Short Communication: Genetic diversity of Indonesian’s sugarcane varieties (Saccharum officinarum) based on RAPD molecular markers

Abstract. Kasiamdari RS, Aristya GR, Prabowo H, Ariesta C, Arif MF. 2019. Genetic diversity of Indonesian’s sugarcane varieties (Saccharum officinarum) based on RAPD molecular markers. Biodiversitas 20: 3005-3010. Sugarcane (Saccharum officinarum L.) belongs to the Poaceae family which are widely used for sweeteners production. In Indonesia, the need for sugarcane continues to increase along with its increased use in the production of bioethanol from molasses, a by-product of sugar production. However, the supply for sugar is still far from enough. Improvement of sugarcane productivity can be done by selecting superior varieties to form a new superior hybrid. Maintaining high genetic diversity in a population is essential. Selection of varieties is important because it can increase productivity without increasing the cost of crop production. Even the selected pest-resistant varieties can reduce the cost of crop production. Indonesia had produced many superior sugarcane plant varieties, but studies on their characters and genetic relationship are still lacking. Several molecular markers have been used to elucidate the genetic diversity among sugarcane varieties. Random Amplified Polymorphism DNA (RAPD) is one of the molecular markers that have been proven to describe genetic diversity among sugarcane plants. This study aimed to determine the genetic diversity among 22 superior sugarcane varieties in Indonesia based on eight RAPD molecular markers. The superior sugarcane varieties in Indonesia in this study were obtained from Indonesian Sweetener and Fiber Crops Research Institute (ISFRI), Malang and Madukismo Sugar Factory, Yogyakarta. DNA products were visualized by using gel electrophoresis and resolved bands were scored as binary data as presence (1) and absence (0). Linkage distance was done based on Jaccard’s similarity coefficient, and clustering analysis was performed based on the unweighted pair- group average (UPGMA) method. Polymorphism Information Content (PIC) analysis showed a high degree of polymorphism ranging from 0.76 to 0.92. Cluster analysis showed that 22 sugarcane varieties were divided into two main clusters and four sub-clusters based on their origin.

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Analysis of genetic diversity in Prunus sibirica L. in inner Mongolia using SCoT molecular markers

Genetic Resources and Crop Evolution ◽

10.1007/s10722-021-01284-4 ◽

2022 ◽

Author(s):

Ha Buer ◽

Sa Rula ◽

Zi Yuan Wang ◽

Shu Fang ◽

Yu´e Bai

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Genetic Differentiation ◽

Inner Mongolia ◽

Start Codon ◽

Group Method ◽

Pair Group ◽

Protection And Utilization ◽

Minimum Number ◽

Polymorphic Bands

AbstractPopulation genetic diversity contributes to the protection and utilization of germplasm resources, especially via genetic breeding. In the present study, start codon targeted polymorphism (SCoT) molecular markers were used to study the genetic diversity of 278 individuals from 10 Prunus sibirica L. populations in Inner Mongolia. A total of 289 polymorphic bands were amplified with 23 SCoT primers, showing a polymorphism percentage of 98.87% and an average of 12.6 polymorphic bands per primer. The SCoT21, SCoT32, and SCoT53 primers amplified up to 17 bands, and the polymorphism percentage was 100%. The minimum number of bands amplified by SCoT25 was 9, and the polymorphism percentage was 90%. Therefore, SCoT molecular markers were shown to be highly polymorphic and suitable for genetic diversity studies of P. sibirica in Inner Mongolia. The analysis of molecular variance showed that 39% of the observed genetic differentiation occurred among populations and 61% occurred within populations, indicating that the genetic differentiation within populations was greater than that among populations. The results of the unweighted pair-group method with an arithmetic cluster analysis, principal coordinate analysis and STRUCTURE analysis were basically the same and divided the 278 individuals from the 10 populations into 2 groups. The results indicated that the efficient SCoT molecular marker-based genetic diversity analysis of P. sibirica in Inner Mongolia can provide a reference for P. sibirica variety breeding and resource development.

