共查询到20条相似文献,搜索用时 15 毫秒
1.
P. Ramu B. Kassahun S. Senthilvel C. Ashok Kumar B. Jayashree R. T. Folkertsma L. Ananda Reddy M. S. Kuruvinashetti B. I. G. Haussmann C. T. Hash 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,119(7):1193-1204
The sequencing and detailed comparative functional analysis of genomes of a number of select botanical models open new doors
into comparative genomics among the angiosperms, with potential benefits for improvement of many orphan crops that feed large
populations. In this study, a set of simple sequence repeat (SSR) markers was developed by mining the expressed sequence tag
(EST) database of sorghum. Among the SSR-containing sequences, only those sharing considerable homology with rice genomic
sequences across the lengths of the 12 rice chromosomes were selected. Thus, 600 SSR-containing sorghum EST sequences (50
homologous sequences on each of the 12 rice chromosomes) were selected, with the intention of providing coverage for corresponding
homologous regions of the sorghum genome. Primer pairs were designed and polymorphism detection ability was assessed using
parental pairs of two existing sorghum mapping populations. About 28% of these new markers detected polymorphism in this 4-entry
panel. A subset of 55 polymorphic EST-derived SSR markers were mapped onto the existing skeleton map of a recombinant inbred
population derived from cross N13 × E 36-1, which is segregating for Striga resistance and the stay-green component of terminal drought tolerance. These new EST-derived SSR markers mapped across all
10 sorghum linkage groups, mostly to regions expected based on prior knowledge of rice–sorghum synteny. The ESTs from which
these markers were derived were then mapped in silico onto the aligned sorghum genome sequence, and 88% of the best hits corresponded to linkage-based positions. This study demonstrates
the utility of comparative genomic information in targeted development of markers to fill gaps in linkage maps of related
crop species for which sufficient genomic tools are not available. 相似文献
2.
A QTL study on late leaf spot and rust revealed one major QTL for molecular breeding for rust resistance in groundnut (Arachis hypogaea L.) 总被引:1,自引:0,他引:1
Y. P. Khedikar M. V. C. Gowda C. Sarvamangala K. V. Patgar H. D. Upadhyaya R. K. Varshney 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2010,120(5):971-984
Late leaf spot (LLS) and rust are two major foliar diseases of groundnut (Arachis hypogaea L.) that often occur together leading to 50–70% yield loss in the crop. A total of 268 recombinant inbred lines of a mapping
population TAG 24 × GPBD 4 segregating for LLS and rust were used to undertake quantitative trait locus (QTL) analysis. Phenotyping
of the population was carried out under artificial disease epiphytotics. Positive correlations between different stages, high
to very high heritability and independent nature of inheritance between both the diseases were observed. Parental genotypes
were screened with 1,089 simple sequence repeat (SSR) markers, of which 67 (6.15%) were found polymorphic. Segregation data
obtained for these markers facilitated development of partial linkage map (14 linkage groups) with 56 SSR loci. Composite
interval mapping (CIM) undertaken on genotyping and phenotyping data yielded 11 QTLs for LLS (explaining 1.70–6.50% phenotypic
variation) in three environments and 12 QTLs for rust (explaining 1.70–55.20% phenotypic variation). Interestingly a major
QTL associated with rust (QTLrust01), contributing 6.90–55.20% variation, was identified by both CIM and single marker analysis (SMA). A candidate SSR marker
(IPAHM 103) linked with this QTL was validated using a wide range of resistant/susceptible breeding lines as well as progeny
lines of another mapping population (TG 26 × GPBD 4). Therefore, this marker should be useful for introgressing the major
QTL for rust in desired lines/varieties of groundnut through marker-assisted backcrossing. 相似文献
3.
