Apple Proliferation Resistance in Apomictic Rootstocks and Its Relationship to Phytoplasma Concentration and Simple Sequence Repeat Genotypes

In an effort to select and characterize apple rootstock resistant to apple proliferation (AP), progenies from seven apomictic rootstock selections and their parental apomictic species, Malus sieboldii and M. sargentii, were compared to standard stocks M 9 and M 11. Seedlings derived from open pollinated mother plants were grafted with cv. Golden Delicious and grown under natural infection conditions. The progenies differed greatly in resistance to the AP agent ‘Candidatus Phytoplasma mali’. Progenies of M. sieboldii and its descendent rootstock selections D2212, 4608, 4551, and D1131 showed a high level of resistance, whereas progenies of M. sargentii and its descendent selections D1111 and C1828 proved susceptible. M 9 and M 11 showed an intermediate level of resistance. Phytoplasma titer in roots of the M. sieboldii and M. sargentii progeny groups was similarly low, whereas the concentration in the standard stocks was 100 to 5,000 times higher. In trees on most of the resistant stocks, only a minority was colonized in the scion, while in trees on susceptible and standard stocks, infection rate was often higher. Also, the titer in the top of trees on resistant stocks was usually lower than in trees on susceptible and standard stocks. Four progenies derived from open pollinated M. sieboldii and M. sieboldii descendents were subjected to DNA typing using simple sequence repeat (SSR) markers. This study revealed that the selected groups consisted mainly of mother-like plants (apomicts) and type I hybrids (unreduced mother genotype plus one male allele at each locus). Type II hybrids (full recombinants) and autopollinated offspring were rare. In the 4608 progeny, trees grown on type I hybrid rootstocks were significantly less affected than trees on mother-like stocks. In other progenies with fewer or no type I hybrids, trees on type II hybrids and autopollinated offspring suffered considerably more from disease than trees on mother-like stocks.

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Simple Sequence Repeat and S-Locus Genotyping to Assist the Genetic Characterization and Breeding of Polyploid Prunus Species, P. spinosa and P. domestica subsp. insititia

Biochemical Genetics ◽

10.1007/s10528-021-10090-7 ◽

2021 ◽

Author(s):

Júlia Halász ◽

Noémi Makovics-Zsohár ◽

Ferenc Szőke ◽

Sezai Ercisli ◽

Attila Hegedűs

Keyword(s):

Simple Sequence Repeat ◽

Principal Component ◽

Sequence Repeat ◽

Breeding Programs ◽

Allele Number ◽

Genetic Potential ◽

Ssr Loci ◽

High Level ◽

Diversity Studies ◽

Simple Sequence

AbstractPolyploid Prunus spinosa (2n = 4 ×) and P. domestica subsp. insititia (2n = 6 ×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programs. In Hungary, 16 cultivar candidates and a recognized cultivar ‘Zempléni’ were selected from wild-growing populations including ten P. spinosa, four P. domestica subsp. insititia and three P. spinosa × P. domestica hybrids (2n = 5 ×) were also created. Genotyping in eleven simple sequence repeat (SSR) loci and the multiallelic S-locus was used to characterize genetic variability and achieve a reliable identification of tested accessions. Nine SSR loci proved to be polymorphic and eight of those were highly informative (PIC values ˃ 0.7). A total of 129 SSR alleles were identified, which means 14.3 average allele number per locus and all accessions but two clones could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified and the complete and partial S-genotype was determined for 10 and 7 accessions, respectively. The DNA sequence was determined for a total of 17 fragments representing 11 S-RNase alleles. ‘Zempléni’ was confirmed to be self-compatible carrying at least one non-functional S-RNase allele (SJ). Our results indicate that the S-allele pools of wild-growing P. spinosa and P. domestica subsp. insititia are overlapping in Hungary. Phylogenetic and principal component analyses confirmed the high level of diversity and genetic differentiation present within the analysed accessions and indicated putative ancestor–descendant relationships. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species but non-related accessions sharing common S-alleles may distort phylogenetic inferences.

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Simple Sequence Repeat Marker Analysis of Genetic Diversity among Progeny of a Biparental Mapping Population of Sweetpotato

HortScience ◽

10.21273/hortsci.50.8.1143 ◽

2015 ◽

Vol 50 (8) ◽

pp. 1143-1147 ◽

Cited By ~ 8

Author(s):

Benard Yada ◽

Gina Brown-Guedira ◽

Agnes Alajo ◽

Gorrettie N. Ssemakula ◽

Robert O.M. Mwanga ◽

...

Keyword(s):

Genetic Diversity ◽

Linkage Analysis ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Polymorphic Information Content ◽

Genetic Distances ◽

Sequence Repeat ◽

Population Improvement ◽

High Level ◽

Simple Sequence

Genetic diversity is critical in sweetpotato improvement as it is the source of genes for desired genetic gains. Knowledge of the level of genetic diversity in a segregating family contributes to our understanding of the genetic diversity present in crosses and helps breeders to make selections for population improvement and cultivar release. Simple sequence repeat (SSR) markers have become widely used markers for diversity and linkage analysis in plants. In this study, we screened 405 sweetpotato SSR markers for polymorphism on the parents and progeny of a biparental cross of New Kawogo × Beauregard cultivars. Thereafter, we used the informative markers to analyze the diversity in this population. A total of 250 markers were polymorphic on the parents and selected progeny; of these, 133 were informative and used for diversity analysis. The polymorphic information content (PIC) values of the 133 markers ranged from 0.1 to 0.9 with an average of 0.7, an indication of high level of informativeness. The pairwise genetic distances among the progeny and parents ranged from 0.2 to 0.9, and they were grouped into five main clusters. The 133 SSR primers were informative and are recommended for use in sweetpotato diversity and linkage analysis.

