Anchoring Linkage Groups of the Rosa Genetic Map to Physical Chromosomes with Tyramide-FISH and EST-SNP Markers

AbstractThe main purposes of the study were i) to develop a first mapping population for bread wheat grown in Kazakhstan, ii) to construct its genetic map for further identification of genes associated with important agronomic traits.To the best of our knowledge this is the first segregating population and genetic map developed for Kazakh bread wheat. The work is an example of how plant breeding programs in Kazakhstan have started successfully deploying next generation plant breeding methods.The KASP (Compatative Allele Specific PCR) technology of LGC Group and SNP DNA-markers have been exploited to genotype and build a genetic map of the segregating population. The total length of the map was 1376 cM. A total 157 out of initial 178 SNP markers used formed 26 linkage groups leaving 1 duplicated and 20 unassigned markers. The threshold distance between markers was set ≤ 30 cM. Therefore, two linkage groups were obtained for chromosomes such as 2A, 2B, 2D, 3A, 5A, 6B and 7A. Despite one duplicated and 20 unassigned markers, the 157 KASP SNP markers that were mapped spanned A, B and D genomes of wheat. Kosambi Mapping function was employed to calculate recombination units between makers. RILs were developed through SSD method up to F4 generation. Almost 97% of identified alleles were useful in evaluating the population’s genetic diversity; the remaining 3% showed no outcome. As a result, 77 DNA markers were mapped for A, 74 for B and 27 for D genomes. The mapping population will be genotyped using high marker density array planform such as Illumina iSelect to obtain a genetic map with a relatively high coverage. Then, the population and high-resolution genetic map will be used to identify genes influencing wheat adaptation in Kazakhstan.

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High-resolution genetic map construction and QTL analysis of important fiber traits in kenaf using RAD-seq

10.21203/rs.3.rs-1072676/v1 ◽

2021 ◽

Author(s):

Li Hui ◽

Chang Li ◽

Tang Huijuan ◽

Luan Mingbao ◽

Pan Gen ◽

...

Keyword(s):

Qtl Mapping ◽

Genetic Map ◽

Fiber Quality ◽

Crop Improvement ◽

Molecular Genetic ◽

Snp Markers ◽

Linkage Groups ◽

Genetic Traits ◽

Map Construction ◽

Fiber Yield

Abstract Quantitative trait locus (QTL) mapping is a useful method for revealing the mechanism of complex genetic traits and identifying new genomic information to accelerate crop improvement. In the present study, 154 F2:3 strains and their parents were used for restriction site-associated DNA sequencing, single-nucleotide polymorphism (SNP) identification, and genetic map construction. After filtering based on stringent filtering standards, 297.5 Gb of clean data were obtained. Further, 5,191 polymorphic SNP markers were identified from each sample, of which 1,997 polymorphic SNP markers were successfully mapped onto 18 different linkage groups. Six QTLs (QPH, QFBW, QDBW, QFW, QFT, and QFC) were identified based on the genetic map using the multiple QTL mapping (MQM) method, which were then assigned to three linkage groups, LG16, LG8, and LG3. QPH, QFBW, QDBW, and QFW were related to fiber yield, while QFT and QFC were related to fiber quality. This is the first study of its kind to map QTL of fiber yield and fiber quality, which will facilitate further understanding of the molecular genetic basis of these traits. However, there are limitations regarding the utilization of this map because several large gaps remain in some linkage groups. Therefore, additional markers need to be developed to further narrow these regions.

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An enhanced molecular marker based genetic map of perennial ryegrass (Lolium perenne) reveals comparative relationships with other Poaceae genomes

Genome ◽

10.1139/g01-144 ◽

2002 ◽

Vol 45 (2) ◽

pp. 282-295 ◽

Cited By ~ 175

Author(s):

Elizabeth S Jones ◽

Natalia L Mahoney ◽

Michael D Hayward ◽

Ian P Armstead ◽

J Gilbert Jones ◽

...

