Phylogenetic Analysis and Lipoxygenase (LOX) Gene Family Variation in The Pistachio

Lipoxygenases (LOX) gene family is a type of nonheme iron-containing dioxygenases, which has a very important aspect in plant development and fruit quality. LOX gene, which is responsible for lipid oxidation, the main role for the biosynthesis pathway of unsaturated fatty acids. Although some studies have investigated the LOX gene family in several species including arabidopsis, soybean, peanut and apple, there is no information from Pistachio; and the phylogeny of this gene family in the Pistacia genus is still not determined. In this study, Arabidopsis thaliana LOX1 gene (NCBI Reference Sequence: NM_104376.3) was selected and used as a query sequence for performing a BLASTN search. Among all sequence query which was found by NCBI platform, 9 sequences were selected for further analysis. Phylogenetic tree of full-length LOX gene sequences from the Pistacia genus was constructed using the Maximum Likelihood method with MEGA software. By using phylogenic analysis, we identified variations in gene structure and revealed the phylogenetic evolutionary relationship of this gene family. Additionally, this may serve as a reference value for assessing the genetic relationships among various LOX genes in Pistacia genus species. This variations provides us the possibility the design the primer to achieve us to find the exact LOX gene in Pistacia genus and future research on the evolutionary history and transgenic research on LOX genes

Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species

Genetic diversity measures in P. terebinthus: allele ranges, number of alleles (Na), number of effective alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), and PIC values of 119 polymorphic SSR loci. (DOCX 38 kb

Yeni nesil sekanslama teknolojisi kullanılarak Pistacia türlerınde SSR markörlerın geliştirilmesi ve türlerarası F1 populasyonu kullanılarak genetik haritalama ve QTL analizleri.

TEZ13041Tez (Doktora) -- Çukurova Üniversitesi, Adana, 2017.Kaynakça (s. 183-200) var., 239 s. :_res. (bzs. rnk.), tablo ;_29 cm.Antepfıstığı (Pistacia vera L.), dünya sert kabuklu meyve üretimi içerisinde önemli bir yere sahiptir. Pistacia cinsi Anacardiaceae familyasının bir üyesi olup içerisinde on birden fazla tür bulunmaktadır. Antepfıstığının genom yapısını belirlemek için yeni nesil sekanslama teknolojisi kullanılarak P. vera’nın Siirt çeşidinde yaklaşık 40 kat yoğunluklu sekanslama yapılmış ve genomun bütünüyle ilgili bilgiler ortaya çıkarılmıştır. Sekanslama sonucunda toplam 26.77 Gb sekans verilerinin birleştirilmesi ile 27.069 adet dizi N50 = 3.4 kb olacak şekilde elde edilmiştir. Bunlar içerisinden 59.280 SSR motifi elde edilmiş ve 8.67 kb’de bir SSR tekrar dizisine rastlanmıştır. Toplam 206 SSR lokusu Pistacia vera’ya ait 24 adet antepfıstığı çeşidi ve 20 yabani Pistacia genotipini karakterize etmek amacıyla kullanılmıştır. Genetik haritalama çalışması Siirt x Pa-18 (monoik atlantik sakızı) F1 populasyonu kullanılarak yapılmıştır. Gerek bu çalışmada gerekse önce yapılan çalışmalarda geliştirilen SSR markörleri kullanılarak toplamda 388 SSR markörü 15 genetik bağlantı grubunda haritalanmıştır. Harita uzunluğu 1.492 cM ve her bir bağlantı grubuna düşen ortalama markör sayısı 3.7 cM olarak hesaplanmıştır. F1 bitkileri 2015 ve 2016 yıllarında yaprak uzunluğu, yaprak genişliği, yaprakçık çifti sayısı, yaprak rengi ve bir yıllık sürgün rengi bakımından karakterize edilmişlerdir. Yapılan QTL analizleri sonucunda yaprak ve sürgün özellikleri ile bağlantılı 17 adet QTL belirlenmiştir.Pistachio (Pistacia vera L.) is one of the most important nut crops in the world. There are about 11 wild species in the genus Pistacia. Genome survey sequences of pistachio was obtained at 40x depth by next generation sequencing to understand genome structure. The assembly of 26.77 Gb Illumina data produced 27,069 scaffolds in the P. vera cv. Siirt genome. A total of 59,280 SSR motifs were detected with a frequency of 8.67 kb. A total of 206 SSRs were used to characterize 24 pistachio cultivars and 20 wild Pistacia genotypes. The novel SSR loci developed from cultivated pistachio were highly transferable to wild Pistacia species. The SSR-based genetic linkage map was constructed using an inter-specific F1 population derived from P. vera L. ‘Siirt’ and monoecious Pistacia atlantica Desf. (Pa-18 genotype). A total of 388 SSR markers were mapped. The length of consensus map was 1,492 cM along with 15 linkage groups with an average marker distance of 3.7 cM. Sex-linked markers in the literature were also mapped with the SSR markers in LG1. Phenotypic data were collected during 2015 and 2016 growing season for five traits: leaf length (LL), leaf width (LW), number of leaflet (NLF), young shoot color (YSC), and leaf color (LC). QTL analysis were performed for the five traits using the the ‘Siirt’ and ‘Pa-18’ SSR-based genetic maps and 17 QTLs were identified. The novel SSR markers, linkage maps, and QTLs reported in this study will be useful resources for future genetic linkage maps and QTL analysis, and for identification of important genes in Pistacia as well as genome sequencing projects.This thesis was financially supported by The Scientific and Technological Research Council of Turkey (Project No: TUBITAK-TOVAG 113 O 962) and University of Çukurova Scientific Research Projects Unit (Project No: FUK-2014-2637, FDK-22015-3642

