Genetic diversity and population structure of Iranian pistachio (Pistacia vera l.) cultivars

Iran has a rich pistachio germplasm, thereby, the diversity and number of Iranian pistachio cultivars is unique in the world. Genetic diversity is crucial for sustainable use of genetic resources and conservation. As one of the oldest nut crops in human history, pistachio nuts have a high nutritional value and are commercially important. In the present study, the genetic variation of pistachio genotypes was investigated by nuclear ISSR markers. In this study, genetic relationships among 11 cultivars was assessed by using 12 inter simple sequence repeat (ISSR) primers. The total of 53 bands of which 44 (83%) were polymorphic were amplified by the 12 primers, an average of 4.4 bands per primer. The total number of amplified fragments was between 2 to 6 and the number of polymorphic fragments ranged from two to six. The amplified allele sizes ranged from 300 to 1600 bp. Pair-wise genetic similarity coefficients varied from 0.70 to 0.95. The UPGMA dendrogram differentiated the genotypes into two major clusters. The Mantel test showed correlation between genetic and geographical distance. AMOVA revealed a significant genetic difference among cultivars and showed that 35% of total genetic variation was due to within- cultivars diversity. The present results may be used for the conservation, core collection and future breeding of the pistachio.

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Genetic Diversity among Isolates of Phytophthora sojae in Anhui Province of China based on ISSR-PCR Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs04398-18 ◽

2018 ◽

Vol 143 (4) ◽

pp. 304-309 ◽

Cited By ~ 2

Author(s):

Dong Liu ◽

Ping Li ◽

Jiulong Hu ◽

Kunyuan Li ◽

Zhenyu Zhao ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Differentiation ◽

Genetic Relationships ◽

Inter Simple Sequence Repeat ◽

Phytophthora Sojae ◽

Anhui Province ◽

Population Variation ◽

Spatial Distance ◽

Similarity Coefficients

To explore genetic differentiation and the genetic relationships of Phytophthora sojae in Anhui Province, the inter-simple sequence repeat (ISSR) technique was used to analyze the genetic diversity of P. sojae. One hundred and sixty ISSR fragments were observed, including 129 (80.6%) polymorphic bands. This suggested that abundant genetic diversity existed among P. sojae in Anhui Province. The pairwise genetic similarity coefficients among the 62 strains ranged from 0.72 to 0.96, with a mean value of 0.85, indicating that there was a high level of genetic variation. Phytophthora sojae strains were divided into five clusters based on neighbor-joining (NJ) analysis, and the clustering was not related to geographic source, according to Mantel’s test (r = 0.3938). In addition, the clustering of strains from the same geographical source had little relationship to the year of collection. Analysis of molecular variance (AMOVA) showed that 16.65% of the genetic variation was derived from the collection area and 83.35% of the genetic variation was within-population variation. The genetic flow between different geographical sources ranged from 0.623 to 2.773, with a mean of 1.325, suggesting that gene exchange was frequent. Genetic distance and the genetic differentiation coefficient were not related to spatial distance.

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Structure and Genetic Diversity of Nine Important Landraces of Capsicum Species Cultivated in the Yucatan Peninsula, Mexico

Agronomy ◽

10.3390/agronomy9070376 ◽

2019 ◽

Vol 9 (7) ◽

pp. 376 ◽

Cited By ~ 3

Author(s):

Lucero del C. López Castilla ◽

René Garruña Hernández ◽

Crescencio de la Cruz Castillo Aguilar ◽

Aida Martínez-Hernández ◽

Matilde Margarita Ortiz-García ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

