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Development of genomic SSR and potential EST-SSR markers in Bupleurum chinense DC.
C Sui, J Wei, S Chen, H Chen, C Yang
African Journal of Biotechnology , 2009,
Abstract: Nineteen genomic SSR markers were developed using inter-simple sequence repeat (ISSR)- suppression PCR technique in Bupleurum chinense DC., a widely used Chinese medicinal plant. A total of 126 alleles were detected across 22 individual plants of B. chinense DC. f. octoradiatum (Bunge) Shan et Sheh, with an average of 3 - 13 alleles per locus. The observed heterozygosity (HO) and the expected heterozygosity (HE) values ranged from 0.23 to 1.00 and from 0.29 to 0.92, respectively. Nine loci deviated from Hardy-Weinberg equilibrium (HWE) (P < 0.05) and eight pairs of loci showed significant linkage disequilibrium (LD) (Fisher’s exact test, P < 0.01). The species transferability of these genomic SSR markers was also detected in seven other Bupleurum species. Eight SSR markers were successfully amplified in all tested species. In addition, forty four EST-SSRs which can be amplified with expected sizes were identified from a B. chinense root cDNA library. The genomic SSR markers and potential EST-SSR markers developed in the present study should be useful for genetic diversity and molecular marker assistant selection breeding research in Bupleurum species.
A White Campion (Silene latifolia) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping
Maria Moccia, Christine Oger-Desfeux, Gabriel AB Marais, Alex Widmer
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-243
Abstract: We obtained a total of 3662 high quality sequences from a normalized Silene cDNA library. These represent 3105 unigenes, with 73% of unigenes matching genes in other species. We found 255 sequences containing one or more SSR motifs. More than 60% of these SSRs were trinucleotides. A total of 30 microsatellite loci were identified from 106 ESTs having sufficient flanking sequences for primer design. The inheritance of these loci was tested via segregation analyses and their usefulness for linkage mapping was assessed in an interspecific cross. Tests for crossamplification of the EST-SSR loci in other Silene species established their applicability to related species.The newly characterized genes and gene-derived markers from our Silene EST library represent a valuable genetic resource for future studies on Silene latifolia and related species. The polymorphism and transferability of EST-SSR markers facilitate comparative linkage mapping and analyses of genetic diversity in the genus Silene.The White Campion, Silene latifolia Poiret, a member of the plant family Caryophyllaceae, is a dioecious herb. The species is diploid, has a large nuclear genome size (1C = 2646 Mbp [1]) and a haploid chromosome number of 12. Sex is determined genetically by heteromorphic sex chromosomes that were first described by Blackburn [2] and Winge [3]. As in humans, females are homogametic, XX, and males are the heterogametic sex, XY. The sex chromosomes are the largest chromosomes and contribute substantially to the large genome size of this species. Although dioecy has evolved many times in different plant lineages [4], well differentiated, heteromorphic sex chromosomes are relatively rare in plants. Over the last decades, Silene latifolia has become a model organism in plant ecology and evolution. Major research avenues include for example the evolution of heteromorphic sex chromosomes in plants [5-7], sexual dimorphism [8,9], plant-pathogen [10] and plant pollinator interactions [11], i
Mapping of the rice (Oryza sativa L.) thermo-sensitive genic male sterile gene tms5 with EST and SSR markers
Dagang Jiang,Sen Lu,Hai Zhou,Xiaojin Wu,Chuxiong Zhuang,Yaoguang Liu,Mantong Mei
Chinese Science Bulletin , 2006, DOI: 10.1007/s11434-006-0417-9
Abstract: With the cDNA suppression subtraction hybridization method, a spikelet-specific cDNA library was constructed that expressed at meiosis stage in rice. A total of 121 cDNA fragments were selected from the library and used as EST (expressed sequence tags) markers to detect the polymorphism between Annong N, a normal fertile Indica rice line and Annong S-1, its spontaneous mutant with thermo-sensitive genic male sterility, using the RFLP (restriction fragment length polymorphism) technique. HN57, one of the EST probes, could detect polymorphism between them. The results of segregation analysis with the F2 population developed from Annong S-1 and Annong N indicate that HN57 co-segregates with the thermo-sensitive genic male-sterility controlled by tms5, the recessive gene in Annong S-1. This marker is located on the 31.2-cM region of the chromosome 2 of RGP (rice genome research program) genetic map. To further determine the location of tms5, 80 SSR (simple sequence repeat) markers around this region were developed, and 12 of them were polymorphic. And finally, the tms5 was mapped within region of 181 kb by using these new markers.
