Genetic analysis of a heritage variety collection

Microsatellite DNA analysis is a powerful tool for assessing population genetics. The main aim of this study was to assess the genetic potential of the peregrine falcon population covered by the restitution program. We characterized individuals from breeders that set their birds for release into the wild and birds that have been reintroduced in previous years. This was done using a well-known microsatellite panel designed for the peregrine falcon containing 10 markers. We calculated the genetic distance between individuals and populations using the UPGMA (unweighted pair group method with arithmetic mean) method and then performed a Principal Coordinates Analysis (PCoA) and constructed phylogenetic trees, to visualize the results. In addition, we used the Bayesian clustering method, assuming 1–15 hypothetical populations, to find the model that best fit the data. Units were segregated into groups regardless of the country of origin, and the number of alleles and observed heterozygosity were different in different breeding groups. The wild and captive populations were grouped independent of the original population.

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AFLP analysis of genetic variation within the two economically important Anatolian grapevine (Vitis vinifera L.) varietal groups

Genome ◽

10.1139/g05-121 ◽

2006 ◽

Vol 49 (5) ◽

pp. 467-475 ◽

Cited By ~ 24

Author(s):

Ali Ergül ◽

Kemal Kazan ◽

Sümer Aras ◽

Volkan Çevik ◽

Hasan Çelik ◽

...

Keyword(s):

Vitis Vinifera ◽

Group Method ◽

Vitis Vinifera L ◽

Aflp Analysis ◽

Pair Group ◽

Length Polymorphisms ◽

Upgma Cluster Analysis ◽

History Of ◽

Historical Role ◽

The Rich

The Anatolian region of modern-day Turkey is believed to have played an important role in the history of grapevine (Vitis vinifera L.) domestication and spread. Despite this, the rich grape germplasm of this region is virtually uncharacterized genetically. In this study, the amplified fragment length polymorphisms (AFLP)-based genetic relations of the grapevine accessions belonging to the 2 economically important Anatolian table grape varietal groups known as V. vinifera 'Misket' (Muscat) and V. vinifera 'Parmak' were studied. Thirteen AFLP primer combinations used in the analyses revealed a total of 1495 (35.5% polymorphic) and 1567 (34.6% polymorphic) DNA fragments for the 'Misket' and 'Parmak' varietal groups, respectively. The unweighted pair-group method with arthimetic averaging (UPGMA) cluster analysis and principal coordinate analysis (PCA) conducted on polymorphic AFLP markers showed that both varietal groups contain a number of synonymous (similar genotypes known by different names) as well as homony mous (genetically different genotypes known by the same name) accessions. Our results also showed that 6 of the Anatolian 'Misket' genotypes were genetically very similar to V. vinifera 'Muscat of Alexandria', implying that these genotypes might have played some role in the formation of this universally known grape cultivar. Finally, the close genetic similarities found here between 'Muscat of Alexandria' and V. vinifera 'Muscat of Hamburg' support the recent suggestion that 'Muscat of Hamburg' probably originated from 'Muscat of Alexandria' through spontaneous hybridizations. Overall, the results of this study have implications for not only preservation and use of the Anatolian grape germplasm, but also better understanding of the historical role that this region has played during the domestication of grapes.Key words: 'Misket', 'Parmak', AFLP, Vitis vinifera L.

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Genetic diversity among Mycobacterium tuberculosis isolates from Mexican patients

Canadian Journal of Microbiology ◽

10.1139/w08-051 ◽

2008 ◽

Vol 54 (8) ◽

pp. 610-618

Author(s):

G. Vázquez-Marrufo ◽

D. Marín-Hernández ◽

M. G. Zavala-Páramo ◽

G. Vázquez-Narvaez ◽

C. Álvarez-Aguilar ◽

...

Keyword(s):

