Molecular Characterization of Pistacia Genus by Microsatellite Markers

Vendramin, Elisa; Dettori, Maria Teresa; Verde, Ignazio; Micali, Simona; Giovinazzi, J.; Mardi, M; Avanzato, D.; Quarta, R.

doi:10.17660/actahortic.2009.825.5

Cited by 13 publications

(11 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In fact, the comparison of gene diversity between different groups yielded significant differences among them (p \ 0.0001), confirming the results of other researchers in separating the different Pistacia species Pazouki et al 2009;Vendramin et al 2009). Cluster analysis of the Pistacia accessions according to their species constructed with UPGMA method based on a coancestry coefficient data matrix (Fig.…”

Section: Discussionsupporting

confidence: 85%

“…To distinguish various species and accessions of Pistacia, phylogenetic analysis of the genus has been attempted using isozyme (Rovira et al 1995); RAPD (Hormaza et al 1998;Kafkas and Perl-Treves 2001;Katsiotis et al 2003;Mirzaei et al 2005); restriction analysis, RFLP of chloroplast DNA (cpDNA) Badenes 1997, 1998); AFLP (GolanGoldhirsh et al 2004;Ahmadi Afzadi et al 2007); SSR Vendramin et al 2009;Pazouki et al 2009Pazouki et al , 2010 and ISSR markers (Noroozi et al 2009). Molecular markers are valuable tools for screening plant morphological and phenotypic characteristics on the grounds that they are ample and independent of tissue or environmental effects that permit trait identification due to diverse appearances at the early stage of crop development.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genetic diversity and phylogenetic relationships between and within wild Pistacia species populations and implications for its conservation

et al. 2015

View full text Add to dashboard Cite

Although cultivation and utilization of Pistacia are fully exploited, the evolutionary history of the Pistacia genus and the relationships among the species and accessions is still not well understood. The aim of this study was to analyze random amplified polymorphic DNA (RAPD) in a total of 50 accessions of wild pistachio species, which included five populations Pistacia vera, Pistacia khinjuk, Pistacia atlantica, Pistacia mutica, and Pistacia eurycarpa. High levels of genetic diversity were detected within wild pistachio accessions, as revealed by using the unweighted pair-group method with arithmetic averaging and supported via analysis of molecular variance. The objectives of this investigation were to estimate marker indices, polymorphic information contents (PICs), and genetic similarities (GS) for RAPD markers; assess the genetic diversity of Pistacia species, using GS estimated from RAPD fingerprints and molecular characterization; and facilitate the use of markers in inter-specific introgression and cultivar improvement. Out of the 149 polymerase chain reaction fragments that were scored, 146 (97.98 %) were polymorphic. Genetic similarities ranged from 0.3 to 0.86 %, marker indices ranged from 2.98 to 17.74 %, and PICs ranged from 0.80 to 0.99 %. Our results provided great molecular identification of all assayed genotypes, which have shown that there is large quantity of genetic diversity among the pistachio accessions. This finding might render striking information in breeding management strategies for genetic conservation and cultivar development.

show abstract

Section: Discussionsupporting

confidence: 85%

Section: Introductionmentioning

confidence: 99%

Genetic diversity and phylogenetic relationships between and within wild Pistacia species populations and implications for its conservation

et al. 2015

View full text Add to dashboard Cite

show abstract

“…Most studies on P. vera have focused on limited SSR and random amplified polymorphic DNA (RAPD) markers development for germplasm characterization and sex determination [ 11 – 14 ], as well as the study of some physiological parameters in pistachio plants under drought and salt stresses [ 15 – 18 ]. However, there is no transcriptomic research and gene discovery at the large scale in this species, and in Anacardiaceae family only two RNA sequencing (RNA-seq) datasets are available from Mangifera indica [ 19 ] and P. chinensis [ 20 ].…”

