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Pistachio is a nut crop domesticated in the Fertile Crescent and a dioecious species with ZW sex chromosomes. We sequenced the genomes of Pistacia vera cultivar (cv.) Siirt, the female parent, and P.vera cv. Bagyolu, the male parent. Two chromosome-level reference genomes of pistachio were generated, and Z and W chromosomes were assembled. The ZW chromosomes originated from an autosome following the first inversion, which occurred approximately 8.18 Mya. Three inversion events in the W chromosome led to the formation of a 12.7-Mb (22.8% of the W chromosome) non-recombining region. These W-specific sequences contain several genes of interest that may have played a pivotal role in sex determination and contributed to the initiation and evolution of a ZW sex chromosome system in pistachio. The W-specific genes, including defA, defA-like, DYT1, two PTEN1, and two tandem duplications of six VPS13A paralogs, are strong candidates for sex determination or differentiation. Demographic history analysis of resequenced genomes suggest that cultivated pistachio underwent severe domestication bottlenecks approximately 7640 years ago, dating the domestication event close to the archeological record of pistachio domestication in Iran. We identified 390, 211, and 290 potential selective sweeps in 3 cultivar subgroups that underlie agronomic traits such as nut development and quality, grafting success, flowering time shift, and drought tolerance. These findings have improved our understanding of the genomic basis of sex determination/differentiation and horticulturally important traits and will accelerate the improvement of pistachio cultivars and rootstocks.

Salinity and drought are the major abiotic stresses that disturb several aspects of maize plants growth at the cellular level, one of these aspects is cell cycle machinery. In our study, we dissected the molecular alterations and downstream effectors of salinity and drought stress on cell cycle regulation and chromatin remodeling. Effects of salinity and drought stress were determined on maize seedlings using 200 mM NaCl (induced salinity stress), and 250 mM mannitol (induced drought stress) treatments, then cell cycle progression and chromatin remodeling dynamics were investigated. Seedlings displayed severe growth defects, including inhibition of root growth. Interestingly, stress treatments induced cell cycle arrest in S-phase with extensive depletion of cyclins B1 and A1. Further investigation of gene expression profiles of cell cycle regulators showed the downregulation of the CDKA, CDKB, CYCA, and CYCB. These results reveal the direct link between salinity and drought stress and cell cycle deregulation leading to a low cell proliferation rate. Moreover, abiotic stress alters chromatin remodeling dynamic in a way that directs the cell cycle arrest. We observed low DNA methylation patterns accompanied by dynamic histone modifications that favor chromatin decondensation. Also, the high expression of DNA topoisomerase 2, 6 family was detected as consequence of DNA damage. In conclusion, in response to salinity and drought stress, maize seedlings exhibit modulation of cell cycle progression, resulting in the cell cycle arrest through chromatin remodeling.

Yield losses to waterlogging are expected to become an increasingly costly and frequent issue in some regions of the world. Despite the extensive work that has been carried out examining the molecular and physiological responses to waterlogging, phenotyping for waterlogging tolerance has proven difficult. This difficulty is largely due to the high variability of waterlogging conditions such as duration, temperature, soil type, and growth stage of the crop. In this review, we highlight use of phenotyping to assess and improve waterlogging tolerance in temperate crop species. We start by outlining the experimental methods that have been utilized to impose waterlogging stress, ranging from highly controlled conditions of hydroponic systems to large-scale screenings in the field. We also describe the phenotyping traits used to assess tolerance ranging from survival rates and visual scoring to precise photosynthetic measurements. Finally, we present an overview of the challenges faced in attempting to improve waterlogging tolerance, the trade-offs associated with phenotyping in controlled conditions, limitations of classic phenotyping methods, and future trends using plant-imaging methods. If effectively utilized to increase crop resilience to changing climates, crop phenotyping has a major role to play in global food security.

