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 High-Quality SNP Linkage Maps Improved QTL Mapping and Genome Assembly in Populus

2020 ◽  
Vol 111 (6) ◽  
pp. 515-530
Author(s):  
Chunfa Tong ◽  
Dan Yao ◽  
Hainan Wu ◽  
Yuhua Chen ◽  
Wenguo Yang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Genome Assembly ◽  
Perfect Match ◽  
Genetic Maps ◽  
Hybrid Population ◽  
Linkage Maps ◽  
Linkage Groups ◽  
High Quality ◽  
F1 Hybrid ◽  
Wide Range

Abstract With the advances in high-throughput sequencing technologies and the development of new software for extracting single nucleotide polymorphisms (SNPs) across a mapping population, it is possible to construct high-quality genetic maps with thousands of SNPs in outbred forest trees. Two parent-specific linkage maps were constructed with restriction site-associated DNA sequencing data from an F1 hybrid population derived from Populus deltoides and Populus simonii, and applied in QTL mapping and genome assembly. The female P. deltoides map contained 4018 SNPs, which were divided into 19 linkage groups under a wide range of LOD thresholds from 7 to 55. The male P. simonii map showed similar characteristics, consisting of 2097 SNPs, which also belonged to 19 linkage groups under LOD thresholds of 7 to 29. The SNP order of each linkage group was optimal among different ordering results from several available software. Moreover, the linkage maps allowed the detection of 39 QTLs underlying tree height and 47 for diameter at breast height. In addition, the linkage maps improved the anchoring of 689 contigs of P. simonii to chromosomes. The 2 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 the excellent performances in QTL mapping and genome assembly. Both approaches for extracting and ordering SNPs could be applied to other species for constructing high-quality genetic maps.

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 Autosomal genetic maps of the Australian Sheep Blowfly, Lucilia cuprina dorsalis R.-D. (Diptera: Calliphoridae), and possible correlations with the linkage maps of Musca domestica L. and Drosophila melanogaster (Mg.)

1981 ◽  
Vol 37 (1) ◽  
pp. 55-69 ◽  
Author(s):  
G. G. Foster ◽  
M. J. Whitten ◽  
C. Konovalov ◽  
J. T. A. Arnold ◽  
G. Maffi
Keyword(s):  
Drosophila Melanogaster ◽  
Musca Domestica ◽  
Genetic Maps ◽  
Lucilia Cuprina ◽  
Linkage Data ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Australian Sheep ◽  
Linkage Relationships

SUMMARYLinkage data and revised maps for 52 autosomal loci in L. cuprina are presented. Examination of the linkage relationships of biochemically and morphologically similar mutations in L. cuprina, Musca domestica L. and Drosophila melanogaster (Mg) suggests that the major linkage groups have survived largely intact during the evolution of the higher Diptera.

scholarly journals Development of an SNP Marker Set for Marker-Assisted Backcrossing Using Genotyping-By-Sequencing in Tetraploid Perilla

2021 ◽  
Author(s):  
Yun-Joo Kang ◽  
Bo-Mi Lee ◽  
Jangmi Kim ◽  
Moon Nam ◽  
Myoung-Hee Lee ◽  
...  
Keyword(s):  
Recurrent Selection ◽  
Diploid Species ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Genome Wide ◽  
A Genome ◽  
Marker Assisted Backcrossing

Abstract High-quality molecular markers are essential for marker-assisted selection to accelerate breeding progress. Compared with diploid species, recently diverged polyploid crop species tend to have highly similar homeologous subgenomes, which is expected to limit the development of broadly applicable locus-specific single-nucleotide polymorphism (SNP) assays. Furthermore, it is particularly challenging to make genome-wide marker sets for species that lack a reference genome. Here, we report the development of a genome-wide set of kompetitive allele specific PCR (KASP) markers for marker-assisted recurrent selection (MARS) in the tetraploid minor crop perilla. To find locus-specific SNP markers across the perilla genome, we used genotyping-by-sequencing (GBS) to construct linkage maps of two F2 populations. The two resulting high-resolution linkage maps comprised 2,326 and 2,454 SNP markers that spanned a total genetic distance of 2,133 cM across 16 linkage groups and 2,169 cM across 21 linkage groups, respectively. We then obtained a final genetic map consisting of 22 linkage groups with 1,123 common markers from the two genetic maps. We selected 96 genome-wide markers for MARS and confirmed the accuracy of markers in the two F2 populations using a high-throughput Fluidigm system. We confirmed that 91.8% of the SNP genotyping results from the Fluidigm assay were the same as the results obtained through GBS. These results provide a foundation for marker-assisted backcrossing and the development of new varieties of perilla.

