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    Construction of new EST-SSRs for Fusarium resistant wheat breeding
    (Elsevier Sci Ltd, 2017) Yumurtaci, Aysen; Sipahi, Hulya; Al-Abdallat, Ayed; Jighly, Abdulqader; Baum, Michael
    Surveying Fusarium resistance in wheat with easy applicable molecular markers such as simple sequence repeats (SSRs) is a prerequest for molecular breeding. Expressed sequence tags (ESTs) are one of the main sources for development of new SSR candidates. Therefore, 18.292 publicly available wheat ESTs were mined and genotyping of newly developed 55 EST-SSR derived primer pairs produced clear fragments in ten wheat cultivars carrying different levels of Fusarium resistance. Among the proved markers, 23 polymorphic EST-SSRs were obtained and related alleles were mostly found on B and D genome. Based on the fragment profiling and similarity analysis, a 327 bp amplicon, which was a product of contig 1207 (chromosome 5BL), was detected only in Fusarium head blight (FHB) resistant cultivars (CM82036 and Sumai) and the amino acid sequences showed a similarity to pathogen related proteins. Another FHB resistance related EST-SSR, Contig 556 (chromosome 1BL) produced a 151 bp fragment in Sumai and was associated to wax2-like protein. A polymorphic 204 bp fragment, derived from Contig 578 (chromosome 1DL), was generated from root rot (FRR) resistant cultivars (2-49; Altay2000 and Sunco). A total of 98 alleles were displayed with an average of 1.8 alleles per locus and the polymorphic information content (PIC) ranged from 0.11 to 0.78. Dendrogram tree with two main and five sub-groups were displayed the highest genetic relationship between FRR resistant cultivars (2-49 and Altay2000), FRR sensitive cultivars (Seri82 and Scout66) and FHB resistant cultivars (CM82036 and Sumai). Thus, exploitation of these candidate EST-SSRs may help to genotype other wheat sources for Fusarium resistance. (C) 2017 Elsevier Ltd. All rights reserved.
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    DEVELOPMENT AND CHARACTERIZATION OF SSR MARKERS FROM FUSARIUM INFECTED BARLEY (HORDEUM VULGARE) CDNA DATA SETS
    (Parlar Scientific Publications (P S P), 2016) Sipahi, Hulya; Yumurtaci, Aysen; Hekimhan, Hakan
    In this study, a collection of 6666 expressed sequence tags (ESTs) deriving from two cDNA libraries (9841 and 24112) constructed under Fusarium infected conditions in Hordeum vulgare were screened to detect and characterize simple sequence repeat (SSR) motifs. Ninety-seven SSRs were identified in ESTs. Trinucleotides were the most frequent repeat (51%), followed by dinucleotides (38%) and tetranucleotides (8%), whereas motif size of pentanucleotides and hexanucleotides was only 1% and 4%, respectively, which is rarely found. Forty-nine SSR-containing EST unigenes were matched with Hordeum vulgare known protein with putative conserved domain via BLASTX. Out of 49 EST-SSRs, 33 of them were successfully used to design primer pairs and further confirmed in seven cultivated barley with significant differences in responses to Fusarium related root rot and head blight diseases. Nineteen of them gave amplification products. A total of 26 alleles were generated from 19 loci. The polymorphic information content (PIC) ranged from 0.28 to 0.60 and the expected heterozygosity (He) varied from 0.22 to 0.61. The seven cultivars were divided into three groups based on 19 SSR markers. These novel EST-SSR markers can be applied for genetic analysis, including marker-assisted selection for fusarium related diseases in barley breeding and genetic diversity analysis.
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    Genetic analysis of microsatellite markers for salt stress in two contrasting maize parental lines and their RIL population
    (Univ Zagreb, Fac Science, Div Biology, 2017) Yumurtaci, Aysen; Sipahi, Hulya; Zhao, Li
    Salt stress considerably hinders the growth and productivity of maize (Zea mays L.). Identifi cation of salt tolerant genotypes and integration of alternative molecular markers have important roles in enhancing breeding processes. In this study, 3308 maize expressed sequence tags (ESTs) from salt stress-related libraries were assembled to mine repetitive sequences for development of applicable markers. In this core EST data, 208 simple and 18 non-simple repetitive regions were detected in 312 contigs and 1121 singletons. The di-nucleotide repeats were the most abundant type and accounted for 79.3%, followed by tri (19.7%), and tetra-nucleotide (1%). Among 59 EST-simple sequence repeats (SSRs), a total of 55 were screened for polymorphism between F35 (salt sensitive) and F63 (salt tolerant) parents and 48 out of 55 were detected as monomorphic. Signifi cantly, seven of them (12.7%) were found to be polymorphic and were used for genotyping of 158 F5 derived recombinant inbred maize lines, and four of them were located on chromosome 1 and 3. Using in silico mapping, 44 out of 59 EST-SSR markers were mapped on 10 maize chromosomes. Analysis of sequence homology revealed different functional groups such as: membrane transport, cell defense, cell division, signaling components, photosynthesis and cell metabolism. These EST-SSRs might be used as new functional molecular markers in the diversity analysis, identifi cation of quantitative trait loci (QTLs) and comparative genomic studies in maize in the future.
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    Genetic diversity within Scorpio maurus (Scorpiones: Scorpionidae) from Turkey
    (Univ Oradea Publ House, 2017) Koc, Halil; Sipahi, Hulya; Yagmur, Ersen Aydin
    In this study, DNA sequence diversity of the mitochondrial (mt) cytochrome oxidase 1 (CO1) gene was investigated in Scorpio maurus specimens from across southeastern Turkey. Nucleotide sequences included 508 conserved sites and 126 variable sites, and the mean nucleotide variation within species was 7.9%. Intraspecific pairwise divergences ranged from 0.5% to 10.7%. Phylogenetic analysis indicated high divergence among specimens. This study is the first mtDNA sequence analysis for Turkish scorpions.