scholarly journals Molecular Linkage Maps: Strategies, Resources and Achievements

2016 ◽  
pp. 139-164 ◽  
Keyword(s):  
Linkage Maps

scholarly journals VfODB: a comprehensive database of ESTs, EST-SSRs, mtSSRs, microRNA-target markers and genetic maps in Vicia faba

AoB Plants ◽  
2020 ◽  
Vol 12 (6) ◽  
Author(s):  
Morad M Mokhtar ◽  
Ebtissam H A Hussein ◽  
Salah El-Din S El-Assal ◽  
Mohamed A M Atia
Keyword(s):  
Vicia Faba ◽  
Faba Bean ◽  
Expressed Sequence Tags ◽  
Genetic Linkage ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Microrna Target ◽  
Genetic Linkage Maps ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract Faba bean (Vicia faba) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibres. Molecular markers tools represent an invaluable tool for faba bean breeders towards rapid crop improvement. Although there have historically been few V. faba genome resources available, several transcriptomes and mitochondrial genome sequence data have been released. These data in addition to previously developed genetic linkage maps represent a great resource for developing functional markers and maps that can accelerate the faba bean breeding programmes. Here, we present the Vicia faba Omics database (VfODB) as a comprehensive database integrating germplasm information, expressed sequence tags (ESTs), expressed sequence tags-simple sequence repeats (EST-SSRs), and mitochondrial-simple sequence repeats (mtSSRs), microRNA-target markers and genetic maps in faba bean. In addition, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps. Collectively, we developed 31 536 EST markers, 9071 EST-SSR markers and 3023 microRNA-target markers based on V. faba RefTrans V2 mining. By mapping 7940 EST and 2282 EST-SSR markers against the KEGG pathways database we successfully developed 107 functional maps. Also, 40 mtSSR markers were developed based on mitochondrial genome mining. On the data curation level, we retrieved 3461 markers representing 12 types of markers (CAPS, EST, EST-SSR, Gene marker, INDEL, Isozyme, ISSR, RAPD, SCAR, RGA, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets. VfODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.

scholarly journals Dense Genetic Linkage Maps of Three Populus Species (Populus deltoides, P. nigra and P. trichocarpa) Based on AFLP and Microsatellite Markers

Genetics ◽  
2001 ◽  
Vol 158 (2) ◽  
pp. 787-809 ◽  
Author(s):  
Maria-Teresa Cervera ◽  
Véronique Storme ◽  
Bart Ivens ◽  
Jaqueline Gusmão ◽  
Ben H Liu ◽  
...  
Keyword(s):  
Populus Deltoides ◽  
Female Parent ◽  
Aflp Markers ◽  
Linkage Maps ◽  
Important Species ◽  
Mapping Strategy ◽  
Sequence Tagged Sites ◽  
Fundamental Research ◽  
Populus Species ◽  
The Individual

Abstract Populus deltoides, P. nigra, and P. trichocarpa are the most important species for poplar breeding programs worldwide. In addition, Populus has become a model for fundamental research on trees. Linkage maps were constructed for these three species by analyzing progeny of two controlled crosses sharing the same female parent, Populus deltoides cv. S9-2 × P. nigra cv. Ghoy and P. deltoides cv. S9-2 × P. trichocarpa cv. V24. The two-way pseudotestcross mapping strategy was used to construct the maps. Amplified fragment length polymorphism (AFLP) markers that segregated 1:1 were used to form the four parental maps. Microsatellites and sequence-tagged sites were used to align homoeologous groups between the maps and to merge linkage groups within the individual maps. Linkage analysis and alignment of the homoeologous groups resulted in 566 markers distributed over 19 groups for P. deltoides covering 86% of the genome, 339 markers distributed over 19 groups for P. trichocarpa covering 73%, and 369 markers distributed over 28 groups for P. nigra covering 61%. Several tests for randomness showed that the AFLP markers were randomly distributed over the genome.

scholarly journals A Consensus Map for Loblolly Pine (Pinus taeda L.). I. Construction and Integration of Individual Linkage Maps From Two Outbred Three-Generation Pedigrees

Genetics ◽  
1999 ◽  
Vol 151 (1) ◽  
pp. 321-330 ◽  
Author(s):  
Mitchell M Sewell ◽  
Bradley K Sherman ◽  
David B Neale
Keyword(s):  
Pinus Taeda ◽  
Loblolly Pine ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Mapping Function ◽  
Genetic Maps ◽  
Linkage Data ◽  
Linkage Maps ◽  
Consensus Map ◽  
Pinus Taeda L

Abstract A consensus map for loblolly pine (Pinus taeda L.) was constructed from the integration of linkage data from two unrelated three-generation outbred pedigrees. The progeny segregation data from restriction fragment length polymorphism, random amplified polymorphic DNA, and isozyme genetic markers from each pedigree were recoded to reflect the two independent populations of parental meioses, and genetic maps were constructed to represent each parent. The rate of meiotic recombination was significantly greater for males than females, as was the average estimate of genome length for males {1983.7 cM [Kosambi mapping function (K)]} and females [1339.5 cM(K)]. The integration of individual maps allows for the synthesis of genetic information from independent sources onto a single consensus map and facilitates the consolidation of linkage groups to represent the chromosomes (n = 12) of loblolly pine. The resulting consensus map consists of 357 unique molecular markers and covers ∼1300 cM(K).