Genetic Diversity ◽

Mycobacterium Tuberculosis ◽

Gene Diversity ◽

Group Method ◽

Tuberculosis Complex ◽

Principal Coordinates Analysis ◽

Strain Distribution Pattern ◽

Pair Group ◽

Principal Coordinates ◽

Unweighted Pair Group Method

Forty-six isolates of the Mycobacterium tuberculosis complex were typified by PCR of the IS6110 region and by Mycobacterium bovis specific primers JB21/JB22. Isolate MVG01 was typified as M. bovis, being the first record of a case of human tuberculosis caused by this species in Mexico. RAPD–PCR was used to describe the genetic diversity of the remaining 45 M. tuberculosis complex isolates. The corrected genotypic diversity value calculated for the analyzed population was 0.96, the estimated mean gene diversity was 0.235, and the corrected Shannon–Weiner index was 2.15. All allele–loci combinations generated showed significant linkage disequilibria. The distribution of genetic variation was analyzed both by the unweighted pair group method with arithmetic averages clustering and by principal coordinates analysis. Unweighted pair group method with arithmetic averages clustering resulted in a tree with four main clusters and one unclustered strain (MVG20), the principal coordinates analysis strain distribution pattern being consistent with this grouping. The obtained results suggest that the studied isolates belong to a clonal population having significant genetic diversity. Our genetic diversity results are comparable with those reported for other populations of M. tuberculosis, although only three RAPD primers were used.

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Genetic Diversity Among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

Sustainability ◽

10.3390/su13126830 ◽

2021 ◽

Vol 13 (12) ◽

pp. 6830

Author(s):

Murat Guney ◽

Salih Kafkas ◽

Hakan Keles ◽

Mozhgan Zarifikhosroshahi ◽

Muhammet Ali Gundesli ◽

...

Keyword(s):

Genetic Diversity ◽

Plant Genetic Resources ◽

Juglans Regia ◽

Genetic Distances ◽

Mean Value ◽

Central Anatolia ◽

Group Method ◽

Arithmetic Average ◽

Pair Group ◽

Principal Coordinates

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

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Microsatellite Characterization of Malaysian Mahseer (Tor spp.) for Improvement of Broodstock Management and Utilization

Animals ◽

10.3390/ani11092633 ◽

2021 ◽

Vol 11 (9) ◽

pp. 2633

Author(s):

Poh Chiang Chew ◽

Annie Christianus ◽

Jaapar M. Zudaidy ◽

Md Yasin Ina-Salwany ◽

Chou Min Chong ◽

...

Keyword(s):

Genetic Variation ◽

Gene Flow ◽

Genetic Differentiation ◽

Genetic Relatedness ◽

Genetic Distances ◽

Group Method ◽

Genetic Management ◽

Principal Coordinates Analysis ◽

Principal Coordinates ◽

Geographical Regions

In this study, a mixture of Tor tambra and T. tambroides with unknown genetic background were collected from 11 localities in Malaysia for broodstock development and sperm cryo-banking. This study aims to assess the microsatellite (simple sequence repeat, SSR) variation, genetic diversity, genetic differentiation, level of gene flow, population structure, genetic relatedness and their demographic aspects among these Tor populations, in addition to establishing their SSR profile by employing 22 SSR markers via fragment analysis. Total genomic DNA was extracted from 181 samples (91 cryopreserved milt samples and 90 scale samples of live broodfish). Results showed the Tor spp. collection retained their genetic variation but exhibited excessive homozygosity among individuals within population. Moderate genetic differentiation was shown among the populations, with highly significant (p < 0.001) fixation indices (FST, FIS and FIT). A low gene flow over all loci (Nm 1.548) indicates little genetic variation transfer between populations. The genetic structures of all the populations were successfully resolved into four main clusters by an unweighted pair group method with arithmetic mean (UPGMA) dendrogram generated based on Nei’s genetic distances. The population structures based on principal coordinates analysis (PCoA) and the Bayesian model also suggested four distinct clusters following geographical regions and eight closely related populations. This study provided a useful baseline reference for better genetic management and utilization of the Tor spp. stocks in their breeding and conservation programmes.

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Kemiripan genetik klon karet (Hevea brasiliensis Muell. Arg.) berdasarkan metode Amplified Fragment Length Polymorphisms (AFLP) Genetic similarity of rubber clones (Hevea brasiliensis Muell. Arg) based on Amplified Fragment Length Polymorphisms (AFLP) method

E-Journal Menara Perkebunan ◽

10.22302/ppbbi.jur.mp.v71i1.180 ◽

2016 ◽

Vol 71 (1) ◽

Author(s):

. NURHAIMI-HARIS ◽

Hajrial ASWIDINNOOR ASWIDINNOOR ◽

Nurita TORUAN-MATHIUS ◽

Agus PURWANTARA

Keyword(s):

