Morphological variation of plantain squirrel Callosciurus notatus (Boddaert, 1785) (Rodentia: Sciuridae) population in West Sumatra, Indonesia

Abstract. Tjong DH, Sari RM, Roesma DI. 2020. Morphological variation of plantain squirrel Callosciurus notatus (Boddaert, 1785) (Rodentia: Sciuridae) population in West Sumatra, Indonesia. Asian J For 21: 54-60. A study about the morphological variation of plantain squirrel among several populations in West Sumatra has been done in West Sumatra. There were 38 specimens of C. notatus collected from Padang, Lubuk Basung, Sangir, and Baso by using a survey and direct collection method. The morphometric measurement was conducted in the Laboratory of Genetic and Biomolecular, Department of Biology, Faculty of Mathematics and Natural Sciences, Andalas University. Morphological measurement data based on 21 external characters and 35 skull characters were analyzed by the Kruskall Wallis test, Principal Component Analysis (PCA), and Unweighted Pair Group Method Arithmetic Average (UPGMA). The result showed that there was morphological variation in ten body characters and nine skull characters. It is necessary to do further research to determine what environmental factors specifically influence certain morphological characters.

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Description and analysis of genetic diversity among squash accessions

Brazilian Archives of Biology and Technology ◽

10.1590/s1516-89132009000200003 ◽

2009 ◽

Vol 52 (2) ◽

pp. 271-283 ◽

Cited By ~ 9

Author(s):

Athanasios L. Tsivelikas ◽

Olga Koutita ◽

Anastasia Anastasiadou ◽

George N. Skaracis ◽

Ekaterini Traka-Mavrona ◽

...

Keyword(s):

Genetic Diversity ◽

Rapd Markers ◽

Clustering Algorithm ◽

Random Amplified Polymorphic Dna ◽

Principal Component ◽

Molecular Data ◽

Optimal Number ◽

Group Method ◽

Arithmetic Average ◽

Pair Group

In this work, the part of the squash core collection, maintained in the Greek Gene Bank, was assessed using the morphological and molecular data. Sixteen incompletely classified accessions of the squash were characterized along with an evaluation of their resistance against two isolates of Fusarium oxysporum. A molecular analysis using Random Amplified Polymorphic DNA (RAPD) markers was also performed, revealing high level of polymorphism. To study the genetic diversity among the squash accessions, a clustering procedure using Unweighed Pair Group Method and Arithmetic Average (UPGMA) algorithm was also adopted. Two independent dendrograms, one for the morphophysiological and one for molecular data were obtained, classifying the accessions into two and three main clusters, respectively. Despite the different number of the clusters there were many similarities between these two dendrograms, and a third dendrogram resulting from their combination was also produced, based on Gower's distance and UPGMA clustering algorithm. In order to determine the optimal number of clusters, the upper tail approach was applied. The more reliable clustering of the accessions was accomplished using RAPD markers as well as the combination of the two different data sets, classifying the accessions into three significantly different groups. These groups corresponded to the three different cultivated species of C. maxima Duch., C. moschata Duch., and C. pepo L. The same results were also obtained using Principal Component Analysis.

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Palynological observations on the genus Gundelia L. (Asteraceae) growing in Turkey

Phytotaxa ◽

10.11646/phytotaxa.502.1.3 ◽

2021 ◽

Vol 502 (1) ◽

pp. 51-66

Author(s):

MEHMET FIRAT ◽

SELAMI SELVİ

Keyword(s):