Yucatan Peninsula ◽

Conservation Status ◽

Sustainable Use ◽

Issr Markers ◽

Southern Mexico ◽

Yucatán Peninsula ◽

Capsicum Spp ◽

Capsicum Species

Mexico has a wealth of Capsicum species, which has led to the development of a large number of chili pepper landraces. A great wealth of Capsicum germplasm can be found in southern Mexico in the Yucatan Peninsula, an important area of diversification of Capsicum annuum. Specifically, in the western Yucatan Peninsula, three of the five domesticated species of Capsicum (C. annuum, C. chinense and C. frutescens) have been reported. However, information on their genetic diversity, conservation status and potential use is lacking. To generate useful information toward the sustainable use, management and conservation of these species, we evaluated the structure, diversity and genetic relationships of nine accessions of Capsicum spp., of major importance cultivated in the western Yucatan Peninsula using 42 ISSR loci. The results indicated that these accessions consisted of three genetic groups that were defined by the respective species of each accession. The level of genetic diversity was moderate and distributed mainly among accessions. The ISSR markers detected a high level of polymorphism and allowed the genetic differentiation of the C. annuum complex. The results indicated that the accessions collected in the western Yucatan Peninsula constitute a valuable genetic resource that can be used in genetic improvement and conservation programs.

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Genetic Diversity of an Alien Invasive Plant Mexican Sunflower (Tithonia diversifolia) in China

Weed Science ◽

10.1614/ws-d-11-00175.1 ◽

2012 ◽

Vol 60 (4) ◽

pp. 552-557 ◽

Cited By ~ 13

Author(s):

Jing Yang ◽

Ling Tang ◽

Ya-Li Guan ◽

Wei-Bang Sun

Keyword(s):

Genetic Diversity ◽

Native Species ◽

Invasive Plant ◽

Genetic Relationships ◽

Geographic Distance ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Chromosome Count ◽

Group Method ◽

Arithmetic Means

Mexican sunflower is a native species of North and Central America that was introduced into China early last century, but it has widely naturalized and become a harmful invasive plant in tropical and subtropical regions in South China. Inter-simple sequence repeat (ISSR) markers were employed to assess genetic diversity and variation in Mexican sunflower populations from China and neighboring regions. The karyotypes of populations were also studied. Our research showed high levels of genetic diversity in all populations. The lowest genetic diversity estimates were represented in two populations in Laos, suggesting prevention of new introductions into Laos is critical. Partitioning of genetic variance revealed that genetic variation was mostly found within populations, and unweighted pair group method with arithmetic means (UPGMA) analysis showed that the introductions into China and Laos were independent. There were no obvious correlations between genetic relationships and geographic distance of populations in China, consistent with the human associated dispersal history of Mexican sunflower. Previous cytological data and our chromosome count (2n = 34) and karyotype analysis showed chromosome stability among populations. The high levels of genetic diversity within invasive Mexican sunflower populations could be challenging for its management in China, and further expansion and potential negative effects on ecological systems of this plant should be monitored.

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Genetic relationships among cultivated and wild bananas from East Kalimantan, Indonesia based on ISSR markers

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d210250 ◽

2020 ◽

Vol 21 (2) ◽

Author(s):

Widi Sunaryo ◽

Wahida ◽

Suria Darma Idris ◽

Ananda Nuryadi Pratama ◽

Kumrop Ratanasut ◽

...

Keyword(s):

Genetic Relationships ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Issr Marker ◽