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High genetic diversity and a new cryptic species within the Ephedrus persicae species group (Hymenoptera: Braconidae: Aphidiinae)

Biologia ◽

10.1515/biolog-2016-0165 ◽

2016 ◽

Vol 71 (12) ◽

Cited By ~ 3

Author(s):

Andjeljko Petrović ◽

Korana Kocić ◽

Katarina Kos ◽

Milan Plećaš ◽

Vladimir Žikić ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Cryptic Species ◽

Species Group ◽

High Genetic Diversity

AbstractIn this study we used molecular markers to characterize various populations of the

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Breeding potential and genetic diversity of "Híbrido do Timor" coffee evaluated by molecular markers

Cropp Breeding and Applied Biotechnology ◽

10.1590/s1984-70332010000400003 ◽

2010 ◽

Vol 10 (4) ◽

pp. 298-304 ◽

Cited By ~ 12

Author(s):

Tesfahun Alemu Setotaw ◽

Eveline Teixeira Caixeta ◽

Guilherme Ferreira Pena ◽

Eunize Maciel Zambolim ◽

Antonio Alves Pereira ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Molecular Markers ◽

Genetic Structure ◽

Gene Diversity ◽

High Genetic Diversity ◽

Breeding Programs ◽

Information Index ◽

Upgma Cluster Analysis ◽

Potential Use

AFLP, RAPD and SSR molecular markers were used to study the genetic diversity and genetic structure of the Híbrido de Timor germplasm. The principal coordinate analysis, UPGMA cluster analysis based on genetic dissimilarity of Jaccard, Bayesian model-based cluster analysis, percentage of polymorphic loci, Shannon's information index and Nei gene diversity were employed to assess the genetic diversity. The analyses demonstrated a high genetic diversity among Híbrido de Timor accessions. UPGMA and Bayesian cluster analyses grouped the accessions into three clusters. The genetic structure of Híbrido de Timor is reported. The management of Híbrido de Timor germplasm variability and its potential use in breeding programs are discussed.

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Genetic diversity and molecular survey of Trypanosoma (Megatrypanum ) theileri in cattle in Brazil’s western Amazon region

Revista Brasileira de Parasitologia Veterinária ◽

10.1590/s1984-296120180049 ◽

2018 ◽

Vol 27 (4) ◽

pp. 579-583 ◽

Cited By ~ 1

Author(s):

Thábata dos Anjos Pacheco ◽

Arlei Marcili ◽

Andrea Pereira da Costa ◽

Rute Witter ◽

Andréia Lima Tomé Melo ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Molecular Diagnosis ◽

Prevalence Rate ◽

Cathepsin L ◽

Ssu Rdna ◽

Amazon Region ◽

Prevalence Rates ◽

High Genetic Diversity ◽

First Time

Abstract Trypanosoma (Megatrypanum) theileri is a flagellated protozoan that infects ruminants and it displays high genetic diversity. In this study, we investigated the prevalence rates of this protozoan based on hemoculture and molecular diagnosis. The isolates of T. theileri thus obtained were characterized by molecular markers SSU rDNA and gGAPDH and molecular diagnosis based on Cathepsin L-like gene (PCR-TthCATL). The PCR-TthCATL and hemoculture indicated an overall prevalence rate of 8.13%, and the CATL derived sequence named IB was identified for the first time in cattle in the western Amazon region, as well as IF in Brazil. We also describe a possible new PCR-TthCATL derived sequence in cattle, designated IL.

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Evaluation of genetic diversity in geranium (Geraniaceae) using RAPD marker

Genetika ◽

10.2298/gensr2101363y ◽

2021 ◽

Vol 53 (1) ◽

pp. 363-378

Author(s):

Juan Yin ◽

Majid Khayatnezhad ◽

Abdul Shakoor

Keyword(s):

Genetic Diversity ◽

Random Amplified Polymorphic Dna ◽

Rapd Marker ◽

Morphological Characters ◽

Mantel Test ◽

Group Method ◽

Plant Resources ◽

High Genetic Diversity ◽

Pair Group ◽

Genetic Structure Of Populations

Genetic diversity studies are essential to understand the conservation and management of plant resources in any environment. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Geranium genetic diversity. Therefore, we collected and analyzed thirteen species from nine provinces. Overall, one hundred and twenty-five plant specimens were collected. Our aims were 1) to assess genetic diversity among Geranium species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. Unweighted pair group method with arithmetic mean and multidimensional scaling divided Geranium species into two groups. G. sylvaticum depicted unbiased expected heterozygosity (UHe) in the range of 0.11. Shannon information was high (0.38) in G. columbinum. G. sylvaticum showed the lowest value, 0.14. The observed number of alleles (Na) ranged from 0.25 to 0.55 in G. persicum and G. tuberosum. The effective number of alleles (Ne) was in the range of 1.020-1.430 for G. tuberosum and G. collinum. Gene flow (Nm) was relatively low (0.33) in Geranium. The Mantel test showed correlation (r = 0.27, p=0.0002) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Geranium species can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in Geranium species.

