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Kuluev BR, Baymiev AK, Gerashchenkov GA, Chemeris DA, Zubov VV, Kuluev AR, Baymiev AK, Chemeris AV. Random Priming PCR Strategies for Identification of Multilocus DNA Polymorphism in Eukaryotes. RUSS J GENET+ 2018. [DOI: 10.1134/s102279541805006x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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2
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Hodoki Y, Ohbayashi K, Kunii H. Analysis of population clonal diversity using microsatellite markers in the salt marsh sedge Carex scabrifolia in western Japan. LANDSCAPE AND ECOLOGICAL ENGINEERING 2013. [DOI: 10.1007/s11355-012-0210-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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Zhou MP, Hayden MJ, Zhang ZY, Lu WZ, Ma HX. Saturation and mapping of a major Fusarium head blight resistance QTL on chromosome 3BS of Sumai 3 wheat. J Appl Genet 2010; 51:19-25. [PMID: 20145296 DOI: 10.1007/bf03195706] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Fusarium head blight (FHB) is a destructive disease in wheat. The major quantitative trait locus (QTL) on 3BS from Sumai 3 and its derivatives has been used as a major source of the resistance to FHB worldwide, but the discrepancy in reported location of the major QTL could block its using in map based cloning and marker assisted selection. In this study, Chinese Spring-Sumai 3 chromosome 3B substitution line was used as resistant parent of the mapping population to reduce the confounded effect of genetic background in Sumai 3. The major QTL region was saturated with the Sequence Tagged Microsatellite (STM) and Sequence Tagged Site (STS) markers. A linkage map of chromosome 3B with 36 markers covering a genetic distance of 112.4 cM was constructed. Twelve new markers were inserted into the chromosome region where the major QTL was located. The average interval distance between markers was 1.5 cM. Multiple QTL Models (MQM) mapping indicated that the major QTL was located in the interval of Xgwm533-Xsts9-1, and explained 45.6% of phenotypic variation of the resistance to FHB. The SSR (simple sequence repeat) marker Xgwm533 and STM marker Xstm748tcac are closely linked to the major QTL.
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Affiliation(s)
- M-P Zhou
- Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Zhongling street 50, Nanjing 210014, P.R.China
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Raman R, Allen H, Diffey S, Raman H, Martin P, McKelvie K. Localisation of quantitative trait loci for quality attributes in a doubled haploid population of wheat (Triticum aestivum L.). Genome 2009; 52:701-15. [PMID: 19767900 DOI: 10.1139/g09-045] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Selection of wheat germplasm for a range of quality traits has been a challenging exercise because of the cost of testing, the variation within testing data, and a poor understanding of the underlying genetics. The objective of this study was to identify quantitative trait loci (QTLs) underlying quality traits in wheat. A doubled haploid population comprising 190 lines from Chara/WW2449 was grown in two different environments and evaluated for various quality traits. A molecular map comprising 362 markers based upon simple sequence repeat, sequence tagged microsatellite, glutenin, and DArT loci was constructed and subsequently exploited to identify QTLs using a whole-genome approach. Fifteen QTLs that were consistent in the two different environments were identified for thousand kernel mass, grain protein content, milling yield, flour protein content, flour colour, flour water absorption, dough development time, dough strength (extensograph height and resistance at 5 cm), and dough extensibility (extensograph length) using the whole genome average interval mapping approach. The amount of genetic variation explained by individual QTLs ranged from 3% to 49%. A number of QTLs associated with dough strength, dough extensibility, dough development time, and flour water absorption were located close to the glutenin Glu-B1 locus on chromosome 1B. Identification of the chromosomal location and effect of the QTLs influencing wheat quality may hasten the development of superior wheats for target markets via marker-assisted selection.
