Evaluation of growth and nutritional value of Brassica microgreens grown under red, blue and green LEDs combinations

39 p.-7 fig.-2 tab.-9 tab. supl.Microgreens are rich functional crops with valuable nutritional elements that have health benefits when used as food supplements. Growth characterization,nutritional composition profile of 21 varieties representing five species of the Brassica genus asmicrogreens were assessed under light-emitting diodes(LEDs) conditions. Microgreens were grown under four different LEDs ratios(%); red:blue 80:20 and 20:80 (R80:B20 and R20:B80), or red:green:blue 70:10:20 and 20:10:70 (R70:G10:B20 and R20:G10:B70). Results indicated that supplemental lighting with green LEDs (R70:G10:B20) enhanced vegetative growth and morphology, while blue LEDs (R20:B80) increased the mineral and vitamin contents. Interestingly, by linking the nutritional content with the growth yield to define the optimal LEDs setup, we found that the best lighting to promote the microgreen growth was the green LEDs combination (R70:G10:B20). Remarkably, under the green LEDs combination (R70:G10:B20) conditions,the microgreens of Kohlrabi purple, Cabbage red, Broccoli, Kale Tucsan, Komatsuna red, Tatsoi and Cabbage green, which can benefit human health in conditions with limited food, had the highest growth and nutritional content.This research work is a part of a project received seed funding from the Dubai Future Foundation through the Guaana.com open research platform(grant no. MBR026). Dr. Mortaza is supported from ERDF project “Plants as a tool from sustainable global development” No. CZ.02.1.01/0.0/0.0/16_019/0000827.Peer reviewe

Sex-linked markers in pistachio

DNA markers have potential to improve the efficiency of conventional plant breeding via marker-assisted selection (MAS). Therefore, MAS can be very effective in pistachio to eliminate undesirable progenies at early stage which can save time, cost, labor, and land. This study aimed to develop sex-linked single nucleotide polymorphism (SNP) markers for MAS, to understand sex determination system and to determine the position of sex locus in pistachio. Eight male and eight female F1 progenies from 'Siirt' × 'Bagyolu' cross, along with the parents, were subjected to RAD (restriction site-associated DNA) sequencing and 38 SNP loci were detected as putative sex-associated ones in pistachio. Validation was performed by SNaPshot minisequencing analysis in mature F1 progenies and in a wide germplasm collection. Seventeen loci successfully distinguished sex in pistachio. To ascertain cost-effective application of markers in a breeding program, high-resolution melting (HRM) analysis was performed; and 10 markers were found to perfectly separate sexes in pistachio. Because of the female heterogamety in all sex-linked SNP loci, pistachio has a ZZ/ZW sex determination system. The sex locus and sex-linked SNP markers were co-segregated in the center of the chromosome at a distance of 30.8 and 31.3 cm, respectively. This study presents sex-linked markers for MAS as well as valuable information about the sex chromosome and sex locus position in pistachio. © 2018 ISHS.Firat University Scientific Research Projects Management UnitThis project was supported by the General Directorate of Agricultural Research and Policies (Project No. TAGEM/ ???ARGE/ ??I at the Republic ofe yTuMrkinistry of Food, Agriculture and Livestock, and the Çukurova University Scientific Research Projects Unit (Project No: FDK- ??? ?- ??? ?? FBA- ?? ? ?- ??? ? and FBA- ??? ?- ? ? ? ?)

Identification of sex-linked SNP markers using RAD sequencing suggests ZW/ZZ sex determination in Pistacia vera L.