Pollen Morphology ◽

Pollen Grains ◽

Principal Component ◽

Polar Axis ◽

Morphological Characters ◽

Group Method ◽

Pair Group ◽

Equatorial Diameter ◽

Polar Diameter ◽

And Cluster Analysis

The pollen morphology of 17 taxa of Gundelia, of which 13 taxa are endemic to Turkey, was investigated by light microscopy (LM) and scanning electron microscopy (SEM). In this study, the pollen morphology of 16 taxa except G. tournefortii was investigated for the first time. The quantitative data were analyzed by descriptive statistics and multivariate statistics. The pollen grains are oblate spheroidal and prolate spheroidal in shape with the polar diameter of 37.01–61.2 μm and the equatorial diameter of 31.2–63.4 μm. The smallest pollen grains were observed in G. anatolica, G. rosea and G. tournefortii, while the largest pollen grains were observed in G. vitekii, G. komagenensis and G. colemerikensis. Pollen ornamentation is echinate in LM and echinate-microperforate in SEM. Statistically, the relationships between pollen characters of the examined taxa were identified using Principal Component Analysis (PCA) and Clustering Analyzis. In addition, a dendrogram was constructed by applying UPGMA based on the determined 15 pollen morphological characters, and the degree of their relationship was discussed. Polar axis, equatorial diameter and colpus length were the major explanations of the pollen morphological characters’ total variation in PCA. Pair group method was used to divide the main pollen taxa into three groups based on the pollen morphology by using arithmetic averages analysis (PCA scatterplot and cluster analysis). As a result, the pollen shape, polar axis, equatorial diameter and spine length were important characters distingushing the taxa from each other. We found some matches and mismatches between pollen and morphological characters, whose significance requires further study.

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GENETIC VARIABILITY OF INDONESIAN PAPAYA ACCESSIONS AS REVEALED BY RANDOM AMPLIFIED POLYMORPHIC DNA AND MORPHOLOGICAL CHARACTERIZATION

Indonesian Journal of Agricultural Science ◽

10.21082/ijas.v20n1.2019.p1-8 ◽

2019 ◽

Vol 20 (1) ◽

pp. 1

Author(s):

Riry Prihatini ◽

Tri Budiyanti ◽

Noflindawati Noflindawati

Keyword(s):

Genetic Diversity ◽

Random Amplified Polymorphic Dna ◽

Principal Component ◽

Accurate Method ◽

Morphological Characters ◽

Morphological Characterization ◽

Fruit Shape ◽

Morphological Data ◽

Group Method ◽

Pair Group

<p class="abstrakinggris">Diverse papaya (<em>Carica</em> sp.) accessions are found in many regions in Indonesia, but their genetic diversity have not yet been studied. Random Amplified Polymorphic DNA (RAPD) is a simple yet accurate method that can be used to examine the genetic diversity of papaya. The study aimed to examine the genetic diversity of Indonesian papaya accessions using RAPD markers and morphological characters. The RAPD was applied on 23 papaya accessions using 30 primers. The appearing bands were further analyzed with the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and Principal Component Analysis (PCA). The molecular results were then compared to the fruit morphological data, including fruit shape, size, flesh color, texture, and flavor. The RAPD analysis revealed that the 23 papaya accessions clustered into six main clades with Dice-Sorensen coefficient similarity ranged from 0.71 to 0.98. The first group consisted of 11 accessions, including both the hybrids and local accessions. The second group consisted of eight accessions especially six Indonesian hybrids, a Mexican Hybrid and a Hawaiian hybrid. The other four groups had a single member namely Sicincin Panjang, Lokal Sumani, Cariso, and Carica. The molecular grouping, however, did not align with the fruit character grouping. Overall, it was implied that the Indonesian papaya accessions were genetically narrow, of which some accessions were closely related to Hawaiian and Mexican accessions. These results can be used as a reference on papaya crossbreeding program in Indonesia.</p>

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Climate Change and Fading Genetic Resources of Parkia biglobosa (Jacq.) in Nigeria Based on SSR Markers

10.20944/preprints201910.0235.v1 ◽

2019 ◽

Author(s):

Jacob Popoola ◽

James Agbolade ◽

Abiodun Ajiboye ◽

Omotolani Akinola ◽

Francis Lewu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Principal Component ◽

