Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik

Permanent URI for this collectionhttps://hdl.handle.net/11147/9

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Publisher: search.filters.publisher.Springer VerlagSubject: search.filters.subject.Molecular markers

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Now showing 1 - 4 of 4
  • Article
    Citation - WoS: 30
    Citation - Scopus: 34
    Gddom: an Online Tool for Calculation of Dominant Marker Gene Diversity
    (Springer Verlag, 2017) Abuzayed, Mazen; El-Dabba, Nourhan; Frary, Anne; Doğanlar, Sami
    Gene diversity (GD), also called polymorphism information content, is a commonly used measure of molecular marker polymorphism. Calculation of GD for dominant markers such as AFLP, RAPD, and multilocus SSRs is valuable for researchers. To meet this need, we developed a free online computer program, GDdom, which provides easy, quick, and accurate calculation of dominant marker GD with a commonly used formula. Results are presented in tabular form for quick interpretation. © 2016, Springer Science+Business Media New York.
  • Article
    Citation - WoS: 21
    Citation - Scopus: 23
    High-Throughput Single Nucleotide Polymorphism (snp) Identification and Mapping in the Sesame (sesamum Indicum L.) Genome With Genotyping by Sequencing (gbs) Analysis
    (Springer Verlag, 2016) Uncu, Ayşe Özgür; Frary, Anne; Karlovsky, Petr; Doğanlar, Sami
    Sesame (Sesamum indicum L. syn. Sesamum orientale L.) is considered to be the first oil seed crop known to man. Despite its versatile use as an oil seed and a leafy vegetable, sesame is a neglected crop and has not been a subject of molecular genetic research until the last decade. There is thus limited knowledge regarding genome-specific molecular markers that are indispensible for germplasm enhancement, gene identification, and marker-assisted breeding in sesame. In this study, we employed a genotyping by sequencing (GBS) approach to a sesame recombinant inbred line (RIL) population for high-throughput single nucleotide polymorphism (SNP) identification and genotyping. A total of 15,521 SNPs were identified with 14,786 SNPs (95.26 %) located along sesame genome assembly pseudomolecules. By incorporating sesame-specific simple sequence repeat (SSR) markers developed in our previous work, 230.73 megabases (99 %) of sequence from the genome assembly were saturated with markers. This large number of markers will be available for sesame geneticists as a resource for candidate polymorphisms located along the physical chromosomes of sesame. Defining SNP loci in genome assembly sequences provides the flexibility to utilize any genotyping strategy to survey any sesame population. SNPs selected through a high stringency filtering protocol (770 SNPs) for improved map accuracy were used in conjunction with SSR markers (50 SSRs) in linkage analysis, resulting in 13 linkage groups that encompass a total genetic distance of 914 cM with 432 markers (420 SNPs, 12 SSRs). The genetic linkage map constitutes the basis for future work that will involve quantitative trait locus (QTL) analyses of metabolic and agronomic traits in the segregating RIL population.
  • Article
    Citation - WoS: 18
    Citation - Scopus: 18
    High Resolution Map of Eggplant (solanum Melongena) Reveals Extensive Chromosome Rearrangement in Domesticated Members of the Solanaceae
    (Springer Verlag, 2014) Doğanlar, Sami; Frary, Amy; Daunay, Marie Christine; Huvenaars, Koen H J; Mank, Rolf A.; Frary, Anne
    A linkage map of eggplant was constructed for an interspecific F2 population derived from a cross between Solanum linnaeanum MM195 and S. melongena MM738. The map contains 400 AFLP® (amplified fragment length polymorphism), 348 RFLP (restriction fragment length polymorphism) and 116 COSII (conserved ortholog set) markers. The 864 mapped markers encompass 12 linkage groups, span 1,518 cM and are spaced at an average interval of 1.8 cM. Use of orthologous markers allowed confirmation of the established syntenic relationships between eggplant and tomato chromosomes and helped delineate the nature of the 33 chromosomal rearrangements and 11 transpositions distinguishing the two species. This genetic map provides a 2- to 3-fold improvement in marker density compared to previously published interspecific maps. Because the interspecific mapping population is rich in morphological variation, this greater genome saturation will be useful for QTL (quantitative trait locus) analyses. The recent release of the tomato genome sequence will provide additional opportunities for exploiting this map for comparative genomics and crop improvement.
  • Article
    Citation - WoS: 64
    Citation - Scopus: 82
    Advanced Backcross Qtl Analysis of a Lycopersicon Esculentum X L. Pennellii Cross and Identification of Possible Orthologs in the Solanaceae
    (Springer Verlag, 2004) Frary, Anne; Fulton, Theresa M.; Zamir, Dani; Tanksley, Steven D.
    In this study, the advanced backcross QTL (AB-QTL) mapping strategy was used to identify loci for yield, processing and fruit quality traits in a population derived from the interspecific cross Lycopersicon esculentum E6203 x Lycopersicon pennellii accession LA1657. A total of 175 BC2 plants were genotyped with 150 molecular markers and BC2F1 plots were grown and phenotyped for 25 traits in three locations in Israel and California, U.S.A. A total of 84 different QTLs were identified, 45% of which have been possibly identified in other wild-species-derived populations of tomato. Moreover, three fruit-weight/size and shape QTLs (fs2b.1, fw3.1/fsz3.1 andfs8.1) appear to have putative orthologs in the related solanaceous species, pepper and eggplant. For the 23 traits for which allelic effects could be deemed as favorable or unfavorable, 26% of the identified loci had L. pennellii alleles that enhanced the performance of the elite parent. Alleles that could be targeted for further introgression into cultivated tomato were also identified.