scholarly journals Lemons: Diversity and Relationships with Selected Citrus Genotypes as Measured with Nuclear Genome Markers

2001 ◽  
Vol 126 (3) ◽  
pp. 309-317 ◽  
Author(s):  
O. Gulsen ◽  
M.L. Roose
Keyword(s):  
Simple Sequence Repeats ◽  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Inter Simple Sequence Repeats ◽  
Ssr Loci ◽  
High Level ◽  
Simple Sequence

Inter-simple sequence repeats (ISSR), simple sequence repeats (SSR) and isozymes were used to measure genetic diversity and phylogenetic relationships among 95 Citrus L. accessions including 57 lemons [C. limon (L.) Burm. f.], related taxa, and three proposed ancestral species, C. maxima (Burm.) Merrill (pummelo), C. medica L. (citron), and C. reticulata Blanco (mandarin). The ancestry of lemons and several other suspected hybrids was also studied. Five isozyme and five SSR loci revealed relatively little variation among most lemons, but a high level of variation among the relatively distant Citrus taxa. Eight ISSR primers amplified a total of 103 polymorphic fragments among the 83 accessions. Similarity matrices were calculated and phylogenetic trees derived using unweighted pair-group method, arithmetic average cluster analysis. All lemons, rough lemons, and sweet lemons, as well as some other suspected hybrids, clustered with citrons. Most lemons (68%) had nearly identical marker phenotypes, suggesting they originated from a single clonal parent via a series of mutations. Citrons contributed the largest part of the lemon genome and a major part of the genomes of rough lemons, sweet lemons, and sweet limes. Bands that characterize C. reticulata and C. maxima were detected in lemons, suggesting that these taxa also contributed to the pedigree of lemon.

Assessment of genetic diversity and differentiation of Elymus nutans indigenous to Qinghai–Tibet Plateau using simple sequence repeats markers

2013 ◽  
Vol 93 (6) ◽  
pp. 1089-1096 ◽  
Author(s):  
Shiyong Chen ◽  
Xinquan Zhang ◽  
Xiao Ma ◽  
Linkai Huang
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeats ◽  
Tibet Plateau ◽  
Group Method ◽  
Similarity Coefficients ◽  
Arithmetic Average ◽  
Pair Group ◽  
Elymus Nutans ◽  
Qinghai Tibet Plateau ◽  
Simple Sequence

Chen, S., Zhang, X., Ma, X. and Huang, L. 2013. Assessment of genetic diversity and differentiation of Elymus nutans indigenous to Qinghai–Tibet Plateau using simple sequence repeats markers. Can. J. Plant Sci. 93: 1089–1096. Elymus nutans Griseb., an important alpine forage grass, is widely distributed in the Qinghai–Tibet Plateau. A total of 50 E. nutans accessions from the eastern Qinghai–Tibet Plateau were analyzed using simple sequence repeats (SSR) markers from wheat and Elymus species. Our results show that a total of 144 reliable bands were generated, of which 132 (91.38%) were found to be polymorphic. Nei-Li's genetic similarity coefficients ranged from 0.515 to 0.870 with an average of 0.719, which shows a high level of genetic diversity and a broad genetic base among accessions. There was a low correlation between genetic distance and geographical distance (r=0.121, P=0.088) in the region, which is consistent with the unweighted pair group method with arithmetic average cluster analysis of accessions. The mountain ridges and river valleys in the eastern Qinghai–Tibet region could serve as genetic barriers for pollinator movement and seed dispersal. The rule of the most genetic diversity at medium altitude of E. nutans in the Qinghai–Tibet Plateau was also validated in the study. The implications of these results for the conservation of E. nutans are discussed.

scholarly journals Genome Wide Characterization, Comparative and Genetic Diversity Analysis of Simple Sequence Repeats in Cucurbita Species

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 143
Author(s):  
Lei Zhu ◽  
Huayu Zhu ◽  
Yanman Li ◽  
Yong Wang ◽  
Xiangbin Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Group Method ◽  
Motif Length ◽  
Pair Group ◽  
Ssr Loci ◽  
Ssr Frequency ◽  
Basic And Applied Research ◽  
Simple Sequence

