Characterization and Identification of Pawpaw Cultivars and Advanced Selections by Simple Sequence Repeat Markers

Pawpaw [Asimina triloba (L.) Dunal.], a tree fruit native to eastern North America, is in the beginning stages of commercialization. Cultivars available in the early 20th century have been lost, and significant genetic erosion may have occurred. Polymorphic microsatellite marker loci were developed from enriched genomic libraries. Five marker loci were used to fingerprint 28 cultivars and 13 selections. For the 41 genotypes, 102 alleles were amplified and major allele frequency (0.16–0.94), number of genotypes (2–27), and allele size (144–343 bp) varied greatly by locus. Four loci were highly polymorphic, as indicated by values for expected heterozygosity (He), observed heterozygosity (Ho), and polymorphism information content, but only two alleles were detected at locus Pp-C104. A high level of genetic diversity was observed in the studied genotypes. The Ho (0.68) and He (0.70) were similar and indicated few null alleles. In the 41 genotypes, 39 unique fingerprints were observed. These new microsatellite marker loci will be useful for cultivar fingerprinting, management of collections, and investigation of genetic diversity in collections and wild populations. Grouping of genotypes in an unweighted pair group method with arithmetic mean dendrogram was generally consistent with their origins.

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Genetic diversity and relationships among Secale L. based on RAMP markers

Chinese Journal of Agricultural Biotechnology ◽

10.1079/cjb200419 ◽

2004 ◽

Vol 1 (2) ◽

pp. 73-78 ◽

Cited By ~ 3

Author(s):

Shang Hai-Ying ◽

Zheng You-Liang ◽

Wei Yu-Ming ◽

Wu Wei ◽

Yan Ze-Hong

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

Pcr Amplification ◽

Group Method ◽

Transitional Region ◽

Arithmetic Average ◽

Pair Group ◽

Broad Leaf ◽

Polymorphic Bands ◽

High Level

AbstractGenetic diversity and relationships among 21 accessions of Secale L., including three species and 10 subspecies, were evaluated using RAMP markers. Forty-one out of 80 (50.5%) RAMP primers, which produced clear and polymorphic bands, were selected for PCR amplification of genomic DNA. A total of 446 bands were amplified from the 41 primers, and 428 of these bands (about 96%) were polymorphic. Three to 19 polymorphic bands could be amplified from each primer, with an average of 10.4 bands. The RAMP-based genetic similarity (GS) values among the 21 Secale accessions ranged from 0.266 to 0.658, with a mean of 0.449. A high level of genetic variation was found between or within the wild populations and the cultivars. Based on the GS matrix, a dendrogram was constructed using the unweighted pair group method with arithmetic average (UPGMA). All 21 accessions could be distinguished by RAMP markers. Clustering results showed that the genetic diversity of Secale based on RAMP markers was correlated with geographical distribution. Six rye cultivars, originating from Poland, Portugal, Mexico, Hungary, Armenia and Ukraine, were clustered into one group. The six countries are all located in the transitional region of broad-leaf forests between maritime and continental temperate zones, with narrow latitude span. In comparison, the other five cultivars from countries scattered over a region with large latitude span were distributed within different groups or subgroups. Genetic relationships based on RAMP markers had great deviation from the original taxonomy. Some subspecies of the same species were distributed within different groups, while some accessions of different species were closely clustered into one subgroup. These results suggest that RAMP markers could be an effective technique for detecting genetic diversity among Secale and give some useful information about its phylogenic relationships.

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Genetic Diversity and Population Structure of Alnus cremastogyne as Revealed by Microsatellite Markers

Forests ◽

10.3390/f10030278 ◽

2019 ◽

Vol 10 (3) ◽

pp. 278 ◽

Cited By ~ 2

Author(s):

Hong-Ying Guo ◽

Ze-Liang Wang ◽

Zhen Huang ◽

Zhi Chen ◽

Han-Bo Yang ◽

...