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Affiliation(s)
- R Raman
- NSW Department of Plant Industries and NSW Agricultural Genomics Centre, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
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Coleman MA, Dolman G, Kelaher BP, Steinberg PD. Characterisation of microsatellite loci in the subtidal habitat-forming alga, Phyllospora comosa (Phaeophyceae, Fucales). CONSERV GENET 2008. [DOI: 10.1007/s10592-007-9437-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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6
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Six newly developed microsatellite markers of Laccaria amethystina, using an improved CSSR approach. Mycol Prog 2008. [DOI: 10.1007/s11557-008-0564-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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7
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Characterisation of microsatellite loci in the habitat-forming kelp, Ecklonia radiata (Phaeophyceae, Laminariales). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9603-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Hayden MJ, Stephenson P, Logojan AM, Khatkar D, Rogers C, Elsden J, Koebner RMD, Snape JW, Sharp PJ. Development and genetic mapping of sequence-tagged microsatellites (STMs) in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:1271-81. [PMID: 16932882 DOI: 10.1007/s00122-006-0381-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Accepted: 07/25/2006] [Indexed: 05/11/2023]
Abstract
The density of SSRs on the published genetic map of bread wheat (Triticum aestivum L.) has steadily increased over the last few years. This has improved the efficiency of marker-assisted breeding and certain types of genetic research by providing more choice in the quality of SSRs and a greater chance of finding polymorphic markers in any cross for a chromosomal region of interest. Increased SSR density on the published wheat genetic map will further enhance breeding and research efforts. Here, sequence-tagged microsatellite profiling (STMP) is demonstrated as a rapid technique for the economical development of anonymous genomic SSRs to increase marker density on the wheat genetic map. A total of 684 polymorphic sequence-tagged microsatellites (STMs) were developed, and 380 were genetically mapped in three mapping populations, with 296 being mapped in the International Triticeae Mapping Initiative W7984 x Opata85 recombinant inbred cross. Across the three populations, a total of 479 STM loci were mapped. Several technological advantages of STMs over conventional SSRs were also observed. These include reduced marker deployment costs for fluorescent-based SSR analysis, and increased genotyping throughput by more efficient electrophoretic separation of STMs and a high amenability to multiplex PCR.
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Affiliation(s)
- M J Hayden
- Plant Functional Genomics Center, University of Adelaide, Hartley Grove, Urrbrae, SA, 5064, Australia.
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Akbari M, Wenzl P, Caig V, Carling J, Xia L, Yang S, Uszynski G, Mohler V, Lehmensiek A, Kuchel H, Hayden MJ, Howes N, Sharp P, Vaughan P, Rathmell B, Huttner E, Kilian A. Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:1409-20. [PMID: 17033786 DOI: 10.1007/s00122-006-0365-4] [Citation(s) in RCA: 286] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 07/06/2006] [Indexed: 05/02/2023]
Abstract
Despite a substantial investment in the development of panels of single nucleotide polymorphism (SNP) markers, the simple sequence repeat (SSR) technology with a limited multiplexing capability remains a standard, even for applications requiring whole-genome information. Diversity arrays technology (DArT) types hundreds to thousands of genomic loci in parallel, as previously demonstrated in a number diploid plant species. Here we show that DArT performs similarly well for the hexaploid genome of bread wheat (Triticum aestivum L.). The methodology previously used to generate DArT fingerprints of barley also generated a large number of high-quality markers in wheat (99.8% allele-calling concordance and approximately 95% call rate). The genetic relationships among bread wheat cultivars revealed by DArT coincided with knowledge generated with other methods, and even closely related cultivars could be distinguished. To verify the Mendelian behaviour of DArT markers, we typed a set of 90 Cranbrook x Halberd doubled haploid lines for which a framework (FW) map comprising a total of 339 SSR, restriction fragment length polymorphism (RFLP) and amplified fragment length polymorphism (AFLP) markers was available. We added an equal number of DArT markers to this data set and also incorporated 71 sequence tagged microsatellite (STM) markers. A comparison of logarithm of the odds (LOD) scores, call rates and the degree of genome coverage indicated that the quality and information content of the DArT data set was comparable to that of the combined SSR/RFLP/AFLP data set of the FW map.