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Assessment of Genetic Diversity of Chinese Sand Pear Landraces (Pyrus pyrifolia Nakai) Using Simple Sequence Repeat Markers

HortScience ◽

10.21273/hortsci.44.3.619 ◽

2009 ◽

Vol 44 (3) ◽

pp. 619-626 ◽

Cited By ~ 9

Author(s):

Zhengwang Jiang ◽

Feiyan Tang ◽

Hongwen Huang ◽

Hongju Hu ◽

Qiliang Chen

Keyword(s):

Genetic Diversity ◽

Principal Component ◽

Central China ◽

Pyrus Pyrifolia ◽

Gene Pools ◽

High Genetic Diversity ◽

Arithmetic Average ◽

Pair Group ◽

Different Origins ◽

Simple Sequence

The sand pear (Pyrus pyrifolia Nakai) is an important fruit crop in China. In this study, simple sequence repeats (SSRs) were used to estimate the level and pattern of genetic diversity among 233 sand pear landraces collected from 10 different geographic regions in China. The results demonstrated that the SSR technique is an effective tool for assessing genetic diversity and the geographic pattern of genetic variation among sand pear landraces of different origins. A total of 184 putative alleles was detected using 14 primer pairs with an average of 13.1 alleles per locus. The mean expected heterozygosity and observed heterozygosity across all loci were 0.705 and 0.671, respectively. High genetic diversity was found in all populations except for that originated from Jiangxi (Ae = 3.149; He = 0.655), whereas at the regional level, those from central China were less diverse than those from other regions. Analysis of molecular variance showed that most genetic differences resided among landraces within populations. Additionally, unweighted pair group with arithmetic average clustering and principal component analysis plotting based on Nei's genetic distance revealed distinct gene pools in agreement with geographic distribution.

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Genetic Variability of 21 Tea Genotypes [Camellia sinensis (L.) O. Kuntze] Based on RAPD Markers

Jurnal Tanaman Industri dan Penyegar ◽

10.21082/jtidp.v5n2.2018.p77-86 ◽

2018 ◽

Vol 5 (2) ◽

pp. 77

Author(s):

Budi Martono ◽

Syafaruddin Syafaruddin

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Similarity ◽

Binary Data ◽

Rapd Markers ◽

Group Method ◽

Breeding Programs ◽

Pair Group ◽

Monomorphic Band ◽

And Cluster Analysis

<em>Knowing the genetic diversity in the tea germplasms collection is one of important conditions for assembling new superior varieties. Information of genetic diversity can be obtained through analysis using RAPD molecular markers. The study aimed to determine the genetic diversity of 21 tea genotypes based on RAPD markers. The research was conducted in Integrated Laboratory, Seameo Biotrop, Bogor, from July to September 2013. Genomic DNA was isolated from 21 tea genotypes leaf samples, then amplified with primer OPA 03, OPA 05, OPB 04, OPB 06, OPC 06, and OPD 08. Electrophoresis result was converted into binary data. The genetic similarity and cluster analysis calculation was done using NTSYS-pc version 2.10. In this research, 50 polymorphic bands (94,34%) and 3 monomorphic band (5,66%) were obtained. Cluster analysis based on Nei's genetic distance using the unweighted pair-group method with arithmatic (UPGMA) divided 21 tea genotypes into two groups at a genetic similarity value of 0,48. Group 1 consisted of 20 tea genotypes, while the second group comprised only a one genotype (Sin 27). The range of genetic similarity matrix was between 28%–92%, the lowest genetic similarity (28%) was found between GMB 4 and Sin 27 genotypes, while the highest (92%) was found between AS 2 and AS 1 genotypes. The information obtained can be utilized in breeding programs with the support of agronomic characters as well as in the conservation of tea germplasm.</em>

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Genetic diversity and morphological variability of fifteen Stachys (Lamiaceae) species from Iran using morphological and ISSR molecular markers

Biologia ◽

10.1515/biolog-2015-0051 ◽

2015 ◽

Vol 70 (4) ◽

Cited By ~ 1

Author(s):

