首页 | 本学科首页   官方微博 | 高级检索  
相似文献
 共查询到20条相似文献，搜索用时 250 毫秒
1.
Radish (Raphanus sativus L.) belongs to Brassicaceae family and is a close relative of Brassica. This species shows a wide morphological diversity, and is an important vegetable especially in Asia. However, molecular research of radish is behind compared to that of Brassica. For example, reports on SSR (simple sequence repeat) markers are limited. Here, we designed 417 radish SSR markers from SSR-enriched genomic libraries and the cDNA data. Of the 256 SSR markers succeeded in PCR, 130 showed clear polymorphisms between two radish lines; a rat-tail radish and a Japanese cultivar, ‘Harufuku’. As a test case for evaluation of the present SSRs, we conducted two studies. First, we selected 16 SSRs to calculate polymorphism information contents (PICs) using 16 radish cultivars and four other Brassicaceae species. These markers detected 3–15 alleles (average = 9.6). PIC values ranged from 0.54 to 0.92 (average = 0.78). Second, part of the present SSRs were tested for mapping using our previously-examined mapping population. The map spanned 672.7 cM with nine linkage groups (LGs). The 21 radish SSR markers were distributed throughout the LGs. The SSR markers developed here would be informative and useful for genetic analysis in radish and its related species.  相似文献   

2.
Elephant grass [Pennisetum purpureum S.; syn. Cenchrus purpureus (Schumach.) Morrone] is an important global forage crop and is recognized for high yields of herbage with good nutritive value. It also has high biomass potential to be utilized as a biofuel feedstock. Whereas several previous genetic studies adapted simple sequence repeat (SSR) markers from pearl millet [Pennisetum glaucum (L.) R.Br.] for investigations in elephant grass, the present study developed SSR markers from 3536 DNA sequences derived from 16 elephant grass entries. A total of 3866 SSRs were identified including 1028 monomeric, 2019 dimeric, 735 trimeric, 49 tetrameric, 20 pentameric and 15 hexameric repeat motifs. Three hundred and seven sequences contained more than one repeated motif, and 154 SSRs were present in compound formation. Susequenctly,  four elephant grass and two pearl millet genotypes were chosen to validate 727 SSR markers. Of these, 628 markers produced visually detectable amplification products, including 73 (11.6%) polymorphic ones across all six genotypes. Polymorphism between the four elephant grass genotypes was revealed by 316 (50.6%) markers with diversity index values ranging from 0.75 to 0.38. Dimeric SSRs had the highest polymorphic rate (48.7%). These validated SSR markers had 58.6% (368 of 628) transferability rate to pearl millet. The availability of these polymorphic SSR markers will support advanced genetic studies in P. purpureum and its relatives.  相似文献   

3.
Simple sequence repeats for genetic analysis in pear   总被引：26，自引：0，他引：26  
The development of highly informative DNA markers, such as simple sequence repeats (SSRs), is essential for breeding to select agronomically important traits and for genetic studies in pear. We developed SSR markers by using two approaches, RAHM (random amplified hybridization microsatellites) and 5' anchored PCR methods. Segregation analysis of the SSRs revealed that amplified fragments were derived from the same loci, using 3 sets of progenies from crosses between pear varieties. Genetic diversity was characterized using 32 varieties, including 10 from Japanese pear (Pyrus pyrifolia), 9 from Chinese pear (P. bretschneideri, P. ussuriensis), 10 from European pear (P. communis) as well as 3 wild relatives (P. calleryana). Diversity of SSR genotypes was observed among species as well as within species and 65 putative alleles were detected. The use of seven SSR markers was sufficient to differentiate between all of the 32 varieties. This revised version was published online in August 2006 with corrections to the Cover Date.  相似文献   

4.
Groundnut (Arachis hypogaea L.) an important oilseed crop in India is known to have narrow genetic base. Therefore, the assessment of genetic diversity and detection of marker-trait association are important objectives for the genetic improvement of groundnut. The present study involved the development of 192 SSR markers from Arachis genomic survey sequences. From these, seven polymorphic SSRs along with 15 other genomic SSRs, 19 genic SSRs, and three STS markers were used to detect genetic diversity among 44 groundnut genotypes. These polymorphic SSR markers amplified 155 bands (76 genomic and 79 genic), of these 128 bands (67 genomic and 61 genic) were polymorphic. The genomic SSR exhibited 88.1% and genic SSRs displayed 77.2% allelic polymorphism. The polymorphic information content (PIC) of the markers ranged from 0.04 to 0.95. The pair-wise genetic similarity ranged from 24.2 to 90.7% for genomic SSR and 32.9 to 97.9% for genic SSR markers. Cluster analysis based on the pooled data from both genomic and genic SSRs revealed a dendrogram which could distinguish all the genotypes. Further, the AMOVA analysis detected 16.7% genetic variation due to differences in seed size and 13.0% due to plant habit. Based on locus-by-locus AMOVA and Kruskal-Wallis ANOVA and further confirmation by discriminant analysis and general linear model, six markers were found to be associated with plant habit and four markers with seed size.  相似文献   