Construction of dense genetic linkage maps of apple cultivars Kasel-41 and Williams' Pride by simple sequence repeat markers

WOS: 000363554800013Almost all commercially grown apple cultivars in Turkey are exotic, with local varieties serving as important genetic resources for breeding and marker development purposes. Among the latter is Amasya, which has a pleasing taste and flavor, but is unsuitable for commercial use because of its small fruit size and alternate-bearing characteristics. Genetic maps of apple cultivars are important resources to facilitate marker-assisted selection. Because of its good eating quality, Amasya is a good genetic resource for marker development to enhance fruit quality, especially flavor. In this study, we constructed a simple sequence repeat (SSR) marker-based genetic map of the Amasya apple cultivar using 96 F1 progenies generated from a cross between Kasel-41 (a selection from Amasya) and Williams' Pride cultivars. Of 187 bacterial artificial chromosome SSRs, 150 expressed sequence tag SSRs, and of 362 genomic SSR primer pairs, 400 markers were mapped, with parental and consensus maps constructed independently. A reference map was also constructed using 207 common SSR markers, thereby producing the most dense SSR-based reference map currently reported for apple. The reference genetic map was 1351 cM long, with a mean marker density of 6.5 cM. The consensus map obtained by mapping 396 markers had a length of 1476.4 cM and a 3.82-cM mean marker density. We also identified the positions of 57 SSR loci previously unmapped in apple. As a result, once additional markers have been incorporated into the maps to increase saturation, the evaluation of phenotypic traits in the mapping population should facilitate linkage between molecular markers and fruit quality traits. Additionally, the constructed apple reference genetic map, with 207 SSR markers, should also assist the construction of new genetic maps and aid integration of various apple linkage maps.Scientific and Technological Research Council of Turkey (TUBITAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [110O093]; Scientific Research Projects Unit of Cukurova UniversityCukurova University [ZF2012YL4]The authors thank the Scientific and Technological Research Council of Turkey (TUBITAK, Project No. 110O093) and the Scientific Research Projects Unit of Cukurova University (Project No. ZF2012YL4) for financial support

First microsatellite markers for Scaligeria lazica Boiss. (Apiaceae) by next-generation sequencing: population structure and genetic diversity analysis

The Apiaceae family includes a few agronomic and medicinal species, one of which is Scaligeria lazica Boiss. In this study, the genetic diversity of S. lazica was analyzed based on novel simple sequence repeat (SSR) markers using next-generation sequencing (NGS). A total of 15.17G clean Illumina data set was obtained and dinucleotide repeats were the most abundant repeats in S. lazica. Of the tested 150 SSR primer pairs, 139 ones produced amplification and 84 ones were polymorphic. Forty polymorphic SSR loci were used in genetic diversity analysis of 40 S. lazica accessions from four locations. A total of 264 alleles were amplified with an average of 6.6 alleles per locus. The polymorphism information content (PIC) was 0.60, while the observed homozygosity (Ho) and expected heterozygosity (He) values were 0.47 and 0.66, respectively. According to cluster and structure analysis, all accessions were grouped into four different clusters according to their collection sites. The SSR markers developed in this study can be tested for other Scaligeria species due to their high transferability and can be used for genetic studies in genus Scaligeria DC