Navaz Kharazian ◽

Somayeh Rahimi ◽

Behrouz Shiran

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Morphological Variability ◽

Natural Habitats ◽

High Genetic Diversity ◽

Morphological Variations ◽

Gene Variation ◽

Germplasm Diversity ◽

Issr Molecular Markers ◽

Zagros Region

AbstractStachys L. (Lamiaceae) exhibits a great range of variation with cosmopolitan distribution. An area extremely rich in taxa including 34 species has been introduced in Iran. This study documents the genetic diversity and morphological variations of 48 accessions from fifteen Stachys species and two subspecies belonging to six sections. All of the specimens were collected from natural habitats in Zagros region of Iran. In order to evaluate morphological variations, 21 characters were used. Eleven ISSR primers with DNA samples of leaves were applied to assess the genetic variations among species and populations of the Stachys genus. Based on the results, from the eleven primers screened, nine primers produced reproducible bands. The highest percentage of polymorphism included 100% in section Aucheriana. Analysis of molecular variance revealed a high proportion of gene variation (42%) among populations within species. In total sections, the UPGMA clustering dendrogram genetically detected different groups. Based on the morphological analysis, each section was definitely positioned. A high genetic diversity and polymorphism was found among Stachys accessions belonging to each section. Based on the findings, the germplasm diversity was due to the wealth genetic resources in the central Zagros region which are important in plant breeding and gene conservation purposes. In addition, morphological and ISSR molecular markers are useful to display the diversity in Stachys genus.

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Genetic relationships in Saccharum complex germplasm collections based on morphological and molecular markers

E-Journal Menara Perkebunan ◽

10.22302/iribb.jur.mp.v89i1.421 ◽

2021 ◽

Vol 89 (1) ◽

Author(s):

Wiwit Budi WIDYASARI ◽

. DAMANHURI

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Genetic Distance ◽

Genetic Relationship ◽

Genetic Similarity ◽

Genetic Relationships ◽

Morphological Markers ◽

Saccharum Complex ◽

High Genetic Diversity ◽

Germplasm Collections

and is a cross-pollinator, so information about the genetic relationship between the accessions in germplasm collections is very important for selecting the prospective parent in crossbreeding. This research aims to determine the phylogenetic relationship of 24 Saccharum complex accessions and to verify the grouping of accessions using 37 morphological and three microsatellite molecular markers. Interpretation of morphological and molecular data was obtained from the analysis using the NTYSYpc-2.02i program. The results show that within the 24 accessions analyzed using morphological markers, some accessions did not cluster as the classification at the conservation time. This difference is due to the morphological markers, descriptions of characters that do not appear are considered as the same variables though in different morphological characters, so this increases the value of genetic similarity among accessions analyzed. In contrast, the grouping of molecular markers shows that each accession was grouped according to the classification at the conservation time. These accessions had a low genetic similarity of 0.20 with a broad genetic distance of 0.80. This broad genetic distance indicates that the twenty-four accessions have a distant genetic relationship with one another, so that the genetic diversity of these accessions is relatively high. The high genetic diversity in germplasm collections improves its potential as a crossing parent to obtain a high heterosis effect.

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Genetic diversity analysis using molecular marker in Terminalia chebula

Journal of Applied and Natural Science ◽

10.31018/jans.v7i2.720 ◽

2015 ◽

Vol 7 (2) ◽

pp. 997-1000

Author(s):

T. N. Ranjini ◽

K. Bhanuprakash ◽

M. A. Suryanarayana ◽

B. G. Yamuna

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Rapd Markers ◽

Molecular Diversity ◽

Crop Improvement ◽

Group Method ◽

Terminalia Chebula ◽

Pair Group ◽

Improvement Programme ◽

Important Medicinal Plant

Terminalia chebula is an important medicinal plant, extensively used in Ayurveda, Unani and Homoeopathic medicines. The present study was aimed to reveal its genetic diversity based on molecular markers from twelve T. chebula accessions. Molecular diversity was studied using RAPD markers. A total of 8 polymorphic primers produced 314 polymorphic bands and 195 monomorphic bands. Unweighted Pair Group Method with Arithmetic Mean (UPMGA) dendrogram divided the accessions into 2 major clusters. Accession IIHRTc2 and IIHRTc10 showed maximum genetic diversity with 55% similarity. This characterization based on molecular markers will help in identification of economically useful accessions for further crop improvement programme.

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