Fragment Length ◽

Genetic Similarity ◽

Numerical Taxonomy ◽

Group Method ◽

Corynespora Cassiicola ◽

Resistant Clone ◽

Expression Study ◽

Multivariate System ◽

Pair Group ◽

Length Polymorphisms

Summary Genetic similarity among ten rubber clones originating from the Wickham collection was studied by Amplified Fragment Length Polymorphism (AFLP) markers. These clones have different levels of resistance to Corynespora cassiicola, one of the major pathogens in rubber plantations. The information resulted from this study will be used to determine resistant and susceptible clones which will be used in expression study of the genes encoding plant resistance to C. cassiicola. Genetic similarity values of clones were calculated from all AFLP markers and used to produce a dendrogram using Unweight Pair-Group Method Arithmetic (UPGMA) based on Numerical Taxonomy and Multivariate System (NTSYS) version 1.8 pc. A total of 481 fragments were detected by using ten pairs of selective AFLP primers, and 233 fragments (48,4 %) of them were polymorphic. The results clearly demonstrated that genetic background of these ten clones were 85.5% similar. At 88.0% similarity level, the clones could be divided into three clusters. Genetic similarity of IRR 100 (resistant clone) with RRIC 103, PPN 2444 and IAN 873 (susceptible clones) was 90.5, 89.5 and 89.0% respectively, while genetic similarity of other three resistant clones (AVROS 2037, PR 255 and BPM 1) to those susceptible clones was 88.0%. The lowest genetic similarity (85.5%) was found between RRIC 100 (resistant clone) and those three susceptible clones. By considering the distribution and the source of clones, AVROS 2037 (resistant) and PPN 2444 (susceptible) clones which have 88.0% genetic similarity will finally be selected for the expression study of the genes. Kemiripan genetik sepuluh klon karet yang berasal dari koleksi Wickham dipelajari dengan menggunakan marka Amplified Fragment Length Polymorphism (AFLP). Kesepuluh klon tersebut memiliki tingkat resistensi berbeda terhadap Corynespora cassiicola, salah satu cendawan patogen penting pada daun tanaman karet. Informasi yang diperoleh dalam penelitian ini akan digunakan untuk menetapkan klon resisten dan klon rentan untuk digunakan dalam mempelajari ekspresi gen yang menyandikan ketahanan tanaman karet terhadap C. cassiicola. Nilai kemiripan genetik kesepuluh klon karet dihitung berdasarkan semua marka AFLP yang diperoleh dan selanjutnya digunakan untuk. membuat dendrogram dengan menggunakan Unweight Pair-Group Method Arithmetic (UPGMA) berdasarkan Numerical Taxonomy and Multivariate System (NTSYS) version 1.8 pc. Dengan menggunakan 10 pasang primer AFLP selektif diperoleh sebanyak 481 fragmen DNA, S 2037, PR 255 and BPM 1) to those susceptible clones was 88.0%. The lowest genetic similarity (85.5%) was found between RRIC 100 (resistant clone) and those three susceptible clones. By considering the distribution and the source of clones, AVROS 2037 (resistant) and PPN 2444 (susceptible) clones which have 88.0% genetic similarity will finally be selected for the expression study of the genes. 233 fragmen (48,4 %) di antaranya polimorfik Dendrogram dengan nyata menunjukkan bahwa 85,5% latar belakang genetik kesepuluh klon karet tersebut adalah sama, dan pada tingkat 88,0% kesepuluh klon terpisah dalam tiga kelompok. Kemiripan genetik klon IRR 100 (resisten) dengan klon rentan RRIC 103, PPN 2444 dan IAN 873 masing-masing adalah 90,5, 89,5 dan 89,0%, sedangkan kemiripan genetik tiga klon resisten lainnya (AVROS 2037, PR 255 dan BPM 1) dengan ketiga klon rentan yang sama adalah 88,0%. Kemiripan genetik terendah (85,5%) terdapat antara klon RRIC 100 (resisten) dengan ketiga klon rentan tersebut. Dengan mempertimbangkan distribusi penyebaran klon dan asal klon maka klon resisten AVROS 2037 dan klon rentan PPN 2444 yang memiliki kemiripan genetik 88,0% akan dipilih untuk digunakan dalam studi ekspresi gen tanaman karet. acerun:yes'> Kesepuluh klon tersebut memiliki tingkat resistensi berbeda terhadap Corynespora cassiicola, salah satu cendawan patogen penting pada daun tanaman karet. Informasi yang diperoleh dalam penelitian ini akan digunakan untuk menetapkan klon resisten dan klon rentan untuk digunakan dalam mempelajari ekspresi gen yang menyandikan ketahanan tanaman karet terhadap C. cassiicola. Nilai kemiripan genetik kesepuluh klon karet dihitung berdasarkan semua marka AFLP yang diperoleh dan selanjutnya digunakan untuk. membuat dendrogram dengan menggunakan Unweight Pair-Group Method Arithmetic (UPGMA) berdasarkan Numerical Taxonomy and Multivariate System(NTSYS) version 1.8 pc. Dengan menggunakan 10 pasang primer AFLP selektif diperoleh sebanyak 481 fragmen DNA, S 2037, PR 255 and BPM 1) to those susceptible clones was 88.0%. The lowest genetic similarity (85.5%) was found between RRIC 100 (resistant clone) and those three susceptible clones. By considering the distribution and the source of clones, AVROS 2037 (resistant) and PPN 2444 (susceptible) clones which have 88.0% genetic similarity will finally be selected for the expression study of the genes.