Similarity Coefficients ◽

Musa Balbisiana ◽

Economic Significance ◽

East Kalimantan ◽

B Genome ◽

A Genome

Abstract. Sunaryo W, Wahida, Idris SD, Pratama AN, Ratanasut K, Nurhasanah. 2020. Genetic relationships among cultivated and wild bananas from East Kalimantan, Indonesia based on ISSR markers. Biodiversitas 21: 824-832. East Kalimantan is one of biodiversity centers for banana in Indonesia including wild or cultivated bananas. This biodiversity is long-historical genetically contributed by the existence of wild cultivars, local/indigenous varieties or introduced accessions from other regions in Indonesia. The existence of cultivated bananas has played an important role in the socio-economic significance of the local people. The genetic contribution of wild and local banana from East Kalimantan to the cultivated bananas or vice versa is very interesting to study. This research reported the genetic relationships among wild and cultivated bananas using Inter Simple Sequence Repeat (ISSR) markers. Thirteen wild and cultivated banana samples collected from different districts of East Kalimantan Province were analyzed using 15 primers of ISSR marker. ISSR primers generated 133 loci, of which 132 were polymorphic (98.98 %) with an average of 9.43 loci per primer. The ISSR marker is very effective and powerful to detect and discriminate the polymorphisms among cultivated and wild bananas. This is supported by PIC value which ranged from 0.60 to 0.91 per primer with an average of 0.80 per primer. The marker index (MI) values were ranged from 1.62 to 11.48 per primer. Primer UBC 855 produced the highest MI value which was 11.48 per primer and UBC 848 resulted in the lowest (1.62 per primer). The similarity coefficients ranged from 0.43 to 0.81. The dendrogram constructed based on UPGMA divided the banana cultivars into 4 clusters, in which the first cluster comprised of the AA/AAA/AB genome bananas (Ambon, Kapas, Tembaga, Liar, and Tanduk). The second cluster composed of only Mauli Banana. The third cluster was comprised of six cultivated banana with AAB or ABB genome i.e., Raja, Rutai, Susu, Kepok, Awak, and Talas banana. The last cluster was only Klutuk Banana (BB genome). Wild bananas (Liar and Klutuk) was the ancestor of cultivated bananas since they contributed for A genome (Musa acuminate) and B genome (Musa balbisiana) to generate many triploid and cultivated bananas. Indigenous banana cultivars from Kalimantan, Rutai is closely related to Susu banana, while Talas banana is related to the AAB genome such as Raja, Rutai, Susu or ABB genome such as Awak and Kepok.

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Different Habitats Show Similar Genetic Structure of Bunias orientalis L. (Brassicaceae)in Lithuania

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha4129186 ◽

2013 ◽

Vol 41 (2) ◽

pp. 396 ◽

Cited By ~ 5

Author(s):

Jolanta PATAMSYTĖ ◽

Tatjana ČĖSNIENĖ ◽

Donatas NAUGŽEMYS ◽

Violeta KLEIZAITĖ ◽

Virginija TUNAITIENĖ ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Genetic Difference ◽

Habitat Type ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Baltic Countries ◽

Bunias Orientalis ◽

The Impact

We studied genetic diversity within and among populations of warty cabbage (Bunias orientalis L.), which is an alien species in Lithuania and other Baltic countries. In Lithuania, this weed colonises two main types of habitats: railway/roadsides and meadows on riversides. The aim of this study was to assess the genetic structure of invasive populations of B. orientalis in Lithuania and consider the impact of diverse habitats on the partitioning of genetic diversity using inter-simple sequence repeat (ISSR) markers. An analysis of molecular variance (AMOVA) carried out on the basis of ISSR showed that there is high genetic differentiation (46%) among populations of B. orientalis, which is probably caused by the founder effect and limited gene flow. However, we observed no impact of habitat on the genetic difference among populations. Similar levels of ISSR polymorphic loci were observed in riverside (P = 31.67%) and railway/roadsides (P = 30.51%) populations. UPGMA cluster analysis and principal coordinate analysis (PCoA) also did not show grouping of studied populations according to habitat type. High genetic differentiation among populations, as indicated by ISSR markers, confirm multiple independent introductions of this species in Lithuania.

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Genetic relatedness among cultivated and wild mulberry (Moraceae: Morus) as revealed by inter-simple sequence repeat analysis in China

Canadian Journal of Plant Science ◽

10.4141/p04-110 ◽

2006 ◽

Vol 86 (1) ◽

pp. 251-257 ◽

Cited By ~ 16

Author(s):

Zhao Weiguo ◽

Zhou Zhihua ◽

Miao Xuexia ◽

Wang Sibao ◽

Zhang Lin ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Genetic Relatedness ◽

Genetic Relationships ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Group Method ◽