Development and incorporation of microsatellite markers into the linkage map of sugar beet (Beta vulgaris spp.) 总被引:1,自引:0,他引:1
S. J. Rae C. Aldam I. Dominguez M. Hoebrechts S. R. Barnes K. J. Edwards 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,100(8):1240-1248
A set of informative simple sequence repeat markers has been identified for use in the marker-assisted breeding of Beta vulgaris. Highly enriched small insert genomic libraries were constructed, consisting of 1536 clones (with inserts of between 250–900
bp). Screening the clones with CA, CT, CAA, CATA and GATA nucleotide-repeat probes revealed positive hybridisation to over
50% of the clones. Of these 340 were sequenced. Primer pairs were designed for sequences flanking the repeats and, of these,
57 pairs revealed length polymorphism with 12 Beta accessions. Heterozygosity levels of the SSR loci ranged from 0.069 to 0.809. Heterozygosity levels were found to be similar
to those detected employing RFLP probes with the same accessions. Phenetic analysis using the markers, indicated relationships
in accordance with known pedigrees. Twenty three of the SSR markers were polymorphic in one or both of two F2 mapping populations, and were placed relative to a framework of RFLP probes. The markers are distributed over all nine linkage
groups of sugar beet.
Received: 14 July 1999 / Accepted: 27 October 1999 相似文献
4.
In the past decade, several molecular maps of cotton have been constructed using diverse DNA molecular markers and mapping populations. In this study, an interspecific linkage map of allotetraploid cotton was developed using a BC1 population ((Gossypium hirsutum x G. barbadense) x G. hirsutum). This map was genome-wide and was based entirely on simple sequence repeat (SSR) markers. Forty-four linkage groups were assigned to 26 chromosomes, with 917 loci spanning 5452.2 cM of the genome. The average distance between loci was 5.9 cM, providing uniform coverage of the A subgenome and D subgenome. Characteristics of this map were analyzed in detail, including the distributions of genomic SSRs, expressed sequence tag (EST)-SSRs, and distorted markers. Furthermore, the relationships between motif characteristics (size, type, length) and the level of polymorphism in EST-SSRs were also surveyed. The results showed that tetranucleotide and dinucleotide repeats had similar levels of polymorphism, and ACAT, AC, and ACT repeats had the highest polymorphism rates. Loci with lengths of 27 bp, 33 bp, and 24 bp were more likely to be polymorphic. This work will provide information to assist in designing future EST-SSRs. 相似文献
5.
Evaluation of inter-simple sequence repeat analysis for mapping in Citrus and extension of the genetic linkage map 总被引:25,自引:0,他引:25
A. A. Sankar G. A. Moore 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,102(2-3):206-214
Inter-simple sequence repeat (ISSR) analysis was evaluated for its usefulness in generating markers to extend the genetic
linkage map of Citrus using a backcross population previously mapped with restriction fragment length polymorphism (RFLP), random amplified polymorphic
DNA (RAPD) and isozyme markers. ISSR markers were obtained through the simple technique of PCR followed by analysis on agarose
gels, using simple sequence repeat (SSR) primers. Optimization of reaction conditions was achieved for 50% of the SSR primers
screened, and the primers amplified reproducible polymorphic bands in the parents and progeny of the backcross population.
Mendelian segregation of the polymorphic bands was demonstrated, with an insignificant number of skewed loci. Most of the
SSR primers produced dominant loci; however co-dominance was observed with loci derived from three primers. A new genetic
map was produced by combining the segregation data for the ISSR markers and data for the RFLP, RAPD and isozyme markers from
the previous map and creating genetic linkages among all the markers using JoinMap 2.0 mapping software. The new map has an
improved distribution of markers along the linkage groups with fewer gaps, and marker order showed partial or complete conservation
in the linkage groups. The incorporation of ISSR markers into the genetic linkage map demonstrates that ISSR markers are suitable
for genetic mapping in Citrus.
Received: 3 February 2000 / Accepted: 12 May 2000 相似文献
6.
Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley 总被引:2,自引:0,他引:2
R. K. Varshney T. Thiel T. Sretenovic-Rajicic M. Baum J. Valkoun P. Guo S. Grando S. Ceccarelli A. Graner 《Molecular breeding : new strategies in plant improvement》2008,22(1):1-13
A ‘core set’ of 28 simple sequence repeat (SSR) and 28 single nucleotide polymorphism (SNP) markers for barley was developed
after screening six diverse genotypes (DGs) representing six countries (Afghanistan, Pakistan, Algeria, Egypt, Jordan and
Syria) with 50 SSR and 50 SNP markers derived from expressed sequence tags (ESTs). The markers of the core set are single
locus with very high quality amplifications, high polymorphism information content (PIC) and are distributed across the barley
genome. PIC values for the selected SSR and SNP markers ranged between 0.32–0.72 (average 0.58) and 0.28–0.50 (average 0.42),
respectively. To make the SNP genotyping cost effective, CAPS (cleaved amplified polymorphic sequence) and indel assays were
developed for 23 markers and the remaining 5 SNP markers were optimized for pyrosequencing. A high coefficient of correlations
(r = 0.96, P < 0.005) between the genetic similarity matrices of SSR and SNP genotyping data of the core set on diverse genotypes (DGs)
and their similar groupings according to the geographical distribution in both SSR and SNP phenograms with high bootstrap
values underline the utility and reliability of the core set. A comparative allelic and sequence diversity for SSR and SNP
markers between the DGs and six elite parental genotypes (PGs) of mapping populations showed comparable diverse nature of
two germplasm sets. However, unique SNPs and indels were observed in both germplasm sets providing more datapoints for analysing
haplotypes in a better way for the corresponding SNP marker.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
7.
Haitao Li Xun Chen Yuan Yang Jinsong Xu Jianxun Gu Jie Fu Xiaoju Qian Shunchang Zhang Jiangsheng Wu Kede Liu 《Molecular breeding : new strategies in plant improvement》2011,28(4):585-596
The availability of whole genome shotgun sequences (WGSs) in Brassica oleracea provides an unprecedented opportunity for development of microsatellite or simple sequence repeat (SSR) markers for genome
analysis and genetic improvement in Brassica species. In this study, a total of 56,465 non-redundant SSRs were identified from the WGSs in B. oleracea, with dinucleotide repeats being the most abundant, followed by tri-, tetra- and pentanucleotide repeats. From these, 1,398
new SSR markers (designated as BoGMS) with repeat length ≥25 bp were developed and used to survey polymorphisms with a panel
of six rapeseed varieties, which is the largest number of SSR markers developed for the C genome in a single study. Of these
SSR markers, 752 (69.5%) showed polymorphism among the six varieties. Of these, 266 markers that showed clear scorable polymorphisms
between B. napus varieties No. 2127 and ZY821 were integrated into an existing B. napus genetic linkage map. These new markers are preferentially distributed on the linkage groups in the C genome, and significantly
increased the number of SSR markers in the C genome. These SSR markers will be very useful for gene mapping and marker-assisted
selection of important agronomic traits in Brassica species. 相似文献
8.
Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.] 总被引:2,自引:0,他引:2
Xiaoping Jia Zhongbao Zhang Yinghui Liu Chengwei Zhang Yunsu Shi Yanchun Song Tianyu Wang Yu Li 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,118(4):821-829
SSR markers are desirable markers in analysis of genetic diversity, quantitative trait loci mapping and gene locating. In
this study, SSR markers were developed from two genomic libraries enriched for (GA)n and (CA)n of foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China. A total of 100 SSR markers among the 193 primer pairs detected
polymorphism between two mapping parents of an F2 population, i.e. “B100” of cultivated S. italica and “A10” of wild S. viridis. Excluding 14 markers with unclear amplifications, and five markers unlinked with any linkage group, a foxtail millet SSR
linkage map was constructed by integrating 81 new developed SSR markers with 20 RFLP anchored markers. The 81 SSRs covered
nine chromosomes of foxtail millet. The length of the map was 1,654 cM, with an average interval distance between markers
of 16.4 cM. The 81 SSR markers were not evenly distributed throughout the nine chromosomes, with Ch.8 harbouring the least
(3 markers) and Ch.9 harbouring the most (18 markers). To verify the usefulness of the SSR markers developed, 37 SSR markers
were randomly chosen to analyze genetic diversity of 40 foxtail millet accessions. Totally 228 alleles were detected, with
an average 6.16 alleles per locus. Polymorphism information content (PIC) value for each locus ranged from 0.413 to 0.847,
with an average of 0.697. A positive correlation between PIC and number of alleles and between PIC and number of repeat unit
were found [0.802 and 0.429, respectively (P < 0.01)]. UPGMA analysis revealed that the 40 foxtail millet cultivars could be grouped into five clusters in which the landraces’
grouping was largely consistent with ecotypes while the breeding varieties from different provinces in China tended to be
grouped together.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
9.
Rui Zhang AnDan Zhu XinJian Wang Jun Yu HongRong Zhang JiangSheng Gao YunJiang Cheng XiuXin Deng 《Plant Molecular Biology Reporter》2010,28(4):646-653
Walnut (Juglans regia), an economically important woody plant, is widely cultivated in temperate regions for its timber and nutritional fruits.
Despite abundant studies in germplasm, systemic molecular evaluations of walnut are sparsely reported mainly due to the limited
molecular markers available. Expressed sequence tags (EST) provide a valuable resource for developing simple sequence repeat
(SSR) markers. In this study, a total of 5,025 walnut ESTs (covering 16.41 Mb) were retrieved from the National Center for
Biotechnology Information database. The SSR motifs were then analyzed by the SSRHunter software. In total, 398 SSRs were obtained
with an average frequency of 1/4.08 kb. Dinucleotide (di-) repeat motifs accounted for 69.85% of all SSRs, followed by trinucleotide
(tri-) with a frequency of 27.64%, while low frequency (2.51%) of tetranucleotide (tetra-) to hexanucleotide (hexa-) was observed.
Meanwhile, GCA and TC motifs were prevalent among di- and tri- loci, respectively. Subsequently, a total of 123 primer pairs
were designed from the non-redundant SSR-containing unigenes with the selection threshold of SSR length set to 10 bp or more.
To examine the efficiency of candidate markers, seven DNA pools were collected from geographically different accessions. Results
demonstrated that 41 SSR primer sets could generate high polymorphic amplification products (33.3%), and these polymorphic
loci were mainly located in the 3′-untranslated region. Annotation analysis revealed that only two of these 41 loci were located
inside open reading frames of characterized proteins (E ≤ 1E−30). 相似文献
10.
M. Venkateswarlu S. Raje Urs B. Surendra Nath H. E. Shashidhar M. Maheswaran T. M. Veeraiah M. G. Sabitha 《Tree Genetics & Genomes》2006,3(1):15-24
To lay the foundation for molecular breeding efforts, the first genetic linkage map of mulberry (2n=2x=28) was constructed with 50 F1 full-sib progeny using randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), and simple sequence repeat (SSR) markers and two-way pseudotestcross mapping strategy. We selected 100 RAPD, 42 ISSR, and 9 SSR primers that amplified 517 markers, of which 188 (36.36%) showed a test-cross configuration, corresponding to the heterozygous condition in one parent and null in the other. Two separate female and male maps were constructed using 94 each of female- and male-specific testcross markers, containing 12 female linkage groups and 14 male linkage groups. At a minimum logarithm of the odds (LOD) score threshold of 6.0 and at a maximum map distance of 20 cM, the female map covered a 1,196.6-cM distance, with an average distance of 15.75 cM and maximum map distance of 37.9 cM between two loci; the male-specific map covered a 1,351.7-cM distance, with an average distance of 18.78 cM and a maximum map distance between two loci is of 34.7 cM. The markers distributed randomly in all linkage groups without any clustering. All 12 linkage groups in the female-specific map consisted of 4–10 loci ranging in length from 0 to 140.4 cM, and in the male-specific map, the 13 largest linkage groups (except linkage group 12, which contained three loci) consisted of 4–12 loci, ranging in length from 53.9 to 145.9 cM and accounting for 97.22% of the total map distance. When mapping, progeny pass through their juvenile phase and assume their adult characters, mapping morphological markers and identification of quantitative trait loci for adaptive traits will be the primary target. In that sense, our map provides reference information for future molecular breeding work on Morus and its relatives. 相似文献
11.
