Assessment of SSR Marker Transfer from the Cultivated Strawberry to Diploid Strawberry Species: Functionality, Linkage Group Assignment, and Use in Diversity Analysis

The cultivated strawberry, Fragaria ×ananassa Duchesne ex Rozier, originated via hybridization between octoploids F. chiloensis (L.) Mill. and F. virginiana Mill. These three octoploid species are thought to share a putative genome composition of AAA`A'BBB`B'. Diploid F. vesca L., is considered to have donated the A genome. Current attention to the development of a diploid model system for strawberry genomics warrants the assessment of simple sequence repeat (SSR) marker transferability between the octoploid and diploid species in Fragaria L. In the present study, 23 SSR primer pairs derived from F. ×ananassa `Earliglow' by genomic library screening were evaluated for their utility in six diploid Fragaria species, including eight representatives of F. vesca, four of F. viridis Weston, and one each of F. nubicola (Hook. f.) Lindl. ex Lacaita, F. mandshurica Staudt, F. iinumae Makino, and F. nilgerrensis Schltdl. ex J. Gay. SSR primer pair functionality, as measured by amplification success rate (= 100% - failure rate) in each species, was ranked (from highest to lowest) as follows: F. vesca (98.4%) > F. iinumae (93.8%) = F. nubicola (93.8%) > F. mandshurica (87.5%) > F. nilgerrensis (75%) > F. viridis (73.4%). The extent to which these octoploid-derived SSR primer pairs generated markers that could be added to the F. vesca linkage map also was assessed. Of the 13 F. ×ananassa SSR markers that segregated codominantly in the F. vesca mapping population, 11 were assigned to linkage groups based upon close linkages to previously mapped loci. These markers were distributed over six of the seven F. vesca linkage groups, and can serve as anchor loci defining these six groups for purposes of comparative mapping between F. vesca and F. ×ananassa.

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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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Microsatellite Marker Development in Rose and its Application in Tetraploid Mapping

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.131.3.380 ◽

2006 ◽

Vol 131 (3) ◽

pp. 380-387 ◽

Cited By ~ 28

Author(s):

L.H. Zhang ◽

D.H. Byrne ◽

R.E. Ballard ◽

S. Rajapakse

Keyword(s):

Ssr Markers ◽

Genomic Library ◽

Cultivar Identification ◽

Genetic Maps ◽

Linkage Groups ◽

Specific Primers ◽

Pcr Products ◽

Ssr Loci ◽

Tetraploid Parent ◽

Simple Sequence

Microsatellite or simple sequence repeat (SSR) markers were developed from Rosa wichurana Crépin to combine two previously constructed tetraploid rose (Rosa hybrida L.) genetic maps. To isolate SSR-containing sequences from rose a small-insert genomic library was constructed from diploid Rosa wichurana and screened with several SSR probes. Specific primers were designed for 43 unique SSR regions, of which 30 primer pairs gave rise to clear PCR products. Seventeen SSR primer pairs (57%) produced polymorphism in the tetraploid rose 90-69 mapping family. These markers were incorporated into existing maps of the parents 86-7 and 82-1134, which were constructed primarily with AFLP markers. The current map of the male parent, amphidiploid 86-7, consists of 286 markers assigned to 14 linkage groups and covering 770 cm. The map of the female tetraploid parent, 82-1134, consists of 256 markers assigned to 20 linkage groups and covering 920 cm. Nineteen rose SSR loci were mapped on the 86-7 map and 11 on the 82-1134 map. Several homeologous linkage groups within maps were identified based on SSR markers. In addition, some of the SSR markers provided anchoring points between the two parental maps. SSR markers were also useful for joining small linkage groups. Based on shared SSR markers, consensus orders for four rose linkage groups between parental maps were generated. Microsatellite markers developed in this study will provide valuable tools for many aspects of rose research including future consolidation of diploid and tetraploid rose genetic linkage maps, genetic, phylogenetic and population analyses, cultivar identification, and marker-assisted selection.