Development of cDNA-derived SSR markers and their efficiency in diversity assessment of Cymbidium accessions
Moe,Kyaw Thu; Hong,Woo-Ju; Kwon,Soon-Wook; Park,Yong-Jin;
Electronic Journal of Biotechnology , 2012,
Abstract: cymbidium spp. are popular ?owering plants. assessment of the genetic diversity in cultivated cymbidium facilitates conservation of germplasm and subsequent cultivar improvement. thus, it is important to develop more efficient polymorphic dna markers. although more motifs (403) were identified and more primers (206) were designed in the genomic library compared to the cdna library, a larger number of successful primers were obtained from the cdna library (59.9%) than from genomic dna library (51.1%). however, higher pic and gene diversity were identified in genomic ssrs. the average allele number per locus was also higher in genomic ssrs (7.3) than est-ssrs (5.2), among the 24 evaluated cymbidium accessions. at/ta was comparatively high in est-ssrs, while this motif was not as common in genomic ssrs. the ctt/aag/tct/aga/ttc/gaa and tgc/gca/gct/agc/ctg/cag motifs were the most abundant tri-nucleotide sequences in est-ssrs, while gtt/aac/tgt/aca/ttg/caa was the most frequent in genomic ssrs. the number of repeats ranged from 3 to 12 in est-ssrs. currently, 52 novel polymorphic ssr markers have been evaluated, which will be useful for germplasm assessments, core set construction, evaluation of genetic diversity, and marker assisted selection (mas) based cymbidium breeding.
Development of new SSR markers from EST of SSH cDNA libraries on rose fragrance
基于差减cDNA文库EST信息的月季花香突变体SSR标记的开发

YAN Hui-Jun,ZHANG Hao,XIE Ji-Rong,LI Shu-Fa,JIAN Hong-Ying,QIU Xian-Qin,WANG Qi-Gang,WANG Ji-Hua,TANG Kai-Xue,
晏慧君
,张颢,谢吉容,李树发,蹇洪英,邱显钦,王其刚,王继华,唐开学

遗传 , 2009,
Abstract: The new SSR markers of rose related fragrance were developed based on the SSH cDNA libraries of rose floral scent mutant. In this study, 10 EST-SSRs (2.6%) from 391 ESTs in the libraries were identified. Six EST-SSRs primers were designed to sequence flanking SSRs. The primer pairs designed were screened on the wild-type Jinyindao, which has flowers full of pleasant scent, and the mutant-type Wangriqinghuai without perceivable floral scent. Five primer pairs were amplified effectively in Jinyindao and Wangriqinghuai, and 3 were polymorphic between Jinyindao and Wangriqinghuai. Eighteen rose cultivars including fragrant roses and nonfragrant roses were identified by the five prime pairs. These results proved that EST-SSR markers are effective markers to identify the polymorphism of the rose.
