A framework linkage map of perennial ryegrass based on SSR markers

Genome ◽  
2006 ◽  
Vol 49 (4) ◽  
pp. 354-364 ◽  
Author(s):  
G P Gill ◽  
P L Wilcox ◽  
D J Whittaker ◽  
R A Winz ◽  
P Bickerstaff ◽  
...  
Keyword(s):  
Linkage Map ◽  
Ssr Markers ◽  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Sequence Repeat ◽  
Linkage Groups ◽  
Marker Loci ◽  
Simple Sequence

A moderate-density linkage map for Lolium perenne L. has been constructed based on 376 simple sequence repeat (SSR) markers. Approximately one third (124) of the SSR markers were developed from GeneThresher® libraries that preferentially select genomic DNA clones from the gene-rich unmethylated portion of the genome. The remaining SSR marker loci were generated from either SSR-enriched genomic libraries (247) or ESTs (5). Forty-five percent of the GeneThresher SSRs were associated with an expressed gene. Unlike EST-derived SSR markers, GeneThresher SSRs were often associated with genes expressed at a low level, such as transcription factors. The map constructed here fulfills 2 definitions of a "framework map". Firstly, it is composed of codominant markers to ensure map transferability either within or among species. Secondly, it was constructed to achieve a level of statistical confidence in the support-for-order of marker loci. The map consists of 81 framework SSR markers spread over 7 linkage groups, the same as the haploid chromosome number. Most of the remaining 295 SSR markers have been placed into their most likely interval on the framework map. Nine RFLP markers and 1 SSR marker from another map constructed using the same pedigree were also incorporated to extend genome coverage at the terminal ends of 5 linkage groups. The final map provides a robust framework with which to conduct investigations into the genetic architecture of trait variation in this commercially important grass species.Key words: Framework map, perennial ryegrass, SSR, simple sequence repeat, GeneThresher, Lolium perenne.

Development and characterisation of simple sequence repeat (SSR) markers for perennial ryegrass (Lolium perenne L.)

2001 ◽  
Vol 102 (2-3) ◽  
pp. 405-415 ◽  
Author(s):  
E. S. Jones ◽  
M. P. Dupal ◽  
R. Kölliker ◽  
M. C. Drayton ◽  
J. W. Forster
Keyword(s):  
Ssr Markers ◽  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Lolium Perenne L ◽  
Simple Sequence

scholarly journals ANALISIS KERAGAMAN GENETIK PLASMA NUTFAH KAKAO (Theobroma cacaoL.) BERDASARKANMARKA SSR / Analysis of Genetic Variability Germplasm of Cacao (Theobroma cacaoL.)Basedon SSR Marker

2020 ◽  
Vol 17 (4) ◽  
pp. 156
Author(s):  
Surti Kurniasih ◽  
Rubiyo Rubiyo ◽  
Asep Setiawan ◽  
Agus Purwantara ◽  
Sudarsono Sudarsono
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Theobroma Cacao ◽  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Gene Diversity ◽  
Sequence Repeat ◽  
Theobroma Cacao L ◽  
Simple Sequence

