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

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.     

RNA isolation from loquat and other recalcitrant woody plants with high quality and yield

RNA isolation is difficult in plants that contain large amounts of polysaccharides and polyphenol compounds. To date, no commercial kit has been developed for the isolation of high-quality RNA from tissues with these characteristics, especially for fruit. The common protocols for RNA isolation are tedious and usually result in poor yields when applied to recalcitrant plant tissues. Here an efficient RNA isolation protocol based on cetyltrimethylammonium bromide (CTAB) and two successive precipitations with 10 M lithium chloride (LiCl) was developed specifically for loquat fruits, but it was proved to work efficiently in other tissues of loquat and woody plants. The RNA isolated by this improved protocol was not only of high purity and integrity (A₂₆₀/A₂₈₀ ratios ranged from 1.90 to 2.04 and A₂₆₀/A₂₃₀ ratios were > 2.0) but also of high yield (up to 720 μg on average [coefficient of variation = 21%] total RNA per gram fresh tissue). The protocol was tested on loquat fruit (different stages of development, postharvest, ripening, and bruising), leaf, root, flower, stem, and bud; quince fruit and root; grapevine cells in liquid culture; and rose petals. The RNA obtained with this method is amenable to enzymatic treatments and can be efficiently applied for research on gene characterization, expression, and function.     

Pollen effects on fruit and seed characteristics in pistachio (Pistacia vera L.)

The agronomic profitability of nut production in pistachio (Pistacia vera L.) is hampered by several factors such as the production of empty nuts, the small size and dry weight of the edible kernel and the low percentage of endocarp dehiscence. The causes underlining these problems are still unknown. The effect of pollinations with pollen from P. atlantica and six different P. vera genotypes on several fruit, nut and embryo characters was compared to study possible xenic and/or metaxenic effects. The use of P. atlantica pollen affected some traits, but there were no clear differences when the pollen of the different P. vera genotypes was used suggesting that, at the intraspecific level, the main limitation to pistachio fruit production problems might not be due to pollen factors.     

Germination of Pistacia vera L. pollen in liquid medium

Summary The osmotic effect of Polyethylene glycol (PEG) has been shown to be sufficient to induce the germination of Pistacia vera L. pollen in liquid medium. The prehydration of the pollen in a saturated atmosphere for approximately 10 h was necessary to obtain maximum in vitro germination. Imbibition of the pollen in water resulted in the rapid leakage of solutes into the medium. These solutes consisted of approximately 50% carbohydrates, of which sucrose (0.65 mol/mg), glucose (0.77 mol/mg) and fructose (0.78 mol/mg) were the major sugars; the remaining 50% comprised proteins with the following major molecular weights 63 kDa, 60 kDa, 59 kDa, 40 kDa, 36 kDa, 35.5 kDa, 31 kDa, other organic matter and minerals.     

Genetic diversity of Pistachio (Pistacia vera, Anacardiaceae) Germplasm based on Randomly Amplified Polymorphic DNA (RAPD) markers

We used Randomly Amplified Polymorphic DNA (RAPD) markers to examine patterns of relatedness among 29 pistachio (Pistacia vera L.) cultivars and accessions. These included 13 cultivars that we had previously described, and an additional 16 items from the USDA National Clonal Germplasm Repository/Davis comprising cultivars and land races originating further east of the cultivars described previously, and material from wild P. vera stands in or near the putative center of origin for pistachio in South Central Asia. The results show high levels of polymorphism in the species emphasizing the importance of preservation of the remaining wild stands of P. vera. Analyses support the concept that cultivars in use west of the Zagros-Caucasus ranges likely originate from a limited germplasm base. The newly examined cultivated material shows greater genetic diversity, consistent with the hypothesis that pistachio cultivation originated in or near South Central Asia. Results also indicate that for at least two cases, material identified differently in two collections are the same clones, thus illustrating the value of molecular marker techniques in describing and maintaining germplasm collections for clonally propagated species.

