scholarly journals Evaluation of Genetic Diversity and Pedigree within Crapemyrtle Cultivars Using Simple Sequence Repeat Markers

2011 ◽  
Vol 136 (2) ◽  
pp. 116-128 ◽  
Author(s):  
Xinwang Wang ◽  
Phillip A. Wadl ◽  
Cecil Pounders ◽  
Robert N. Trigiano ◽  
Raul I. Cabrera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Interspecific Hybrids ◽  
Size Variation ◽  
Sequence Repeat ◽  
Allele Size ◽  
Low Genetic Diversity ◽  
Ssr Loci ◽  
Diversity Estimates ◽  
Simple Sequence

Genetic diversity was estimated for 51 Lagerstroemia indica L. cultivars, five Lagerstroemia fauriei Koehne cultivars, and 37 interspecific hybrids using 78 simple sequence repeat (SSR) markers. SSR loci were highly variable among the cultivars, detecting an average of 6.6 alleles (amplicons) per locus. Each locus detected 13.6 genotypes on average. Cluster analysis identified three main groups that consisted of individual cultivars from L. indica, L. fauriei, and their interspecific hybrids. However, only 18.1% of the overall variation was the result of differences between these groups, which may be attributable to pedigree-based breeding strategies that use current cultivars as parents for future selections. Clustering within each group generally reflected breeding pedigrees but was not supported by bootstrap replicates. Low statistical support was likely the result of low genetic diversity estimates, which indicated that only 25.5% of the total allele size variation was attributable to differences between the species L. indica and L. fauriei. Most allele size variation, or 74.5%, was common to L. indica and L. fauriei. Thus, introgression of other Lagestroemia species such as Lagestroemia limii Merr. (L. chekiangensis Cheng), Lagestroemia speciosa (L.) Pers., and Lagestroemia subcostata Koehne may significantly expand crapemyrtle breeding programs. This study verified relationships between existing cultivars and identified potentially untapped sources of germplasm.

scholarly journals GENETIC VARIATION OF E. oleifera POPULATION AND POPULATION E. guineensis x E. oleifera ON NUTFAH PLASMA COLLECTION PPKS

2016 ◽  
Vol 24 (1) ◽  
pp. 13-22
Author(s):  
Rokhana Faizah ◽  
Sri Wening ◽  
Hernawan Yuli Rahmadi ◽  
Abdul Razak Purba
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Interspecific Hybrids ◽  
Hybrid Population ◽  
Interspecific Crosses ◽  
Sequence Repeat ◽  
Elaeis Oleifera ◽  
Palm Species ◽  
Plasma Collection ◽  
Simple Sequence

The oil palm species of Elaeis oleifera have some superior characters not possessed by E. guineensis species. The cross between E. oleifera x E. guineensis (E. o x E. g.) Is carried out to insert the superior character of E. oleifera into the E. guineensis species and to obtain individuals who possess a superior characteristic blend of both species. This study aims to determine the genetic diversity within and between populations of E. oleifera, as well as relationships between E. oleifera, E. guineensis and its interspecific hybrids. A total of 8 germplasm populations used were E. oleifera originating from Suriname and Brazil, E. guineensis population of Dura Deli and SP540T, and interspecific crosses of hybrid E. guineensis x E. oleifera from Colombia, hybrid E. guineensis x E. oleifera which is presumably from Colombia, as well as hybrid E. guineensis x E. oleifera from Brazil. A total of sixteen Simple Sequence Repeat (SSR) markers were used to analyze 92 individuals from 8 populations. PCoA results show that 8 Elaeis populations cluster in each group. The hybrid population of E. guineensis x E. oleifera suspected of Colombia has a very close kinship relationship with hybrid E. guineensis x E. oleifera from Colombia and clumped in the same quadrant. This suggests that the hybrid is indeed a hybrid of E. guineensis x E. oleifera from Colombia. The population of E. oleifera from Suriname showed the lowest genetic diversity, with the number of different alleles, specific alleles, heterozygosity values, and the percentages of polymorphic loci sequentially were 1.37, 0.18, 0.09, and 37.50%. While the population of interspecific interspecific crossbreeds of the E. oleifera species showed the highest genetic diversity with values ​​of 3.81, 0.43, 0.62 and 100%.