Keyword(s):

Molecular Marker ◽

Linkage Map ◽

Genetic Map ◽

Lolium Perenne ◽

Perennial Ryegrass ◽

Genetic Linkage Map ◽

Population Based ◽

Genetic Maps ◽

Linkage Groups ◽

Integrated Genetic Map

A molecular-marker linkage map has been constructed for perennial ryegrass (Lolium perenne L.) using a one-way pseudo-testcross population based on the mating of a multiple heterozygous individual with a doubled haploid genotype. RFLP, AFLP, isoenzyme, and EST data from four collaborating laboratories within the International Lolium Genome Initiative were combined to produce an integrated genetic map containing 240 loci covering 811 cM on seven linkage groups. The map contained 124 codominant markers, of which 109 were heterologous anchor RFLP probes from wheat, barley, oat, and rice, allowing comparative relationships between perennial ryegrass and other Poaceae species to be inferred. The genetic maps of perennial ryegrass and the Triticeae cereals are highly conserved in terms of synteny and colinearity. This observation was supported by the general agreement of the syntenic relationships between perennial ryegrass, oat, and rice and those between the Triticeae and these species. A lower level of synteny and colinearity was observed between perennial ryegrass and oat compared with the Triticeae, despite the closer taxonomic affinity between these species. It is proposed that the linkage groups of perennial ryegrass be numbered in accordance with these syntenic relationships, to correspond to the homoeologous groups of the Triticeae cereals.Key words: Lolium perenne, genetic linkage map, RFLP, AFLP, conserved synteny.

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Genetic map of eight microsatellite markers comprising two linkage groups on rat chromosome 6

Cytogenetic and Genome Research ◽

10.1159/000133901 ◽

1995 ◽

Vol 68 (1-2) ◽

pp. 107-111 ◽

Cited By ~ 4

Author(s):

Y. Du ◽

E.F. Remmers ◽

H. Zha ◽

E.A. Goldmuntz ◽

P. Mathern ◽

...

Keyword(s):

Microsatellite Markers ◽

Genetic Map ◽

Chromosome 6 ◽

Linkage Groups

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Centromere-Linkage Analysis and Consolidation of the Zebrafish Genetic Map

Genetics ◽

10.1093/genetics/142.4.1277 ◽

1996 ◽

Vol 142 (4) ◽

pp. 1277-1288

Author(s):

Stephen L Johnson ◽

Michael A Gates ◽

Michele Johnson ◽

William S Talbot ◽

Sally Horne ◽

...

Keyword(s):

Linkage Group ◽

Linkage Analysis ◽

Genetic Analysis ◽

Linkage Map ◽

Rapid Method ◽

Genetic Map ◽

Dna Polymorphisms ◽

Linkage Groups

Abstract The ease of isolating mutations in zebrafish will contribute to an understanding of a variety of processes common to all vertebrates. To facilitate genetic analysis of such mutations, we have identified DNA polymorphisms closely linked to each of the 25 centromeres of zebrafish, placed centromeres on the linkage map, increased the number of mapped PCR-based markers to 652, and consolidated the number of linkage groups to the number of chromosomes. This work makes possible centromere-linkage analysis, a novel, rapid method to assign mutations to a specific linkage group using half-tetrads.

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Genetic map of 16 polymorphic markers forming three linkage groups assigned to rat Chromosome 4

Mammalian Genome ◽

10.1007/bf00360654 ◽

1995 ◽

Vol 6 (7) ◽

pp. 459-463 ◽

Cited By ~ 7

Author(s):

E. A. Goldmuntz ◽

E. F. Remmers ◽

Y. Du ◽

H. Zha ◽

P. Mathern ◽

...

Keyword(s):

Genetic Map ◽

Polymorphic Markers ◽

Chromosome 4 ◽

Linkage Groups

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Combined QTL and GWAS Analysis to Identify the Growth-Related Gene in Rhopilema Esculentum with the Help of 2b-RAD Sequencing

10.21203/rs.3.rs-902725/v1 ◽

2021 ◽

Author(s):

Bailing Chen ◽

Yulong Li ◽

Meilin Tian ◽

Hao Su ◽

Wei Sun ◽

...