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Résumé  En este trabajo se ha empleado la técnica del ADN polimórfico amplificado al azar (RAPD) para examinar la similitud genética entre 29 cultivares y accesiones de pistachero (Pistacia vera L). Este material incluye 13 cultivares considerados en un trabajo anterior y 16 nuevas accesiones del Banco Nacional de Germoplasma Clonal del USDA en Davis que incluyen cultivares y razas locales de regiones más orientales que las consideradas anteriormente así como material procedente de basques naturales de P. vera situados en las proximidades del presunto centro de origen del pistachero. Los resultados obtenidos muestran un alto grado de polimorfismo, lo que indica la necesidad de conservar el germoplasma de P. vera todavía existente en estado natural. Además se confirma la hipótesis de que los cultivares procedentes del oeste de la zona Caucásica y del Zagros se originaron a partir de una base genética limitada. El nuevo material estudiado muestra una mayor diversidad genética lo que corrobora la idea de que el cultivo del pistachero se inició en Asia Central. Al menos en dos de los casos estudiados, el material identificado en dos colecciones diferentes como distintos genotipos, en realidad se trata del mismo clon, lo que demuestra la utilidad de los marcadores moleculares en la descripción y mantenimiento de colecciones de germoplasma en especies de reproducción vegetativa.

     

Isolation of high quality RNA from bilberry (Vaccinium myrtillus L.) fruit

A simple and efficient method is described for isolating high quality RNA from bilberry fruit. The procedure is based on the use of hexadecyltrimethyl ammonium bromide (CTAB), polyvinylpyrrolidone (PVP), and β-mercaptoethanol in an extraction buffer in order to eliminate the polysaccharides and prevent the oxidation of phenolic compounds. This method is a modification of the one described for pine trees, and yields high-quality RNA suitable for cDNA based methodologies. This method is applicable for a variety of plant tissues.     

Micrografting of pistachio (Pistacia vera L. cv. Mateur)

A successful micrografting technique was developed for Pistacia vera. High levels of graft union were achieved when shoots from Stage II cultures of four-year-old P. vera. cv. Mateur were grafted onto in vitro-raised seedling rootstocks. Light and fluorescence microscopy investigations revealed that vascular continuity was established across grafts by three weeks.     

Antioxidant activity and phenolic profile of pistachio (Pistacia vera L., variety Bronte) seeds and skins

Pistachio (Pistacia vera L.; Anacardiaceae) is native of aride zones of Central and West Asia and distributed throughout the Mediterranean basin. In Italy, a pistachio cultivar of high quality is typical of Bronte (Sicily), an area around the Etna volcano, where the lava land and climate allow the production of a nut with intense green colour and aromatic taste, very appreciated in international markets. Pistachio nuts are a rich source of phenolic compounds, and have recently been ranked among the first 50 food products highest in antioxidant potential. Pistachio nuts are often used after removing the skin, which thus represents a significant by-product of pistachio industrial processing. The present study was carried out to better characterize the phenolic composition and the antioxidant activity of Bronte pistachios, with the particular aim to evaluate the differences between pistachio seeds and skins. The total content of phenolic compounds in pistachios was shown to be significantly higher in skins than in seeds. By HPLC analysis, gallic acid, catechin, eriodictyol-7-O-glucoside, naringenin-7-O-neohesperidoside, quercetin-3-O-rutinoside and eriodictyol were found both in pistachio seeds than in skins; furthermore, genistein-7-O-glucoside, genistein, daidzein and apigenin appeared to be present only in pistachio seeds, while epicatechin, quercetin, naringenin, luteolin, kaempferol, cyanidin-3-O-galactoside and cyanidin-3-O-glucoside are contained only in pistachio skins. The antioxidant activity of pistachio seeds and skins were determined by means of four different assays (DPPH assay, Folin-Ciocalteau colorimetric method and TEAC assay, SOD-mimetic assay). As expected on the basis of the chemical analyses, pistachio skins have shown to possess a better activity with respect to seeds in all tests. The excellent antioxidant activity of pistachio skins can be explained by its higher content of antioxidant phenolic compounds. By HPLC-TLC analysis, gallic acid, catechin, cyanidin-3-O-galactoside, eriodictyol-7-O-glucoside and epicatechin appeared to be responsible for the antioxidant activity of pistachio skin, together with other unidentified compounds. In conclusion, our work has contributed to clarify some particular characteristics of Bronte pistachios and the specific antioxidant power of pistachio skins. Introduction of pistachios in daily diet may be of undoubted utility to protect human health and well-being against cancer, inflammatory diseases, cardiovascular pathologies and, more generally, pathological conditions related to free radical overproduction. On the other hand, pistachio skins could be successfully employed in food, cosmetic and pharmaceutical industry.     