Sub Saharan Africa ◽

Group Method ◽

Parkia Biglobosa ◽

Arithmetic Average ◽

Ecological Zones ◽

Pair Group

African locust bean (Parkia biglobosa (Jacq.) is a multi-purpose economic tree with genetic potentials in sub-Saharan Africa. Its cultivation and production is declining with increased aging and genetically threatened throughout its natural ranges. Research efforts are needed to change the present scenario to sustainable cultivation and utilization, hence this present study. This study was aimed at evaluating genetic diversity and geographical spread relationships of twenty landraces collected from different ecological zones of Nigeria using simple sequence repeat (SSR) markers. Ten SSR markers were screened and five primers (PbL02, PbL03, PbL04, PbL05 and PbL09) were selected based on clear amplification products and reproducible scorable bands. The SSR primers detected a total of 55 alleles ranged from 10 to 14 alleles with a mean of 11. The percentage polymorphisms were high and ranged from 68.75 % in PbL04 to 84.21 % in PbL05 with a mean of 74.16 %. The polymorphic information content (PIC) was in the range of 0.31 in PbL02 to 0.37 in PbL09. The genetic diversity and heterozygosity values ranged from 0.39 to 0.50 and 0.00 to 0.68 while the average genetic distance for all pair wise comparisons was 0.31.The first five Principal Component (PC) accounted for 70.20 % of the total variation out of which PC1 (31.50%) and PC2 (19.20%) extracted 49.70% molecular similarity. The dendrogram resulted in separation of the 19 landraces into three major clusters based on unweighted pair group method with arithmetic average. Cluster I comprised of five landraces: ABNo130 and BENo023; OYNo11, KANo125 and NiNo262 while cluster II had only one (BANo116). Cluster III was diverse comprising 13 landraces: ZANo188, KNNo162, KENo220, GMNo076 and EbNo260, ADNo64, EdNo164, KANo137, KENo217, KwNo270, NiNo241, OsNo206 and PLNo120. The homogeneity of alleles among the studied landraces suggested suspicion of loss of genetic intra-specific variation among the landraces of P. biglobosa which calls for concerted efforts toward better cultivation, conservation, management, utilization and genetic improvement of the species in Nigeria.

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Hubungan Kekerabatan Kultivar Talas (Colocasia esculenta) Berdasarkan Karakter Morfologi Organ Vegetatif (The Phenetic Relationship among Taro Cultivar (Colocasia esculenta) Based on Vegetative Morphological Characters)

JURNAL BIOS LOGOS ◽

10.35799/jbl.4.1.2014.4838 ◽

2014 ◽

Vol 4 (1) ◽

Author(s):

Hafsah Hafsah ◽

Topik Hidayat ◽

Kusdianti Kusdianti

Keyword(s):

Computer Software ◽

Morphological Characters ◽

Colocasia Esculenta ◽

Group Method ◽

Dominant Position ◽

Arithmetic Average ◽

Pair Group ◽

Close Relationship ◽

Length Width ◽

Vegetative Characters

Abstrak Telah dilakukan penelitian mengenai hubungan kekerabatan pada delapan kultivar talas (Colocasia esculenta) berdasarkan karakter morfologi organ vegetatif. Kultivar-kultivar tersebut yakni talas kaliurang, burkok, bentul, bogor, sutra, kudo, lampung dan semir. Total karakter yang diamati berjumlah 35 karakter. Karakter-karakter tersebut kemudian dibuat skoring. Hasil skoring dianalisis dengan metode UPGMA (Unwight Pair Group Method with Arithmetic Average) menggunakan program komputer PAUP versi 4.0b10 sehingga terbentuk fenogram. Hasil penelitian menunjukkan variasi morfologi organ vegetatif yang cukup tinggi. Dari seluruh karakter, hanya lima karakter yang tidak menunjukkan adanya perbedaan. Karakter tersebut yaitu bentuk daun dan ujung daun, rasio panjang terhadap lebar daun, pola tepi pelepah dan posisi dominan bentuk helai daun tua. Dari fenogram diketahui bahwa seluruh kultivar yang diamati membentuk dua kelompok utama. Kelompok pertama terdiri dari kaliurang, burkok, bentul, bogor, lampung dan sutra, yang membentuk tiga subkelompok. Kelompok kedua terdiri dari kudo dan semir. Hasil analisis fenetik menunjukkan kultivar bogor dan lampung merupakan dua kultivar yang sangat dekat hubungan kekerabatannya dengan nilai kesamaan sebesar 80%. Kata kunci : Colocasia esculenta, fenetik, kultivar, organ vegetatif Abstract This research was conducted to find out relationship on eight cultivars of taro (Colocasia esculanta) based on vegetative morphological characters. They were kaliurang, burkok, bentul, bogor, sutra, kudo, lampung and semir. Total characters observed were 35 characters and the scoring was also performed. In order to form a phenogram, the scoring then were analyzed using computer software PAUP version 4.0b10, the UPGMA method (Unwight Pair Group Method with Arithmetic Average). Results showed that morphological variation of vegetative characters are quite high. Of all the characters, only five characters that indicated any significant differences. These characters were leaves shape, leaves tip shape, length-width leaves ratio, midrib leaves, and dominant position of the old leaves. From the phenogram, it was known that all cultivars observed were form into two main groups. The first group consists of kaliurang, burkok, bentul, bogor, lampung and sutra, which formed three subgroups. The second group consists of kudo and semir. The results of the phenetic analysis showed the cultivar bogor and lampung are two cultivars that are very close relationship ties with the similarity value of 80%. Keywords : Colocasia esculenta , phenetic, cultivars, vegetative