Sequence Repeat ◽

Pair Group ◽

Simple Sequence

The genetic diversity of 27 mulberry (Morus spp.) genotypes mainly from China was investigated using inter-simple sequence repeat (ISSR) markers to assist in addressing breeding objectives and conserving existing genetic resources. Of the 22 primers screened, 15 produced highly reproducible ISSR bands. Using these 15 primers, 138 discernible DNA fragments were generated with 126 (91.3%) being polymorphic, indicating considerable genetic variation among the mulberry genotypes studied. Genetic similarity ranged from 0.6014 between Yu 2 and Yu 711 to 0.9493 between Cuizhisang and Dejiang 10. The phenetic dendrogram based on ISSR data generated by the unweighed pair group method with arithmetical averages (UPGMA) method grouped the 27 accessions into two major clusters: cluster I, cultivated mulberry species (M. multicaulis Perr., M. alba Linn., M. atropurpurea oxb., M. bombycis Kiodz., M. australis Poir., M. rotundiloba Kiodz., M. alba var. pendula Dipp., M. alba var. macrophylla Loud., and M. alba var. venose Delile.); and cluster II, wild mulberry species (M. cathayana Hemsl., M. laevigata Wall., M. wittiorum Hand-Mazz., M. nigra Linn., and M. mongolica Schneid.). Our molecular analyses agree with the existing morphological classification of Morus and clarify the genetic relationships among mulberry species. Key words: Morus L., genetic diversity, inter-simple sequence repeat, relatedness

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Genetic variability of Orobanche aegyptiaca infesting tobacco in Iran by Bayesian analysis

Biologia ◽

10.2478/s11756-014-0473-6 ◽

2014 ◽

Vol 69 (12) ◽

Author(s):

Samaneh Abedi ◽

Reza Darvishzadeh ◽

Iraj Bernousi ◽

Babak Abdollahi Mandoulakani ◽

Hamid Hatami Maleki ◽

...

Keyword(s):

Genetic Variation ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Similarity Coefficients ◽

Genetic Groups ◽

Wide Range ◽

Orobanche Aegyptiaca ◽

Simple Sequence ◽

Issr Primers

AbstractBroomrapes (Orobanche L.) are holoparasitic plants, parasitizing roots of a wide range of host plants. In this study, genetic polymorphism among 44 Orobanche aegyptiaca Pers. individuals collected from different regions of northwest Iran was investigated using inter-simple sequence repeat (ISSR) markers. Two hundred-sixty one discernible bands were amplified using 20 ISSR primers which 245 (94%) was polymorphic, indicating considerable genetic variation among the examined individuals. The number of polymorphic bands per primer ranged from 4 to 17, averaging 12.25. UPGMA clustering using Jaccard’s similarity coefficients revealed six main groups. Genetic similarity coefficients varied from 0.71 (between individuals 23 and 27) to 0.34 (between 13 and 30). A model-based Bayesian approach subdivided 38 out of 44 broomrape genotypes into 2 genetic groups and the remaining ones were categorized as mixed genotypes based on Q values. According to an analysis of molecular variance, 99% of the total variation was partitioned within genetic groups. The results demonstrated the potential usefulness of ISSR markers for determination of genetic variation in O. aegyptiaca. Understanding the variability in broomrape is important when attempting to develop resistant host crops against this parasite.

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Determination of genetic diversity among some almond accessions

Genetika ◽

10.2298/gensr1501013p ◽

2015 ◽

Vol 47 (1) ◽

pp. 13-22 ◽

Cited By ~ 1

Author(s):

Hasan Pinar ◽

Sezai Ercisli ◽

Mustafa Unlu ◽

Mustafa Bircan ◽

Aydın Uzun ◽

...

Keyword(s):

Genetic Diversity ◽

Cultivar Identification ◽

Genetic Relationships ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Geographical Isolation ◽

Fruit Species ◽

Rapd And Issr ◽

Simple Sequence

More recently the use of different molecular markers in fruit species to determine particularly genetic diversity, genetic relationships and cultivar identification has been gained more importance. In the study, 13 randomly amplified polimorfic DNA (RAPD) and 4 inter-simple sequence repeat (ISSR) markers were used to evaluate genetic relationships among 95 almong accessions (26 foreign cultivars and 69 national cultivars and selections). The all plant material found in Almond Germplasm Repository in Gaziantep, Turkey. Both RAPD and ISSR markers distinguished the almond cultivars and selections in various levels. 17 RAPD and ISSR markers yielded a total of 73 scorable bands, which 51 are polymorphic. The two marker system exhibited variation with regard to average band sizes and polymorphism ratio. The average polymorphism was higher in ISSR (88%) compared to RAPD (74%). RAPD and ISSR marker systems were found to be useful for determining genetic diversity among almong genotypes and cultivars. Combining of two dendrograms obtained through these markers show different clustering of 96 almond specimens without geographical isolation. These results supported that almonds in Turkey indicated considerable genetic diversity.