Antibacterial, antifungal, and antiviral activities of the lipophylic extracts of Pistacia vera

In the present study, antibacterial, antifungal, and antiviral properties of 15 lipohylic extracts obtained from different parts (leaf, branch, stem, kernel, shell skins, seeds) of Pistacia vera were screened against both standard and the isolated strains of Escherichia coli, Pseudomonas aeruginosa, Enterococcus faecalis, Staphylococcus aureus, Candida albicans and C. parapsilosis by microdilution method. Both Herpes simplex (DNA) and Parainfluenza viruses (RNA) were used for the determination of antiviral activity of the P. vera extracts by using Vero cell line. Ampicilline, ofloxocine, ketoconazole, fluconazole, acyclovir and oseltamivir were used as the control agents. The extracts showed little antibacterial activity between the range of 128-256 microg/ml concentrations whereas they had noticeable antifungal activity at the same concentrations. Kernel and seed extracts showed significant antiviral activity compared to the rest of the extracts as well as the controls.     

Isolation of RNA from blackcurrant (Ribes nigrum L.) fruit

Extraction of high-quality RNA from blackcurrant fruit has hitherto proved difficult, probably owing to high levels of phenolic and polysaccharide components in the berries. The procedure described here is a modification of one described for grape berries, and yields RNA suitable for in vitro translations, RNA blot analysis, and cDNA library construction.     

A Rapid and effective method for RNA extraction from different tissues of grapevine and other woody plants

Introduction –  RNA quality and integrity are critical for many studies in plant molecular biology. High‐quality RNA extraction from grapevine and other woody plants is problematic due to the presence of polysaccharides, polyphenolics and other compounds that bind or co‐precipitate with the RNA. Objective  – To develop an optimised cetyltrimethylammonium bromide (CTAB)‐based protocol, to reduce the time and cost of extraction without reducing quality and yield of RNA extracted from polysaccharide‐rich tissues of several plants. Methodology  – Several changes were introduced to the original CTAB protocol. All centrifugation steps were carried out at 4°C, the sample weight was decreased and the concentrations of PVP‐40 and LiCl were increased reducing incubation time prior to RNA precipitation. This rapid CTAB protocol was compared with six different RNA extraction methods from three grapevine tissues, namely, in vitro plantlets, and leaves and mature canes from actively growing field vines. Results –  The rapid CTAB method gave high‐quality RNA in only 3 h at low cost with efficiency equal to or higher than that obtained with other time‐consuming and expensive protocols. The procedure was applied to RNA extraction from other grapevine tissues and other woody species including olive, lemon, poplar, chestnut, apple, pear, peach, cherry, apricot, plum and kiwi fruit. RNA of high quality could be isolated from all tissues and from all species. Conclusion –  The study has shown that the improvement of a CTAB‐based protocol allows the rapid isolation of high‐quality RNA from grapevine and many woody species. Copyright © 2008 John Wiley & Sons, Ltd.     