Keyword(s):

Genetic Diversity ◽

Geographical Distribution ◽

Mantel Test ◽

Group Method ◽

Arithmetic Means ◽

Mountain Area ◽

Pair Group ◽

Hill Area ◽

Population Genetic Variation ◽

High Level

Alnus cremastogyne Burk. is a nonleguminous, nitrogen-fixing tree species. It is also the most important endemic species of Alnus Mill. in China, possessing important ecological functions. This study investigated population genetic variation in A. cremastogyne using 175 trees sampled from 14 populations native to Sichuan Province with 25 simple sequence repeat (SSR) markers. Our analysis showed that A. cremastogyne has an average of 5.83 alleles, 3.37 effective alleles, an expected heterozygosity of 0.63, and an observed heterozygosity of 0.739, indicating a relatively high level of genetic diversity. The A. cremastogyne populations in Liangshan Prefecture (Meigu, Mianning) showed the highest level of genetic diversity, whereas the Yanting population had the lowest. Our analysis also showed that the average genetic differentiation of 14 A. cremastogyne populations was 0.021. Analysis of molecular variance (AMOVA) revealed that 97% of the variation existed within populations; only 3% was among populations. Unweighted pair-group method with arithmetic means (UPGMA) clustering and genetic structure analysis showed that the 14 A. cremastogyne populations could be clearly divided into three clusters: Liangshan Prefecture population, Ganzi Prefecture population, the other population in the mountain area around the Sichuan Basin and central Sichuan hill area, indicating some geographical distribution. Further analysis using the Mantel test showed that this geographical distribution was significantly correlated with elevation.

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Genetic Diversity in Populations of Phytophthora citricola Associated with Horticultural Crops in California

Plant Disease ◽

10.1094/pdis-91-12-1556 ◽

2007 ◽

Vol 91 (12) ◽

pp. 1556-1563 ◽

Cited By ~ 11

Author(s):

R. G. Bhat ◽

G. T. Browne

Keyword(s):

Genetic Diversity ◽

Fragment Length Polymorphism ◽

Group Method ◽

Aflp Data ◽

Analysis Of Molecular Variance ◽

Molecular Variance ◽

Horticultural Crops ◽

Pair Group ◽

Phytophthora Citricola ◽

High Level

California populations of the plant pathogen Phytophthora citricola were examined for amplified fragment length polymorphism (AFLP), pathogenicity on almond, and sensitivity to mefenoxam. The characterizations of AFLP variation and mefenoxam sensitivity were based on 86 isolates (44 from almond, 11 from avocado, 3 from strawberry, 18 from walnut, and 10 from six other hosts). Cluster analysis of the AFLP data using the unweighted pair group method indicated a high level of genetic diversity among the isolates, and four main clusters were identified—one dominated by isolates from almond, another including all isolates from avocado, and two including isolates from several hosts other than avocado. Analysis of molecular variance revealed that 38.4 and 24.9% of the AFLP variation were associated with host and geographical factors, respectively. Of 24 isolates, including those from almond, avocado, strawberry, and walnut, 22 were aggressive on almond shoots; there was no evidence of host specificity. All but 1 of the 86 isolates grew at different rates on V8 juice medium amended with mefenoxam at 1 ppm, indicating partial tolerance to the fungicide. Isolates of P. citricola from California populations are genetically diverse, and much of the variation is associated with host and geography. These populations are all potentially pathogenic on almond and tolerant to mefenoxam.