Genetic mapping of resistance factors to Phytophthora palmivora in cocoa

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 79-85 ◽  
Author(s):  
M -H Flament ◽  
I Kebe ◽  
D Clément ◽  
I Pieretti ◽  
A -M Risterucci ◽  
...  
Keyword(s):  
Quantitative Trait ◽  
Natural Infection ◽  
Genetic Maps ◽  
Aflp Markers ◽  
Phytophthora Palmivora ◽  
Good Prediction ◽  
Linkage Groups ◽  
Genetic Determination ◽  
Total Length ◽  
Adult Trees

Phytophthora palmivora causes pod rot, a serious disease on cocoa widespread throughout the producing regions. In order to ascertain the genetic determination of cocoa resistance to P. palmivora, a study was carried out on two progenies derived from crosses between a heterozygous, moderately resistant Forastero clone, T60/887, and two closely related and highly susceptible Forastero clones, one completely homozygous, IFC2, and one partially heterozygous, IFC5. The cumulative size of both progenies was 112 individuals. Plants were subjected to natural and artificial inoculation of P. palmivora in Côte d'Ivoire. The genetic maps of T60/887 and of IFC5 were constructed using amplified fragment length polymorphism (AFLP) markers and microsatellites. The map of T60/887 comprised 198 markers assembled in 11 linkage groups and representing a total length of 793 cM. The map of IFC5 comprised 55 AFLP markers that were assembled into six linkage groups for a total length of 244 cM. Ratio of rotten over total number of fruit under natural infection was measured for each tree over two harvests. Artificial inoculations were performed on leaves and pods. These tests were weakly correlated with the pod rot rate in the field. Five quantitative trait loci (QTLs) of resistance were detected for T60/887 but none were common between the three traits measured. Stability and reliability of the experimental procedures are discussed and revealed the difficult use of these artificial tests on adult trees for a good prediction of field resistance.Key words: Theobroma cacao, Phytophthora palmivora, cocoa black pod disease, genetic map, quantitative trait locus (QTL).

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.

scholarly journals Novel fluorescent sequence-related amplified polymorphism(FSRAP) markers for the construction of a genetic linkage map of wheat(Triticum aestivum L.)

Genetika ◽  
2017 ◽  
Vol 49 (3) ◽  
pp. 1081-1093 ◽  
Author(s):  
Lingbo Zhao ◽  
Zhang Li ◽  
Jipeng Qu ◽  
Yan Yu ◽  
Lu Lu ◽  
...  
Keyword(s):  
Genetic Linkage Map ◽  
Average Distance ◽  
Triticum Aestivum L ◽  
Genetic Maps ◽  
The Novel ◽  
Linkage Groups ◽  
D Genome ◽  
Wheat Varieties ◽  
B Genome ◽  
A Genome

Novel fluorescent sequence-related amplified polymorphism (FSRAP) markers were developed based on the SRAP molecular marker. Then, the FSRAP markers were used to construct the genetic map of a wheat (Triticum aestivumL.) recombinant inbred line population derived from a Chuanmai 42?Chuannong 16 cross. Reproducibility and polymorphism tests indicated that the FSRAP markers have repeatability and better reflect the polymorphism of wheat varieties compared with SRAP markers. A total of 430 polymorphic loci between Chuanmai 42 and Chuannong 16 were detected with 189 FSRAP primer combinations. A total of 281 FSARP markers and 39 SSR markers re classified into 20 linkage groups. The maps spanned a total length of 2499.3cM with an average distance of 7.81cM between markers. A total of 201 markers were mapped on the B genome and covered a distance of 1013cM. On the A genome, 84 markers were mapped and covered a distance of 849.6cM. On the D genome, however, only 35 markers were mapped and covered a distance of 636.7cM. No FSRAP markers were distributed on the 7D chromosome. The results of the present study revealed that the novel FSRAP markers can be used to generate dense, uniform genetic maps of wheat.