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Achene Morphology and Anatomy of Clematis L. (Ranunculaceae) in Korea and Its Taxonomic Implications

Plants ◽

10.3390/plants9101279 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1279

Author(s):

Balkrishna Ghimire ◽

Beom Kyun Park ◽

Dong Chan Son ◽

Seung-Hwan Oh

Keyword(s):

Principal Component ◽

Morphological Characters ◽

Point Of View ◽

Group Method ◽

Pair Group ◽

Light Yellow ◽

Alternative Means ◽

Electron And Light Microscopy ◽

Qualitative Characters ◽

Taxonomic Point

Clematis, a widely distributed genus in Ranunculaceae, is one of the most difficult groups of taxa in the family from a taxonomic point of view. A comprehensive study on achene morphology and the anatomy of 19 taxa of Clematis from Korea was carried out using scanning electron and light microscopy to evaluate the taxonomic significance of achene characters. Clematis achenes are elliptical, obovate or fusiform in shape, light yellow or brown to black in color and completely or sparsely covered with hairs. The permanent style is elongated and plumose in all the studied taxa except C. brachyura. We found that the size, indument, permanent style, surface sculpture, shape in cross-section, and nature and thickness of the exocarp, and endocarp were valuable achene features for species delimitation and may contribute to the unraveling of the taxonomic problems in the genus Clematis. One-way analysis of variance (ANOVA) indicated that the quantitative achene variables among the species were highly significant (p < 0.001). Principal component analyses based on seven quantitative characters and UPGMA (unweighted pair-group method with arithmetic mean) analysis based on seven quantitative and 18 qualitative characters also signify the utility of achene features for taxonomic discriminations of the Clematis taxa within the genus. Similar to other morphological characters in the genus Clematis, achene morphological and anatomical characters with the limited taxonomic value alone cannot be expected to resolve the infrageneric relationships but certain achene features combined with other morphological features could be useful as an alternative means of determining the infrageneric relationships within the genus.

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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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Optimal use of SSR markers for varietal identification of upland cotton

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2015000700007 ◽

2015 ◽

Vol 50 (7) ◽

pp. 571-581 ◽

Cited By ~ 1

Author(s):

Guilherme da Silva Pereira ◽

Ana Luíza Ramos Cazé ◽

Michelle Garcia da Silva ◽

Vanessa Cavalcante Almeida ◽

Fernanda Oliveira da Cunha Magalhães ◽

...

Keyword(s):

Genetic Distance ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Group Method ◽

Discrimination Power ◽

Arithmetic Average ◽

Pair Group ◽

Varietal Identification ◽

The World ◽

The Mean

Abstract: The objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the varieties. Initially, 92 SSR markers were genotyped in 20 Brazilian cotton cultivars. Of this total, 38 loci were polymorphic, two of which were amplified by one primer pair; the mean number of alleles per locus was 2.2. The values of polymorphic information content (PIC) and discrimination power (DP) were, on average, 0.374 and 0.433, respectively. The mean genetic distance was 0.397 (minimum of 0.092 and maximum of 0.641). A panel of 96 varieties originating from different regions of the world was assessed by 21 polymorphic loci derived from 17 selected primer pairs. Among these varieties, the mean genetic distance was 0.387 (minimum of 0 and maximum of 0.786). The dendrograms generated by the unweighted pair group method with arithmetic average (UPGMA) did not reflect the regions of Brazil (20 genotypes) or around the world (96 genotypes), where the varieties or lines were selected. Bootstrap resampling shows that genotype identification is viable with 19 loci. The polymorphic markers evaluated are useful to perform varietal identification in a large panel of cotton varieties and may be applied in studies of the species diversity.