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Assessment of ISSR Markers for Tagging Genetic Variability for Yield Components in Small Cardamom (Elettaria cardamomum Maton)

Indian Journal of Agricultural Research ◽

10.18805/ijare.a-5414 ◽

2020 ◽

Author(s):

Sherin Jose ◽

Anusha Prasannan

Keyword(s):

Genetic Diversity ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Similarity Coefficients ◽

Marker Data ◽

Linkage Algorithm ◽

Average Linkage ◽

Breeding Programmes ◽

High Yielding Varieties ◽

Simple Sequence

Genetic diversity among ten small cardamom accessions having variability in yield traits was investigated using inter simple sequence repeat markers (ISSR). A better understanding of the variability in yield is essential for the proper utilization of genotypes in breeding programmes. Of the 10 primers analysed, 5 reported polymorphisms and generated a total of 47 scorable loci, of which 32 were polymorphic revealing 68% polymorphism. The molecular weight of the fragments ranged from 200-1100 bp. Specific banding pattern was observed in high yielding group using ISSR7 (800bp) and with ISSR 3 (800bp) for low yielding group. Genetic diversity analysis within and among the two groups showed maximum diversity in high yielding varieties based on the values of Nei’ s genetic diversity (h) and Shannon’s informative index (I). Dendrogram based on Jaccard’s similarity coefficients were generated based on an average linkage algorithm (UPGMA) using marker data. Clear grouping of the ten accessions of small cardamom into two clusters was observed. These results suggested that ISSR markers could efficiently differentiate the small cardamom genotypes based on yield and can be useful for future cardamom improvement programmes.

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Assessment of the Utility of ISSR Markers for Evaluating Genetic Relationships Among Members of Asimina and Annona

HortScience ◽

10.21273/hortsci.39.4.786a ◽

2004 ◽

Vol 39 (4) ◽

pp. 786A-786

Author(s):

Danielle Rascoe ◽

Kirk W. Pomper* ◽

Jeremiah Lowe ◽

Sheri B. Crabtree ◽

Har Mahdeem ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

The United States ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Asimina Triloba ◽

The North ◽

Research Priority ◽

Custard Apple ◽

Issr Pcr

The genus Asimina has the only temperate representatives of the tropical Annonaceae, or Custard Apple family, and includes eight species that are indigenous to North America. The North American pawpaw Asimina triloba (L.) Dunal has the largest edible fruit native to the United States and is the best-known of these species. The USDA National Clonal Germplasm Repository for Asimina species is located at Kentucky State Univ. (KSU); therefore, assessment of genetic diversity is an important research priority for KSU. The inter-simple sequence repeat PCR (ISSR-PCR) methodology has been used successfully to characterize genetic diversity within and among populations of many plant species. The objective of this study was to assess the utility of ISSR markers in evaluating genetic relationships in members of the Asimina genus, as well as closely related tropical relatives in the Annona genus. Leaf samples were collected from three plants each of Asimina longifolia, A. obovata, A. parviflora, A. reticulata, A. tetramera and A. triloba. Leaf samples were also collected from three plants each of Annona cherimola, A. squamosa, A. reticulata, A. muricata, A. glabra, A. diversifolia, and A. montana. DNA was extracted from leaf samples and subjected to ISSR-PCR using the REDExtract-N-Amp™ Plant PCR Kit. DNA samples were screened with ISSR primers using the Univ. of British Columbia microsatellite primer set #9. Three primers, UBC812, UBC841, and UBC873 were found to produce 84 scorable ISSR markers and allowed the determination of genetic relationships among Asimina and Annona members examined.

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