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A preliminary genetic structure study of the non-native weed, common tansy (Tanacetum vulgare)

Canadian Journal of Plant Science ◽

10.4141/cjps10203 ◽

2011 ◽

Vol 91 (4) ◽

pp. 717-723 ◽

Cited By ~ 1

Author(s):

Benjamin Clasen ◽

Nicole Moss ◽

Monika Chandler ◽

Alan Smith

Keyword(s):

Genetic Structure ◽

North America ◽

Small Variation ◽

Structure Study ◽

Inter Simple Sequence Repeat ◽

Principal Coordinates Analysis ◽

Tanacetum Vulgare ◽

Pair Group ◽

Principal Coordinates ◽

Disturbed Areas

Clasen, B. M., Moss, N. G., Chandler, M. A. and Smith, A. G. 2011. A preliminary genetic structure study of the non-native weed, common tansy (Tanacetum vulgare). Can. J. Plant Sci. 91: 717–723. Common tansy is an herbaceous perennial member of the Asteraceae and is considered a weed in North America. Common tansy was introduced deliberately for use as a funerary herb, medicine, preservative, and animal and insect repellent. It is known to escape cultivation and invade disturbed areas, spreading both sexually and asexually. This paper reports a preliminary analysis of the genetic structure of 10 invasive common tansy populations in Minnesota and Montana, USA, and Alberta, Canada. Ninety polymorphic loci were found using six inter simple sequence repeat (ISSR) primers used to amplify DNA from 40 individuals from 10 discrete populations. The diversity within and among populations was assessed using the Dice coefficient of similarity and AMOVA. The AMOVA showed that diversity within populations was generally high and that there was relatively small variation among populations. An unweighted pair-group with arithmetic mean (UPGMA) dendrogram was constructed based on the distance between populations, and demonstrated substantial and distinct clustering of a population from Ramsey County, Minnesota. A principal coordinates analysis clustered all individuals from Ramsey County distinctly from other individuals, indicating a possible limited gene flow among this population and the other populations sampled in this study. Understanding genetic diversity and the distribution of diversity within and among populations may help predict the potential for successful management of common tansy populations in North America.

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Kemiripan genetik klon karet (Hevea brasiliensis Muell. Arg.) berdasarkan metode Amplified Fragment Length Polymorphisms (AFLP) Genetic similarity of rubber clones (Hevea brasiliensis Muell. Arg) based on Amplified Fragment Length Polymorphisms (AFLP) method

E-Journal Menara Perkebunan ◽

10.22302/iribb.jur.mp.v71i1.180 ◽

2016 ◽

Vol 71 (1) ◽

Author(s):

. NURHAIMI-HARIS ◽

Hajrial ASWIDINNOOR ASWIDINNOOR ◽

Nurita TORUAN-MATHIUS ◽

Agus PURWANTARA

Keyword(s):