5.
Simple sequence repeat (SSR) or microsatellite markers are a valuable tool for several purposes such as evaluation of genetic diversity, fingerprinting, marker‐assisted selection and breeding. In this study, a SSR genomic enriched library was developed in Lathyrus sativus (grass pea) by affinity capture of restriction fragments to biotinylated microsatellite oligonucleotides. About 400 randomly selected clones were sequenced, and SSRs were present in approximately 30% of them. Clones contained 75%, 9% and 16% of simple, interrupted and compound SSRs, respectively. Of the 10 SSRs tested, 7 primer pairs produced clearly distinguishable DNA banding patterns. Successively, SSR primer pairs were successfully tested to reveal polymorphism in a set of four different grass pea germplasm accessions. The transferability of SSR markers was high among three related species of Lathyrus, namely Lathyrus cicera, Lathyrus ochrus and Lathyrus tingitanus, and the legume crop, Pisum sativum. These results indicate that the novel SSR markers are informative and will be useful and convenient for genetic analysis in grass pea and related species.  相似文献   

6.
Cultivated peanut (Arachis hypogaea L.) consists of six botanical varieties. Identification of DNA markers associated with botanical varieties would be useful in plant genotyping, germplasm management, and evolutionary studies. We have developed 130 simple sequence repeat (SSR) markers in peanut, 38 of which were used in this study because of their ability in detecting genetic polymorphism among 24 peanut accessions. Eight SSR markers were found useful to classify botanical varieties. Among them, six SSR markers were specific to botanical varieties fastigiata and vulgaris, one to botanical varieties hypogaea and hirsuta, and one to botanical varieties peruviana, and aequatoriana. Also, three of them derived from peanut expressed sequence tags (ESTs) were associated with putative genes. As botanical varieties have different morphological traits and belong to different subspecies in A. hypogaea, these markers might be associated with genes involved in the expression of morphological traits. The results also suggested that SSRs (also called microsatellites) might play a role in shaping evolution of cultivated peanut. Multiplex PCR of botanical variety-specific markers could be applied to facilitate efficient genotyping of the peanut lines.  相似文献   

7.
  相似文献   

8.
  相似文献   

9.
Watermelon, Citrullus lanatus Thunb. Matsum. & Nakai is an important vegetable crop worldwide. Due to its narrow genetic base, detection and utilization of the genetic variations, cultivar identification and increasing genetic diversity are some important tasks for watermelon breeders. Molecular markers, especially microsatellites or simple sequence repeats (SSRs) are playing increasingly important roles for these purposes. In the present study, a core set of 23 highly informative SSR markers was developed for watermelon genetic diversity analysis. Based on whole genome sequencing of 17 watermelon inbred lines, we identified 3.9 million single nucleotide polymorphisms (SNPs) which were used to construct a SNP-based dendrogram for the 17 lines. Meanwhile, from the sequenced genome, 13,744 SSRs were developed, of which 704 were placed on a high-resolution watermelon linkage map. To develop the core set SSR markers, 78 of the 704 mapped SSRs were selected as the candidate markers. Using the SNP-based dendrogram as calibration, 23 SSR markers evenly distributed across the genome were identified as the core marker set for watermelon genetic diversity analysis. Each marker was able to detect 2–7 alleles with polymorphism information content values ranging from 0.45 to 0.82. The dendrograms of 17 watermelon lines based on SNPs, the base set of 78 SSRs and the core set of 23 SSRs were highly consistent. The utility of this core set SSRs was demonstrated in 100 commercial watermelon cultivars and elite lines, which could be placed into six clusters that were largely consistent with previous classification based on morphology and parentage data. This core set of SSR markers should be very useful for genotyping and genetic variation analysis in watermelon.  相似文献   

10.
红麻是最重要的自然纤维作物之一,然而SSR标记的匮乏限制了其遗传改良。本研究从红麻90 175个EST序列中挑出含有转录因子的EST,开发了94对SSR引物。以24份不同红麻种质资源的DNA为模板,利用9%非变性聚丙烯酰胺凝胶电泳检测多态性。结果表明,85对引物(占90.4%)至少在2个材料之间存在多态性,表明开发的EST-SSR具有很好的多态性。其中,三核苷酸重复所占比例最多,重复基元AAT和ATG的多态性较高。聚类分析表明,24份红麻种质资源的遗传相似系数变化在0.62~0.92之间,表现出丰富的遗传基础。这些结果不仅丰富了红麻的分子标记数量,而且为红麻的遗传分析提供资源。  相似文献   