Ding-Qin Tang Jiang-Jie Lu Wei Fang Shan Zhang Ming-Bing Zhou 《Molecular breeding : new strategies in plant improvement》2010,25(2):299-311
Public sequence databases provide a rapid, simple and cost-effective source of microsatellite markers. We analyzed 1,532 bamboo
(Phyllostachys pubescens) sequences available in public domain DNA databases, and found 3,241 simple sequence repeat (SSR) loci comprising repeats
of two or more nucleotides in 920 genomic survey sequences (GSSs) and 68 cDNA sequences. This corresponded to one SSR per
336 bp of GSS DNA and one SSR per 363 bp of cDNA. The SSRs consisted of 76.6 and 74.5% dinucleotide repeats, 20.0 and 22.3%
trinucleotide repeats, and 3.4 and 3.2% higher-number repeats in the GSS DNA and cDNA sequences, respectively. The repeat
motif AG/CT (or GA/TC) was the most abundant. Nineteen microsatellite markers were developed from Class I and Class II SSRs,
showing that the limited polymorphism in Ph. pubescens cultivars and provenances could be attributed to clonal propagation of the bamboo plant. The transferability of the microsatellites
reached 75.3%, and the polymorphism of loci successfully transferred was 66.7% for six additional Phyllostachys species. Microsatellite PBM014 transferred successfully to all six species, showed rich polymorphism, and could serve as species-specific
alleles for the identification of Phyllostachys interspecies hybrids. 相似文献
12.
Microsatellites (i.e., simple sequence repeats [SSRs]) are highly variable genetic markers that are widely used at an intraspecific
level in population genetic studies. Here we employed an enrichment strategy for microsatellite isolation by using microsatellite
oligoprobes and magnetic capture of the fragments (Fischer and Bachmann, 1998) inProsopis chilensis (Mol.) Stuntz (Fabaceae). We analyzed the obtained level of enrichment by sequencing 120 enriched genomic fragments. A total
of 521 SSR motives were detected. According to specific search criteria (SSR motifs ≥3 repeat units and ≥6 bp length), 95.8%
of the clones contained SSR motifs. Of these, 7.8% showed homology to chloroplast sequences and 92.2% to nuclear sequences.
When regarding only nuclear SSRs with 5 or more repeat units and a minimum length of 10 bp, the level of enrichment was 30.8%.
A FASTA search against the European Molecular Biology Laboratory (EMBL) database univocally revealed 4 clones in transcribed
regions, 102 clones in genomic regions with unknown function, and 9 clones in chloroplast regions. Among the loci with longer
repeat units (≥10 bp, ≥5 repeat units), 3 were in transcribed regions and 65 were in other genomic regions. We discuss the
applicability of these markers for population genetic studies. 相似文献
13.
The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.) 总被引:1,自引:0,他引:1
R. K. Varshney D. J. Bertioli M. C. Moretzsohn V. Vadez L. Krishnamurthy R. Aruna S. N. Nigam B. J. Moss K. Seetha K. Ravi G. He S. J. Knapp D. A. Hoisington 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,118(4):729-739
Molecular markers and genetic linkage maps are pre-requisites for molecular breeding in any crop species. In case of peanut
or groundnut (Arachis hypogaea L.), an amphidiploid (4X) species, not a single genetic map is, however, available based on a mapping population derived
from cultivated genotypes. In order to develop a genetic linkage map for tetraploid cultivated groundnut, a total of 1,145
microsatellite or simple sequence repeat (SSR) markers available in public domain as well as unpublished markers from several
sources were screened on two genotypes, TAG 24 and ICGV 86031 that are parents of a recombinant inbred line mapping population.