Linkage maps for Arabidopsis lyrata subsp. lyrata and Arabidopsis lyrata subsp. petraea combining anonymous and Arabidopsis thaliana–derived markers

Genome ◽  
2007 ◽  
Vol 50 (2) ◽  
pp. 142-150 ◽  
Author(s):  
Julien Beaulieu ◽  
Martine Jean ◽  
François Belzile
Keyword(s):  
Arabidopsis Thaliana ◽  
Aflp Markers ◽  
Close Relative ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Arabidopsis Lyrata ◽  
Model Plant Arabidopsis Thaliana ◽  
Caps Markers ◽  
Simple Sequence ◽  
Plant Arabidopsis Thaliana

Arabidopsis lyrata, a close relative of the model plant Arabidopsis thaliana, is 1 of a few plant species for which the genome is to be entirely sequenced, which promises to yield important insights into genome evolution. Only 2 sparse linkage maps have been published, and these were based solely on markers derived from the A. thaliana genome. Because the genome of A. lyrata is practically twice as large as that of A. thaliana, the extent of map coverage of the A. lyrata genome remains uncertain. In this study, a 2-way pseudo-testcross strategy was used to construct genetic linkage maps of A. lyrata subsp. petraea and A. lyrata subsp. lyrata, using simple sequence repeat (SSR) and cleaved amplified polymorphic sequence (CAPS) markers from the A. thaliana genome, and anonymous amplified fragment length polymorphism (AFLP) markers that could potentially uncover regions unique to the A. lyrata genome. The SSR and CAPS markers largely confirmed the relationships between linkage groups in A. lyrata and A. thaliana. AFLP markers slightly increased the coverage of the A. lyrata maps, but mostly increased marker density on the linkage groups. We noted a much lower level of polymorphism and a greater segregation distortion in A. lyrata subsp. lyrata markers. The implications of these findings for the sequencing of the A. lyrata genome are discussed.

Common bunt resistance gene Bt10 located on wheat chromosome 6D

2006 ◽  
Vol 86 (Special Issue) ◽  
pp. 1409-1412 ◽  
Author(s):  
J. G. Menzies ◽  
R. E. Knox ◽  
Z. Popovic ◽  
J. D. Procunier
Keyword(s):  
Microsatellite Markers ◽  
Resistance Gene ◽  
Doubled Haploid ◽  
Chromosomal Location ◽  
Wheat Chromosome ◽  
Common Bunt ◽  
Tilletia Tritici ◽  
Doubled Haploid Lines ◽  
The Individual ◽  
Bunt Resistance

Knowledge of the chromosomal location of disease resistance genes assists in their identification and classification. The determination of the chromosomal location in wheat of the common bunt (Tilletia tritici and T. laevis) resistance gene Bt10 was the goal of this study. Doubled haploid lines were developed from a cross between bunt susceptible Glenlea and bunt resistant AC Taber carrying Bt10. The doubled haploid lines were inoculated with T. tritici race T19, grown in a growth room and rated for bunt near maturity. A series of 50 wheat microsatellite markers were tested on DNA of the individual lines. The population segregated 1:1 for bunt reaction with clear separation between resistant and susceptible classes. A trait related DNA polymorphism generated by gwm469 located in chromosome 6D fit a 1:1 segregation. Combined segregation of bunt resistance and the gwm469 polymorphism differed significantly from a 1:1: 1:1 ratio with a preponderance of parental types confirming linkage of gwm469 with Bt10. The map distance between gwm469 and Bt10was estimated at 19.3 cM by MAPMAKER. The microsatellite markers wmc749, barc54 and cfd0033, located on chromosome 6D, also were significantly associated with the bunt resistance and gwm469. In total, six markers previously located to chromosome 6D were in the linkage group with the Bt10 common bunt resistance. The linkage of these markers with each other and Bt10 indicated that Bt10 is located on the short arm of chromosome 6D. Key words: Tilletia tritici, Tilletia laevis, Triticum aestivum, wheat, microsatellite, doubled haploid

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