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Affiliation(s)
- Mona Akbari
- Triticarte P/L, 1 Wilf Crane Crescent, Yarralumla, Canberra, ACT, 2600, Australia
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Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006. [PMID: 17033786 DOI: 10.1007/s00122‐006‐0365‐4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
Despite a substantial investment in the development of panels of single nucleotide polymorphism (SNP) markers, the simple sequence repeat (SSR) technology with a limited multiplexing capability remains a standard, even for applications requiring whole-genome information. Diversity arrays technology (DArT) types hundreds to thousands of genomic loci in parallel, as previously demonstrated in a number diploid plant species. Here we show that DArT performs similarly well for the hexaploid genome of bread wheat (Triticum aestivum L.). The methodology previously used to generate DArT fingerprints of barley also generated a large number of high-quality markers in wheat (99.8% allele-calling concordance and approximately 95% call rate). The genetic relationships among bread wheat cultivars revealed by DArT coincided with knowledge generated with other methods, and even closely related cultivars could be distinguished. To verify the Mendelian behaviour of DArT markers, we typed a set of 90 Cranbrook x Halberd doubled haploid lines for which a framework (FW) map comprising a total of 339 SSR, restriction fragment length polymorphism (RFLP) and amplified fragment length polymorphism (AFLP) markers was available. We added an equal number of DArT markers to this data set and also incorporated 71 sequence tagged microsatellite (STM) markers. A comparison of logarithm of the odds (LOD) scores, call rates and the degree of genome coverage indicated that the quality and information content of the DArT data set was comparable to that of the combined SSR/RFLP/AFLP data set of the FW map.
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Lian CL, Abdul Wadud M, Geng Q, Shimatani K, Hogetsu T. An improved technique for isolating codominant compound microsatellite markers. JOURNAL OF PLANT RESEARCH 2006; 119:415-7. [PMID: 16636745 DOI: 10.1007/s10265-006-0274-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Accepted: 02/14/2006] [Indexed: 05/08/2023]
Abstract
An approach for developing codominant polymorphic markers (compound microsatellite (SSR) markers), with substantial time and cost savings, is introduced in this paper. In this technique, fragments flanked by a compound SSR sequence at one end were amplified from the constructed DNA library using compound SSR primer (AC)6(AG)5 or (TC)6(AC)5 and an adaptor primer for the suppression-PCR. A locus-specific primer was designed from the sequence flanking the compound SSR. The primer pairs of the locus-specific and compound SSR primers were used as a compound SSR marker. Because only one locus-specific primer was needed for design of each marker and only a common compound SSR primer was needed as the fluorescence-labeled primer for analyzing all the compound SSR markers, this approach substantially reduced the cost of developing codominant markers and analyzing their polymorphism. We have demonstrated this technique for Dendropanax trifidus and easily developed 11 codominant markers with high polymorphism for D. trifidus. Use of the technique for successful isolation of codominant compound SSR markers for several other plant species is currently in progress.
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Affiliation(s)
- Chunlan L Lian
- Asian Natural Environmental Science Center, The University of Tokyo, 1-1-8 Midori-cho, Nishitokyo, Tokyo, 188-0002, Japan,
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KEIPER FELICITYJ, HAYDEN MATTHEWJ, WALLWORK HUGH. Development of sequence tagged microsatellites (STMs) for the barley scald pathogen Rhynchosporium secalis. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01249.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ellwood SR, D'Souza NK, Kamphuis LG, Burgess TI, Nair RM, Oliver RP. SSR analysis of the Medicago truncatula SARDI core collection reveals substantial diversity and unusual genotype dispersal throughout the Mediterranean basin. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:977-83. [PMID: 16402186 DOI: 10.1007/s00122-005-0202-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2005] [Accepted: 12/14/2005] [Indexed: 05/04/2023]
Abstract
The world's oldest and largest Medicago truncatula collection is housed at the South Australian Research and Development Institute (SARDI). We used six simple sequence repeat (SSR) loci to analyse the genetic diversity and relationships between randomly selected individuals from 192 accessions in the core collection. M. truncatula is composed of three subspecies (ssp.): ssp. truncatula, ssp. longeaculeata, and ssp. tricycla. Analysis at the level of six SSR loci supports the concept of ssp. tricycla, all the samples of which showed unique alleles at two loci. Contingency Chi-squared tests were significant between ssp. tricycla and ssp. truncatula at four loci, suggesting a barrier to gene flow between these subspecies. In accessions defined as ssp. longeaculeata, no unique allelic distribution or diagnostic sizes were observed, suggesting this apparent ssp. is a morphological variant of ssp. truncatula. The data also suggest M. truncatula that exhibits unusually wide genotype dispersal throughout its native Mediterranean region, possibly due to animal and trade-related movements. Our results showed the collection to be highly diverse, exhibiting an average of 25 SSR alleles per locus, with over 90% of individuals showing discrete genotypes. The rich diversity of the SARDI collection provides an invaluable resource for studying natural allelic variation of M. truncatula. To efficiently exploit the variation in the SARDI collection, we have defined a subset of accessions (n = 61) that maximises the diversity.