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Chromosome structural changes in diploid and tetraploid A genomes of Gossypium

Genome ◽

10.1139/g05-116 ◽

2006 ◽

Vol 49 (4) ◽

pp. 336-345 ◽

Cited By ~ 44

Author(s):

Aparna Desai ◽

Peng W Chee ◽

Junkang Rong ◽

O Lloyd May ◽

Andrew H Paterson

Keyword(s):

Genome Evolution ◽

Linkage Mapping ◽

Structural Variation ◽

Structural Changes ◽

Diploid Species ◽

Gossypium Arboreum ◽

Linkage Groups ◽

Recombination Rates ◽

A Genome ◽

Polyploid Genome

The genus Gossypium, which comprises a divergent group of diploid species and several recently formed allotetraploids, offers an excellent opportunity to study polyploid genome evolution. In this study, chromosome structural variation among the A, At, and D genomes of Gossypium was evaluated by comparative genetic linkage mapping. We constructed a fully resolved RFLP linkage map for the diploid A genome consisting of 275 loci using an F2 interspecific Gossypium arboreum × Gossypium herbaceum family. The 13 chromosomes of the A genome are represented by 12 large linkage groups in our map, reflecting an expected interchromosomal translocation between G. arboreum and G. herbaceum. The A-genome chromosomes are largely collinear with the D genomes, save for a few small inversions. Although the 2 diploid mapping parents represent the closest living relatives of the allotetraploid At-genome progenitor, 2 translocations and 7 inversions were observed between the A and At genomes. The recombination rates are similar between the 2 diploid genomes; however, the At genome shows a 93% increase in recombination relative to its diploid progenitors. Elevated recombination in the Dt genome was reported previously. These data on the At genome thus indicate that elevated recombination was a general property of allotetraploidy in cotton.Key words: comparative mapping, polyploidy, genome evolution, inversions, translocations, RFLP.

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A framework linkage map of perennial ryegrass based on SSR markers

Genome ◽

10.1139/g05-120 ◽

2006 ◽

Vol 49 (4) ◽

pp. 354-364 ◽

Cited By ~ 43

Author(s):

G P Gill ◽

P L Wilcox ◽

D J Whittaker ◽

R A Winz ◽

P Bickerstaff ◽

...

Keyword(s):

Linkage Map ◽

Ssr Markers ◽

Lolium Perenne ◽

Perennial Ryegrass ◽

Simple Sequence Repeat ◽

Ssr Marker ◽

Sequence Repeat ◽

Linkage Groups ◽

Marker Loci ◽

Simple Sequence

A moderate-density linkage map for Lolium perenne L. has been constructed based on 376 simple sequence repeat (SSR) markers. Approximately one third (124) of the SSR markers were developed from GeneThresher® libraries that preferentially select genomic DNA clones from the gene-rich unmethylated portion of the genome. The remaining SSR marker loci were generated from either SSR-enriched genomic libraries (247) or ESTs (5). Forty-five percent of the GeneThresher SSRs were associated with an expressed gene. Unlike EST-derived SSR markers, GeneThresher SSRs were often associated with genes expressed at a low level, such as transcription factors. The map constructed here fulfills 2 definitions of a "framework map". Firstly, it is composed of codominant markers to ensure map transferability either within or among species. Secondly, it was constructed to achieve a level of statistical confidence in the support-for-order of marker loci. The map consists of 81 framework SSR markers spread over 7 linkage groups, the same as the haploid chromosome number. Most of the remaining 295 SSR markers have been placed into their most likely interval on the framework map. Nine RFLP markers and 1 SSR marker from another map constructed using the same pedigree were also incorporated to extend genome coverage at the terminal ends of 5 linkage groups. The final map provides a robust framework with which to conduct investigations into the genetic architecture of trait variation in this commercially important grass species.Key words: Framework map, perennial ryegrass, SSR, simple sequence repeat, GeneThresher, Lolium perenne.