Keyword(s):

Body Weight ◽

High Resolution ◽

Genetic Map ◽

Calcium Binding ◽

Genome Wide Association Study ◽

Snp Markers ◽

Fishery Resource ◽

Genetic Breeding ◽

Marine Fishery ◽

Genome Wide

Abstract R. esculentum is a popular seafood in Asian countries and an economic marine fishery resource in China. However, the high-resolution genetic map and growth-related molecular markers still lack, hindering the process of the genetic breeding of R. esculentum. Therefore, we firstly used the 2b-RAD method to sequence 152 R. esculentum specimens, identified 9100 single nucleotide polymorphism (SNP) markers and constructed a high-resolution genetic map with a marker interval of 0.58 cM, covering 98.68% of the genome. Then, we separately detected four and three quantitative trait loci (QTLs) associated with umbrella diameter and body weight based on the linkage map, which is located on linkage group (LG) 4, 13, 14 and 15. Finally, 27 genes were found both associated with umbrella diameter and body weight of R. esculentum by genome-wide association study (GWAS), in which one gene named RE13670 containing calcium-binding EGF-like domain may play an important role in controlling the growth. This study will be beneficial for underlying the growth mechanism of R. esculentum and also provide background knowledge for guiding its genetic breeding.

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

10.21203/rs.3.rs-1177284/v1 ◽

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.

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Genetic mapping of male sterility and pollen fertility QTLs in triticale with sterilizing Triticum timopheevii cytoplasm

Journal of Applied Genetics ◽

10.1007/s13353-020-00595-z ◽

2020 ◽

Author(s):

Marzena Wasiak ◽

Agnieszka Niedziela ◽

Henryk Woś ◽

Mirosław Pojmaj ◽

Piotr Tomasz Bednarek

Keyword(s):

Male Sterility ◽

Genetic Map ◽

Pollen Sterility ◽

Snp Markers ◽

Hybrid Seed Production ◽

Triticum Timopheevii ◽

Crop Species ◽

Sugar Beets ◽

Map Construction ◽

Explained Variance

AbstractCytoplasmic male sterility (CMS) phenomenon is widely exploited in commercial hybrid seed production in economically important crop species, including rye, wheat, maize, rice, sorghum, cotton, sugar beets, and many vegetables. Although some commercial successes, little is known about QTLs responsible for the trait in case of triticale with sterilizing Triticum timopheevii (Tt) cytoplasm. Recombinant inbred line (RIL) F6 mapping population encompassing 182 individuals derived from the cross of individual plants representing the HT352 line and cv Borwo was employed for genetic map construction using SNP markers and identification of QTLs conferring pollen sterility in triticale with CMS Tt. The phenotypes of the F1 lines resulting from crossing of the HT352 (Tt) with HT352 (maintainer) × Borwo were determined by assessing the number of the F2 seeds per spike. A genetic map with 21 linkage groups encompasses 29,737 markers and spanned over the distance of 2549 cM. Composite (CIM) and multiple (MIM) interval mappings delivered comparable results. Single QTLs mapped to the 1A, 1B, 2A, 2R, 3B, 3R, 4B, and 5B chromosomes, whereas the 5R and 6B chromosomes shared 3 and 2 QTLs, respectively. The QTLs with the highest LOD score mapped to the 5R, 3R, 1B, and 4B chromosomes; however, the QRft-5R.3 has the highest explained variance of the trait.

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Chromosomal regions which control sporulation in Bacillus subtilis

Canadian Journal of Microbiology ◽

10.1139/m69-137 ◽

1969 ◽

Vol 15 (7) ◽

pp. 787-790 ◽

Cited By ~ 6

Author(s):

Marvin Rogolsky

Keyword(s):

Bacillus Subtilis ◽

Linkage Group ◽

Genetic Map ◽

Gene Clusters ◽

Linkage Groups ◽

The Third ◽

The Right

Large quantities of sporulation mutants have been isolated with a variety of mutagens. The genetic sites for asporogeny have been localized on the chromosome of Bacillus subtilis through transduction with phage PBSI. Through these procedures specific portions of the chromosome which are associated with sporulation have been identified. Although asporogenic (Sp−) defects were observed to be scattered throughout the four linkage groups of the genetic map of B. subtilis, only three extensive Sp− linkage groups were identified. The first linkage group of Sp− markers is located at the proximal end of the chromosome between the cys A and ery markers. The second cluster of spore genes mapped to the right of ura, and the third linkage group of spore markers mapped to the left of lys-2. Defects within specific regions of the first and third spore gene clusters obstructed some early products of sporogenesis.

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