Simple sequence repeats in watermelon (Citrullus lanatus (Thunb.) Matsum. &Nakai)

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 433-441 ◽  
Author(s):  
R. L. Jarret ◽  
L. C. Merrick ◽  
T. Holms ◽  
J. Evans ◽  
M. K. Aradhya
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeats ◽  
Genetic Relatedness ◽  
Genomic Library ◽  
Citrullus Lanatus ◽  
Dinucleotide Repeats ◽  
Length Polymorphisms ◽  
Ssr Loci ◽  
Diversity Studies ◽  
Simple Sequence

Simple sequence repeat length polymorphisms were utilized to examine genetic relatedness among accessions of watermelon (Citrullus lanatus (Thunb.) Matsum. &Nakai). A size-fractionated TaqI genomic library was screened for the occurrence of dimer and trimer simple sequence repeats (SSRs). A total of 96 (0.53%) SSR-bearing clones were identified and the inserts from 50 of these were sequenced. The dinucleotide repeats (CT)n and (GA)n accounted for 82% of the SSRs sequenced. PCR primer pairs flanking seven SSR loci were used to amplify SSRs from 32 morphologically variable watermelon genotypes from Africa, Europe, Asia, and Mexico and a single accession of Citrullus colocynthis from Chad. Cluster analysis of SSR length polymorphisms delineated 4 groups at the 25% level of genetic similarity. The largest group contained C. lanatus var. lanatus accessions. The second largest group contained only wild and cultivated "citron"-type or C. lanatus var. citroides accessions. The third group contained an accession tentatively identified as C. lanatus var. lanatus but which perhaps is a hybrid between C. lanatus var. lanatus and C. lanatus var. citroides. The fourth group consisted of a single accession identified as C. colocynthis. "Egusi"-type watermelons from Nigeria grouped with C. lanatus var. lanatus. The use of SSRs for watermelon germplasm characterization and genetic diversity studies is discussed.Key words: Citrullus, watermelon, simple sequence repeats, genetic diversity.

scholarly journals Genome Wide Characterization, Comparative and Genetic Diversity Analysis of Simple Sequence Repeats in Cucurbita Species

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 143
Author(s):  
Lei Zhu ◽  
Huayu Zhu ◽  
Yanman Li ◽  
Yong Wang ◽  
Xiangbin Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Group Method ◽  
Motif Length ◽  
Pair Group ◽  
Ssr Loci ◽  
Ssr Frequency ◽  
Basic And Applied Research ◽  
Simple Sequence

Simple sequence repeats (SSRs) are widely used in mapping constructions and comparative and genetic diversity analyses. Here, 103,056 SSR loci were found in Cucurbita species by in silico PCR. In general, the frequency of these SSRs decreased with the increase in the motif length, and di-nucleotide motifs were the most common type. For the same repeat types, the SSR frequency decreased sharply with the increase in the repeat number. The majority of the SSR loci were suitable for marker development (84.75% in Cucurbita moschata, 94.53% in Cucurbita maxima, and 95.09% in Cucurbita pepo). Using these markers, the cross-species transferable SSR markers between C. pepo and other Cucurbitaceae species were developed, and the complicated mosaic relationships among them were analyzed. Especially, the main syntenic relationships between C. pepo and C. moschata or C. maxima indicated that the chromosomes in the Cucurbita genomes were highly conserved during evolution. Furthermore, 66 core SSR markers were selected to measure the genetic diversity in 61 C. pepo germplasms, and they were divided into two groups by structure and unweighted pair group method with arithmetic analysis. These results will promote the utilization of SSRs in basic and applied research of Cucurbita species.

scholarly journals Simple Sequence Repeat Marker Analysis of Genetic Relationships within Hydrangea macrophylla

2007 ◽  
Vol 132 (3) ◽  
pp. 341-351 ◽  
Author(s):  
Sandra M. Reed ◽  
Timothy A. Rinehart
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Allelic Diversity ◽  
Sequence Repeat ◽  
Hydrangea Macrophylla ◽  
Total Genetic Diversity ◽  
Ssr Loci ◽  
Diversity Studies ◽  
Simple Sequence