Opuntia spp. is an economically important crop from the Cactaceae family and native to the tropical and subtropical regions of America. It is cultivated for various uses such as fresh fruit, pharmaceutical, cosmetic, or in the form of beverage. Opuntia spp. is well known for its anatomical and physiological characters to conserve water and tolerate extreme drought conditions. The production of Opuntia has been extended around the world and it has become an alternative crop in the areas with low-quality soil and water deficit. The ability to tolerate the extreme environments of Opuntia species makes them also valuable to study molecular mechanisms underlying abiotic stress tolerance. Opuntia is crassulacean acid metabolism (CAM) species with high water-use efficiencies (WUE) that makes it to be able to grow in areas with insufficient precipitation and less water availability to support traditional C3 or C4 bioenergy crops. Studies of photosynthesis have shown that these species use a particular photosynthetic pathway known as CAM for the fixation of atmospheric CO2 during the dry season. Indeed, in the CAM pathway as an adaptation mechanism in plants to water deficit, all or part of the atmospheric CO2 uptake occurs at the nighttime that remains stomata closer at daytime when the temperature is a higher and consequent reduction in the evapotranspiration rates. Atmospheric CO2 uptake ratio can affect the biomass production in plants. Despite, CO2 fixation in CAM plants is 15% more efficient than C3 plants, CAM species often grow slowly due to their extra enzymatic reactions for carbon fixation. In C3 plants, 3 ATP and 2 NADPH require for each CO2 molecular fixation, while in CAM plants for each CO2 fixation, 5.5–6.5 ATP and 2 NADPH are required. In CAM plants net carbon fixation efficiency is 10% less than C4 plants. However, under optimal growth conditions, Opuntia has the potential to produce higher biomass rivaling that of C3 and C4 crops. Moreover, growth character and CAM pathway in genera Opuntia, allow these species to operate at near-maximum productivity with relatively low water requirement. Cultivation of CAM species from the genera Opuntia can provide an alternative to product feedstocks and food in the arid and semiarid regions. For this purpose, here in this chapter, we will discuss (a) the crassulacean acid metabolism pathway; (b) the molecular mechanism of CAM; (c) physiological attributes of CAM during the drought tolerance period; (d) CAM improve Opuntia biomass production. Furthermore, screening Opuntia species that qualify with water use efficiency and high productivity will be interesting to be reviewed in this chapter to provide the alternative feedstock bioenergy crops that preserve and expand feedstock production in water-limited areas.

Natural plant-derived phenolic extract recently received much attention in the food industry to obtain bioactive compounds for food and pharmaceutical industries. These compounds are of considerable interest due to their medicinal and nutrition properties. In this line, cactus pear (Opuntia spp.) is considered for its potentially active nutrients and its multifunctional properties to produce health-promoting food supplements. These beneficial effects are related to its potential bioactive compounds like phenolic acids and flavonoids possessing antioxidant traits. As secondary metabolites, phenolic compounds can mitigate oxidative damage caused by cancer, cardiovascular diseases, and diabetes. The phenolic structure contains an aromatic ring with one or more hydroxyl groups that cause their therapeutic activity. Two classes of phenolic compounds are extensively investigated in the plants, including hydroxybenzoic acid and hydroxycinnamic acid. However, phenylpropanoid serves as a precursor for synthesizing the other phenolic compounds. Several phenolic compounds were found to display different health benefits, including antioxidant, anti-inflammatory, and anticancer activities. Phenolic acids and flavonoids from the genus Opuntia have been recognized as antioxidants. Phenolic acids such as vanillic, ferulic, p-coumaric, p-hydroxybenzoic, syringic, protocatechuic, caffeic, salicylic, gallic, and sinapic, as well as flavonoids such as rutin, isoquercitrin, kaempferol, and narcissi are found in plants from the genus Opuntia. The antioxidant properties of phenolic compounds in Opuntia spp. plants make them an essential product for preventing human health against degenerative diseases such as cancer, diabetes, hypercholesterolemia, arteriosclerosis, cardiovascular and gastric diseases. Nowadays, the food and agricultural processing include phenolic compounds as an essential part of the human diet. This chapter discusses the medicinal importance of phenolic compounds in Opuntia spp. as a natural antioxidant. The article highlights the extractions methods and manufacturing processing, including backing, cooking, and frying, in the food and beverage industry and their effects on these compounds’ stability and activity. This information would help identify Opuntia species rich in phenolics and their therapeutic properties. Besides, the chemical structure, properties, and health benefits of phenolic compounds of cactus pear fruit and their influences in agro-industrial wastes as natural sources of antioxidants with application in food industries have been reviewed.

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.

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 Unit This 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- ??? ?- ? ? ? ?).

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 +113O962 Acknowledgments 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).

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-113O962 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-2015-3641). The authors declare that they have no conflict of interest.

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.

Background 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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3359-x) contains supplementary material, which is available to authorized users.

Genetic diversity measures in P. atlantica: allele ranges, number of alleles (Na), number of effective alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), and PIC values of 161 polymorphic SSR loci. (DOCX 37 kb)

Genetic diversity measures in P. chinensis: allele ranges, number of alleles (Na), number of effective alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), and PIC values of 142 polymorphic SSR loci. (DOCX 37 kb)

Genetic diversity measures in P. lentiscus: allele ranges, number of alleles (Na), number of effective alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), and PIC values of 83 polymorphic SSR loci. (DOCX 34 kb)

Genetic diversity measures in P. vera: allele ranges, number of alleles (Na), number of effective alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphic information content (PIC) of 200 polymorphic SSR loci. (DOCX 40 kb)

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)

Genetic diversity measures in P. integerrima: allele ranges, number of alleles (Na), number of effective alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), and PIC values of 157 polymorphic SSR loci. (DOCX 37 kb)

PubMedID: 25765114 Background: 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.