11.
  相似文献   

12.
小豆SSR引物在绿豆基因组中的通用性分析   总被引：5，自引：1，他引：4  
分析了187对小豆SSR引物在绿豆基因组中的可转移性,以期为绿豆分子遗传育种研究提供分析工具.结果表明,约75%的小豆SSR引物可在绿豆中有效扩增,但不同小豆连锁群SSR引物的可转移率存在差异.多态性分析发现80对引物中有28对在60份绿豆种质中可以检测到多态性,等位变异数从2～7不等,平均为2.9,PIC指数从0.02～0.69,平均为0.36.UPGMA聚类及主坐标分析表明,尽管同一省份的种质不能紧密聚在一起,但大多在聚类图上成簇状分布,说明相同来源的绿豆种质具有相似的遗传背景;此外,国外及我国边远地区的绿豆种质在遗传背景上与内部省份间存在明显差异.这些多态性SSR不仅可以有效用于绿豆分子遗传学研究,还可以用于不同来源绿豆种质资源的辅助鉴别.  相似文献   

13.
  相似文献   

14.
Microsatellite polymorphism in Pisum sativum   总被引：8，自引：0，他引：8  
J. Burstin    G. Deniot    J. Potier    C. Weinachter    G. Aubert  A. Barranger   《Plant Breeding》2001,120(4):311-317
Pisum sativum sequences were retrieved from Genbank/EMBL databases and searched for all possible dinucleotide and trinucleotide tandem repeats. One‐hundred and seventy‐one simple sequence repeats (SSRs) were found among 663 sequences. The different dinucleotide or trinucleotide motifs occurred at varying frequencies. CT/AG was the most frequent dinucleotide, and TCT/AGA the most frequent trinucleotide. Forty‐three microsatellite markers were generated from these sequences and used to assess the genetic variability among 12 pea genotypes. Thirty‐one were polymorphic among the genotypes and the average number of variants per marker was 3.6 when considering only polymorphic markers. Overall, the number of variants for a given SSR marker was correlated with the length of the SSR but some 12‐bp long SSRs showed the same degree of polymorphism as longer ones. The groupings resulting from the SSR genotyping among the 12 genotypes gave an interesting insight into the possible origin of one recent cultivar. Database‐derived SSR markers are highly variable. They can provide useful information on the genetic diversity among P. sativum cultivated types.  相似文献   

15.
Summary The first genetic linkage map of Japanese bunching onion (Allium fistulosum) based primarily on AFLP markers was constructed using reciprocally backcrossed progenies. They were 120 plants each of (P1)BC1 and (P2)BC1 populations derived from a cross between single plants of two inbred lines: D1s-15s-22 (P1) and J1s-14s-20 (P2). Based on the (P2)BC1 population, a linkage map of P1 was constructed. It comprises 164 markers – 149 amplified fragment length polymorphisms (AFLPs), 2 cleaved amplified polymorphic sequences (CAPSs), and 12 simple sequence repeats (SSRs) from Japanese bunching onion, and 1 SSR from bulb onion (A. cepa) – on 15 linkage groups covering 947 centiMorgans (cM). The linkage map of P2 was constructed with the (P1)BC1 population and composed of 120 loci – 105 AFLPs, 1 CAPS, and 13 SSRs developed from Japanese bunching onion and 1 SSR from bulb onion – on 14 linkage groups covering 775 cM. Both maps were not saturated but were considered to cover the majority of the genome. Nine linkage groups in P2 map were connected with their counterparts in P1 map using co-dominant anchor markers, 13 SSRs and 1 CAPS.  相似文献   

16.
A total of 16,619 ESTs sequences (SSRs) of sesame (Sesamum indicum L.) were mined from Genbank. From sequences, 156 primer pairs were designed and characterized to determine the diversity among 49 sesame accessions. Twenty SSRs were found to be polymorphic and the number of alleles ranged from two to five per locus. The allele size varied from 101 to 399 bp. The average PIC value of the 20 SSR loci was 0.72 ranging from 0.49 (SEM-12-68) to 0.90 (SEM-12-27). Dendrogram analysis grouped the 49 genotypes into five separate clusters exhibiting a genetic similarity coefficient from 0.59 to 1.0. Hence, these EST-derived SSRs markers could be useful in assessing the diversity of sesame accessions and could also help in identifying diverse parents for sesame improvement programs.  相似文献   