PubMedID: 25765114Background: Pistachio (Pistacia vera L.) is a dioecious species that has a long juvenility period. Therefore, development of marker-assisted selection (MAS) techniques would greatly facilitate pistachio cultivar-breeding programs. The sex determination mechanism is presently unknown in pistachio. The generation of sex-linked markers is likely to reduce time, labor, and costs associated with breeding programs, and will help to clarify the sex determination system in pistachio. Results: Restriction site-associated DNA (RAD) markers were used to identify sex-linked markers and to elucidate the sex determination system in pistachio. Eight male and eight female F1 progenies from a Pistacia vera L. Siirt × Bağyolu cross, along with the parents, were subjected to RAD sequencing in two lanes of a Hi-Seq 2000 sequencing platform. This generated 449 million reads, comprising approximately 37.7 Gb of sequences. There were 33,757 polymorphic single nucleotide polymorphism (SNP) loci between the parents. Thirty-eight of these, from 28 RAD reads, were detected as putative sex-associated loci in pistachio. Validation was performed by SNaPshot analysis in 42 mature F1 progenies and in 124 cultivars and genotypes in a germplasm collection. Eight loci could distinguish sex with 100% accuracy in pistachio. To ascertain cost-effective application of markers in a breeding program, high-resolution melting (HRM) analysis was performed; four markers were found to perfectly separate sexes in pistachio. Because of the female heterogamety in all candidate SNP loci, we report for the first time that pistachio has a ZZ/ZW sex determination system. As the reported female-to-male segregation ratio is 1:1 in all known segregating populations and there is no previous report of super-female genotypes or female heteromorphic chromosomes in pistachio, it appears that the WW genotype is not viable. Conclusion: Sex-linked SNP markers were identified and validated in a large germplasm and proved their suitability for MAS in pistachio. HRM analysis successfully validated the sex-linked markers for MAS. For the first time in dioecious pistachio, a female heterogamety ZW/ZZ sex determination system is suggested. © 2015 Kafkas et al.; licensee BioMed Central

Development and linkage mapping of novel sex-linked markers for marker-assisted cultivar breeding in pistachio (Pistacia vera L.)

The dioecious character of Pistacia vera L (the pistachio tree) limits its breeding capacity. Thus, early stage selection of males can save time, labor, and land. This study aimed to develop sex-linked single nucleotide polymorphism (SNP) markers, together with expressed sequence tag-derived simple sequence repeats (EST-SSRs), to determine position of the sex locus in pistachio by constructing a linkage map of its sex chromosome for the first time. Nine novel sex-linked SNP markers were successfully identified by SNaPshot minisequencing analysis of 25 SNP loci from 17 restriction site-associated DNA (RAD) reads in 309 individuals. All nine markers were heterozygous in females and homozygous in males supporting a ZW/ZZ sex determination system in pistachio. A total of 105 segregating SSRs and sex-linked markers were used to identify the sex chromosome and the position of the sex locus through analysis of a Siirt × Bağyolu F1 population with 122 progenies. Of these 105 markers, four common and four paternal SSRs were mapped onto the sex chromosome, along with the phenotypic sex locus and sex-linked markers. The resulting consensus map had a total length of 65.19 cM. The sex locus and sex-linked SNP markers were located in the center of the chromosome at a distance of 31.86 and 31.92 cM, respectively. This study presents valuable information about the sex chromosome and sex locus position as well as novel polymorphic EST-SSRs and nine sex-linked SNP markers in pistachio. © 2017, Springer Science+Business Media B.V

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)

Genetic relationships among Pistacia vera L. Cultivars based on simple sequence repeat markers

Pistacia belongs to the family Anacardiaceae (cashew family), and consists of 11 species. Pistachio (Pistacia vera L.) is the commercially grown species within the genus Pistacia. In this study, phylogenetic relationships among 24 P. vera cultivars were used to test simple sequence repeat (SSR) markers. Within 200 SSR loci analysed in 24 pistachio cultivars, the best 25 were used futher analysis. The 25 SSR loci produced 203 polymorphic alleles with an average of 8.12 alleles per locus. The effective number of alleles ranged from 2.57 to 7.60. Averages of Ne, Ho, He and PIC values in P. vera were calculated as 4.22, 0.64, 0.74 and 0.71, respectively. The constructed unweighted pair group method with arithmetic averages (UPGMA) dendrogram separated 24 pistachio cultivars based on their origins. © 2019 International Society for Horticultural Science. All rights reserved.Firat University Scientific Research Projects Management Unit: FBA-2015-4538, FUK-2014-2637, FDK-2015-3642 Türkiye Bilimsel ve Teknolojik Araştirma KurumuThe authors thank The Scientific and Technological Research Council of Turkey (Project No: TUBITAK-TOVAG ??? O ???), Cukurova University Scientific Research Projects (Project No: FUK-2014-2637, FDK-2015-3642 and FBA-2015-4538) for providing financial support. We also thank The Scientific and Technological Research Council of Turkey for providing a Ph.D. scholarship to Elmira Ziya-Motalebipour