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Affiliation(s)
- S R Ellwood
- Australian Centre for Nectrotropic Fungal Pathogens, Health Sciences, Murdoch University, 6150 Perth, Western Australia.
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Abstract
A white-grained wheat accession, AUS1408, is a current major source of pre-harvest sprouting (PHS) tolerance in Australian breeding programs. This study has located 2 significant quantitative trait loci (QTLs) for its grain dormancy on 4AL and 5BL. Their associations with seed dormancy have been determined from population-level marker-trait associations (with 3 years of phenotype data) and confirmed by transmission/disequilibrium test on selected advanced breeding lines. The 4AL QTL was expressed in all years of testing, with phenotypic variance ranging from 5 to 15%, indicating a strong genotype × environment interaction. This QTL has been reported in wheat cultivars of diverse origin and was also found to be strongly influenced by the environment. The 5BL QTL was found to have a remarkably consistent effect on the trait at a phenotypic variance of around 10%. The successful outcome in this study was facilitated by high throughput DArT mapping, which complemented mapping with microsatellite markers for critical QTL identification. Identification of these QTLs from AUS1408 should enable sprouting tolerance derived from this source to be incorporated into advanced breeding lines, with the use of molecular markers reducing the requirement for multi-year field testing.
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Hayden MJ, Kuchel H, Chalmers KJ. Sequence tagged microsatellites for the Xgwm533 locus provide new diagnostic markers to select for the presence of stem rust resistance gene Sr2 in bread wheat ( Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:1641-7. [PMID: 15340687 DOI: 10.1007/s00122-004-1787-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Accepted: 08/03/2004] [Indexed: 05/09/2023]
Abstract
The stem rust resistance gene Sr2 has provided durable broad-spectrum, adult-plant resistance to the fungal pathogen Puccinia graminis Pers. f. sp. tritici throughout wheat-growing regions of the world for more than 50 years. The ability to select for Sr2 in wheat breeding programs was recently improved by the identification of a tightly linked microsatellite marker gwm533. This marker typically amplifies a 120-bp polymerase chain reaction fragment from wheat lines carrying Sr2. In instances where the 120-bp fragment is not associated with the presence of Sr2, DNA sequence analysis has shown that a second allele was amplified, differing in the structure of the microsatellite repeat. To discriminate this allelic homoplasy (alleles identical in size, but not identical by descent), sequence-tagged microsatellites (STM) markers were developed for the Xgwm533 locus. These markers were shown to be diagnostic for the presence of Sr2 in a wide range of germplasm, representative of all major wheat varieties historically grown in Australia. The STMs will be particularly useful for marker-assisted selection in Southern Australian breeding programs, where the use of the marker gwm533 is often precluded by the presence of the non- Sr2-associated 120-bp allele in the pedigree of current breeding germplasm. The STMs also revealed a high incidence of previously undetected allelic homoplasy at the Xgwm533 locus and may have broader utility in genetic research and breeding, as this locus is also reported to be strongly associated with a major gene conferring resistance to Fusarium head blight.
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Affiliation(s)
- M J Hayden
- Plant Genomics Center, University of Adelaide, Hartley Grove, Urrbrae, SA, 5064, Australia.
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