In silico polymorphic novel SSR marker development and the first SSR-based genetic linkage map in pistachio

Simple sequence repeats (SSRs) are co-dominant markers, and are very useful in constructing consensus maps in heterozygous perennial plant species like pistachio. Pistacia vera L. is the only cultivated species in the genus Pistacia. It is dioecious with a haploid chromosome count of n = 15. Saturated genetic linkage maps can be a reference to identify markers linked to economically important phenotypic traits that could be useful for early breeding and selection programs. Therefore, this study aimed to develop polymorphic SSR markers in silico and to construct the first SSR-based genetic linkage map in pistachio. The DNA sequences of three cultivars (Siirt, Ohadi, and Bagyolu) of P. vera and one genotype belonging to P. atlantica (Pa-18) were obtained by next-generation sequencing, and 625 polymorphic SSR loci were identified from 750 screened in silico polymorphic SSR primer pairs. The novel SSRs were used to construct SSR-based genetic linkage maps in pistachio along with published SSRs in Siirt × Bagyolu F1 population. Most (71.4%) of the SSRs were common markers that were used to construct consensus and parental maps spanning 15 linkage groups (LGs). A total of 384, 317, and 341 markers were mapped in the consensus, female, and male genetic maps with total lengths of 1511.3, 1427.0, and 1453.4 cM, respectively. The large number of SSR markers discovered and the first SSR-based genetic linkage map constructed in this study will be useful for anchoring loci for map integration, and will facilitate marker-assisted selection efforts for important horticultural traits in the genus Pistacia. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature.Firat University Scientific Research Projects Management Unit: FDK-2015-3641 Türkiye Bilimsel ve Teknolojik Araştirma Kurumu: TUBITAK-TOVAG-113O962This work was supported by the Scientific and Technological Research Council of Turkey (Project No: TUBITAK-TOVAG-113O962), and the Cukurova University Scientific Research Projects Unit (Project No: FDK-2015-3641). The authors declare that they have no conflict of interest

SSR-based genetic linkage map construction in pistachio using an interspecific F1 population and QTL analysis for leaf and shoot traits

Pistachio is one of the most commercially important nut trees in the world. To characterize the genetic controls of horticultural traits and facilitate marker-assisted breeding in pistachio, we constructed an SSR-based linkage map using an interspecific F1 population derived from a cross between the cultivar “Siirt” (Pistacia vera L.) and the monoecious Pa-18 genotype of Pistacia atlantica Desf. This population was also used for the first QTL analysis in pistachio on leaf and shoot characters. In total, 1312 SSR primers were screened, and 388 loci were successfully integrated into parental linkage maps. The Siirt maternal map contained 306 markers, while the “Pa-18” paternal map included 285 markers along the 15 linkage groups. The Siirt map spanned 1410.4 cM, with an average marker distance of 4.6 cM; the Pa-18 map covered 1362.5 cM with an average marker distance of 4.8 cM. Phenotypic data were collected during the growing seasons of 2015 and 2016 for four traits: leaf length (LL), leaf width (LW), leaf length/leaf width ratio (LWR), number of leaflet pairs (NLL), and young shoot color (YSC). A total of 17 QTLs were identified in the parental maps. Four QTLs for LL and LW were located on LG2 and LG4, while four QTLs for LWR ratio on LG13 and LG14, two QTLs for NLL and two QTLs for YSC were on LG7 and LG9, respectively, with similar positions in both parental maps. The SSR markers, linkage maps, and QTLs reported here will provide a valuable resource for future molecular and genetic studies in pistachio. © 2018, Springer Nature B.V.Firat University Scientific Research Projects Management Unit: FDK-2015-3642 TUBITAK-TOVAG +113O962Acknowledgments This work was supported by the Scientific and Technological Research Council of Turkey (Project No. TUBITAK-TOVAG +113O962), and the Cukurova University Scientific Research Projects Unit (Project No.: FDK-2015-3642)

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. © 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group

In vitro propogation of Physalis peruviana (L.) using apical shoot explants [Rozmnazanie in vitro Physalis peruviana (L.) przy uzyciu eksplantów ze szczytowych pedów]

Physalis 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 l-1 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. © by Wydawnictwo Uniwersytetu Przyrodniczego w Lublinie, Lublin 2016

QTL mapping for flower characters using 'Guara' × 'Nurlu' F1 population in almond

Almond is the only nut tree in Rosaceae family and it is one of the most important nut crops in Turkey. Construction of genetic linkage maps and quantitative trait locus (QTLs) analysis are important tools to develop markers linked to economically important phenotypic characters. Simple sequence repeat (SSR) based linkage map in almond using 'Guara' × 'Nurlu' F1 population was constructed and flower characters such as color, full blooming date and position of anthers were phenotypically characterized in the population during three consecutive years. The consensus map included a total of 153 SSR markers in eight linkage groups (LGs). The number of mapped markers changed between 15 (LG4) and 25 (LG2), and the length of the LGs varied from 49.8 (LG6) cm to 85.1 cm (LG1). An average number of SSR markers per linkage group was 19. The average distance between markers was 3.2. Two QTLs for full blooming in LG1 and LG7, two QTLs for the position of anthers in LG3 and in LG8, and one QTL for flower color in LG6 were detected. © 2018 ISHS