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Implementing molecular marker technology in forage improvement

Proceedings of the New Zealand Grassland Association ◽

10.33584/jnzg.2003.65.2498 ◽

2003 ◽

pp. 229-238

Author(s):

M. Faville ◽

B. Barrett ◽

A. Griffiths ◽

M. Schreiber ◽

C. Mercer ◽

...

Keyword(s):

Quantitative Trait Locus ◽

Genetic Variation ◽

White Clover ◽

Simple Sequence Repeat ◽

Sequence Repeat ◽

Linkage Groups ◽

Seedling Vigour ◽

Genome Map ◽

Trait Locus ◽

Simple Sequence

Accelerated improvement of two cornerstones of New Zealand's pastoral industries, per ennial ryegrass (Lolium perenne L.) and white clover (Trifolium repens L.), may be realised through the application of markerassisted selection (MAS) strategies to enhance traditional plant breeding programmes. Genome maps constructed using molecular markers represent the enabling technology for such strategies and we have assembled maps for each species using EST-SSR markers - simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) representing genes. A comprehensive map of the white clover genome has been completed, with 464 EST-SSR and genomic SSR marker loci spanning 1125 cM in total, distributed across 16 linkage groups. These have been further classified into eight pairs of linkage groups, representing contributions from the diploid progenitors of this tetraploid species. In perennial ryegrass a genome map based exclusively on EST-SSR loci was constructed, with 130 loci currently mapped to seven linkage groups and covering a distance of 391 cM. This map continues to be expanded with the addition of ESTSSR loci, and markers are being concurrently transferred to other populations segregating for economically significant traits. We have initiated gene discovery through quantitative trait locus (QTL) analysis in both species, and the efficacy of the white clover map for this purpose was demonstrated with the initial identification of multiple QTL controlling seed yield and seedling vigour. One QTL on linkage group D2 accounts for 25.9% of the genetic variation for seed yield, and a putative QTL accounting for 12.7% of the genetic variation for seedling vigour was detected on linkage group E1. The application of MAS to forage breeding based on recurrent selection is discussed. Keywords: genome map, marker-assisted selection, perennial ryegrass, QTL, quantitative trait locus, SSR, simple sequence repeat, white clover

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Chromosomal organization of a sequence related to LTR-like elements of Ty1-copia retrotransposons in Avena species

Genome ◽

10.1139/g99-007 ◽

1999 ◽

Vol 42 (4) ◽

pp. 706-713 ◽

Cited By ~ 10

Author(s):

Concha Linares ◽

Antonio Serna ◽

Araceli Fominaya

Keyword(s):

In Situ Hybridization ◽

Diploid Species ◽

D Genome ◽

Specific Sequence ◽

Chromosomal Organization ◽

Intergenomic Translocations ◽

A Genome ◽

Slot Blot Analysis ◽

Copia Retrotransposons

A repetitive sequence, pAs17, was isolated from Avena strigosa (As genome) and characterized. The insert was 646 bp in length and showed 54% AT content. Databank searches revealed its high homology to the long terminal repeat (LTR) sequences of the specific family of Ty1-copia retrotransposons represented by WIS2-1A and Bare. It was also found to be 70% identical to the LTR domain of the WIS2-1A retroelement of wheat and 67% identical to the Bare-1 retroelement of barley. Southern hybridizations of pAs17 to diploid (A or C genomes), tetraploid (AC genomes), and hexaploid (ACD genomes) oat species revealed that it was absent in the C diploid species. Slot-blot analysis suggested that both diploid and tetraploid oat species contained 1.3 × 104 copies, indicating that they are a component of the A-genome chromosomes. The hexaploid species contained 2.4 × 104 copies, indicating that they are a component of both A- and D-genome chromosomes. This was confirmed by fluorescent in situ hybridization analyses using pAs17, two ribosomal sequences, and a C-genome specific sequence as probes. Further, the chromosomes involved in three C-A and three C-D intergenomic translocations in Avena murphyi (AC genomes) and Avena sativa cv. Extra Klock (ACD genomes), respectively, were identified. Based on its physical distribution and Southern hybridization patterns, a parental retrotransposon represented by pAs17 appears to have been active at least once during the evolution of the A genome in species of the Avena genus.Key words: chromosomal organization, in situ hybridization, intergenomic translocations, LTR sequence, oats.