As a result, 144 (12.6%) polymorphic markers were identified and these amplified a total of 150 loci. A total of 135 SSR loci
could be mapped into 22 linkage groups (LGs). While six LGs had only two SSR loci, the other LGs contained 3 (LG_AhXV) to
15 (LG_AhVIII) loci. As the mapping population used for developing the genetic map segregates for drought tolerance traits,
phenotyping data obtained for transpiration, transpiration efficiency, specific leaf area and SPAD chlorophyll meter reading
(SCMR) for 2 years were analyzed together with genotyping data. Although, 2–5 QTLs for each trait mentioned above were identified,
the phenotypic variation explained by these QTLs was in the range of 3.5–14.1%. In addition, alignment of two linkage groups
(LGs) (LG_AhIII and LG_AhVI) of the developed genetic map was shown with available genetic maps of AA diploid genome of groundnut
and Lotus and Medicago. The present study reports the construction of the first genetic map for cultivated groundnut and demonstrates its utility
for molecular mapping of QTLs controlling drought tolerance related traits as well as establishing relationships with diploid
AA genome of groundnut and model legume genome species. Therefore, the map should be useful for the community for a variety
of applications.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
14.
James W. Olmstead Audrey M. Sebolt Antonio Cabrera Suneth S. Sooriyapathirana Sue Hammar Gloria Iriarte Dechun Wang Charles Y. Chen Esther van der Knaap Amy F. Iezzoni 《Tree Genetics & Genomes》2008,4(4):897-910
Linkage maps of the sweet cherry cultivar ‘Emperor Francis’ (EF) and the wild forest cherry ‘New York 54’ (NY) were constructed
using primarily simple sequence repeat (SSR) markers and gene-derived markers with known positions on the Prunus reference map. The success rate for identifying SSR markers that could be placed on either the EF or NY maps was only 26%
due to two factors: a reduced transferability of other Prunus-species-derived markers and a low level of polymorphism in the mapping parents. To increase marker density, we developed
four cleaved amplified polymorphic sequence markers (CAPS), 19 derived CAPS markers, and four insertion–deletion markers for
cherry based on 101 Prunus expressed sequence tags. In addition, four gene-derived markers representing orthologs of a tomato vacuolar invertase and
fruit size gene and two sour cherry sorbitol transporters were developed. To complete the linkage analysis, 61 amplified fragment
length polymorphism and seven sequence-related amplified polymorphism markers were also used for map construction. This analysis
resulted in the expected eight linkage groups for both parents. The EF and NY maps were 711.1 cM and 565.8 cM, respectively,
with the average distance between markers of 4.94 cM and 6.22 cM. A total of 82 shared markers between the EF and NY maps
and the Prunus reference map showed that the majority of the marker orders were the same with the Prunus reference map suggesting that the cherry genome is colinear with that of the other diploid Prunus species.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
15.
Small yellow croaker (Larimichthys polyactis) is an important economic species of marine fishery. We developed and evaluated simple sequence repeat (SSR) markers from
expressed sequence tags (ESTs) of Pseudosciaena crocea, Paralichthys olivaceus and Psetta maxima. Characteristics of nine EST–SSR loci were investigated using 46 L. polyactis individuals. The number of alleles per locus ranged from 2 to 6. The observed heterozygosity ranged from 0.0652 to 0.7391,
while the expected heterozygosity ranged from 0.0638 to 0.7754. Seven loci departed from Hardy–Weinberg equilibrium (P < 0.01) significantly. These loci and markers will be useful for population genetics and systemic evolution among species
of small yellow croaker. 相似文献
16.
Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.) 总被引:49,自引:0,他引:49
X. Chen S. Temnykh Y. Xu Y. G. Cho S. R. McCouch 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,95(4):553-567
Ninety-four newly developed microsatellite markers were integrated into existing RFLP framework maps of four rice populations,
including two doubled haploid, a recombinant inbred, and an interspecific backcross population. These simple sequence repeats
(SSR) were predominantly poly(GA) motifs, targetted because of their abundance in rice. They were isolated from a previously
described sheared library and a newly constructed enzyme-digested library. Differences in the average length of poly(GA) tracts
were observed for clones isolated from the two libraries. The length of GA motifs averaged 21 repeat units for clones isolated
from the Tsp-509-digested library, while motifs averaged 17 units for clones from the sheared library. There was no evidence of clustering
of microsatellite markers near centromeres or telomeres. Mapping of the 94 newly developed markers as well as of 27 previously
reported microsatellites provided genome-wide coverage of the 12 chromosomes, with an average distance of 1 SSLP (simple sequence
repeat polymorphism) per 16–20 cM.
Received: 13 February 1997/Accepted: 28 February 1997 相似文献
17.
Development and characterisation of simple sequence repeat (SSR) markers for perennial ryegrass (Lolium perenne L.) 总被引:2,自引:0,他引:2
E. S. Jones M. P. Dupal R. Kölliker M. C. Drayton J. W. Forster 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,102(2-3):405-415
Enrichment methods were optimised in order to isolate large numbers of simple sequence repeat (SSR) markers for perennial
ryegrass (Lolium perenne L.), with the aim of developing a comprehensive set of loci for trait mapping and cultivar identification. Two libraries
were constructed showing greater than 50% enrichment for a variety of SSR-motif types. Sequence characterisation of 1853 clones
identified 859 SSR-containing clones, of which 718 were unique. Truncation of flanking sequences limited potential primer
design to 366 clones. One-hundred selected SSR primer pairs were evaluated for amplification and genetic polymorphism across
a panel of diverse genotypes. The efficiency of amplification was 81%. A relatively high level of SSR polymorphism was detected
(67%), with a range of 2–7 alleles per locus. Mendelian segregation of alleles detected by selected SSR-locus primer pairs
was demonstrated in the F1 progeny of a pair cross. Cross-species amplification was detected in a number of related pasture and turfgrass species, with
high levels of transfer to other Lolium species and members of the related genus Festuca. The identity of putative SSR ortholoci in these related species was confirmed by DNA sequence analysis. These loci constitute
a valuable resource of ideal markers for the molecular breeding of ryegrasses and fescues.
Received: 8 May 2000 / Accepted: 13 June 2000 相似文献
18.
Genetic diversity and population structure of a diverse set of rice germplasm for association mapping 总被引:4,自引:0,他引:4
Liang Jin Yan Lu Peng Xiao Mei Sun Harold Corke Jinsong Bao 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2010,121(3):475-487
Germplasm diversity is the mainstay for crop improvement and genetic dissection of complex traits. Understanding genetic diversity,
population structure, and the level and distribution of linkage disequilibrium (LD) in target populations is of great importance
and a prerequisite for association mapping. In this study, 100 genome-wide simple sequence repeat (SSR) markers were used
to assess genetic diversity, population structure, and LD of 416 rice accessions including landraces, cultivars and breeding
lines collected mostly in China. A model-based population structure analysis divided the rice materials into seven subpopulations.
63% of the SSR pairs in these accessions were in LD, which was mostly due to an overall population structure, since the number
of locus pairs in LD was reduced sharply within each subpopulation, with the SSR pairs in LD ranging from 5.9 to 22.9%. Among
those SSR pairs showing significant LD, the intrachromosomal LD had an average of 25–50 cM in different subpopulations. Analysis
of the phenotypic diversity of 25 traits showed that the population structure accounted for an average of 22.4% of phenotypic
variation. An example association mapping for starch quality traits using both the candidate gene mapping and genome-wide
mapping strategies based on the estimated population structure was conducted. Candidate gene mapping confirmed that the Wx and starch synthase IIa (SSIIa) genes could be identified as strongly associated with apparent amylose content (AAC) and pasting temperature (PT), respectively.
