativa L.) is important to food security and is also an excellent model plant for numerous cereal crops. A functional genomics study in rice includes characterization of the expression dynamics of genes by quantitative real-time PCR (qPCR) analysis; this is a significant key for developing rice varieties that perform well in the face of adverse climate change. The qPCR analysis requires the use of appropriate reference genes in order to make any quantitative interpretations meaningful. Here, the new potential reference genes were selected from a huge public database of rice microarray experiments. The expression stability of 14 candidates and 4 conventional reference genes was validated by geNorm PLUS and NormFinder software. Seven candidates are superior to the conventionally used reference genes in qPCR and three genes can be used reliably for quantitating the expression of genes involved in abiotic stress responses. These high-quality references EP (LOC_Os05g08980), HNR (LOC_Os01g71770), and TBC (LOC_Os09g34040) worked very well in three indica genotypes and one japonica genotype. One of indica genotypes including the Jasmine rice, KDML105 developed in Thailand for which no reference genes have been reported until now.  相似文献   

17.
Breeding rice with high water use efficiency (WUE) can ameliorate water shortage through water-saving irrigation.However,WUE is a complex quantitative trait and very few studies have been conducted to measure WUE directly.In this study,a recombined inbred line population derived from a cross between an indica lowland rice and upland japonica rice was used to dissect the genetic control of WUE by fine-monitored water supply experiments.Quantitative trait loci (QTL) were scanned for 10 traits including heading date (HD),water-consumption per day (water/d),shoot weight gain per day (shootw/d),root weight gain per day (rootw/d),kernel weight gain per day (kernelw/d),average WUE at whole plant level (WUEwhole/d),average WUE for up-ground biomass (WUEup/d),average WUE for grain yield (WUEyield/d),average economic index (econindex/d),and average root/shoot ratio per day (ratio/d).The results show that most of the traits were significantly correlated to each other.Twenty-four QTL (LOD ≥ 2.0) were detected for econindex,econindex/d,WUEyield,WUEyield/d,WUEup,WUEup/d,WUEwhole,WUEwhole/d,kernelw,kernelw/d,rootw,and water/d by composite interval mapping.These QTLs are located on chromosomes 1,2,4,6,7,8,and 12.Individual QTLs accounted for 4.97%-10.78% of the phenotypic variation explained.Some of these QTLs overlapped with previously reported drought resistance QTLs detected in this population.These results provide useful information for further dissection of the genetic basis and marker-assisted selection of WUE in rice.  相似文献   

18.
Indica is not only an important rice subspecies widely planted in Asia and the rest of the world,but it is also the genetic background of the majority of hybrid varieties in China.Studies on genetic structure and genetic diversity in indica germplasm resources are important for the classification and utilization of cultivated rice in China.Using a genetically representative core collection comprising 1482 Chinese indica landraces,we analysed the genetic structure,geographic differentiation and diversity.Model-based structure analysis of varieties within three ecotypes revealed nine eco-geographical types partially accordant with certain ecological zones in China.Differentiation of eco-geographical types was attributed to local ecological adaption and physical isolation.These groups may be useful for developing heterotic groups of indica.To facilitate the identification of different ecotypes and eco-geographical types,we identified characteristic SSR alleles of each ecotype and eco-geographical type and a rapid index of discrimination based on characteristic alleles.The characteristic alleles and rapid discrimination index may guide development of heterotic groups,and selection of hybrid parents.  相似文献   

19.
The pubescence of the leaf blade surface is an important agronomic characteristic for rice morphology and significantly influences rice growth as well as physiological characteristics. This characteristic was analyzed in F1 and F2 plants derived by crossing cultivar 75-1-127 with the indica cultivar Minghui 63, as well as the glabrous cultivar Lemont and indica cultivar 9311. Results indicated that the pubescence of the leaf blade surface was a dominant trait and controlled by a single gene. The GL6 gene was primarily mapped on rice chromosome 6 with recessive F2 population derived from 75-1-127/Minghui 63 by combining bulked segregation analysis and recessive class analysis using the Mapmaker3.0/MapDraw software. The genetic distances between the simple sequence repeat markers RM20491 and RM20547 were 7.2 and 2.2 cM, respectively. The GL6 gene was fine mapped in the interval between InDel-106 and InDel-115 at genetic distances of 0.3 and 0.1 cM, respectively. The large, recessive F2 population was derived from 75-1-127/Minghui 63. A high-resolution genetic and physical map of GL6 was constructed. Derived from the map-based sequences published by the International Rice Genome Sequencing Project, the GL6 gene was localized at an interval of 79 (japonica) and 116.82 kb (9311) bracketed by InDel-106 and InDel-115 within the BAC accession numbers AP008403 and AP005760. Seven annotated genes (japonica) and eight annotated genes (9311) were present. The basis was further set for GL6 cloning and function analysis.  相似文献   

20.
Using multi-color fluorescencein situ hybridization (FISH), we localized transferredbarnase-ps1 andpHctinG DNA sequences onto chromosomes of two transgenic rice plants, named Q12 and Q13, both of which were produced by micro-projectile bombardment. In both Q12 and Q13, each detected cell showed 2–3 signal spots on their chromosomes respectively. The signals of bothbarnase-ps1 andpHctinG were mostly detected in the adjacent chromosomal sites in which their signals were overlapped and could be recognized by the signal color on the metaphase chromosomes. Fiber FISH further demonstrated that the multiple copies in each of the two DNA sequences distributed adjacently on the DNA fiber in Q13. Combined with the results of Southern hybridization, the possible integration patterns in transgenic rice co-transformed by micro-projectile bombardment have been discussed.  相似文献   

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