Molecular genetic linkage maps for allotetraploid Leymus wildryes (Gramineae: Triticeae)

Genome ◽  
2003 ◽  
Vol 46 (4) ◽  
pp. 627-646 ◽  
Author(s):  
Xiaolei Wu ◽  
Steven R Larson ◽  
Zanmin Hu ◽  
Antonio J Palazzo ◽  
Thomas A Jones ◽  
...  
Keyword(s):  
Molecular Genetic ◽  
Perennial Grass ◽  
Perennial Grasses ◽  
Genetic Maps ◽  
Aflp Markers ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Genetic Linkage Maps ◽  
Leymus Triticoides ◽  
Leymus Cinereus

Molecular genetic maps were constructed for two full-sib populations, TTC1 and TTC2, derived from two Leymus triticoides × Leymus cinereus hybrids and one common Leymus triticoides tester. Informative DNA markers were detected using 21 EcoRI–MseI and 17 PstI–MseI AFLP primer combinations, 36 anchored SSR or STS primer pairs, and 9 anchored RFLP probes. The 164-sib TTC1 map includes 1069 AFLP markers and 38 anchor loci in 14 linkage groups spanning 2001 cM. The 170-sib TTC2 map contains 1002 AFLP markers and 36 anchor loci in 14 linkage groups spanning 2066 cM. Some 488 homologous AFLP loci and 24 anchor markers detected in both populations showed similar map order. Thus, 1583 AFLP markers and 50 anchor loci were mapped into 14 linkage groups, which evidently correspond to the 14 chromosomes of allotetraploid Leymus (2n = 4x = 28). Synteny of two or more anchor markers from each of the seven homoeologous wheat and barley chromosomes was detected for 12 of the 14 Leymus linkage groups. Moreover, two distinct sets of genome-specific STS markers were identified in these allotetraploid Leymus species. These Leymus genetic maps and populations will provide a useful system to evaluate the inheritance of functionally important traits of two divergent perennial grass species.Key words: AFLP, perennial grasses, RFLP, STS, SSR.

scholarly journals Genetic maps of Saccharum officinarum L. and Saccharum robustum Brandes & Jew. ex grassl

1999 ◽  
Vol 22 (1) ◽  
pp. 125-132 ◽  
Author(s):  
Claudia T. Guimarães ◽  
Rhonda J. Honeycutt ◽  
Gavin R. Sills ◽  
Bruno W.S. Sobral
Keyword(s):  
Dna Markers ◽  
Genetic Model ◽  
Saccharum Officinarum ◽  
Genetic Maps ◽  
Breeding Ecology ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Genetic Linkage Maps ◽  
Arbitrarily Primed Pcr ◽  
Saccharum Robustum

Genetic analysis was performed in a population composed of 100 F1 individuals derived from a cross between a cultivated sugarcane (S. officinarum `LA Purple') and its proposed progenitor species (S. robustum `Mol 5829'). Various types (arbitrarily primed-PCR, RFLPs, and AFLPs) of single-dose DNA markers (SDMs) were used to construct genetic linkage maps for both species. The LA Purple map was composed of 341 SDMs, spanning 74 linkage groups and 1,881 cM, while the Mol 5829 map contained 301 SDMs, spanning 65 linkage groups and 1,189 cM. Transmission genetics in these two species showed incomplete polysomy based on the detection of 15% of SDMs linked in repulsion in LA Purple and 13% of these in Mol 5829. Because of this incomplete polysomy, multiple-dose markers could not be mapped for lack of a genetic model for their segregation. Due to inclusion of RFLP anchor probes, conserved in related species, the resulting maps will serve as useful tools for breeding, ecology, evolution, and molecular biology studies within the Andropogoneae.

