Comparative genetic mapping of allotetraploid cotton and its diploid progenitors

Genome ◽  
1999 ◽  
Vol 42 (2) ◽  
pp. 184-203 ◽  
Author(s):  
C L Brubaker ◽  
A H Paterson ◽  
J F Wendel
Keyword(s):  
Fragment Length Polymorphism ◽  
Genetic Maps ◽  
Linkage Groups ◽  
Reciprocal Translocations ◽  
Physical Size ◽  
Cotton Species ◽  
A Genome ◽  
Duplicated Loci ◽  
Comparative Genetic Mapping ◽  
Allotetraploid Cotton

Allotetraploid cotton species (Gossypium) belong to a 1-2 million year old lineage that reunited diploid genomes that diverged from each other 5-10 million years ago. To characterize genome evolution in the diploids and allotetraploids, comparative RFLP mapping was used to construct genetic maps for the allotetraploids (AD genome; n = 26) and diploids (A and D genomes; n = 13). Comparisons among the 13 suites of homoeologous linkage groups permitted comparisons of synteny and gene order. Two reciprocal translocations were confirmed involving four allotetraploid At genome chromosomes, as was a translocation between the two extant A genome diploids. Nineteen locus order differences were detected among the two diploid and two allotetraploid genomes. Conservation of colinear linkage groups among the four genomes indicates that allopolyploidy in Gossypium was not accompanied by extensive chromosomal rearrangement. Many inversions include duplicated loci, suggesting that the processes that gave rise to inversions are not fully conservative. Allotetraploid At and Dt genomes and the A and D diploid genomes are recombinationally equivalent despite a nearly two-fold difference in physical size. Polyploidization in Gossypium is associated with enhanced recombination, as genetic lengths for allotetraploid genomes are over 50% greater than those of their diploid counterparts.Key words: restriction fragment length polymorphism (RFLP), Gossypium, evolution, polyploidy.

Applications of genetic markers in cytogenetic manipulation of the wheat genomes

Genome ◽  
1989 ◽  
Vol 31 (1) ◽  
pp. 137-142 ◽  
Author(s):  
M. D. Gale ◽  
P. J. Sharp ◽  
S. Chao ◽  
C. N. Law
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Genetic Maps ◽  
Linkage Groups ◽  
Large Genome ◽  
Large Genome Size ◽  
Restriction Fragment Length

A molecular map of wheat, Triticum aestivum, is being developed. Problems associated with the large genome size, the large number of linkage groups, polyploidy, and limited polymorphism at the DNA level are being overcome. In addition to the breeding applications expected from the map, various uses for restriction fragment length polymorphism markers as tools in cytogenetic manipulation of wheat chromosomes and those from related species are being found. These include identification of aneuploid genotypes, added precision in intervarietal chromosome manipulations, tests of chromosome stability, identification of alien chromosomes, and marker-aided introgression of genes of agronomic importance from related species.Key words: wheat, restriction fragment length polymorphism, genetic maps, aneuploidy, alien chromosomes.

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.

scholarly journals Detailed Alignment of Saccharum and Sorghum Chromosomes: Comparative Organization of Closely Related Diploid and Polyploid Genomes

Genetics ◽  
1998 ◽  
Vol 150 (4) ◽  
pp. 1663-1682 ◽  
Author(s):  
R Ming ◽  
S-C Liu ◽  
Y-R Lin ◽  
J da Silva ◽  
W Wilson ◽  
...  
Keyword(s):  
Molecular Analysis ◽  
Saccharum Officinarum ◽  
Dna Probes ◽  
Genetic Maps ◽  
Linkage Groups ◽  
Structural Polymorphism ◽  
Sorghum Genome ◽  
F1 Progeny ◽  
Duplicated Loci ◽  
Intrachromosomal Rearrangements

Abstract The complex polyploid genomes of three Saccharum species have been aligned with the compact diploid genome of Sorghum (2n = 2x = 20). A set of 428 DNA probes from different Poaceae (grasses) detected 2460 loci in F1 progeny of the crosses Saccharum officinarum Green German × S. spontaneum IND 81-146, and S. spontaneum PIN 84-1 × S. officinarum Muntok Java. Thirty-one DNA probes detected 226 loci in S. officinarum LA Purple × S. robustum Molokai 5829. Genetic maps of the six Saccharum genotypes, including up to 72 linkage groups, were assembled into “homologous groups” based on parallel arrangements of duplicated loci. About 84% of the loci mapped by 242 common probes were homologous between Saccharum and Sorghum. Only one interchromosomal and two intrachromosomal rearrangements differentiated both S. officinarum and S. spontaneum from Sorghum, but 11 additional cases of chromosome structural polymorphism were found within Saccharum. Diploidization was advanced in S. robustum, incipient in S. officinarum, and absent in S. spontaneum, consistent with biogeographic data suggesting that S. robustum is the ancestor of S. officinarum, but raising new questions about the antiquity of S. spontaneum. The densely mapped Sorghum genome will be a valuable tool in ongoing molecular analysis of the complex Saccharum genome.