Mapping of the rice (Oryza sa-tiva L.) thermo-sensitive genic male sterile gene tms5 with EST and SSR markers
Mapping of the rice (Oryza sativa L.) thermo-sensitive genic male sterile gene tms5 with EST and SSR markers

JIANG Dagang,LU Sen,ZHOU Hai,WU Xiaojin,ZHUANG Chuxiong,LIU Yaoguang,MEI Mantong,
JIANG
,Dagang,LU,Sen,ZHOU,Hai,WU,Xiaojin,ZHUANG,Chuxiong,LIU,Yaoguang

科学通报(英文版) , 2006,
Abstract: With the cDNA suppression subtraction hybridization method, a spikelet-specific cDNA library was constructed that expressed at meiosis stage in rice. A total of 121 cDNA fragments were selected from the library and used as EST (expressed se-quence tags) markers to detect the polymorphism between Annong N, a normal fertile Indica rice line and Annong S-1, its spontaneous mutant with thermo-sensitive genic male sterility, using the RFLP (restriction fragment length polymorphism) technique. HN57, one of the EST probes, could detect poly-morphism between them. The results of segregation analysis with the F2 population developed from An-nong S-1 and Annong N indicate that HN57 co-seg- regates with the thermo-sensitive genic male-sterility controlled by tms5, the recessive gene in Annong S-1. This marker is located on the 31.2-cM region of the chromosome 2 of RGP (rice genome research pro-gram) genetic map. To further determine the location of tms5, 80 SSR (simple sequence repeat) markers around this region were developed, and 12 of them were polymorphic. And finally, the tms5 was mapped within region of 181 kb by using these new markers.
Studies of new EST-SSRs derived from Gossypium barbadense
YanXin Zhang,ZhongXu Lin,Wu Li,LiLi Tu,YiChun Nie,XianLong Zhang
Chinese Science Bulletin , 2007, DOI: 10.1007/s11434-007-0399-2
Abstract: Existing cotton EST-SSR markers are mostly derived from Gossypium arboreum and Gossypium hirsutum, but EST-SSR markers from Gossypium barbadense are scarce. One hundred and nineteen EST-SSRs were developed based on 98 unique ESTs from a cDNA library constructed in our laboratory using developing fibers from G. barbadense cv. Pima3–79. Among the SSRs, trinucleotide AAG appeared at a high frequency of 11.76%. 36 accessions (consisting of 13 diploids of the A genome, 11 diploids of the D genome and 12 allotetraploids of the AD genome) were employed to test new EST-SSRs. 76 EST-SSRs were successfully amplified, and 313 polymorphic fragments were yielded, with an average of 4.11 fragments per primer pair. The PIC ranged from 0.17 to 0.95 with an average of 0.53. Based on Jaccard’s genetic similarity coefficient, these 36 accessions were clustered into three groups. 21 EST-SSRs exhibited polymorphisms in BC1 population ((Emian22 × Pima3–79) × Emian22), 24 polymorphic loci were generated, while 22 of the 24 polymorphic loci were integrated with our interspecific BC1 backbone genetic linkage map, and anchored in 12 chromosomes. This study effectively proved that EST-SSRs from G. barbadense are valuable for genetic diversity analysis and genetic mapping.
火炬松热胁迫cDNA文库的EST-SSR预测  [PDF]
华南农业大学学报 , 2009, DOI: 10.7671/j.issn.1001-411X.2009.03.083
Abstract: 以火炬松热胁迫cDNA文库的EST序列为材料,对EST序列进行聚类、拼接等处理后,再进行EST-SSR标记的预测.结果表明:火炬松热胁迫eDNA文库4283条EST序列经CAP3拼接后,获得2062个UniGene,其中934个Contig,1128个Singletons.对UniGene利用SSRIT在线软件分析得到110条EST-SSR.拼接后的UniGene含有SSR位点的频率为4.32%,SSR在火炬松EST上的分布密度为每14.6kb出现1个SSR.这些EST重复基元中,二核苷酸重复和三核苷酸重复最多,分别占60.90%和36.36%;四、六核苷酸重复分别占0.91%、2.73%;没有五核苷酸的重复基序.所有的核苷酸重复基元中,二核苷酸AT所占比例最高,约占42.73%;三核苷酸重复中,比例最高的是AAG和AGG,均占7.33%.上述研究结果对于开发火炬松新分子标记与开展分子辅助育种的研究具有一定的指导意义.