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Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut

BMC Plant Biology ◽

10.1186/s12870-021-02875-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Liuyang Fu ◽

Qian Wang ◽

Lina Li ◽

Tao Lang ◽

Junjia Guo ◽

...

Keyword(s):

In Situ Hybridization ◽

Physical Mapping ◽

Tandem Repeats ◽

Genetic Research ◽

Diploid Species ◽

Reference Sequence ◽

A Genome ◽

Genome Map ◽

Chromosomal Variants

Abstract Background Chromosomal variants play important roles in crop breeding and genetic research. The development of single-stranded oligonucleotide (oligo) probes simplifies the process of fluorescence in situ hybridization (FISH) and facilitates chromosomal identification in many species. Genome sequencing provides rich resources for the development of oligo probes. However, little progress has been made in peanut due to the lack of efficient chromosomal markers. Until now, the identification of chromosomal variants in peanut has remained a challenge. Results A total of 114 new oligo probes were developed based on the genome-wide tandem repeats (TRs) identified from the reference sequences of the peanut variety Tifrunner (AABB, 2n = 4x = 40) and the diploid species Arachis ipaensis (BB, 2n = 2x = 20). These oligo probes were classified into 28 types based on their positions and overlapping signals in chromosomes. For each type, a representative oligo was selected and modified with green fluorescein 6-carboxyfluorescein (FAM) or red fluorescein 6-carboxytetramethylrhodamine (TAMRA). Two cocktails, Multiplex #3 and Multiplex #4, were developed by pooling the fluorophore conjugated probes. Multiplex #3 included FAM-modified oligo TIF-439, oligo TIF-185-1, oligo TIF-134-3 and oligo TIF-165. Multiplex #4 included TAMRA-modified oligo Ipa-1162, oligo Ipa-1137, oligo DP-1 and oligo DP-5. Each cocktail enabled the establishment of a genome map-based karyotype after sequential FISH/genomic in situ hybridization (GISH) and in silico mapping. Furthermore, we identified 14 chromosomal variants of the peanut induced by radiation exposure. A total of 28 representative probes were further chromosomally mapped onto the new karyotype. Among the probes, eight were mapped in the secondary constrictions, intercalary and terminal regions; four were B genome-specific; one was chromosome-specific; and the remaining 15 were extensively mapped in the pericentric regions of the chromosomes. Conclusions The development of new oligo probes provides an effective set of tools which can be used to distinguish the various chromosomes of the peanut. Physical mapping by FISH reveals the genomic organization of repetitive oligos in peanut chromosomes. A genome map-based karyotype was established and used for the identification of chromosome variations in peanut following comparisons with their reference sequence positions.

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SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napusThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽

10.1139/g10-079 ◽

2010 ◽

Vol 53 (11) ◽

pp. 948-956 ◽

Cited By ~ 35

Author(s):

G. Durstewitz ◽

A. Polley ◽

J. Plieske ◽

H. Luerssen ◽

E. M. Graner ◽

...

Keyword(s):