<p>Microsatellite or simple sequence repeat (SSR) markers have proven to be an excellent tool for cultivar identification, pedigree analysis, and genetic distance evaluations among organisms. The objectives of this research were to characterize cacao collection of Indonesian Coffee and Cacao Research Institute (ICCRI) and to analyze their genetic diversity using SSR markers. In this research, 39 SSR primer pairs were used to amplify genomic DNA of 29 cacao clones. Amplified SSR fragments for each primer pair were scored as individual band and used to determine genetic distance among evaluated cacao clones. Results of the experiment indicated that all SSR primer pairs evaluated were able to produce SSR markers for 29 cacao clones. The results also indicated that 34 out of 39 microsatellite loci evaluated were polymorphic, while 5 others were monomorphic. The total number of observed alleles among 29 clones was 132. Number of alleles per locus ranged from 4-8, with an average of 5.5 alelles per locus. Results of data analysis indicated that the PIC value was 0.665, the observed heterozigosity (Ho) was 0.651, and the gene diversity (He) was 0.720. The PIC, Ho, and He values were considered high. Genetic distances were evaluated using NTSys version 2.1 and dendrogram was constructed. Results of analysis indicated that 12 cacao clones evaluated were clustered in the first group with diversity coefficient of &lt; 3.75. Nine cacao clones were in the second group but with the same value of diversity coefficient (&lt;7.50). The rest of the cacao clones were in the third group with diversity coefficient of&gt;7.50. Based on those finding, all SSR primer pairs evaluated could be used to analyze cacao genome and be useful for genetic diversity analysis of cacao germplasm. The SSR marker analysis in ICCRI cacao collections resulted in high PIC, high observed heterozygosity, and high genetic diversity.</p><p>Key words: Theobroma cacao L, microsatelite, molecular marker, genetic diversity, heterozygosity</p><p> </p><p><strong>Abstrak</strong></p><p>Marka mikrosatelit atau sekuens sederhana berulang (simple sequence repeat = SSR) terbukti merupakan alat yang bagus untuk identifikasi kultivar, analisis pedigree, dan evaluasi jarak genetik berbagai organisme. Penelitian ini bertujuan untuk:1) karakterisasi kakao koleksi Pusat penelitian Kopi dan Kakao Indonesia menggunakan marka SSR dan 2) analisis keragaman genetik klon-klon kakao koleksi dengan menggunakan marka SSR. Dalam penelitian ini, 39 pasangan primer SSR telah digunakan untuk amplifikasi DNA genomik dari 29 klon kakao. Skoring pita SSR hasil amplifikasi menggunakan masing-masing pasangan primer dilakukan secara terpisah dan digunakan untuk menentukan jarak genetik di antara klon kakao yang dievaluasi. Hasil percobaan menunjukkan bahwa semua pasangan primer SSR yang digunakan mampu menghasilkan pita DNA hasil amplifikasi (marka SSR) untuk 29 klon kakao yang diuji. Hasil penelitian juga menunjukkan bahwa 34 dari 39 lokus SSR yang dianalisis bersifat polimorfik sedangkan lima primer yang lain bersifat monomorfik. Dari 29 klon kakao yang dievaluasi, telah berhasil diamplifikasi sebanyak 132 alel, dengan kisaran antara 4-8 alel/lokus. Rataan jumlah alel per lokus sebanyak 5,50. Hasil analisis data yang dilakukan juga menunjukkan nilai PIC untuk marka SSR yang digunakan sebesar 0,665. Untuk populasi klon kakao yang dievaluasi, diperoleh nilai rataan heterosigositas pengamatan (Ho) sebesar 0,651 dan rataan diversitas gen (He) sebesar 0,720. Nilai PIC Ho dan He yang didapat tergolong tinggi. Berdasarkan analisis keragaman dengan menggunakan program NTSys, diperoleh hasil 12 klon kakao berada dalam grup pertama (koefisien keragaman&lt;3,75) dan9 klon berada dalam grup kedua, dengan koefisien keragaman &lt; 7,50. Sedangkan klon-klon lainnya mempunyai koefisien keragaman &gt; 7,50. Berdasarkan hasil penelitian dan analisis data disimpulkan bahwa marka SSR dapat digunakan untuk menganalisis keragaman genetik plasma nutfah kakao. Tingkat polimorfisme yang dihasilkan marka SSR relatif tinggi. Tingkat heterosigositas plasma nutfah kakao koleksi Puslit Kopi dan Kakao Indonesiarelatif tinggi, dan keragaman genetiknyacukup tinggi.</p><p>Kata kunci : Theobroma cacao L, mikrosatelit, marka molekuler, keragaman genetik, heterosigositas</p>

scholarly journals A new intervarietal linkage map and its application for quantitative trait locus analysis of "gigas" features in bread wheat

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 65-75 ◽  
Author(s):  
Kazuhiro Suenaga ◽  
Mireille Khairallah ◽  
H M William ◽  
David A Hoisington
Keyword(s):  
Quantitative Trait Locus ◽  
Linkage Map ◽  
Qtl Analysis ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Linkage Groups ◽  
Spike Number ◽  
Trait Locus ◽  
Dh Lines ◽  
Simple Sequence

A doubled-haploid (DH) population from an intervarietal cross between the Japanese cultivar 'Fukuho-komugi' and the Israeli wheat line 'Oligoculm' was produced by means of wheat × maize crosses. One hundred seven DH lines were genotyped to construct a simple sequence repeat (SSR) based linkage map with RFLP, RAPD, and inter-simple sequence repeat markers. Out of 570 loci genotyped, 330 were chosen based on their positions on the linkage map to create a "framework" map for quantitative trait locus (QTL) analysis. Among the 28 linkage groups identified, 25 were assigned to the 21 chromosomes of wheat. The total map length was 3948 cM, including the three unassigned linkage groups (88 cM), and the mean interval between loci was 12.0 cM. Loci with segregation distortion were clustered on chromosomes 1A, 4B, 4D, 5A, 6A, 6B, and 6D. After vernalization, the DH lines were evaluated for spike number per plant (SN) and spike length (SL) in a greenhouse under 24-h daylength to assess the "gigas" features (extremely large spikes and leaves) of 'Oligoculm'. The DH lines were also autumn-sown in the field in two seasons (1990–1991 and 1997–1998) for SN and SL evaluation. QTL analysis was performed by composite interval mapping (CIM) with the framework map to detect QTLs for SN and SL. A major QTL on 1AS, which was stable in both greenhouse and field conditions, was found to control SN. This QTL was close to the glume pubescence locus (Hg) and explained up to 62.9% of the total phenotypic variation. The 'Oligoculm' allele restricted spike number. The SSR locus Xpsp2999 was the closest locus to this QTL and is considered to be a possible marker for restricted tillering derived from 'Oligoculm'. Eight QTLs were detected for SL. The largest QTL detected on 2DS was common to the greenhouse and field environments. It explained up to 33.3% of the total phenotypic variation. The second largest QTL on 1AS was common to the greenhouse and the 1997–1998 season. The position of this QTL was close to that for the SN detected on 1AS. The association between SN and SL is discussed.Key words: linkage map, microsatellite, QTL, spike length, spike number.