Construction of three linkage maps in bread wheat, Triticum aestivum

2001 ◽  
Vol 52 (12) ◽  
pp. 1089 ◽  
Author(s):  
K. J. Chalmers ◽  
A. W. Campbell ◽  
J. Kretschmer ◽  
A. Karakousis ◽  
P. H. Henschke ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Doubled Haploid ◽  
Wheat Breeding ◽  
Genetic Maps ◽  
Aflp Markers ◽  
Linkage Maps ◽  
Linkage Groups ◽  
D Genome ◽  
Doubled Haploid Lines ◽  
Wide Range

Genetic maps were compiled from the analysis of 160–180 doubled haploid lines derived from 3 crosses: Cranbrook Halberd, CD87 Katepwa, and Sunco Tasman. The parental wheat lines covered a wide range of the germplasm used in Australian wheat breeding. The linkage maps were constructed with RFLP, AFLP, microsatellite markers, known genes, and proteins. The numbers of markers placed on each map were 902 for Cranbrook Halberd, 505 for CD87 Katepwa, and 355 for Sunco Tasman. Most of the expected linkage groups could be determined, but 10–20% of markers could not be assigned to a specific linkage group. Homologous chromosomes could be aligned between the populations described here and linkage groups reported in the literature, based around the RFLP, protein, and microsatellite markers. For most chromosomes, colinearity of markers was found for the maps reported here and those recorded on published physical maps of wheat. AFLP markers proved to be effective in filling gaps in the maps. In addition, it was found that many AFLP markers defined specific genetic loci in wheat across all 3 populations. The quality of the maps and the density of markers differs for each population. Some chromosomes, particularly D genome chromosomes, are poorly covered. There was also evidence of segregation distortion in some regions, and the distribution of recombination events was uneven, with substantial numbers of doubled haploid lines in each population displaying one or more parental chromosomes. These features will affect the reliability of the maps in localising loci controlling some traits, particularly complex quantitative traits and traits of low heritability. The parents used to develop the mapping populations were selected based on their quality characteristics and the maps provide a basis for the analysis of the genetic control of components of processing quality. However, the parents also differ in resistance to several important diseases, in a range of physiological traits, and in tolerance to some abiotic stresses.

scholarly journals Development, Linkage Mapping, and Use of Microsatellites in Bermudagrass

2010 ◽  
Vol 135 (6) ◽  
pp. 511-520 ◽  
Author(s):  
Karen R. Harris-Shultz ◽  
Brian M. Schwartz ◽  
Wayne W. Hanna ◽  
Jeff A. Brady
Keyword(s):  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Linkage Mapping ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Marker Data ◽  
Genetic Linkage Maps ◽  
Expressed Sequence ◽  
Simple Sequence

Genetic linkage maps of bermudagrass (Cynodon spp.) species using 118 triploid individuals derived from a cross of T89 [C. dactylon (2n = 4x = 36)] and T574 [C. transvaalensis (2n = 2x = 18)] were enriched with expressed sequence tags-derived simple sequence repeat (EST-SSR) markers. Primers were developed from 53 ESTs containing SSRs producing 75 segregating markers from which 28 could be mapped to the T89 and T574 genetic maps. With the addition of previously generated marker data, 26 T89 linkage groups and eight T574 linkage groups were formed using a log-of-odds (LOD) value of 4.0. The T89 and T574 linkage maps spanned 1055 cM and 311.1 cM and include 125 and 36 single-dose amplified fragments (SDAFs), respectively. Many of the SDAFs displayed disomic segregation and thus T89 may be a segmental allotetraploid or an allotetraploid. The additional EST-SSR markers add value to the maps by increasing marker density and provide markers that can be easily transferred to other bermudagrass populations. Furthermore, EST-SSRs can be immediately used to assess genetic diversity, identify non-mutated cultivars of bermudagrass, confirm pedigrees, and differentiate contaminants from cultivars derived from ‘Tifgreen’.

Construction of High-quality Linkage Maps in Populus with RADseq Data and their Application in QTL Mapping and Genome Assembly

2019 ◽  
Author(s):  
Chunfa Tong ◽  
Dan Yao ◽  
Hainan Wu ◽  
Yuhua Chen ◽  
Wenguo Yang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Genome Assembly ◽  
Genetic Linkage ◽  
High Density ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Linkage Groups ◽  
High Quality ◽  
Populus Simonii ◽  
Genetic Linkage Maps