Prevalence and infection intensity of Nosema in honey bee (Apis mellifera L.) colonies in Virginia

Nosema ceranae is a recently described pathogen of Apis mellifera and Apis cerana. Relatively little is known about the distribution or prevalence of N. ceranae in the United States. To determine the prevalence and potential impact of this new pathogen on honey bee colonies in Virginia, over 300 hives were sampled across the state. The samples were analyzed microscopically for Nosema spores and for the presence of the pathogen using real-time PCR. Our studies indicate that N. ceranae is the dominant species in Virginia with an estimated 69.3% of hives infected. Nosema apis infections were only observed at very low levels (2.7%), and occurred only as co-infections with N. ceranae. Traditional diagnoses based on spore counts alone do not provide an accurate indication of colony infections. We found that 51.1% of colonies that did not have spores present in the sample were infected with N. ceranae when analyzed by real-time PCR. In hives that tested positive for N. ceranae, average C_T values were used to diagnose a hive as having a low, moderate, or a heavy infection intensity. Most infected colonies had low-level infections (73%), but 11% of colonies had high levels of infection and 16% had moderate level infections. The prevalence and mean levels of infection were similar in different regions of the state.     

Isolation and characterization of cDNA clones encoding ADP-glucose pyrophosphorylase (AGPase) large and small subunits from chickpea (Cicer arietinum L.)

Four cDNA clones encoding two large subunits and two small subunits of the starch regulatory enzyme ADP-glucose pyrophosphorylase (AGPase) were isolated from a chickpea (Cicer arietinum L.) stem cDNA library. DNA sequence and Southern blot analyses of these clones, designated CagpL1, CagpL2 (large subunits) and CagpS1 and CagpS2 (small subunits), revealed that these isoforms represented different AGPase large and small subunits. RNA expression analysis indicated that CagpL1 was expressed strongly in leaves with reduced expression in the stem. No detectable expression was observed in seeds and roots. CagpL2 was expressed moderately in seeds followed by weak expression in leaves, stems and roots. Similar analysis showed that CagpS1 and CagpS2 displayed a spatial expression pattern similar to that observed for CagpL2 with the exception that CagpS1 showed a much higher expression in seeds than CagpS2. The spatial expression patterns of these different AGPase subunit sequences indicate that different AGPase isoforms are used to control starch biosynthesis in different organs during chickpea development.     

Plant morphology and root hydraulics are altered by nutrient deficiency in Pistacia lentiscus (L.)

The plants in arid and semiarid areas are often limited by water and nutrients. Morpho-functional adjustments to improve nutrient capture may have important implications on plant water balance, and on plant capacity to withstand drought. Several studies have shown that N and P deficiencies may decrease plant hydraulic conductance. Surprisingly, studies on the implications of nutrient limitations on water use in xerophytes are scarce. We have evaluated the effects of strong reductions in nitrogen and phosphorus availability on morphological traits and hydraulic conductance in seedlings of a common Mediterranean shrub, Pistacia lentiscus L.. Nitrogen deficiency resulted in a decrease in aboveground biomass accumulation, but it did not affect belowground biomass accumulation or root morphology. Phosphorus-deficient plants showed a decrease in leaf area, but no changes in aboveground biomass. Root length, root surface area, and specific root length were higher in phosphorus-deficient plants than in control plants. Nitrogen and phosphorus deficiency reduced both root hydraulic conductance and root hydraulic conductance scaled by total root surface area. On the other hand, nutrient limitations did not significantly affect root conductance per unit of foliar surface area. Thus, adaptation to low nutrient availability did not affect seedling capacity for maintaining water supply to leaves. The implications for drought resistance and survival during seedling establishment in semi-arid environments are discussed.     

A simple and efficient protocol for isolation of functional RNA from plant tissues rich in secondary metabolites

A protocol is described for rapid RNA isolation from various plant species and tissues rich in polyphenolics and polysaccharides. The method is based on the Nucleon PhytoPure^™ system without the use of phenol. The procedure can be completed within 1 h and many samples can be processed at the same time. The yield ranged from 240 μg up to 3 mg per gram of tissue with an average purity measured as A_260/280 of 1.85. The RNA was of sufficient quality for use in RT-PCR reactions. Quantitation of single-stranded cDNA was carried out with the RiboGreen^™ reagent and of PCR products with the PicoGreen^™ reagent.