Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Research Project Solanaceae'de kıyaslamalı genom analizleri: model sistem olarak patlıcan (Solanum melongena L.)(2010) Doğanlar, Sami; Mutlu, Sevgi; Frary, Anne; Eanes, Ritchie C.; Daunay, Marie ChristineKıyaslamalı genom analizleri aynı ailenin değişik türleri arasındaki gen ve genomların yapısını ve fonksiyonlarındaki benzerlikleri ve farklılıkları incelemektedir. Esas olarak kıyaslamalı genomiks (1) her türdeki her bir genin rolünü, (2) bir türü diğer bir türden (örneğin fenotipik, büyüme şekli ve çevreye adaptasyon gibi) ayırmadaki önemli değişikliklerin ne olduğunu ve (3) bu değişikliklerin nasıl oluştuğunu (evrimsel işlemleri) araştırmaktadır. Son yirmi yıllık süre içerinde değişik bitki taxa’larında yapılan kıyaslamalı genom analizleri sonucunda, 130-240 milyon yıl süren angiospem evrimi sonrası ortaya çıkan morfolojik, gelişim ve biyokimyasal seviyelerdeki son derece dramatik değişikliklere rağmen, çok değişik bitki türlerinin gen içerikleri ve kromozom boyunca gen sıralarının korunduğu ortaya konmuştur. Dolayısıyla, heterologous DNA markörlerinin ve hatta sekanz bilgilerinin akraba türler arasında kullanımı mümkündür. Türler arasındaki genom bilgilerinin birbirine çevirebilme yeteneği minor öneme sahip çok sayıda diğer bitki türlerinde de genom analizlerini hızlandırmıştır.Article Citation - WoS: 18Citation - Scopus: 18High 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, AnneA 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: 54Citation - Scopus: 61Qtl Hotspots in Eggplant (solanum Melongena) Detected With a High Resolution Map and Cim Analysis(Springer Verlag, 2014) Frary, Amy; Frary, Anne; Daunay, Marie Christine; Huvenaars, Koen; Mank, Rolf; Doğanlar, SamiFifty-eight F2 individuals derived from an interspecific cross between cultivated eggplant, Solanum melongena, and its wild relative, S. linnaeanum, were phenotyped for 42 plant, leaf, flower, and fruit traits. Composite interval mapping analysis using genotypic data from 736 molecular markers revealed the positions of 71 statistically significant (P ≤ 0.05) quantitative trait loci (QTL) influencing 32 of the morphological traits. Although most QTL were location-specific, QTL governing three traits (leaf lobing, leaf prickles and prickle anthocyanin) were detected in both experimental locations. Analysis of three additional traits (stem prickles, fruit calyx prickles and fruit length) in both locations yielded QTL in similar but non-overlapping map positions. The majority (69 %) of the QTL corresponded closely with those detected in previous analyses of this data set. However the increased resolution of the linkage map combined with advances in QTL mapping permitted more precise localization, such that the average interval length of these QTL was reduced by 93 %. Thirty-one percent of the QTL were novel, suggesting that simple linear regression with a low density linkage map (the method used in previous studies of this population) missed a substantial portion of significant QTL. Hotspots of QTL affecting plant hairiness, prickliness, and pigmentation were identified on chromosomes 3, 6, and 10, respectively, and may reflect the pleiotropic activity of single structural or regulatory genes at these positions. Based on synteny between the eggplant, tomato, potato and pepper genomes, putative orthologs were identified for 35 % of the QTL suggesting strong conservation of gene function within the Solanaceae. These results should make it easier to target particular loci for map-based cloning and marker-assisted selection studies.Article Citation - WoS: 71Citation - Scopus: 86Genetic Mapping of a Major Dominant Gene for Resistance To Ralstonia Solanacearum in Eggplant(Springer Verlag, 2013) Lebeau, A.; Gouy, M.; Daunay, Marie Christine; Wicker, E.; Chiroleu, F.; Prior, P.; Frary, Anne; Dintinger, J.Resistance of eggplant against Ralstonia solanacearum phylotype I strains was assessed in a F6 population of recombinant inbred lines (RILs) derived from a intra-specific cross between S. melongena MM738 (susceptible) and AG91-25 (resistant). Resistance traits were determined as disease score, percentage of wilted plants, and stem-based bacterial colonization index, as assessed in greenhouse experiments conducted in Réunion Island, France. The AG91-25 resistance was highly efficient toward strains CMR134, PSS366 and GMI1000, but only partial toward the highly virulent strain PSS4. The partial resistance found against PSS4 was overcome under high inoculation pressure, with heritability estimates from 0. 28 to 0. 53, depending on the traits and season. A genetic map was built with 119 AFLP, SSR and SRAP markers positioned on 18 linkage groups (LG), for a total length of 884 cM, and used for quantitative trait loci (QTL) analysis. A major dominant gene, named ERs1, controlled the resistance to strains CMR134, PSS366, and GMI1000. Against strain PSS4, this gene was not detected, but a significant QTL involved in delay of disease progress was detected on another LG. The possible use of the major resistance gene ERs1 in marker-assisted selection and the prospects offered for academic studies of a possible gene for gene system controlling resistance to bacterial wilt in solanaceous plants are discussed.Article Citation - WoS: 25Citation - Scopus: 25Application of Est-Ssrs To Examine Genetic Diversity in Eggplant and Its Close Relatives(TUBITAK, 2011) Tümbilen, Yeliz; Frary, Anne; Daunay, Marie Christine; Doğanlar, SamiWithin the genus Solanum, the term 'eggplant' encompasses several cultivated species that are used for food and, to a lesser extent, for medicine. Th e use of one common name to describe more than one species and the existence of many related wild species have led to taxonomic confusion which, in turn, have complicated analyses of evolutionary relationships and genetic diversity within this groups of species. A further challenge for eggplant research is that, despite the fact that the use of molecular markers for phylogenetic studies is well-established, very few studies have described the development of new markers for eggplant. In our work, genic microsatellite (SSR) markers were identified from an expressed sequence tag library of S. melongena and used for analysis of 47 accessions of eggplant and closely related species. Th e markers had very good polymorphism in the 18 species tested including 8 S. melongena accessions. Moreover, genetic analysis performed with these markers showed concordance with previous research and knowledge of eggplant domestication. Th ese markers are expected to be a valuable resource for studies of genetic relationships, fingerprinting, and gene mapping in eggplant.