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Genetic Diversity and Origin of Slovene Common Bean (Phaseolus vulgaris L.) Germplasm as Revealed by AFLP Markers and Phaseolin Analysis

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.131.2.242 ◽

2006 ◽

Vol 131 (2) ◽

pp. 242-249 ◽

Cited By ~ 21

Author(s):

Jelka Šustar-Vozlič ◽

Marko Maras ◽

Branka Javornik ◽

Vladimir Meglič

Keyword(s):

Genetic Diversity ◽

Phaseolus Vulgaris ◽

Common Bean ◽

Seed Protein ◽

Fragment Length Polymorphism ◽

Aflp Markers ◽

Group Method ◽

Phaseolus Vulgaris L ◽

Pair Group ◽

High Level

There is a long tradition of common bean cultivation in Slovenia, which has resulted in the development of numerous landraces in addition to newly established cultivars. The genetic diversity of 100 accessions from the Genebank of the Agricultural Institute of Slovenia (AIS) were evaluated with amplified fragment length polymorphism (AFLP) markers and phaseolin seed protein. Twenty-seven standard accessions of known Mesoamerican and Andean origin, 10 wild Phaseolus vulgaris accessions and two related species, P. coccineus L. and P. lunatus L., were also included. Ten AFLP primer combinations produced 303 polymorphic bands, indicating a relatively high level of genetic diversity. Based on the marker data, unweighted pair group method with arithmethic mean (UPGMA) analysis and principal coordinate analysis (PCoA) all P. vulgaris accessions were separated into three well-defined groups. Two groups consisted of accessions of Mesoamerican and Andean origin, while the third was comprised of only four wild P. vulgaris accessions. A set of Slovene accessions formed a well-defined sub-group within the Andean cluster, showing their unique genetic structure. These data were supported by phaseolin analysis, which also revealed additional variants of “C” and “T” phaseolin types. The results are in agreement with previous findings concerning diversification of common bean germplasm introduced in Europe.

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Genetic Diversity of Iranian Clones of Common Reed (Phragmites australis) Based on Morphological Traits and RAPD Markers

Weed Science ◽

10.1614/ws-d-10-00163.1 ◽

2011 ◽

Vol 59 (3) ◽

pp. 366-375 ◽

Cited By ~ 2

Author(s):

Marjan Diyanat ◽

Ali A. S. Booshehri ◽

Hassan M. Alizadeh ◽

Mohammad R. Naghavi ◽

Hamid R. Mashhadi

Keyword(s):

Genetic Diversity ◽

Rapd Markers ◽

Rapd Analysis ◽

Common Reed ◽

Group Method ◽

Successful Management ◽

Morphological Comparison ◽

Pair Group ◽

High Level ◽

Methods Of Control

The genetic diversity of 39 clones of common reed originating from different geographical areas of Iran were evaluated using morphological and RAPD analyses. High level of morphological variation was observed among clones. The 16 primers used in this study amplified 149 scorable RAPD loci among which 123 were polymorphic (83.1%). A dendrogram was prepared on the basis of a similarity matrix of RAPD data using the unweighted pair-group method with arithmetic averages (UPGMA) algorithm and separated the 39 clones into four groups, which mainly were in accordance with geographical origins. The results of the morphological comparison mostly corresponded with the results of RAPD analysis. It is possible that these variations among clones will affect successful management of common reed using chemical or the other methods of control.

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Analysis of genetic diversity of African yam bean using SSR markers derived from cowpea

Plant Genetic Resources ◽

10.1017/s1479262115000064 ◽

2015 ◽

Vol 14 (1) ◽

pp. 50-56 ◽

Cited By ~ 3

Author(s):

Ndenum S. Shitta ◽

Michael T. Abberton ◽

Adenubi I. Adesoye ◽

Daniel B. Adewale ◽

Olaniyi Oyatomi

Keyword(s):