Genetic diversity studies using 39 simple-sequence repeat (SSR) markers were carried out with 114 taxa of Hydrangea macrophylla (Thunb.) Ser., including 87 H. macrophylla ssp. macrophylla cultivars and 20 members of H. macrophylla ssp. serrata (Thunb.) Makino. The SSR loci were highly variable among the taxa, producing a mean of 8.26 alleles per locus. Overall allelic richness was relatively high at 5.12 alleles per locus. H. macrophylla ssp. serrata contained nearly twice the allelic diversity of H. macrophylla ssp. macrophylla. The majority of genetic diversity was found to reside within the subspecies, with only 12% of the total genetic diversity observed occurring between subspecies. Although the elevation of H. macrophylla ssp. serrata to species level has recently been recommended by several hydrangea authorities, these data support the subspecies designation. Four cultivars (Preziosa, Pink Beauty, Tokyo Delight, and Blue Deckle) appeared to be hybrids between the two subspecies. Genetic similarities were found among five remontant cultivars (Bailmer, Oak Hill, David Ramsey, Decatur Blue, and Penny Mac) and several nonremontant cultivars, including General Vicomtesse de Vibraye, Nikko Blue, All Summer Beauty, and La France. No close genetic relationship was found between the remontant cultivar Early Sensation and other remontant cultivars. Genetic similarities were found among variegated and double-flower cultivars. Within H. macrophylla ssp. macrophylla, cultivars with mophead inflorescences clustered separately from most lacecap cultivars. This indicates the cultivars with lacecap inflorescences that were among some of the earliest introductions to Europe were not widely used in the breeding of mophead forms. Some presumed synonyms were found to be valid (‘Preziosa’ and ‘Pink Beauty’, ‘Rosalba’ and ‘Benigaku’, ‘Geoffrey Chadbund’ and ‘Mowe’), whereas others were not (‘Harlequin’ and ‘Monrey’, ‘Nigra’ and ‘Mandschurica’). This study identified potentially unexploited sources of germplasm within H. macrophylla and relationships between existing cultivars of this popular shrub. This information should be of value when selecting parents for breeding programs.

scholarly journals Genome Wide Characterization and Comparative Analysis of Simple Sequence Repeats in Cucurbita Genomes

2020 ◽  
Author(s):  
Lei Zhu ◽  
Hua yu Zhu ◽  
Yan man Li ◽  
Xiang bin Wu ◽  
Jin tao Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Comparative Genomics ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Diversity Analysis ◽  
Motif Length ◽  
Genetic Diversity Analysis ◽  
Genome Wide ◽  
Ssr Loci ◽  
Simple Sequence

Abstract Background The Cucurbita genus contains important economic crops in the world, while limited molecular markers have been developed in the past years. Simple sequence repeats (SSR) markers are powerful tools for the study of genetic mapping construction, genetic diversity analysis and genome wide association. The availability of pumpkin genome information has made it possible to analyze SSRs in genome wide across three Cucurbita species. Results In this paper, based on the whole genome sequences, 34,375 SSR loci were found in C. moschata, 30,577 SSR loci were found in C. maxima and 38,104 SSR loci were found in C. pepo. C. pepo has the maximum density of SSRs with an average of 145 SSR/Mb. In general, the frequency in total SSR loci decreased with the increase of the motif length, dinucleotide motifs were the most common motifs in the three species, and for the same repeat types, the SSR frequency decreased sharply with the increase of the repeat number. Most of those SSR loci were suitable for marker development (84.75% in C. moscata, 94.53% in C. maxima and 95.09% in C. pepo). Based on those markers, we compared and analyzed the cross-species SSR markers between C. pepo and other Cucurbitaceae species by silico-PCR. Using these cross-species primers, the high collinear relationships between C. pepo and the other two species were detected, respectively. Furthermore, the application of SSR markers in genetic diversity analysis was tested in C. pepo, the results showed that they were good tools to be used in genetic diversity analysis. Conclusion In this study, the genome wide SSR markers were detected from three Cucurbita species, and some of their applications were proved by comparative genomics and genetic diversity analysis. The large number of genome-wide SSR markers and crossspecies markers would promote the basic and applied studies of Cucurbita species, such as gene mapping, QTLs mapping, comparative genomics and marker-assisted breeding.

scholarly journals Simple Sequence Repeats (SSRs) in Watermelon (Citrullus lanatus L.)