scholarly journals Assessment of Genetic Relationship among Male and Female Fig Genotypes Using Simple Sequence Repeat (SSR) Markers

2017 ◽  
Vol 45 (1) ◽  
pp. 172-178
Author(s):  
Sevin TEOMAN ◽  
Meryem IPEK ◽  
Umran ERTURK ◽  
Nesrin Aktepe TANGU ◽  
Erdem DURGUT ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Genetic Relationship ◽  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Aegean Sea ◽  
Gene Pools ◽  
Sequence Repeat ◽  
Expected Heterozygosity ◽  
Male Tree ◽  
Simple Sequence

Fig (Ficus carica L.) is a traditional crop in Turkey and widely cultivated around the Mediterranean areas. The gynodioecious fig species is present in two sexual forms, i.e. the domesticated fig (female tree) and the caprifig (male tree). Caprifigs are crucial for high quality fig production and breeding while, the studies on assessment of genetic relationship among caprifigs is limited. The aim of this study was to determine genetic diversity among 45 caprifigs and 2 female figs collected from four provinces in Marmara and Aegean Sea Regions of Turkey using simple sequence repeat (SSR) markers. In this work, 24 SSR markers were tested, one was monomorphic and the remaining markers amplified 82 alleles. The number of polymorphic alleles per SSR marker ranged from 2 to 7. The observed heterozygosity (Ho) differed from 0.18 to 0.76 and expected heterozygosity (He) ranged between 0.24 and 0.81. The polymorphism information content (PIC) varied from 0.42 to 0.98. A UPGMA analysis based on Dice similarity matrix clustered fig genotypes into two main groups and similarly, STRUCTURE analysis placed fig genotypes into two different gene pools (K=2). Fig genotypes collected from the same region were not clustered together in a group indicating that the fig genotypes did not cluster on the basis of their collection sites. Our results demonstrated that caprifigs and female figs are not genetically distinct and they clustered together in a group. All fig genotypes had distinct SSR marker profiles suggesting that there were no synonyms or homonyms. These results revealed a high genetic variation among fig genotypes and 23 SSR markers were enough to discriminate all fig genotypes analysed in this study demonstrating that SSR marker system is suitable for genetic analysis in figs.

A genetic linkage map for hazelnut (Corylus avellana L.) based on RAPD and SSR markers

Genome ◽  
2006 ◽  
Vol 49 (2) ◽  
pp. 122-133 ◽  
Author(s):  
Shawn A Mehlenbacher ◽  
Rebecca N Brown ◽  
Eduardo R Nouhra ◽  
Tufan Gökirmak ◽  
Nahla V Bassil ◽  
...  
Keyword(s):  
Linkage Map ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Random Amplified Polymorphic Dna ◽  
Corylus Avellana ◽  
Sequence Repeat ◽  
Starting Point ◽  
Ssr Loci ◽  
Corylus Avellana L ◽  
Simple Sequence

A linkage map for European hazelnut (Corylus avellana L.) was constructed using random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers and the 2-way pseudotestcross approach. A full-sib population of 144 seedlings from the cross OSU 252.146 × OSU 414.062 was used. RAPD markers in testcross configuration, segregating 1:1, were used to construct separate maps for each parent. Fifty additional RAPD loci were assigned to linkage groups as accessory markers whose exact location could not be determined. Markers in intercross configuration, segregating 3:1, were used to pair groups in one parent with their homologues in the other. Eleven groups were identified for each parent, corresponding to the haploid chromosome number of hazelnut (n = x = 11). Thirty of the 31 SSR loci were able to be assigned to a linkage group. The maternal map included 249 RAPD and 20 SSR markers and spanned a distance of 661 cM. The paternal map included 271 RAPD and 28 SSR markers and spanned a distance of 812 cM. The maps are quite dense, with an average of 2.6 cM between adjacent markers. The S-locus, which controls pollen-stigma incompatibility, was placed on chromosome 5S where 6 markers linked within a distance of 10 cM were identified. A locus for resistance to eastern filbert blight, caused by Anisogramma anomala, was placed on chromosome 6R for which two additional markers tightly linked to the dominant allele were identified and sequenced. These maps will serve as a starting point for future studies of the hazelnut genome, including map-based cloning of important genes. The inclusion of SSR loci on the map will make it useful in other populations.Key words: Corylus avellana, hazelnut, filbert, linkage map, pseudotestcross, pollen-stigma incompatibility, random amplified polymorphic DNA, simple sequence repeat, microsatellite.

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