More importantly, we revealed that the Wx gene was also strongly associated with PT. In addition to the major genes, we found five and seven SSRs were associated with
AAC and PT, respectively, some of which have not been detected in previous linkage mapping studies. The results suggested
that the population may be useful for the genome-wide marker–trait association mapping. This new association population has
the potential to identify quantitative trait loci (QTL) with small effects, which will aid in dissecting complex traits and
in exploiting the rich diversity present in rice germplasm. 相似文献
19.
Nivedita Singh Debjani Roy Choudhury Amit Kumar Singh Sundeep Kumar Kalyani Srinivasan R. K. Tyagi N. K. Singh Rakesh Singh 《PloS one》2013,8(12)
Simple sequence repeat (SSR) and Single Nucleotide Polymorphic (SNP), the two most robust markers for identifying rice varieties were compared for assessment of genetic diversity and population structure. Total 375 varieties of rice from various regions of India archived at the Indian National GeneBank, NBPGR, New Delhi, were analyzed using thirty six genetic markers, each of hypervariable SSR (HvSSR) and SNP which were distributed across 12 rice chromosomes. A total of 80 alleles were amplified with the SSR markers with an average of 2.22 alleles per locus whereas, 72 alleles were amplified with SNP markers. Polymorphic information content (PIC) values for HvSSR ranged from 0.04 to 0.5 with an average of 0.25. In the case of SNP markers, PIC values ranged from 0.03 to 0.37 with an average of 0.23. Genetic relatedness among the varieties was studied; utilizing an unrooted tree all the genotypes were grouped into three major clusters with both SSR and SNP markers. Analysis of molecular variance (AMOVA) indicated that maximum diversity was partitioned between and within individual level but not between populations. Principal coordinate analysis (PCoA) with SSR markers showed that genotypes were uniformly distributed across the two axes with 13.33% of cumulative variation whereas, in case of SNP markers varieties were grouped into three broad groups across two axes with 45.20% of cumulative variation. Population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD) derived Δk was plotted against the K to determine the number of populations. In case of SSR maximum Δk was at K=5 whereas, in case of SNP maximum Δk was found at K=15, suggesting that resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis. 相似文献
20.
Fernandez-Silva I Eduardo I Blanca J Esteras C Picó B Nuez F Arús P Garcia-Mas J Monforte AJ 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2008,118(1):139-150
We report the development of 158 primer pairs flanking SSR motifs in genomic (gSSR) and EST (EST-SSR) melon sequences, all
yielding polymorphic bands in melon germplasm, except one that was polymorphic only in Cucurbita species. A similar polymorphism level was found among EST-SSRs and gSSRs, between dimeric and trimeric EST-SSRs, and between
EST-SSRs placed in the open reading frame or any of the 5′- or 3′-untranslated regions. Correlation between SSR length and
polymorphism was only found for dinucleotide EST-SSRs located within the untranslated regions, but not for trinucleotide EST-SSRs.
Transferability of EST-SSRs to Cucurbita species was assayed and 12.7% of the primer pairs amplified at least in one species, although only 5.4% were polymorphic.
A set of 14 double haploid lines from the cross between the cultivar “Piel de Sapo” and the accession PI161375 were selected
for the bin mapping approach in melon. One hundred and twenty-one SSR markers were newly mapped. The position of 46 SSR loci
was also verified by genotyping the complete population. A final bin-map was constructed including 80 RFLPs, 212 SSRs, 3 SNPs
and the Nsv locus, distributed in 122 bins with an average bin length of 10.2 cM and a maximum bin length of 33 cM. Map density
was 4.2 cM/marker or 5.9 cM/SSR.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献