Genetic Analysis ◽

Oilseed Rape ◽

Expressed Sequence Tag ◽

Diploid Species ◽

Amplicon Sequencing ◽

Snp Markers ◽

Snp Analysis ◽

Genome Wide ◽

A Genome ◽

Illumina Goldengate

Oilseed rape ( Brassica napus ) is an allotetraploid species consisting of two genomes, derived from B. rapa (A genome) and B. oleracea (C genome). The presence of these two genomes makes single nucleotide polymorphism (SNP) marker identification and SNP analysis more challenging than in diploid species, as for a given locus usually two versions of a DNA sequence (based on the two ancestral genomes) have to be analyzed simultaneously during SNP identification and analysis. One hundred amplicons derived from expressed sequence tag (ESTs) were analyzed to identify SNPs in a panel of oilseed rape varieties and within two sister species representing the ancestral genomes. A total of 604 SNPs were identified, averaging one SNP in every 42 bp. It was possible to clearly discriminate SNPs that are polymorphic between different plant varieties from SNPs differentiating the two ancestral genomes. To validate the identified SNPs for their use in genetic analysis, we have developed Illumina GoldenGate assays for some of the identified SNPs. Through the analysis of a number of oilseed rape varieties and mapping populations with GoldenGate assays, we were able to identify a number of different segregation patterns in allotetraploid oilseed rape. The majority of the identified SNP markers can be readily used for genetic mapping, showing that amplicon sequencing and Illumina GoldenGate assays can be used to reliably identify SNP markers in tetraploid oilseed rape and to convert them into successful SNP assays that can be used for genetic analysis.

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Patterns of genome duplication within the Brassica napus genome

Genome ◽

10.1139/g03-006 ◽

2003 ◽

Vol 46 (2) ◽

pp. 291-303 ◽

Cited By ~ 96

Author(s):

I A.P Parkin ◽

A G Sharpe ◽

D J Lydiate

Keyword(s):

Brassica Napus ◽

Genome Duplication ◽

Chromosomal Rearrangements ◽

Centric Fusion ◽

Linkage Groups ◽

Gross Chromosomal Rearrangements ◽

A Genome ◽

C Genome ◽

Homologous Locus ◽

Duplicate Loci

The progenitor diploid genomes (A and C) of the amphidiploid Brassica napus are extensively duplicated with 73% of genomic clones detecting two or more duplicate sequences within each of the diploid genomes. This comprehensive duplication of loci is to be expected in a species that has evolved through a polyploid ancestor. The majority of the duplicate loci within each of the diploid genomes were found in distinct linkage groups as collinear blocks of linked loci, some of which had undergone a variety of rearrangements subsequent to duplication, including inversions and translocations. A number of identical rearrangements were observed in the two diploid genomes, suggesting they had occurred before the divergence of the two species. A number of linkage groups displayed an organization consistent with centric fusion and (or) fission, suggesting this mechanism may have played a role in the evolution of Brassica genomes. For almost every genetically mapped locus detected in the A genome a homologous locus was found in the C genome; the collinear arrangement of these homologous markers allowed the primary regions of homoeology between the two genomes to be identified. At least 16 gross chromosomal rearrangements differentiated the two diploid genomes during their divergence from a common ancestor.Key words: genome evolution, Brassicaeae, polyploidy, homoeologous linkage groups.

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Marker-trait association study for root-related traits in chickpea (Cicer arietinum L.)

Acta agriculturae Slovenica ◽

10.14720/aas.2021.117.1.2167 ◽

2021 ◽

Vol 117 (3) ◽

pp. 1

Author(s):

Zahra SHEKARI ◽

Zahra TAHMASEBI ◽

Homayoun KANOUNI ◽

Ali ashraf MEHRABI

Keyword(s):

Cicer Arietinum ◽

Ssr Markers ◽

Agronomic Traits ◽

Nutrient Deficiency ◽

Root Traits ◽

Root Structure ◽

Structure Modification ◽

Linkage Groups ◽

Research Findings ◽

Simple Sequence

Root structure modification can improve important agronomic traits including yield, drought tolerance and nutrient deficiency resistance. The aim of the present study was to investigate the diversity of root traits and to find simple sequence repeat (SSR) markers linked to root traits in chickpea (Cicer arietinum L.). This research was performed using 39 diverse accessions of chickpea. The results showed that there is significant variation in root traits among chickpea genotypes. A total of 26 alleles were detected 26 polymorphic bands were produced by 10 SSR markers in the eight linkage groups (LG). The results indicated that there is substantial variability present in chickpea germplasm for root traits. By analyzing the population structure, four subpopulations were identified. PsAS2, AF016458, 16549 and 19075 SSR markers on LG1, LG3, LG2 and LG1 linkage group respectively were associated with root traits. The research findings provide valuable information for improving root traits for chickpea breeders.

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