In vitro PROPOGATION OF Physalis peruviana (L.) USING APICAL SHOOT EXPLANTS

WOS: 000391345700008Physalis peruviana L. is belongs to Solanaceae family and commonly known as Cape gooseberry. More recently it is very popular and widely used as medicinal plant to treat malaria, asthma, hepatitis, dermatitis and rheumatism and has diuretic and antiinflammatory properties. In this study, it was aimed to develop in vitro propagation protocol for P. peruviana L. using apical shoots as an explant sources. Regenerated plants were evaluated based on their multiplication rate and shoot length using various concentration of BAP (1, 2, 3 mg l(-1)) in combination with IBA (0, 0.1, 0.2, 0.4 mg l(-1)) and NAA (0, 0.1, 0.2, 0.4 mg l(-1)). In addition, efficiency of various auxin concentrations of (1 and 2 mg l(-1) IBA and NAA) was also applied on root formation of P. peruviana L. The highest shoot numbers were obtained from 2 mg l(-1) BAP with 0.4 mg l(-1) IBA (6.00) combinations 'and shoot length obtained in 2 mg l(-1) BAP with 0.2 mg 14 IBA combinations (3.30 cm). As for the effects of BAP and NAA combinations; the highest shoot length were obtained from 2 mg l(-1) BAP without NAA combinations (3.33 cm) while the lowest one was in 3 mg l(-1) BAP with 0.4 mg/I NAA combinations. The highest root numbers were obtained from NAA application (2 mg l(-1) and 1 mg l(-1), respectively). In vitro derived plants were acclimatized to the soil smoothly. The present study highlights the importance of plant tissue culture in order to be used for large-scale production of P. peruviana (L.) due to the elimination of sexual propagation

First microsatellite markers for <i>Scaligeria lazica</i> Boiss. (Apiaceae) by next-generation sequencing: population structure and genetic diversity analysis

<p>The Apiaceae family includes a few agronomic and medicinal species, one of which is <i>Scaligeria lazica</i> Boiss. In this study, the genetic diversity of <i>S</i>. <i>lazica</i> was analyzed based on novel simple sequence repeat (SSR) markers using next-generation sequencing (NGS). A total of 15.17G clean Illumina data set was obtained and dinucleotide repeats were the most abundant repeats in <i>S. lazica</i>. Of the tested 150 SSR primer pairs, 139 ones produced amplification and 84 ones were polymorphic. Forty polymorphic SSR loci were used in genetic diversity analysis of 40 <i>S. lazica</i> accessions from four locations. A total of 264 alleles were amplified with an average of 6.6 alleles per locus. The polymorphism information content (PIC) was 0.60, while the observed homozygosity (<i>Ho</i>) and expected heterozygosity (<i>He</i>) values were 0.47 and 0.66, respectively. According to cluster and structure analysis, all accessions were grouped into four different clusters according to their collection sites. The SSR markers developed in this study can be tested for other <i>Scaligeria</i> species due to their high transferability and can be used for genetic studies in genus <i>Scaligeria</i> DC.</p

Construction of a Dense Genetic Linkage Map and Identification of QTLs for Aroma Compounds in the Apple Progeny ‘Kasel-37 X Delbarestivale’

In the focus of the discipline of environmental ethics stands the moral relationship between human beings and the environment. The development of this science was necessary due to the traditional anthropocentrical approach, which provided an excellent moral base for the exploitation of our natural environment. Although nature was the focus of much of nineteenth and twentieth century philosophy, contemporary environmental ethics only emerged as an academic discipline in the 1970s. Basically two main lines can be distinguished: the invidualistic and the holistic approach. The main idea of individualism (biocentric), similarly to traditional anthropocentrical paradigm, is that only individuals can represent value, which must be respected by others. These individuals are not only human beings, but all living being?, because each individual living thing in nature - whether it is an animal, a plant, or a micro-organism - is a ‘teleological-center-of-life’ having a good or well-being of its own which can be enhanced or damaged, and that all individuals who are teleological-centers-of life have equal intrinsic value (or ‘inherent worth’) which entitles them to moral respect. The holistic approach offers a totally different solution by extending the moral concern to the whole biosphere. Hereinafter this article, along with the most popular disciplines of environmental ethics, examines whether non human beings can have legal standing or not.In the focus of the discipline of environmental ethics stands the moral relationship between human beings and the environment. The development of this science was necessary due to the traditional anthropocentrical approach, which provided an excellent moral base for the exploitation of our natural environment. Although nature was the focus of much of nineteenth and twentieth century philosophy, contemporary environmental ethics only emerged as an academic discipline in the 1970s. Basically two main lines can be distinguished: the invidualistic and the holistic approach. The main idea of individualism (biocentric), similarly to traditional anthropocentrical paradigm, is that only individuals can represent value, which must be respected by others. These individuals are not only human beings, but all living being?, because each individual living thing in nature - whether it is an animal, a plant, or a micro-organism - is a ‘teleological-center-of-life’ having a good or well-being of its own which can be enhanced or damaged, and that all individuals who are teleological-centers-of life have equal intrinsic value (or ‘inherent worth’) which entitles them to moral respect. The holistic approach offers a totally different solution by extending the moral concern to the whole biosphere. Hereinafter this article, along with the most popular disciplines of environmental ethics, examines whether non human beings can have legal standing or not