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AFLP-based assessment of genetic diversity among nine alfalfa germplasms using bulk DNA templates

Genome ◽

10.1139/g02-100 ◽

2003 ◽

Vol 46 (1) ◽

pp. 51-58 ◽

Cited By ~ 46

Author(s):

A Segovia-Lerma ◽

R G Cantrell ◽

J M Conway ◽

I M Ray

Keyword(s):

Genetic Diversity ◽

Medicago Sativa ◽

High Throughput ◽

Genetic Distances ◽

Group Method ◽

Aflp Analysis ◽

Dna Templates ◽

Arithmetic Average ◽

Pair Group ◽

Large Numbers

Improving commercial utilization of perennial Medicago collections requires developing approaches that can rapidly and accurately characterize genetic diversity among large numbers of populations. This study evaluated the potential of using amplified fragment length polymorphism (AFLP) DNA markers, in combination with DNA bulking over multiple genotypes, as a strategy for high-throughput characterization of genetic distances (D) among alfalfa (Medicago sativa L.) accessions. Bulked DNA templates from 30 genotypes within each of nine well-recognized germplasms (African, Chilean, Flemish, Indian, Ladak, Medicago sativa subsp. falcata, Medicago sativa subsp. varia, Peruvian, and Turkistan) were evaluated using 34 primer combinations. A total of 3754 fragments were identified, of which 1541 were polymorphic. The number of polymorphic fragments detected per primer combination ranged from 20 to 85. Pairwise D estimates among the nine germplasms ranged from 0.52 to 1.46 with M. sativa subsp. falcata being the most genetically dissimilar. Unweighted pair-group method arithmetic average (UPGMA) analysis of the marker data produced two main clusters, (i) M. sativa subsp. sativa and M. sativa subsp. varia, and (ii) M. sativa subsp. falcata. Cluster-analysis results and D estimates among the Chilean, Peruvian, Flemish, and M. sativa subsp. varia germplasms supported the hypothesis that Peruvian was more similar to original Spanish introductions into Central and South America than Chilean. Hierarchical arrangement of the nine germplasms was supported by their respective geographic, subspecific, and intersubspecific hybrid origins. Subsets of as few as seven highly informative primer pairs were identified that produced comparable D estimates and similar heirarchical arrangements compared with the complete dataset. The results indicate that use of primer-pair subsets for AFLP analysis of bulk DNA templates could serve as a high-throughput system for accurately characterizing genetic diversity among large numbers of alfalfa populations.Key words: Medicago sativa, DNA bulking, genetic distance.

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Partial diallel and genetic divergence analyses in maize inbred lines

Acta Scientiarum Agronomy ◽

10.4025/actasciagron.v43i1.53540 ◽

2020 ◽

Vol 43 ◽

pp. e53540

Author(s):

Maria Fernanda de Souza Dias Maioli ◽

Ronald José Barth Pinto ◽

Tereza Aparecida da Silva ◽

Diego Ary Rizzardi ◽

Robson Akira Matsuzaki ◽

...

Keyword(s):

Grain Yield ◽

Genetic Divergence ◽

Block Design ◽

Inbred Lines ◽

Group Method ◽

Arithmetic Average ◽

Pair Group ◽

Maize Inbred Lines ◽

Randomized Block Design ◽

Partial Diallel

In this study, we aimed to estimate general and specific combining abilities (GCA and SCA, respectively) and to verify genetic divergence (Rogers distance, Unweighted Pair-Group Method Using Arithmetic Average - UPGMA) using microsatellite markers in maize inbred lines. Using a partial diallel scheme, a total of 19 inbred lines were crossed as (9 x 10), which were derived from the single hybrids SG6015 and P30F53, respectively. The 90 hybrids were evaluated in an incomplete randomized block design with common checks and three replications during the 2017-2018 growing season. Flowering time, average plant height, ear height insertion, average ear diameter, ear length, number of lodged and broken plants, mass of 100 grains and grain yield were measured. According to the analysis of variance, GCA, and SCA were significant (p < 0.05) in all the measured traits; inbred line B as well as 1 and 8, derived from the single hybrids SG6015 and P30F53, respectively, were selected due to their higher GCA values in grain yield to be used in crosses as testers, while the single cross hybrid (B x 1) was selected due to their higher SCA value in grain yield to be used in future breeding programs. The molecular marker analysis divided the inbred lines into two groups, where the highest dissimilarity (0.74) was observed between lines A and 9; however, these did not result in a high SCA value, therefore the hybrids obtained by such crossings were not selected for grain yield.

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