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

PubMedID: 27923352Background: 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, and they have importance as rootstock seed sources for cultivated P. vera and forest trees. Published information on the pistachio genome is limited. Therefore, a genome survey is necessary to obtain knowledge on the genome structure of pistachio by next generation sequencing. Simple sequence repeat (SSR) markers are useful tools for germplasm characterization, genetic diversity analysis, and genetic linkage mapping, and may help to elucidate genetic relationships among pistachio cultivars and species. Results: To explore the genome structure of pistachio, a genome survey was performed using the Illumina platform at approximately 40× coverage depth in the P. vera cv. Siirt. The K-mer analysis indicated that pistachio has a genome that is about 600 Mb in size and is highly heterozygous. The assembly of 26.77 Gb Illumina data produced 27,069 scaffolds at N50 = 3.4 kb with a total of 513.5 Mb. 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 P. vera cultivars and 20 wild Pistacia genotypes (four genotypes from each five wild Pistacia species) belonging to P. atlantica, P. integerrima, P. chinenesis, P. terebinthus, and P. lentiscus genotypes. Overall 135 SSR loci amplified in all 44 cultivars and genotypes, 41 were polymorphic in six Pistacia species. The novel SSR loci developed from cultivated pistachio were highly transferable to wild Pistacia species. Conclusions: The results from a genome survey of pistachio suggest that the genome size of pistachio is about 600 Mb with a high heterozygosity rate. This information will help to design whole genome sequencing strategies for pistachio. The newly developed novel polymorphic SSRs in this study may help germplasm characterization, genetic diversity, and genetic linkage mapping studies in the genus Pistacia. © 2016 The Author(s)

In silico polymorphism analysis for the development of simple sequence repeat markers in pistachio

Pistacia vera L. is one of the most important nut crops. There are a limited number of simple sequence repeat (SSR) markers in the literature for pistachio. The short Illumina DNA sequences of three cultivars (‘Siirt’, ‘Ohadi’ and ‘Bagyolu’) in P. vera and one genotype belongs to P. atlantica (Pa-18) were produced by next-generation sequencing, and a total of 750 polymorphic loci were detected in silico and the primers were designed. Seventy-nine (10.5%) did not have amplification product and they were discarded. The remaining loci were subjected to PCR and then capillary electrophoresis for polymorphism in 18 pistachio cultivars as well as in six P. atlantica genotypes. Fifty-three SSR loci produced complex patterns, and were unable to score. Among the remaining (618) SSR primer pairs, seven had multilocus amplifications, and in total 625 SSR loci were produced from 618 SSR primer pairs. The newly developed novel polymorphic SSRs in this study may help germplasm characterization, genetic diversity, and genetic linkage mapping studies in the genus Pistacia. © 2019 International Society for Horticultural Science. All rights reserved.Firat University Scientific Research Projects Management Unit: FUK-2014-2637, FDK-2015-3641 Türkiye Bilimsel ve Teknolojik Araştirma Kurumu: TUBITAK-TOVAG 113 O 962This research was supported by The Scientific and Technological Research Council of Turkey (Project No: TUBITAK-TOVAG 113 O 962) and Cukurova University Scientific Research Projects Unit (Project No: FUK-2014-2637 and FDK-2015-3641)