Integrating Genetic Linkage Maps With Pachytene Chromosome Structure in Maize

Genetics ◽  
2004 ◽  
Vol 166 (4) ◽  
pp. 1923-1933 ◽  
Author(s):  
Lorinda K Anderson ◽  
Naser Salameh ◽  
Hank W Bass ◽  
Lisa C Harper ◽  
W Z Cande ◽  
...  
Keyword(s):  
Genetic Linkage ◽  
Chromosome Structure ◽  
Single Copy ◽  
Chromosome 9 ◽  
Linkage Maps ◽  
Cytogenetic Map ◽  
Recombination Nodules ◽  
Novel Approach ◽  
Genetic Linkage Maps ◽  
High Degree

Abstract Genetic linkage maps reveal the order of markers based on the frequency of recombination between markers during meiosis. Because the rate of recombination varies along chromosomes, it has been difficult to relate linkage maps to chromosome structure. Here we use cytological maps of crossing over based on recombination nodules (RNs) to predict the physical position of genetic markers on each of the 10 chromosomes of maize. This is possible because (1) all 10 maize chromosomes can be individually identified from spreads of synaptonemal complexes, (2) each RN corresponds to one crossover, and (3) the frequency of RNs on defined chromosomal segments can be converted to centimorgan values. We tested our predictions for chromosome 9 using seven genetically mapped, single-copy markers that were independently mapped on pachytene chromosomes using in situ hybridization. The correlation between predicted and observed locations was very strong (r2 = 0.996), indicating a virtual 1:1 correspondence. Thus, this new, high-resolution, cytogenetic map enables one to predict the chromosomal location of any genetically mapped marker in maize with a high degree of accuracy. This novel approach can be applied to other organisms as well.

Constructing linkage maps in autotetraploid species using simulated annealing

2003 ◽  
Vol 106 (6) ◽  
pp. 1107-1115 ◽  
Author(s):  
C. A. Hackett ◽  
B. Pande ◽  
G. J. Bryan
Keyword(s):  
Simulated Annealing ◽  
Linkage Maps

Associations of SRAP markers with dried-shrink disease resistance in a germplasm collection of sea buckthorn (Hippophae L.)

Genome ◽  
2010 ◽  
Vol 53 (6) ◽  
pp. 447-457 ◽  
Author(s):  
He Li ◽  
Cheng-Jiang Ruan ◽  
Jaime A. Teixeira da Silva ◽  
Bao-Quan Liu
Keyword(s):  
Woody Plant ◽  
Germplasm Collection ◽  
Sea Buckthorn ◽  
Linkage Maps ◽  
Dice Coefficient ◽  
Viable Option ◽  
Breeding Programs ◽  
Srap Markers ◽  
Hippophae Salicifolia ◽  
Pioneer Plant

Sea buckthorn ( Hippophae L.) is a woody, outcrossing dioecious pioneer plant, being widely planted as a new berry crop with rich nutritional and medicinal compounds. This long-juvenile and long-lived woody plant can be more difficult to cultivate than other crop plants. Dried-shrink disease (DSD) is a dangerous pathogen that destroys sea buckthorn and halts commercial production. We estimated variability of sequence-related amplified polymorphism (SRAP) markers in 77 accessions of 22 sea buckthorn cultivars to seek markers associated with DSD resistance and help to identify potential breeding cultivars. Seventeen SRAP primer combinations generated 289 bands, with a mean of 17 bands per primer combination. At a Dice coefficient of 0.852, the dendrogram generated with 191 polymorphic bands clustered 73 accessions of Hippophae rhamnoides into 2 groups and 4 accessions of Hippophae salicifolia into 1 group. Eleven SRAP markers (Me1-Em3600, Me1-Em1680, Me2-Em1650, Me2-Em1950, Me3-Em61300, Me2-Em6320, Me2-Em6400, Me1-Em2600, Me1-Em11200, Me1-Em11700, Me2-Em2250) were significantly correlated with DSD resistance (P < 0.001). These markers provide a viable option for breeding programs that select lineages with DSD resistance, especially when no other genetic information, such as linkage maps and quantitative trait loci, are available.

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