Simple sequence repeats (SSRs) are widely used in mapping constructions and comparative and genetic diversity analyses. Here, 103,056 SSR loci were found in Cucurbita species by in silico PCR. In general, the frequency of these SSRs decreased with the increase in the motif length, and di-nucleotide motifs were the most common type. For the same repeat types, the SSR frequency decreased sharply with the increase in the repeat number. The majority of the SSR loci were suitable for marker development (84.75% in Cucurbita moschata, 94.53% in Cucurbita maxima, and 95.09% in Cucurbita pepo). Using these markers, the cross-species transferable SSR markers between C. pepo and other Cucurbitaceae species were developed, and the complicated mosaic relationships among them were analyzed. Especially, the main syntenic relationships between C. pepo and C. moschata or C. maxima indicated that the chromosomes in the Cucurbita genomes were highly conserved during evolution. Furthermore, 66 core SSR markers were selected to measure the genetic diversity in 61 C. pepo germplasms, and they were divided into two groups by structure and unweighted pair group method with arithmetic analysis. These results will promote the utilization of SSRs in basic and applied research of Cucurbita species.

scholarly journals Genetic Diversity of Iraqi Date Palms Revealed By Microsatellite Polymorphism

2011 ◽  
Vol 136 (4) ◽  
pp. 282-287 ◽  
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.

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

2001 ◽  
Vol 126 (1) ◽  
pp. 72-77 ◽  
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.

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

2004 ◽  
Vol 1 (2) ◽  
pp. 73-78 ◽  
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.

scholarly journals Molecular Analysis of Genetic Diversity and Geographic Origin within an Ex Situ Germplasm Collection of Cherimoya by Using SSRs

2007 ◽  
Vol 132 (3) ◽  
pp. 357-367 ◽  
Author(s):  
P. Escribano ◽  
M.A. Viruel ◽  
J.I. Hormaza
Keyword(s):  
Genetic Diversity ◽  
Geographic Origin ◽  
Germplasm Collection ◽  
Ex Situ ◽  
Group Method ◽  
Pair Group ◽  
Ssr Primers ◽  
Upgma Cluster Analysis ◽  
Ssr Loci ◽  
Simple Sequence

Cherimoya (Annona cherimola Mill.) is an underused fruit crop with a clear niche for expansion in subtropical climates. In this study, 16 simple sequence repeat (SSR) loci were used to find molecular polymorphisms among 279 cherimoya accessions from a worldwide ex situ field germplasm collection. A total of 79 amplification fragments were amplified with 16 pairs of SSR primers, with an average of 4.9 bands/SSR. Mean expected and observed heterozygosities averaged 0.53 and 0.44, respectively. The total value for the probability of identity was 4.34 × 10−8. The SSRs studied resulted in 267 different fingerprinting profiles, of which 258 were unique genotypes; the rest were putative cases of synonymies or mislabeling errors. Unweighted pair group method with arithmetic averages (UPGMA) cluster analysis indicated the relationships among the analyzed accessions, showing some specific groups related to their geographical origins. Analysis of molecular variance (AMOVA) was performed to examine the distribution of genetic variation of the 148 accessions collected from putative cherimoya origin areas in Ecuador and Peru, showing that the major variations occurred within valleys in each country. The results confirmed the usefulness of microsatellites for identification of genetic diversity and geographic origin of cherimoya and are discussed in terms of their implications for ex situ conservation of cherimoya genetic resources.

Identification and structure analysis of three tilapia species using microsatellite markers

2009 ◽  
Vol 6 (2) ◽  
pp. 119-125
Author(s):  
Song Hong-Mei ◽  
Bai Jun-Jie ◽  
Quan Ying-Chun ◽  
Li Sheng-Jie
Keyword(s):  
Microsatellite Markers ◽  
Clustering Analysis ◽  
Phylogenetic Trees ◽  
Mean Value ◽  
Group Method ◽  
Oreochromis Aureus ◽  
Arithmetic Average ◽  
Pair Group ◽  
Expected Heterozygosity ◽  
The Mean