Fragment Length ◽

Genetic Similarity ◽

Numerical Taxonomy ◽

Group Method ◽

Corynespora Cassiicola ◽

Resistant Clone ◽

Expression Study ◽

Multivariate System ◽

Pair Group ◽

Length Polymorphisms

Summary Genetic similarity among ten rubber clones originating from the Wickham collection was studied by Amplified Fragment Length Polymorphism (AFLP) markers. These clones have different levels of resistance to Corynespora cassiicola, one of the major pathogens in rubber plantations. The information resulted from this study will be used to determine resistant and susceptible clones which will be used in expression study of the genes encoding plant resistance to C. cassiicola. Genetic similarity values of clones were calculated from all AFLP markers and used to produce a dendrogram using Unweight Pair-Group Method Arithmetic (UPGMA) based on Numerical Taxonomy and Multivariate System (NTSYS) version 1.8 pc. A total of 481 fragments were detected by using ten pairs of selective AFLP primers, and 233 fragments (48,4 %) of them were polymorphic. The results clearly demonstrated that genetic background of these ten clones were 85.5% similar. At 88.0% similarity level, the clones could be divided into three clusters. Genetic similarity of IRR 100 (resistant clone) with RRIC 103, PPN 2444 and IAN 873 (susceptible clones) was 90.5, 89.5 and 89.0% respectively, while genetic similarity of other three resistant clones (AVROS 2037, PR 255 and BPM 1) to those susceptible clones was 88.0%. The lowest genetic similarity (85.5%) was found between RRIC 100 (resistant clone) and those three susceptible clones. By considering the distribution and the source of clones, AVROS 2037 (resistant) and PPN 2444 (susceptible) clones which have 88.0% genetic similarity will finally be selected for the expression study of the genes. Kemiripan genetik sepuluh klon karet yang berasal dari koleksi Wickham dipelajari dengan menggunakan marka Amplified Fragment Length Polymorphism (AFLP). Kesepuluh klon tersebut memiliki tingkat resistensi berbeda terhadap Corynespora cassiicola, salah satu cendawan patogen penting pada daun tanaman karet. Informasi yang diperoleh dalam penelitian ini akan digunakan untuk menetapkan klon resisten dan klon rentan untuk digunakan dalam mempelajari ekspresi gen yang menyandikan ketahanan tanaman karet terhadap C. cassiicola. Nilai kemiripan genetik kesepuluh klon karet dihitung berdasarkan semua marka AFLP yang diperoleh dan selanjutnya digunakan untuk. membuat dendrogram dengan menggunakan Unweight Pair-Group Method Arithmetic (UPGMA) berdasarkan Numerical Taxonomy and Multivariate System (NTSYS) version 1.8 pc. Dengan menggunakan 10 pasang primer AFLP selektif diperoleh sebanyak 481 fragmen DNA, S 2037, PR 255 and BPM 1) to those susceptible clones was 88.0%. The lowest genetic similarity (85.5%) was found between RRIC 100 (resistant clone) and those three susceptible clones. By considering the distribution and the source of clones, AVROS 2037 (resistant) and PPN 2444 (susceptible) clones which have 88.0% genetic similarity will finally be selected for the expression study of the genes. 233 fragmen (48,4 %) di antaranya polimorfik Dendrogram dengan nyata menunjukkan bahwa 85,5% latar belakang genetik kesepuluh klon karet tersebut adalah sama, dan pada tingkat 88,0% kesepuluh klon terpisah dalam tiga kelompok. Kemiripan genetik klon IRR 100 (resisten) dengan klon rentan RRIC 103, PPN 2444 dan IAN 873 masing-masing adalah 90,5, 89,5 dan 89,0%, sedangkan kemiripan genetik tiga klon resisten lainnya (AVROS 2037, PR 255 dan BPM 1) dengan ketiga klon rentan yang sama adalah 88,0%. Kemiripan genetik terendah (85,5%) terdapat antara klon RRIC 100 (resisten) dengan ketiga klon rentan tersebut. Dengan mempertimbangkan distribusi penyebaran klon dan asal klon maka klon resisten AVROS 2037 dan klon rentan PPN 2444 yang memiliki kemiripan genetik 88,0% akan dipilih untuk digunakan dalam studi ekspresi gen tanaman karet. acerun:yes'> Kesepuluh klon tersebut memiliki tingkat resistensi berbeda terhadap Corynespora cassiicola, salah satu cendawan patogen penting pada daun tanaman karet. Informasi yang diperoleh dalam penelitian ini akan digunakan untuk menetapkan klon resisten dan klon rentan untuk digunakan dalam mempelajari ekspresi gen yang menyandikan ketahanan tanaman karet terhadap C. cassiicola. Nilai kemiripan genetik kesepuluh klon karet dihitung berdasarkan semua marka AFLP yang diperoleh dan selanjutnya digunakan untuk. membuat dendrogram dengan menggunakan Unweight Pair-Group Method Arithmetic (UPGMA) berdasarkan Numerical Taxonomy and Multivariate System(NTSYS) version 1.8 pc. Dengan menggunakan 10 pasang primer AFLP selektif diperoleh sebanyak 481 fragmen DNA, S 2037, PR 255 and BPM 1) to those susceptible clones was 88.0%. The lowest genetic similarity (85.5%) was found between RRIC 100 (resistant clone) and those three susceptible clones. By considering the distribution and the source of clones, AVROS 2037 (resistant) and PPN 2444 (susceptible) clones which have 88.0% genetic similarity will finally be selected for the expression study of the genes.