Development and characterization of EST-derived simple sequence repeat (SSR) markers for pasture grass endophytes

Genome ◽  
2003 ◽  
Vol 46 (2) ◽  
pp. 277-290 ◽  
Author(s):  
Eline van Zijll de Jong ◽  
Kathryn M Guthridge ◽  
German C Spangenberg ◽  
John W Forster
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Simple Sequence Repeat ◽  
Fragment Length Polymorphism ◽  
Sequence Repeat ◽  
Pasture Grass ◽  
Ssr Loci ◽  
Expressed Sequence ◽  
Simple Sequence

Fungal endophytes of the genus Neotyphodium are common in temperate pasture grass species and confer both beneficial and deleterious agronomic characteristics to their hosts. The aim of this study was to develop molecular markers based on simple sequence repeat (SSR) loci for the identification and assessment of genetic diversity among Neotyphodium endophytes in grasses. Expressed sequence tags (ESTs) from both Neptyphodium coenophialum and Neotyphodium lolii were examined, and unique SSR loci were identified in 9.7% of the N. coenophialum sequences and 6.3% of the N. lolii sequences. A variety of SSRs were present, although perfect trinucleotide repeat arrays were the most common. Primers were designed to 50 SSR loci from N. coenophialum and 57 SSR loci from N. lolii and were evaluated using 20 Neotyphodium and Epichloë isolates. A high proportion of the N. coenophialum and N. lolii primers produced amplification products from the majority of isolates and most of these primers detected genetic variation. SSR markers from both N. coenophialum and N. lolii detected high levels of polymorphism between Neotyphodium and Epichloë species, and low levels of polymorphism within N. coenophialum and N. lolii. SSR markers may be used in appropriate combinations to discriminate between species. Comparison with amplified fragment length polymorphism (AFLP) data demonstrated that the SSR markers were informative for the assessment of genetic variation within and between endophyte species. These markers may be used to identify endophyte taxa and to evaluate intraspecific population diversity, which may be correlated with variation for endophyte-derived agronomic traits.Key words: Neotyphodium, simple sequence repeats, expressed sequence tags, amplified fragment length polymorphism, genetic diversity.

scholarly journals Simple Sequence Repeat Marker Analysis of Genetic Relationships within Hydrangea macrophylla

2007 ◽  
Vol 132 (3) ◽  
pp. 341-351 ◽  
Author(s):  
Sandra M. Reed ◽  
Timothy A. Rinehart
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Allelic Diversity ◽  
Sequence Repeat ◽  
Hydrangea Macrophylla ◽  
Total Genetic Diversity ◽  
Ssr Loci ◽  
Diversity Studies ◽  
Simple Sequence

Genetic diversity studies using 39 simple-sequence repeat (SSR) markers were carried out with 114 taxa of Hydrangea macrophylla (Thunb.) Ser., including 87 H. macrophylla ssp. macrophylla cultivars and 20 members of H. macrophylla ssp. serrata (Thunb.) Makino. The SSR loci were highly variable among the taxa, producing a mean of 8.26 alleles per locus. Overall allelic richness was relatively high at 5.12 alleles per locus. H. macrophylla ssp. serrata contained nearly twice the allelic diversity of H. macrophylla ssp. macrophylla. The majority of genetic diversity was found to reside within the subspecies, with only 12% of the total genetic diversity observed occurring between subspecies. Although the elevation of H. macrophylla ssp. serrata to species level has recently been recommended by several hydrangea authorities, these data support the subspecies designation. Four cultivars (Preziosa, Pink Beauty, Tokyo Delight, and Blue Deckle) appeared to be hybrids between the two subspecies. Genetic similarities were found among five remontant cultivars (Bailmer, Oak Hill, David Ramsey, Decatur Blue, and Penny Mac) and several nonremontant cultivars, including General Vicomtesse de Vibraye, Nikko Blue, All Summer Beauty, and La France. No close genetic relationship was found between the remontant cultivar Early Sensation and other remontant cultivars. Genetic similarities were found among variegated and double-flower cultivars. Within H. macrophylla ssp. macrophylla, cultivars with mophead inflorescences clustered separately from most lacecap cultivars. This indicates the cultivars with lacecap inflorescences that were among some of the earliest introductions to Europe were not widely used in the breeding of mophead forms. Some presumed synonyms were found to be valid (‘Preziosa’ and ‘Pink Beauty’, ‘Rosalba’ and ‘Benigaku’, ‘Geoffrey Chadbund’ and ‘Mowe’), whereas others were not (‘Harlequin’ and ‘Monrey’, ‘Nigra’ and ‘Mandschurica’). This study identified potentially unexploited sources of germplasm within H. macrophylla and relationships between existing cultivars of this popular shrub. This information should be of value when selecting parents for breeding programs.