A gene controlling sex in grapevines placed on a molecular marker-based genetic map

Genome ◽  
2000 ◽  
Vol 43 (2) ◽  
pp. 333-340 ◽  
Author(s):  
M A Dalbó ◽  
G N Ye ◽  
N F Weeden ◽  
H Steinkellner ◽  
K M Sefc ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Dna Markers ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Basic Number ◽  
Genetic Maps ◽  
Hybrid Population ◽  
Linkage Groups ◽  
Starting Point ◽  
Map Distance

Genetic maps of Vitis (2n = 38) have been constructed from an interspecific hybrid population of 58 seedlings of the cross 'Horizon' ('Seyval' × 'Schuyler') × Illinois 547-1 (V. cinerea B9 × V. rupestris B38). The maps were initially constructed based on 277 RAPD (random amplified polymorphic DNA) markers using a double-pseudotestcross strategy. Subsequently, 25 microsatellites, 4 CAPS (cleaved amplified polymorphic sequence), and 12 AFLP (amplified fragment length polymorphism) markers were added to the maps. Another 120 markers, mostly those segregating 3:1, were also assigned but not positioned on the linkage groups in the two maps. The 'Horizon' map consisted of 153 markers covering 1199 cM, with an average map distance of 7.6 cM between markers. The Illinois 547-1 map had 179 markers covering 1470 cM, with an average map distance of 8.1 cM. There were 20 linkage groups in each map, one more than the basic number of chromosomes in grapes. Ten linkage groups in each map were identified as homologous using 16 microsatellite and 2 CAPS markers polymorphic in both parents. A single locus controlling sex in grapes mapped close to a microsatellite marker. These maps provide enough coverage of the genome for QTL (quantitative trait loci) analysis and as a starting point for positional gene cloning in grapes. Key words: Vitis, RAPD, microsatellite, SSR, CAPS.

scholarly journals Genetic analysis of phenotype in Trypanosoma brucei : a classical approach to potentially complex traits

2002 ◽  
Vol 357 (1417) ◽  
pp. 89-99 ◽  
Author(s):  
Andy Tait ◽  
Dan Masiga ◽  
Johnstone Ouma ◽  
Annette MacLeod ◽  
Juergen Sasse ◽  
...  
Keyword(s):  
Genetic Mapping ◽  
Trypanosoma Brucei ◽  
Complex Traits ◽  
Positional Cloning ◽  
Genetic Maps ◽  
Linkage Groups ◽  
Physical Size ◽  
Large Numbers ◽  
Number Of Genes ◽  
Allelic Segregation

The genome of the African trypanosome, Trypanosoma brucei , is currently being sequenced, raising the question of how the data generated can be used to determine the function of the large number of genes that will be identified. There is a range of possible approaches, and in this paper we discuss the use of a classical genetic approach coupled with positional cloning based on the ability of trypanosomes to undergo genetic exchange. The genetics of these parasites is essentially similar to a conventional diploid Mendelian system with allelic segregation and an independent assortment of markers on different chromosomes. Data are presented showing that recombination occurs between markers on the same chromosome allowing the physical size of the unit of recombination to be determined. Analysis of the available progeny clones from a series of crosses shows that, in principal, large numbers of progeny can readily be isolated from existing cryopreserved products of mating and, taking these findings together, it is clear that genetic mapping of variable phenotypes is feasible. The available phenotypes for analysis are outlined and most are relevant to the transmission and pathogenesis of the parasite. Genetic maps from two crosses are presented based on the use of the technique of AFLP; these maps comprise 146 and 139 markers in 30 and 21 linkage groups respectively. Segregation distortion is exhibited by some of the linkage groups and the possible reasons for this are discussed. The general conclusion, from the results presented, is that a genetic-mapping approach is feasible and will, in the future, allow the genes determining a number of important traits to be identified.

scholarly journals Genetic mapping in Xenopus laevis: eight linkage groups established.

Genetics ◽  
1989 ◽  
Vol 123 (2) ◽  
pp. 389-398
Author(s):  
J D Graf
Keyword(s):  
Linkage Group ◽  
Xenopus Laevis ◽  
Malic Enzyme ◽  
Fumarate Hydratase ◽  
Genetic Maps ◽  
Linkage Groups ◽  
Heterozygous Parent ◽  
A Genome ◽  
Group 5 ◽  
Group 1