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Phenetic Characterization of Plum Cultivars by High Multiplex Ratio Markers: Amplified Fragment Length Polymorphisms and Inter-simple Sequence Repeats

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.126.1.72 ◽

2001 ◽

Vol 126 (1) ◽

pp. 72-77 ◽

Cited By ~ 19

Author(s):

Luís Goulão ◽

Luisa Monte-Corvo ◽

Cristina M. Oliveira

Keyword(s):

Fragment Length ◽

Simple Sequence Repeats ◽

Group Method ◽

Similarity Coefficients ◽

Pair Group ◽

Multiple Loci ◽

Inter Simple Sequence Repeats ◽

Length Polymorphisms ◽

Amplified Fragment Length Polymorphisms ◽

Simple Sequence

Variability of commercial plum (Prunus L. sp.) cultivars is unknown since breeding often involves intercrossing hybrids with several species but has been based on a low number of parents. Molecular markers like amplified fragment length polymorphisms (AFLP) and inter-simple sequence repeats (ISSR), which sample multiple loci simultaneously, have become increasingly popular, and were used to characterize 24 diploid and four hexaploid cultivars of plum. Seven AFLP and six ISSR primers were used, and resulted in amplification of 379 and 270 products, respectively. Unweighted pair-group method with arithmetic averages (UPGMA) dendrograms, based on similarity coefficients, reflected a clear separation between diploid and hexaploid plums. Among diploid plums, two pairs of cultivars were relatively distinct from the rest, namely `Golden Japan' and `Methley' and `Ozark Premier' and `Songold'. Furthermore, several cultivars were grouped together both with AFLP and ISSR analysis: 1) `Ambra', `Red Beaut', and `Black Beaut', 2) `Black Diamond' and `Royal Diamond', 3) `June Rose', `Santa Rosa', and `Royal Red', and iv) `Freedom', `Larry Ann', and `Queen Rosa'. Although the phenetic classification obtained by the two methods were similar (r = 0.73, for the diploid group), ISSR had a higher reproducibility and percentage of polymorphisms (87.4% vs. 62.8%) than AFLP. Methodological aspects of both markers systems are discussed. Results obtained suggest that the AFLP and ISSR approaches are valuable tools for identification of specific genotypes and analysis of phenetic relationships in plum.

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Preserving Biodiversity in Marginal Rural Areas: Assessment of Morphological and Genetic Variability of a Sicilian Common Bean Germplasm Collection

Plants ◽

10.3390/plants9080989 ◽

2020 ◽

Vol 9 (8) ◽

pp. 989

Author(s):

Maria Carola Fiore ◽

Francesco Maria Raimondo ◽

Francesco Mercati ◽

Ignazio Digangi ◽

Francesco Sunseri ◽

...

Keyword(s):

Common Bean ◽

Rural Areas ◽

Germplasm Collection ◽

Genetic Distances ◽

Ex Situ ◽

Group Method ◽

Gene Pools ◽

Mountain Areas ◽

Pair Group ◽

Principal Coordinates

The historical cultivation of common bean (Phaseolus vulgaris L.) has resulted in the development of local populations/cultivars in restricted Italian rural areas. Many common bean landraces, still cultivated in small mountain areas from Sicily, have become outdated and endangered due to the commercial varieties spreading. These accessions are poorly known but often represent a genetic heritage to be preserved and enhanced. The ex situ conservation of fifty-seven Sicilian common bean landraces was carried out at the “Living Plants Germplasm Bank” at Ucria (Messina, Italy), founded by the Nebrodi Regional Park, together with the “Sicilian Plant Germplasm Repository” of University of Palermo (SPGR/PA). To assess the germplasm genetic diversity, nineteen morphological traits and eight Simple Sequence Repeats (SSRs) were used. Genetic distances among landraces were calculated to construct a clustering tree by using unweighted pair group method arithmetic (UPGMA). Seed germplasm diversity of Sicilian common bean varied from 80.7% to 93.3%, based on six seed descriptors and six leaf, flower, and pod descriptors, respectively, while cluster genetic analysis depicted a clear separation among all the 57 landraces. Principal coordinates (PCoA) and STRUCTURE analyses showed a prevalent rate of admixture between Mesoamerican and Andean gene pools in Sicilian common bean collection, confirming its heterogeneity. The observed high level of diversity evidenced the needs to adopt accurate criterion to plan a definitive ex situ germplasm collection to share agrobiodiversity with local farmers and to avoid any further loss of genetic resources in rural and protected areas.

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