Genetic Diversity ◽

Polymorphic Information Content ◽

Group Method ◽

Arithmetic Average ◽

African Yam Bean ◽

Pair Group ◽

Ssr Primers ◽

Nutritional Qualities ◽

High Level ◽

Average Cluster

African yam bean, AYB (Sphenostylis stenocarpa Hochst. ex. A. Rich Harms), is a tuberous legume of tropical Africa. AYB has the potential to significantly boost food security due to its considerable nutritional qualities. However, the crop is underutilized. To efficiently utilize AYB genetic resources for its improvement, it is necessary to understand the crop's diversity. This study investigated the amplification ability of 36 cowpea simple sequence repeat (SSR) primers across AYB genomic DNA, extracted from 67 accessions. Thirteen (36%) of the cowpea SSRs showed transferability in AYB. Eight of these SSRs amplified above 60% of AYB accessions and generated 55 polymorphic fragments with an average of 6.9 per primer. Polymorphic information content ranged from 0.6691 to 0.8857 with an average of 0.7791. This study also assessed the genetic diversity within 67 AYB accessions using eight cowpea (Vigna unguiculata L. Walp)-derived SSR primers. The result revealed a high level of genetic diversity with simple matching coefficient ranging from 0.458 to 1.000. A dendrogram depicting three main clusters was generated based on unweighted pair group method with arithmetic average. Cluster 1 was the most diverse with a dissimilarity range of 0.517–1.000. The level of genetic diversity revealed in this study indicates that the studied AYB germplasm can be exploited for genetic improvement. Additionally, the transferable markers will aid AYB genome research and also make possible the comparative mapping between AYB and cowpea.

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Genetic diversity of Juglans sigillata Dode germplasm in Yunnan Province, China, as revealed by SSRs

Plant Genetic Resources ◽

10.1017/s1479262120000441 ◽

2020 ◽

pp. 1-10

Author(s):

Shaoyu Chen ◽

Tao Wu ◽

Liangjun Xiao ◽

Delu Ning ◽

Li Pan

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Yunnan Province ◽

Allelic Richness ◽

Geographic Distance ◽

Group Method ◽

Pair Group ◽

Ssr Loci ◽

Juglans Sigillata ◽

High Level

Abstract Iron walnut, Juglans sigillata Dode, restricted to southwestern China, has its centre of distribution in Yunnan Province which has a varied climate, geography and rich plant diversity. Yunnan contains abundant J. sigillata germplasm. In this study, a provincial-scale set of walnut germplasm resources (14 populations comprising 1122 individuals) was evaluated for genetic diversity based on 20 simple sequence repeat (SSR) loci. The number of SSR alleles per locus ranged from 7 to 27, with an average of 17.55. Mean allelic richness and mean private allelic richness ranged from 3.40 to 4.62 and 0.11 to 0.36, with average of 3.93 and 0.30, respectively. Expected heterozygosity (He) varied from 0.26 to 0.78, with an average of 0.57. Polymorphism information content ranged from 0.22 to 0.79, with an average of 0.57. Genetic differentiation (FST) was 0.05, indicating that only 5% of total genetic variability was inter-populational, a finding supported by an analysis of molecular variance and STRUCTURE analysis. Relatively high gene flow (Nm = 6.70) was observed between populations. A unweighted pair-group method with arithmetic analysis classified the 14 populations into two major groups. Mantel testing uncovered a significant correlation between geographic distance and genetic distance (r = 0.33, P = 0.04). Overall, the research revealed a moderately high level of genetic diversity in the germplasm and low genetic differentiation among populations, which showed great potential for further development and exploitation of this resource.

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Genetic Diversity of Iraqi Date Palms Revealed By Microsatellite Polymorphism

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.136.4.282 ◽

2011 ◽

Vol 136 (4) ◽

pp. 282-287 ◽

Cited By ~ 19

Author(s):

Hussam S.M. Khierallah ◽

Saleh M. Bader ◽

Michael Baum ◽

Alladin Hamwieh

Keyword(s):

Genetic Diversity ◽

Date Palm ◽

Phoenix Dactylifera ◽

Principal Coordinate Analysis ◽

Group Method ◽

Arithmetic Average ◽

Pair Group ◽

Ssr Primers ◽

High Level ◽

Simple Sequence

Genetic diversity in 30 date palm (Phoenix dactylifera L.) cultivars in Iraq representing 24 female and six male cultivars was investigated using 22 microsatellite [simple sequence repeat (SSR)] primers. The tested SSR markers showed a high level of polymorphism. A total of 188 alleles were detected at the 22 loci ranging from three to 21 with an average of 8.54 alleles per locus. The average of heterozygosity for all cultivars was 0.503; genetic distance among cultivars varied from 0.171 to 0.938 indicating diverse relationships. The cultivar Ghanami Akhder was highly divergent from ‘Ghnami Ahmer’, whereas ‘Jamal Al-Dean’ was very closely related to ‘Qitaz’. Unweighted pair group method arithmetic average ordered date palm cultivars into two main clusters. Principal coordinate analysis exhibited the similar clusters of cultivars as in the dendrogram.