Abstract Inheritance of alleles at 29 electrophoretically detected protein loci and one pigment locus (albinism) was analyzed in Xenopus laevis by backcrossing multiply heterozygous individuals generated by intersubspecies hybridization. Pairwise linkage tests revealed eight classical linkage groups. These groups have been provisionally numbered from 1 to 8 in an arbitrarily chosen order. Linkage group 1 includes ALB-2 (albumin), ADH-1 (alcohol dehydrogenase), NP (nucleoside phosphorylase), and ap (periodic albinism). Linkage group 2 contains ALB-1 and ADH-2, and probably is homeologous to group 1. Linkage group 3 comprises PEP-B (peptidase B), MPI-1 (mannosephosphate isomerase), SORD (sorbitol dehydrogenase), and mIDH-2 (mitochondrial isocitrate dehydrogenase). Linkage group 4 contains GPI-1 (glucosephosphate isomerase) and EST-4 (esterase 4). Linkage group 5 contains GPI-2 and PEP-D (peptidase D). Linkage group 6 comprises ACP-3 (acid phosphatase), sME (cytosolic malic enzyme), and GLO-2 (glyoxalase). Linkage group 7 consists of sSOD-1 (cytosolic superoxide dismutase), GPD-2 (glycerol-3-phosphate dehydrogenase), mME (mitochondrial malic enzyme), and the sex determining locus. Linkage group 8 includes FH (fumarate hydratase) and TRF (transferrin). Recombination frequencies between linked loci showed differences related to the genomic constitution (parental subspecies) and to the sex of the heterozygous parent. Independent assortment was observed between the duplicate ALB loci. This is true for the duplicate ADH, GLO, and MPI loci as well, supporting the view that these genes have been duplicated as part of a genome duplication that occurred in the evolutionary history of X. laevis. Comparative analysis of genetic maps reveals a possible conservation of several linkages from the Xenopus genome to the human genome.

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.

scholarly journals Analysis of a detailed genetic linkage map of Lactuca sativa (lettuce) constructed from RFLP and RAPD markers.

Genetics ◽  
1994 ◽  
Vol 136 (4) ◽  
pp. 1435-1446
Author(s):  
R V Kesseli ◽  
I Paran ◽  
R W Michelmore
Keyword(s):  
Lactuca Sativa ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Genetic Linkage Map ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Maps ◽  
Morphological Markers ◽  
Linkage Groups ◽  
F2 Population

Abstract A detailed genetic map has been constructed from the F2 population of a single intraspecific cross of Lactuca sativa (n = 9). It comprises 319 loci, including 152 restriction fragment length polymorphism (RFLP), 130 random amplified polymorphic DNA (RAPD), 7 isozyme, 19 disease resistance, and 11 morphological markers. Thirteen major, four minor linkage groups and several unlinked markers are identified for this genome which is estimated to be approximately 1950 cM. RFLP and RAPD markers show similar distributions throughout the genome and identified similar levels of polymorphism. RAPD loci were much quicker to identify but more difficult to order. Procedures for generating accurate genetic maps and their limitations are described.

An RFLP-based linkage map of oats based on a cross between two diploid taxa (Avena atlantica × A. hirtula)

Genome ◽  
1992 ◽  
Vol 35 (5) ◽  
pp. 765-771 ◽  
Author(s):  
L. S. O'Donoughue ◽  
Z. Wang ◽  
M. Röder ◽  
B. Kneen ◽  
M. Leggett ◽  
...  
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Rflp Markers ◽  
Linkage Groups ◽  
Marker Selection ◽  
A Genome ◽  
Restriction Fragment Length

A restriction fragment length polymorphism (RFLP) map for the A genome of Avena has been developed using F3 families from the cross A. atlantica × A. hirtula. The main source of markers were an oat cDNA and a barley cDNA library. A total of 194 RFLP markers was used, 192 of which were mapped or assigned to linkage groups. Seven main linkage groups, presumably corresponding to the seven chromosomes of the haploid genome, were identified. The linkage groups varied in size from 30 to 118 cM for a total map length of 614 cM. This map provides a tool for the interpretation of genome organization in Avena and for marker selection in the development of a map of hexaploid oats.Key words: restriction fragment length polymorphism, Avena, mapping.

scholarly journals Collinearity Analysis of Allotetraploid Gossypium Tomentosum and Gossypium Darwinii

2015 ◽  
Author(s):  
Fang Liu ◽  
Zhong-li Zhou ◽  
Chun-ying Wang ◽  
Yu-hong Wang ◽  
Xiao-yan Cai ◽  
...  
Keyword(s):  
Genome Structure ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Genome Research ◽  
Cotton Species ◽  
Fiber Fineness ◽  
Genetic Linkage Maps ◽  
Gossypium Tomentosum ◽  
Open The Doors ◽  
Allotetraploid Cotton

G. tomentosum and G. darwinii are wild allotetraploid cotton species, characterized with many excellent traits including finer fiber fineness, drought tolerance, Fusarium wilt and Verticillium wilt resistance. Based on construction of F2 linkage groups of G. hirsutum ?? G. tomentosum and G. hirsutum × G. darwinii, two genetic linkage maps were compared. As a result we found a total of 7 inversion fragments on chr02, chr05, chr08, chr12, chr14, chr16 and chr25, 3 translocation fragments on chr05, chr14 and chr26. Further comparing the inversion and translocation fragments, we noticed four of seven markers orientation of G. tomentosum consistent with G. hirsutum or G. raimondii, one of seven inversion markers orientation of G. darwinii consistent with G. hirsutum；meanwhile one of three translocation marker orientation of G. tomentosum consistent with G. raimondii. The result indicate，compare G. darwinii, G. tomentosum has closer genetic relationship to G. hirsutum. This study will play an important role in understanding the genome structure of G. tomentosum and G. darwinii, and open the doors for further in-depth genome research such as fine mapping, tagging genes of interest from wild relatives and evolutionary study.

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