Targetting microsatellites (SSRs) in genetic linkage maps of bread wheat

2001 ◽  
Vol 52 (12) ◽  
pp. 1143 ◽  
Author(s):  
M. J. Hayden ◽  
S. Khatkar ◽  
P. J. Sharp
Keyword(s):  
Bread Wheat ◽  
Ssr Markers ◽  
Genetic Linkage ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Intraspecific Polymorphism ◽  
Chromosomal Origin ◽  
Genetic Linkage Maps ◽  
Genomic Regions ◽  
Simple Sequence

The construction of genetic linkage maps from intraspecific crosses of bread wheat is slow and difficult due to very limited levels of polymorphism, which hinder the assignment of linkage groups to chromosomes and leave large genomic regions without markers. Simple sequence repeats (SSRs) reveal a higher incidence of polymorphism and are more informative than any other DNA marker, and are therefore considered a marker of choice for self-pollinating crops with little intraspecific polymorphism. However, the availability of SSRs in bread wheat is still limited. In this study, selectively amplified microsatellite (SAM) analysis was used to develop informative SSR markers to assist in the construction of an intraspecific wheat map. Three markers were developed for under-represented regions in the genetic map, and 7 for unassigned linkage groups. The latter SSRs permitted the chromosomal origin of 4 unassigned linkage groups to be determined. These results demonstrate the utility of SAM analysis for the targetted development of informative SSR markers to genomic regions of interest, and assignment of linkage groups to chromosomes. Furthermore, SAM analysis facilitates the development of markers for relatively short (<11) dinucleotide repeat sequences, a class of SSRs generally inaccessible to traditional hybridisation-based methods used to develop these markers.

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’.

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

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.

scholarly journals Randomly Amplified Polymorphic DNA-based Genetic Linkage Maps of Three Apple Cultivars

1997 ◽  
Vol 122 (3) ◽  
pp. 350-359 ◽  
Author(s):  
Patrick J. Conner ◽  
Susan K. Brown ◽  
Norman F. Weeden
Keyword(s):  
Skin Color ◽  
Genetic Linkage ◽  
Average Distance ◽  
Scab Resistance ◽  
Linkage Maps ◽  
Randomly Amplified Polymorphic Dna ◽  
Linkage Groups ◽  
Single Linkage ◽  
Genetic Linkage Maps ◽  
Using Data

Genetic linkage maps were created for three apple (Malus ×domestica Borkh.) cultivars using data from two progenies (`Wijcik McIntosh' xNY 75441-67 and `Wijcik McIntosh' xNY 75441-58). The maps consist primarily of randomly amplified polymorphic DNA (RAPD) markers, but also contain six isozyme loci and four morphological markers (Rf, fruit skin color; Vf, scab resistance; Co, columnar growth habit; Ma, malic acid). Maps were constructed using a double pseudotestcross mapping format and JoinMap mapping software. An integrated `Wijcik McIntosh' map was produced by combining marker data from both progenies into a single linkage map. Homologous linkage groups from paternal maps were paired with their counterparts in the `Wijcik McIntosh' map using locus bridges composed of markers heterozygous in both parents of a progeny. The `Wijcik McIntosh' map consists of 238 markers arranged in 19 linkage groups spanning 1206 cM. The NY 75441-67 map contains 110 markers in 16 linkage groups and the NY 75441-58 map consists of 183 markers in 18 linkage groups. The average distance between markers in the maps was ≈5.0 cM.

Integration of the Cytogenetic and Genetic Linkage Maps of Brassica oleracea

Genetics ◽  
2002 ◽  
Vol 161 (3) ◽  
pp. 1225-1234 ◽  
Author(s):  
Elaine C Howell ◽  
Guy C Barker ◽  
Gareth H Jones ◽  
Michael J Kearsey ◽  
Graham J King ◽  
...  
Keyword(s):  
Linkage Map ◽  
Brassica Oleracea ◽  
Genetic Map ◽  
Genetic Linkage ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Opposite Orientation ◽  
Cytogenetic Map ◽  
Specific Pcr ◽  
Genetic Linkage Maps

Abstract We have assigned all nine linkage groups of a Brassica oleracea genetic map to each of the nine chromosomes of the karyotype derived from mitotic metaphase spreads of the B. oleracea var. alboglabra line A12DHd using FISH. The majority of probes were BACs, with A12DHd DNA inserts, which give clear, reliable FISH signals. We have added nine markers to the existing integrated linkage map, distributed over six linkage groups. BACs were definitively assigned to linkage map positions through development of locus-specific PCR assays. Integration of the cytogenetic and genetic linkage maps was achieved with 22 probes representing 19 loci. Four chromosomes (2, 4, 7, and 9) are in the same orientation as their respective linkage groups (O4, O7, O8, and O6) whereas four chromosomes (1, 3, 5, and 8) and linkage groups (O3, O9, O2, and O1) are in the opposite orientation. The remaining chromosome (6) is probably in the opposite orientation. The cytogenetic map is an important resource for locating probes with unknown genetic map positions and is also being used to analyze the relationships between genetic and cytogenetic maps.

Genetic linkage maps of the ground crickets Allonemobius fasciatus and Allonemobius socius using RAPD and allozyme markers

Genome ◽  
1998 ◽  
Vol 41 (6) ◽  
pp. 841-847 ◽  
Author(s):  
Jiming Chu ◽  
Daniel J Howard
Keyword(s):  
Hybrid Zone ◽  
Genetic Linkage ◽  
Sex Chromosome ◽  
Average Distance ◽  
Linkage Maps ◽  
Eastern United States ◽  
Linkage Groups ◽  
Genetic Linkage Maps ◽  
Allonemobius Fasciatus ◽  
Allonemobius Socius

The ground crickets, Allonemobius fasciatus and A. socius are sister species and form a mosaic hybrid zone in the eastern United States. In this study, we developed RAPD markers and constructed genetic linkage maps for the two species, as a first step toward mapping quantitative trait loci that control conspecific sperm precedence. The A. fasciatus map consists of 25 markers mapped to 8 linkage groups, spanning 400.1 contiguous centiMorgans (cM). The average distance between two framework markers is 23.5 cM. The A. socius map consists of 20 markers mapped to 6 linkage groups, spanning 400.5 contiguous cM. The average distance between two framework markers is 30.4 cM. A sex chromosome was identified in the A. socius map. These are the first reported genetic linkage maps for Orthoptera.Key words: Allonemobius, allozyme, cricket, hybrid zone, linkage maps, RAPD.

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