17.
A core set of 21 simple sequence repeats (SSR) markers was developed for Pak‐choi (Brassica rapa ssp. chinensis var. communis) variety identification. We initially selected 74 SSR markers which exhibited high polymorphism and reproducibility in SSR detection from 2129 SSRs. Using the 74 SSR‐based dendrogram for 45 inbred lines as calibration, 21 core SSRs were selected out. The utility of this core set SSRs was firstly tested in 45 inbred lines and finally verified in 102 commercial varieties. We also constructed a molecular ladder for each core SSR as a reference standard. Diversity analysis of this core SSR panel in 102 varieties demonstrated that each marker generates 2–3 alleles (averaged 2.33), with polymorphism information content values ranging from 0.01 to 0.56 (averaged 0.31). The averaged values of Shannon information index, observed heterozygosity, expected heterozygosity and Wright's fixation index were 0.59, 0.43, 0.38 and −0.09, respectively. Furthermore, the 21 SSR‐based classifications for 102 varieties were consistent with traditional classification based on morphology. This core SSR panel represents an effective tool for genetic variation analysis in Pak‐choi.  相似文献   

18.
L. R. Pinto    K. M. Oliveira    T. Marconi    A. A. F. Garcia    E. C. Ulian    A. P. de Souza   《Plant Breeding》2006,125(4):378-384
Microsatellites or simple sequence repeats (SSRs) are one of the most suitable markers for genome analysis as they have great potential to aid breeders to develop new improved sugarcane varieties. The development of SSR derived from expressed sequence tags (EST) opens new opportunities for genetic investigations at a functional level. In the present work, the polymorphism obtained with a subset of 51 EST–SSRs derived from sucest was compared with those generated by 50 genomic SSRs (gSSR) in terms of number of alleles, polymorphism information content, discrimination power and their ability to establish genetic relationships among 18 sugarcane clones including three Saccharum species (S. officinarum, S. barberi, S. sinense). The majority of EST–SSRs loci had four to six alleles in contrast to the seven to nine observed for the gSSRs loci. Approximately, 35% of the gSSRs had PIC values around 0.90 in contrast to 15% of the EST–SSRs. However, the mean discrimination power of the two types of SSR did not differ significantly as much as the average genetic similarity (GS) based on Dice coefficient. The correlation between GS of the two types of SSRs was high (r = 0.71/P = 0.99) and significant. Although differences were observed between dendrograms obtained with each SSR type, both were in good agreement with pedigree information. The S. officinarum clone IJ76‐314 was grouped apart from the other clones evaluated. The results here demonstrate that EST–SSRs can be successfully used for genetic relationship analysis, extending the knowledge of genetic diversity of sugarcane to a functional level.  相似文献   

19.
黄麻是世界上重要的天然韧皮部纤维作物之一。然而, SSR标记的缺乏限制了黄麻的遗传改良。本研究从圆果种黄麻测序品种CVL-1的基因组、基因、CDS和cDNA中挖掘SSR信息,利用SSR Primer软件查找SSR位点,并分析其分布特征。结果表明,基于基因组序列共开发了153,242个基因组SSR,平均密度为467.20个SSRMb~(–1);基于cDNA序列开发了10,747个SSR,平均密度为260.85 SSR Mb~(–1)。大部分重复基元为二至四核苷酸,占76.91%,其中cDNA序列SSR中三核苷酸重复基元数量较多而基因组SSR中二核苷酸重复基元数量较多。对于不同类型的SSR重复基元,随着重复单元数量的增加,其基因组和cDNA的SSR分布频率呈现逐步降低特征。黄麻全基因组SSR标记鉴定,不仅可以丰富黄麻分子标记的数量,而且为剖析黄麻重要农艺性状的遗传机制奠定基础。  相似文献   

20.
EST–SSRs of Gossypium barbadense are mainly developed using traditional Sanger sequencing. However, due to the high cost and low throughput of Sanger sequencing, it is necessary to use high throughput sequencing technology for the development of more ESTs to more effectively analyze the structure and function of this species. In this study, a G. barbadense acc. 3–79 unnormalized fiber cDNA library (219.63 Mb) and a G. barbadense cv. Hai7124 normalized root cDNA library (204.61 Mb) were obtained by 454 sequencing. EST–SSRs were identified from the two libraries, and only 7,255 SSRs were obtained from the unnormalized library, with an average frequency of 1/31.00 kb. In contrast, 16,087 SSRs were obtained from the normalized library, with an average frequency of 1/13.02 kb. The frequencies of dinucleotides and tetranucleotides in the two libraries were very different. Comparing the two libraries, we found that a normalized cDNA library is more efficient for mining SSRs. Integrating the two libraries allowed the development of 1,129 EST–SSR markers, and 311 polymorphic loci were integrated into our interspecific BC1 genetic linkage map. The mapping results showed that the distribution of EST–SSRs on sub-genomes and chromosomes was uneven; however, the distribution of the mapped G. barbadense EST–SSRs on homologous chromosomes was similar, with the exception of Chr05 versus Chr19 and Chr12 versus Chr26. This study provided new EST–SSR markers that will facilitate studies on cotton genetics and breeding.  相似文献   

设为首页 | 免责声明 | 关于勤云 | 加入收藏

Copyright©北京勤云科技发展有限公司  京ICP备09084417号