Section: Introductionmentioning

confidence: 99%

A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery

et al. 2017

View full text Add to dashboard Cite

BackgroundPistachio (Pistacia vera L.) is one of the most important commercial nut crops worldwide. It is a salt-tolerant and long-lived tree, with the largest cultivation area in Iran. Climate change and subsequent increased soil salt content have adversely affected the pistachio yield in recent years. However, the lack of genomic/global transcriptomic sequences on P. vera impedes comprehensive researches at the molecular level. Hence, whole transcriptome sequencing is required to gain insight into functional genes and pathways in response to salt stress.ResultsRNA sequencing of a pooled sample representing 24 different tissues of two pistachio cultivars with contrasting salinity tolerance under control and salt treatment by Illumina Hiseq 2000 platform resulted in 368,953,262 clean 100 bp paired-ends reads (90 Gb). Following creating several assemblies and assessing their quality from multiple perspectives, we found that using the annotation-based metrics together with the length-based parameters allows an improved assessment of the transcriptome assembly quality, compared to the solely use of the length-based parameters. The generated assembly by Trinity was adopted for functional annotation and subsequent analyses. In total, 29,119 contigs annotated against all of five public databases, including NR, UniProt, TAIR10, KOG and InterProScan. Among 279 KEGG pathways supported by our assembly, we further examined the pathways involved in the plant hormone biosynthesis and signaling as well as those to be contributed to secondary metabolite biosynthesis due to their importance under salinity stress. In total, 11,337 SSRs were also identified, which the most abundant being dinucleotide repeats. Besides, 13,097 transcripts as candidate stress-responsive genes were identified. Expression of some of these genes experimentally validated through quantitative real-time PCR (qRT-PCR) that further confirmed the accuracy of the assembly. From this analysis, the contrasting expression pattern of NCED3 and SOS1 genes were observed between salt-sensitive and salt-tolerant cultivars.ConclusionThis study, as the first report on the whole transcriptome survey of P. vera, provides important resources and paves the way for functional and comparative genomic studies on this major tree to discover the salinity tolerance-related markers and stress response mechanisms for breeding of new pistachio cultivars with more salinity tolerance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3989-7) contains supplementary material, which is available to authorized users.

show abstract

“…Following year the same research group was experienced 32 arbitrary primers for RAPD analysis and mentioned FPK 106 and FPK 105 but there was no data related to primer sequence. Vedramin et al carried out the SSR study covering 4 species [51]. Their analysis contains 50 P. vera, 4 P. integerrima, 12 P. mutica and 16 P. terebinthus for a total of 82 accessions but the tested markers were insu cient for gender base discrimination.…”

Section: Discussionmentioning

confidence: 99%

Molecular sexual determinants in Pistacia genus by KASP assay

Sahin

Şahin

Aydın

et al. 2021

Preprint

View full text Add to dashboard Cite

I. Background: Pistacia is kind of unisexual plant species that can take 4–5 years to initiate bearing stage of trees in terms of economic value. The fruits of species have an extreme importance in food, health and baking industry as a raw material. So, identify the individual in early juvenile period for pollination and position of trees is very crucial for growers. The objective of this study is developing markers for each Pistacia species which helps the screening the sex of plant seedling quickly before they reach reproduction stage without waiting morphological data. II. Methods and Results: Within the context, by using the power of KASP (Kompetitive Allele Specific PCR) assay technology as a marker screening system, we successfully discriminate 7 Pistacia species out of 8 which are P. atlantica, P. integerrima, P. khinjuk, P. mutica, P. terebinthus, P. vera and P. lentiscus. We have used a high-throughput DNA sequence read archive (SRA) to assemble a reference genome to use in our studies as de novo bioinformatics method. 4 genomic regions were sequenced with collected plant material from Antepfıstıgı Research Institute Collection Garden predominantly and 8 species were aligned intraspecifically for Single Nucleotide Polymorphism (SNP) mining. 12 SNP markers are converted to KASP markers and 5 of them (SNP-PIS-133396, SNP-PIS-167992, P-ATL-91951-565, P-INT-91951-256, P-KHI-91951-115) showed obvious allelic discrimination between male and female species. SNP-PIS-167992 and P-ATL-91951-565 were identified as best marker assays due to the allelic frequency differences in graphs which are apparent for all individuals and homozygosis/heterozygosis observed clearly. These markers could be most comprehensive for whole genus because the discriminability power of several species in once. III. Conclusions: As a conclusion, this study is reported first Pistacia gender discrimination by KASP, besides the precursor study for sex discrimination by KASP in plants.

show abstract

Molecular Characterization of Pistacia Genus by Microsatellite Markers

Cited by 13 publications

References 0 publications

Genetic diversity and phylogenetic relationships between and within wild Pistacia species populations and implications for its conservation

Genetic diversity and phylogenetic relationships between and within wild Pistacia species populations and implications for its conservation

A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery

Molecular sexual determinants in Pistacia genus by KASP assay

Contact Info

Product

Resources

About