scholarly journals Molecular characterization of indigenous olive genotypes based on SSR analysis

Genetika ◽  
2016 ◽  
Vol 48 (3) ◽  
pp. 1017-1025
Author(s):  
Hulya Unver ◽  
Ebru Sakar ◽  
Mehmet Ulas ◽  
Sezai Ercisli ◽  
Bekir Ak
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Ssr Analysis ◽  
Olive Cultivars ◽  
Ssr Loci ◽  
Similarity Ratio ◽  
Repeat Primer ◽  
Simple Sequence

Trees of 25 widely grown olive genotypes were analyzed using a set of 10 SSR (simple sequence repeat) primer pairs and to evaluate genetic diversity and reveal inter-cultivar relationships. Two well-known international olive cultivars (Chetoni and Manzanilla) and four widely grown Turkish standard cultivars (Aycalik, Edincik Su, Gemlik, Kilis Yaglik) are also included in the study to compare Kilis genotypes. The 10 polymorphic SSR loci exhibited 4 (UDO4) to 17 alleles (UDO43), with expected heterozygozity (He) ranging from 0.510 to 0.887 and a mean of 0.692 presenting high polymorphism. In this study we did not determine identical genotypes and Polateli4 and Kilis Ya?l?k (0.75), Polateli3 and Polateli7 (0.75) and Polateli6 and Manzanilla (0.70) revealed the highest similarity ratio each other. The most genetically divergent cultivars were Elbeyli8 and Musabeyli5 (0.10); Elbeyli3 and Musabeyli7 (0.15) and Musabeyli6 and Elbeyli7 (0.15), respectively.

scholarly journals Differentiation of “CandidatusLiberibacter asiaticus” Isolates by Variable-Number Tandem-Repeat Analysis

2011 ◽  
Vol 77 (5) ◽  
pp. 1910-1917 ◽  
Author(s):  
Hiroshi Katoh ◽  
Siti Subandiyah ◽  
Kenta Tomimura ◽  
Mitsuru Okuda ◽  
Hong-Ji Su ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Tandem Repeat ◽  
Simple Sequence Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Sequence Repeat ◽  
Repeat Analysis ◽  
Ssr Loci ◽  
Liberibacter Asiaticus ◽  
Simple Sequence

ABSTRACTFour highly polymorphic simple sequence repeat (SSR) loci were selected and used to differentiate 84 Japanese isolates of “CandidatusLiberibacter asiaticus.” The Nei's measure of genetic diversity values for these four SSRs ranged from 0.60 to 0.86. The four SSR loci were also highly polymorphic in four isolates from Taiwan and 12 isolates from Indonesia.

scholarly journals Genetic structure of populations of several endangered and endemic Dianthus species revealed by microsatellite markers

2018 ◽  
Vol 77 (2) ◽  
pp. 181-188 ◽  
Author(s):  
Anca Butiuc-Keul ◽  
Cornelia Crăciunaș ◽  
Irina Goia ◽  
Anca Farkas ◽  
Liliana Jarda ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Genetic Structure Of Populations ◽  
Ssr Loci ◽  
Different Populations ◽  
The Mean ◽  
Simple Sequence