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 840E-840
Author(s):  
R.L. Jarret ◽  
S. Kresovich ◽  
T. Holms ◽  
Janelle Evans ◽  
Z. Liu
Keyword(s):  
New Hampshire ◽  
Simple Sequence Repeats ◽  
Genomic Dna ◽  
Citrullus Lanatus ◽  
Germplasm Characterization ◽  
Dna Library ◽  
Automated Dna Sequencing ◽  
Ssr Loci ◽  
Genomic Dna Library ◽  
Simple Sequence

Simple sequence repeats (SSRs) were isolated from a size-fractionated genomic DNA library of watermelon (Citrullus lanatus L. cv. New Hampshire Midget). Screening of the library with five oligonucleotide probes, including (GT)11, (AT)11, (CT)11, (GC)11, and (TAA)8, detected the occurrence of 96 positive colonies among ≈8000 recombinants. Automated DNA sequencing revealed the presence of SSRs. PCR primer pairs homologous to the regions flanking the SSR loci were synthesized commercially and used to screen 56 watermelon genotypes for the occurrence of SSR polymorphisms. Amplification products were separated using nondenaturing PAGE. Eighty percent of the primer pairs produced amplification products of the expected size and detected polymorphisms among the genotypes examined. The use of SSRs for watermelon germplasm characterization is discussed.

scholarly journals Simple Sequence Repeat and S-Locus Genotyping to Assist the Genetic Characterization and Breeding of Polyploid Prunus Species, P. spinosa and P. domestica subsp. insititia

2021 ◽  
Author(s):  
Júlia Halász ◽  
Noémi Makovics-Zsohár ◽  
Ferenc Szőke ◽  
Sezai Ercisli ◽  
Attila Hegedűs
Keyword(s):  
Simple Sequence Repeat ◽  
Principal Component ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Allele Number ◽  
Genetic Potential ◽  
Ssr Loci ◽  
High Level ◽  
Diversity Studies ◽  
Simple Sequence

AbstractPolyploid Prunus spinosa (2n = 4 ×) and P. domestica subsp. insititia (2n = 6 ×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programs. In Hungary, 16 cultivar candidates and a recognized cultivar ‘Zempléni’ were selected from wild-growing populations including ten P. spinosa, four P. domestica subsp. insititia and three P. spinosa × P. domestica hybrids (2n = 5 ×) were also created. Genotyping in eleven simple sequence repeat (SSR) loci and the multiallelic S-locus was used to characterize genetic variability and achieve a reliable identification of tested accessions. Nine SSR loci proved to be polymorphic and eight of those were highly informative (PIC values ˃ 0.7). A total of 129 SSR alleles were identified, which means 14.3 average allele number per locus and all accessions but two clones could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified and the complete and partial S-genotype was determined for 10 and 7 accessions, respectively. The DNA sequence was determined for a total of 17 fragments representing 11 S-RNase alleles. ‘Zempléni’ was confirmed to be self-compatible carrying at least one non-functional S-RNase allele (SJ). Our results indicate that the S-allele pools of wild-growing P. spinosa and P. domestica subsp. insititia are overlapping in Hungary. Phylogenetic and principal component analyses confirmed the high level of diversity and genetic differentiation present within the analysed accessions and indicated putative ancestor–descendant relationships. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species but non-related accessions sharing common S-alleles may distort phylogenetic inferences.

scholarly journals The new use of Sorghum bicolor-derived SSR markers to evaluate genetic diversity in 17 Australian Sorghum species

2005 ◽  
Vol 3 (1) ◽  
pp. 19-28 ◽  
Author(s):  
Sally L. Dillon ◽  
Peter K. Lawrence ◽  
Robert J. Henry
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Ssr Markers ◽  
Diversity Indices ◽  
Basic Knowledge ◽  
Apparent Lack ◽  
Breeding Programmes ◽  
Diversity Studies ◽  
Potential Use ◽  
Simple Sequence

The Sorghum genus is extremely diverse both morphologically and geographically, however, relatively few of the 25 recognized species have been evaluated genetically. The apparent lack of basic knowledge pertaining to the levels of genetic diversity both within and between the 17 Australian wild species is a major obstacle to both their effective conservation and potential use in breeding programmes. Twelve Sorghum bicolor-derived simple sequence repeat (SSR) markers were evaluated for cross-species amplification in all 25 Sorghum species. The SSR markers were highly polymorphic, with diversity indices ranging from 0.59 to 0.99 with mean of 0.91. Five markers combined were able to differentiate 24 of the 25 Sorghum species, with intra-species polymorphism apparent. Sorghum bicolor-derived SSRs have proven to be an efficient source of markers for genetic diversity studies of the relatively poorly characterized Australian indigenous Sorghum species.

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