Abstract Background: Although great efforts have been made to construct genetic linkage maps in Populus using traditional molecular markers, these maps are typically sparse, and the number of linkage groups does not match the karyotype of Populus . With the advances in high-throughput sequencing technologies and new software packages available for extracting single nucleotide polymorphisms (SNPs) across a mapping population, it is possible to construct high-quality, high-density genetic linkage maps with thousands of SNPs in such outbred species. Results: Two parent-specific linkage maps were constructed with restriction site-associated DNA sequencing (RADseq) data from an F 1 hybrid population from Populus de l toides and Populus simonii and were applied to identify growth trait loci and facilitate genome assembly. The female Populus deltoides map contained 4,018 SNPs, which were divided into 19 linkage groups under a wide range of LOD thresholds from 7 to 55, perfectly matching the karyotype of Populus . The male Populus simonii map showed similar characteristics, consisting of 2,097 SNPs, which also belonged to 19 linkage groups under LOD thresholds of 7 to 29. The SNP genotype data for linkage analysis were confirmed to be of high quality. The SNP order of each linkage group was optimal among different ordering results from several available software platforms. Moreover, the linkage maps allowed the detection of 39 QTLs underlying tree height and 47 for diameter at breast height, some of which were strongly associated with QTLs identified in previous studies. In addition, the linkage maps enabled the anchoring of 671 contigs of a draft genome assembly of Populus simonii to chromosomes, corresponding to approximately 83.6% of the genome and showing a high level of collinearity with the genetic maps. Conclusions: The two parental genetic maps of Populus are of high quality, especially in terms of SNP data quality, the SNP order within linkage groups, and the perfect match between the number of linkage groups and the karyotype of Populus as well as performance in QTL mapping and genome assembly. The adopted approaches for both extracting and ordering SNPs could be applied to other species to construct high-density, high-quality genetic 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.

Genetic Linkage Maps of the Guppy ( Poecilia reticulata ): Assignment of RAPD Markers to Multipoint Linkage Groups

2003 ◽  
Vol 5 (3) ◽  
pp. 279-293 ◽  
Author(s):  
Gideon Khoo ◽  
Meng Huat Lim ◽  
Haridas Suresh ◽  
Damien K. Y. Gan ◽  
Kok Fang Lim ◽  
...  
Keyword(s):  
Genetic Linkage ◽  
Rapd Markers ◽  
Poecilia Reticulata ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Multipoint Linkage ◽  
Genetic Linkage Maps

Molecular genetic linkage maps of mouse chromosomes 4 and 6

Genomics ◽  
1991 ◽  
Vol 11 (1) ◽  
pp. 33-47 ◽  
Author(s):  
Nathan Bahary ◽  
Georgia Zorich ◽  
Jane E. Pachter ◽  
Rudolph L. Leibel ◽  
Jeffrey M. Friedman
Keyword(s):  
Genetic Linkage ◽  
Molecular Genetic ◽  
Linkage Maps ◽  
Genetic Linkage Maps

Two genetic linkage maps of mungbean using RFLP and RAPD markers

2000 ◽  
Vol 51 (4) ◽  
pp. 415 ◽  
Author(s):  
C. J. Lambrides ◽  
R. J. Lawn ◽  
I. D. Godwin ◽  
J. Manners ◽  
B. C. Imrie
Keyword(s):  
Linkage Map ◽  
Segregation Distortion ◽  
Recombinant Inbred ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Rflp Markers ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Genetic Linkage Maps ◽  
Map Distance

Two genetic linkage maps of mungbean derived from the cross Berken ACC 41 are reported. The F2 map constructed from 67 individuals consisted of 110 markers (52 RFLP and 56 RAPD) that grouped into 12 linkage groups. The linked markers spanned a total map distance of 758.3 cM. A recombinant inbred (RI) population derived from the 67 F2 individuals was used for the generation of an additional linkage map. The RI map, composed entirely of RAPD markers, consisted of 115 markers in 12 linkage groups. The linked markers spanned a total map distance of 691.7 cM. Using a framework set of RFLP markers, the F2 map was compared with another F2 mungbean map constructed in Minnesota. In general, the order of these markers was consistent between maps. Segregation distortion was observed for some markers. 14.5% (16/110) of mapped F2 markers and 24% (28/115) of mapped RI markers segregated with distorted ratios. Segregation distortion occurred in each successive generation after the F2 . The regions of distortion identified in the Australian maps did not coincide with regions of the Minnesota map.

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