Abstract In order to develop a proper conservation programme for several endangered, rare or endemic species of Dianhtus from Romania, molecular characterization by simple sequence repeat (SSR) markers has been accomplished. Amplification of SSR loci in individuals belonging to different populations of D. callizonus, D. glacialis ssp. gelidus, D. henteri, D. nardiformis and D. tenuifolius revealed 23 polymorphic alleles. D. callizonus and D. tenuifolius showed particular sets of SSR alleles. D. glacialis ssp. gelidus, D. henteri and D. nardiformis proved to share almost the same alleles in most of the loci. The highest genetic diversity was observed in D. glacialis ssp. gelidus and D. tenuifolius in locus MS-DINMADSBOX. Allelic patterns across Dianthus species indicate that the mean number of different alleles was highest in D. glacialis ssp. gelidus, while the number of effective alleles was highest in D. tenuifolius. There are no particular differences in individuals belonging to the same species. Genetic diversity is generally low, ranging from 0.18 (D. callizonus) to 0.44 (D. henteri). Regarding the genetic diversity within populations of the same species, no differences were revealed by the use of the SSR markers tested in the present study.

scholarly journals GENETIC VARIATION OF E. oleifera POPULATION AND POPULATION E. guineensis x E. oleifera ON NUTFAH PLASMA COLLECTION PPKS

2018 ◽  
Vol 24 (1) ◽  
pp. 13-22
Author(s):  
Rokhana Faizah ◽  
Sri Wening ◽  
Hernawan Yuli Rahmadi ◽  
Abdul Razak Purba
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Interspecific Hybrids ◽  
Hybrid Population ◽  
Interspecific Crosses ◽  
Sequence Repeat ◽  
Elaeis Oleifera ◽  
Palm Species ◽  
Plasma Collection ◽  
Simple Sequence

The oil palm species of Elaeis oleifera have some superior characters not possessed by E. guineensis species. The cross between E. oleifera x E. guineensis (E. o x E. g.) Is carried out to insert the superior character of E. oleifera into the E. guineensis species and to obtain individuals who possess a superior characteristic blend of both species. This study aims to determine the genetic diversity within and between populations of E. oleifera, as well as relationships between E. oleifera, E. guineensis and its interspecific hybrids. A total of 8 germplasm populations used were E. oleifera originating from Suriname and Brazil, E. guineensis population of Dura Deli and SP540T, and interspecific crosses of hybrid E. guineensis x E. oleifera from Colombia, hybrid E. guineensis x E. oleifera which is presumably from Colombia, as well as hybrid E. guineensis x E. oleifera from Brazil. A total of sixteen Simple Sequence Repeat (SSR) markers were used to analyze 92 individuals from 8 populations. PCoA results show that 8 Elaeis populations cluster in each group. The hybrid population of E. guineensis x E. oleifera suspected of Colombia has a very close kinship relationship with hybrid E. guineensis x E. oleifera from Colombia and clumped in the same quadrant. This suggests that the hybrid is indeed a hybrid of E. guineensis x E. oleifera from Colombia. The population of E. oleifera from Suriname showed the lowest genetic diversity, with the number of different alleles, specific alleles, heterozygosity values, and the percentages of polymorphic loci sequentially were 1.37, 0.18, 0.09, and 37.50%. While the population of interspecific interspecific crossbreeds of the E. oleifera species showed the highest genetic diversity with values ​​of 3.81, 0.43, 0.62 and 100%.

Genetic diversity of Symplocos paniculata of Hunan province revealed by inter-simple sequence repeat (ISSR)

2019 ◽  
Vol 51 (5) ◽  
Author(s):  
Huifang Cao ◽  
Qiang Lin ◽  
Peiwang Li ◽  
Jingzhen Chen ◽  
Changzhu Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Hunan Province ◽  
Sequence Repeat ◽  
Simple Sequence
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