EST and EST-SSR marker resources for Iris
Shunxue Tang, Rebecca A Okashah, Marie-Michele Cordonnier-Pratt, Lee H Pratt, Virgil Ed Johnson, Christopher A Taylor, Michael L Arnold, Steven J Knapp
BMC Plant Biology , 2009, DOI: 10.1186/1471-2229-9-72
Abstract: Collectively, 6,530 ESTs were produced from normalized leaf and root cDNA libraries of I. brevicaulis (IB72) and I. fulva (IF174), and assembled into 4,917 unigenes (1,066 contigs and 3,851 singletons). We identified 1,447 SSRs in 1,162 unigenes and developed 526 EST-SSR markers, each tracing a different unigene. Three-fourths of the EST-SSR markers (399/526) amplified alleles from IB72 and IF174 and 84% (335/399) were polymorphic between IB25 and IF174, the parents of I. brevicaulis × I. fulva mapping populations. Forty EST-SSR markers were screened for polymorphisms among 39 ecotypes or cultivars of seven species – 100% amplified alleles from wild collected ecotypes of Louisiana Iris (I.brevicaulis, I.fulva, I. nelsonii, and I. hexagona), whereas 42–52% amplified alleles from cultivars of three horticulturally important species (I. pseudacorus, I. germanica, and I. sibirica). Ecotypes and cultivars were genetically diverse – the number of alleles/locus ranged from two to 18 and mean heterozygosity was 0.76.Nearly 400 ortholog-specific EST-SSR markers were developed for comparative genetic mapping and other genotyping applications in Iris, were highly polymorphic among ecotypes and cultivars, and have broad utility for genotyping applications within the genus.Iris, a genus of 200–300 species in the Iridaceae (Asparagales), is one of the most widely admired and earliest cultivated garden flowers, having appeared in ancient Eygptian artifacts as early as 1950 B.C. [1]. The most widely cultivated, hybridized, and horticulturally important species are I.germanica (tall-bearded Iris), I.pseudacorus (yellow-flag Iris), and I.sibirica (Siberian Iris), each with numerous commercially important cultivars. Iris species are found in diverse habitats on every continent in the Northern Hemisphere and have been important models for the study of plant evolution, ecology, and hybrid speciation [2-8]. Chromosome numbers and ploidy are highly variable among and within species in the
Construction of full-length cDNA library of white flower Salvia miltiorrhiza bge f.alba root and partial EST sequence analysis
G Hao, R Shi, J Wang, B Qi
African Journal of Biotechnology , 2009,
Abstract: In order to screen and isolate secondary metabolite biosynthesis related gene, we construct a cDNA library of white flower Salvia miltiorrhiza bge. f.alba. High quality of total RNA was successfully isolated from roots of white flower S. miltiorrhiza using modified CTAB method. Double strand cDNA was cloned into pDNR-LIB vector. The number of clones, recombinant rate and length of insert fragments were determined. Results showed that the capacity of the original library was 1.8×107 with a recombinant rate of 91% and the inserted cDNA fragments ranged from 0.5 to 2.0 kb. Partial cDNAs chosen by random were sequenced. After BLAST analysis of some cDNAs, their possible functions were predicted. It is found that most of these cDNAs were similar to homological genes of Arabidopsis thaliana, Oryza sativa, and other plants. Most of the genes were related to cell metabolism, stress resistance, cell growth and development, etc. More importantly, some key enzymes and factors involved in secondary metabolism of S. miltiorrhiza, such as EST fragments of phenylalanine ammonialyase (SmPAL1), chorismate synthase (SmCHS), 3-hydroxy-3-methylglutaryl CoA reductase (SmHMGR), 4-Coumaratecoenzyme A ligase (Sm4CL1) and SmMYB90, were found from this library. These results indicated that the library has enough capacity, high recombinant rate and long insert fragment. This study provided a base for further study on the structure and function of these cDNAs.
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