AbstractSeventeen special loci were selected from 77 microsatellite markers to distinguish three varieties of tilapias, including the six differential loci UNH636, UNH117, UNH172, UNH738, UNH878 and UNH896 in Oreochromis aureus; five differential loci UNH913, UNH907, UNH222, UNH980 and UNH880 in O. niloticus; and six differential loci of UNH876, UNH899, UNH853, UNH932, UNH933 and UNH773 in O. mossambicus. Any one of the 17 loci could amplify particular bands to distinguish one tilapia from the other two. The genetic structure of O. aureus, O. niloticus and O. mossambicus stocks and their phylogenetic relationships were also analysed using these 17 loci. In total 142 alleles were detected, and the average number of alleles per locus was 8.35. Additionally, a clustering analysis was performed based on the result of the Popgen32 software package and phylogenetic trees were constructed by MEGA4 using the unweighted pair group method using arithmetic average (UPGMA). The results showed that the mean value of observed heterozygosity was 0.0941, 0.5490 and 0.2588, the mean value of expected heterozygosity was 0.1089, 0.7230 and 0.1965, and the polymorphism information content was 0.0869, 0.7149 and 0.1643, in O. aureus, O. niloticus and O. mossambicus, respectively. The UPGMA tree demonstrated that O. aureus was more closely related to O. mossambicus than to O. niloticus.

RAPD analysis of cultivated and wild yellow nutsedge (Cyperus esculentusL.)

Weed Science ◽  
1998 ◽  
Vol 46 (3) ◽  
pp. 318-321 ◽  
Author(s):  
Paloma Abad ◽  
Bernardo Pascual ◽  
José V. Maroto ◽  
Salvador López-Galarza ◽  
María J. Vicente ◽  
...  
Keyword(s):  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Wild Populations ◽  
Arithmetic Average ◽  
Yellow Nutsedge ◽  
Pair Group ◽  
High Level ◽  
Unweighted Pair Group Method

Cultivated and weedy clones of yellow nutsedge were analyzed using random amplified polymorphic DNA (RAPD) markers to assess the polymorphism within the species and determine if this approach was suitable for identification of cultivar and wild populations. The RAPD markers unambiguously identified all studied clones. Nei-Li similarities were computed and used in an unweighted pair group method using arithmetic average (UPGMA) cluster analyses. Cultivated and weedy clones were clustered in two groups, but two cultivated clones were more closely related to weedy clones than to cultivated clones. The results showed a high level of genetic variability among the clones tested, particularly among the cultivated ones. Identification of yellow nutsedge cultivars and analysis of genetic diversity within and among weedy populations is possible by using only a small number of primers. In this study, seven selected primers discriminated among the 10 tested clones.

scholarly journals Genetic Characterization of an Endangered Chilean Endemic Species, Prosopis burkartii Muñoz, Reveals its Hybrids Parentage

Plants ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 744
Author(s):  
Roberto Contreras ◽  
Liesbeth van den Brink ◽  
Boris Burgos ◽  
Marlene González ◽  
Sandra Gacitúa
Keyword(s):  
Endemic Species ◽  
Genetic Material ◽  
Inter Simple Sequence Repeat ◽  
Group Method ◽  
Trnl Intron ◽  
Arithmetic Average ◽  
Pair Group ◽  
Upgma Cluster Analysis ◽  
Species Specific ◽  
Simple Sequence

The hybridization of Prosopis burkartii, a critically endangered endemic species, and the identification of its paternal species has not been genetically studied before. In this study we aimed to genetically confirm the origin of this species. To resolve the parental status of P. burkartii, inter-simple sequence repeat (ISSR), simple sequence repeats (SSR) and intron trnL molecular markers were used, and compared with Chilean species from the Algarobia and Strombocarpa sections. Out of seven ISSRs, a total of 70 polymorphic bands were produced in four species of the Strombocarpa section. An Multi-dimensional scaling (MDS) and Bayasian (STRUCTURE) analysis showed signs of introgression of genetic material in P. burkartii. Unweighted pair group method with arithmetic average (UPGMA) cluster analysis showed three clusters, and placed the P. burkartii cluster nested within the P. tamarugo group. Sequencing of the trnL intron showed a fragment of 535 bp and 529 bp in the species of the Algarobia and Strombocarpa sections, respectively. Using maximum parsimony (MP) and maximum likelihood (ML) trees with the trnL intron, revealed four clusters. A species-specific diagnostic method was performed, using the trnL intron Single Nucleotide Polymorphism (SNP). This method identified if individuals of P. burkartii inherited their maternal DNA from P. tamarugo or from P. strombulifera. We deduced that P. tamarugo and P. strombulifera are involved in the formation of P. burkartii.

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

2015 ◽  
Vol 14 (1) ◽  
pp. 50-56 ◽  
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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