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High level of genetic diversity among spelt germplasm revealed by microsatellite markers

Genome ◽

10.1139/g04-065 ◽

2004 ◽

Vol 47 (6) ◽

pp. 1043-1052 ◽

Cited By ~ 14

Author(s):

P Bertin ◽

D Grégoire ◽

S Massart ◽

D de Froidmont

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum L ◽

Genetic Distances ◽

Group Method ◽

Germplasm Collections ◽

Pair Group ◽

Genetic Diversity And Structure ◽

The Mean ◽

High Level ◽

Shared Alleles

The genetic diversity of spelt (Triticum aestivum (L.) Thell. subsp. spelta (L.) Thell.) cultivated presently is very narrow. Although the germplasm collections of spelt are extensive, the related genetic knowledge is often lacking and makes their use for genetic improvement difficult. The genetic diversity and structure of the spelt gene pool held in gene banks was determined using 19 simple sequence repeat (SSR) markers applied to 170 spelt accessions collected from 27 countries and 4 continents. The genetic distances (1 – proportion of shared alleles) were calculated and an unweighted pair-group method with arithmetic averaging (UPGMA)-based dendrogram was generated. The genetic diversity was high: 259 alleles were found and the mean interaccession genetic distance was 0.782 ± 0.141. The dendrogram demonstrated the much higher genetic diversity of spelt held in germplasm collections than in the currently used genotypes. Accessions with the same geographical origin often tended to cluster together. Those from the Middle East were isolated first. All but one of the Spanish accessions were found in a unique subcluster. Most accessions from eastern Europe clustered together, while those from northwestern Europe were divided into two subclusters. The accessions from Africa and North America were not separated from the European ones. This analysis demonstrates the extent of genetic diversity of spelts held in germplasm collections and should help to widen the genetic basis of cultivated spelt in future breeding programs.Key words: spelt, SSR, microsatellites, genetic diversity, germplasm.

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Genetic Diversity and Population Structure of Japanese Plum-Type (Hybrids of P. salicina) Accessions Assessed by SSR Markers

Agronomy ◽

10.3390/agronomy11091748 ◽

2021 ◽

Vol 11 (9) ◽

pp. 1748

Author(s):

Brenda I. Guerrero ◽

M. Engracia Guerra ◽

Sara Herrera ◽

Patricia Irisarri ◽

Ana Pina ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Group Method ◽

Japanese Plum ◽

Pair Group ◽

Prunus Salicina ◽

Wide Range ◽

High Level ◽

Informative Content

Japanese plum (Prunus salicina Lindl.) is widely distributed in temperate zones across the world. Since its introduction to USA in the late 19th century, this species has been hybridized with up to 15 different diploid Prunus species. This high level of introgression has resulted in a wide range of traits and agronomic behaviors among currently grown cultivars. In this work, 161 Japanese plum-type accessions were genotyped using a set of eight Simple Sequence Repeats (SSR) markers to assess the current genetic diversity and population structure. A total of 104 alleles were detected, with an average of 13 alleles per locus. The overall Polymorphic Informative Content (PIC) value of SSR markers was 0.75, which indicates that these SSR markers are highly polymorphic. The Unweighted Pair Group Method with Arithmetic (UPGMA) dendrogram and the seven groups inferred by Discriminant Analysis of Principal Components (DAPC) revealed a strong correlation of the population structure to the parentage background of the accessions, supported by a moderate but highly significant genetic differentiation. The results reported herein provide useful information for breeders and for the preservation of germplasm resources.

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