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Genetic variation in Hydrangea macrophylla (Thunb.) Ser. in Russia based on simple sequence repeat markers

Bangladesh Journal of Botany ◽

10.3329/bjb.v47i4.47389 ◽

2018 ◽

Vol 47 (4) ◽

pp. 937-943

Author(s):

Natalia Sukhikh ◽

Valentina Malyarovskaya ◽

Anastasiya Kamionskaya ◽

Lidia Samarina ◽

Svetlana Vinogradova

Keyword(s):

Simple Sequence Repeat ◽

Genetic Relationships ◽

Effective Number ◽

Sequence Repeat ◽

Base Pairs ◽

Breeding Programs ◽

Simple Sequence Repeat Markers ◽

Hydrangea Macrophylla ◽

High Level ◽

Simple Sequence

Genetic diversity and genetic relationships among 39 accessions of Hydrangea macrophylla (Thunb.) Ser. were analyzed using 38 previously developed simple sequence repeat markers (SSRs). A total of 38 polymorphic primers representing 166 bands with an average of 4.53 polymorphic bands per primer were selected. The number of alleles detected per locus ranged from two to eight with a total of 163 alleles amplified. The size of the amplified fragments ranged from 70 to180 base pairs. The effective multiallelic markers with high level of heterozygosity (more than 0.7) and effective number of alleles (more than 3.5) were identified. In this study nine SSR markers showed clear polymorphisms. The dendrogram grouped all hybrids in three major clusters, and two of these clusters included only mophead cultivars. The lacecap cultivars clustered more closely to each other. The results of this research could be used in breeding programs of H. macrophylla.

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Genetic diversity of ten Moroccan populations of Tetraclinis articulata as revealed by Inter Simple Sequence Repeat (ISSR) markers

BOIS & FORETS DES TROPIQUES ◽

10.19182/bft2020.345.a31927 ◽

2020 ◽

Vol 345 ◽

pp. 15-25

Author(s):

Meryem MAKKAOUI ◽

Younes ABBAS ◽

Salwa EL ANTRY-TAZY ◽

Leila MEDRAOUI ◽

Mohammed ALAMI ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Mantel Test ◽

Conservation Strategies ◽

Sequence Repeat ◽

Tetraclinis Articulata ◽

High Level ◽

Simple Sequence

Tetraclinis articulata (Vahl) Masters is one of Morocco's most important forest species. It is also found occasionally in Malta and Spain, showing significant adaptability to different bio-climatic conditions. However, the species is being affected by anthropogenic fragmentation, logging and neglect from authorities, which could lead to the irretrievable loss of this resource. In this study, the genetic diversity and genetic structure of ten Moroccan populations of T. articulata were assessed. Fifteen Inter-Simple Sequence Repeat (ISSR) markers were used. These generated 271 polymorphic fragments with an average of 18.06 per primer and showed 79.59% of polymorphism. The 129 individuals revealed a high level of genetic diversity (Hs = 0.221; Ht = 0.254) and 85% of genetic variation within populations. However, the genetic differentiation level was low (Gst = 0.13), which is consistent with the lack of correlation between genetic and geographic distances revealed by the Mantel test, resulting in a high level of gene flow (Nm = 3.294). Based on PCoA and neighbour-joining methods, the ten populations clustered under the effect of continental and marine climates. Compared with other conifers, the current genetic diversity and the pattern of T. articulata population structure indicate an important gene pool requiring efficient conservation strategies.

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Molecular phylogeny of genus Musa determined by simple sequence repeat markers

Plant Genetic Resources ◽

10.1017/s1479262115000222 ◽

2015 ◽

Vol 14 (3) ◽

pp. 192-199 ◽

Cited By ~ 1

Author(s):

Huimin Feng ◽

You Chen ◽

Bo Li ◽

Yaoting Wu

Keyword(s):

Simple Sequence Repeat ◽

Polymorphic Information Content ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Molecular Data ◽

Sequence Repeat ◽

Wide Range ◽

Molecular Marker Analysis ◽

High Level ◽

Simple Sequence

Musa L. was previously separated into five sections (Eumusa, Rhodochlamys, Callimusa, Australimusa and Ingentimusa) based on basic chromosome numbers and morphological characters. However, several molecular analyses currently support restructuring of Musa species into two sections, Musa and Callimusa. The application of simple sequence repeat molecular marker analysis to Musa phylogeny provided valuable, supplemental information about the classification of, and relationships between, Musa species and subspecies. Totally, 28 accessions of Musa acuminata Colla subspecies and varieties and 25 accessions of other Musa species were evaluated; 12 primers produced 91 polymorphic bands, polymorphic information content ranged from 0.4473 to 0.8394 (average = 0.7226), indicating that the primers showed a high level of polymorphism. Our results generally agreed with previous phylogenetic analyses based on molecular data. One clade comprised species of sections Australimusa and Callimusa (X= 10/9); most species of sections Eumusa and Rhodochlamys (X= 11) formed the other clade. The relationships between most species were as expected; however, some species did not conform to findings of previous studies. A wide range of variability was observed in the M. acuminata complex. M. acuminata var. chinensis and M. acuminata subsp. 522 showed the most distant relationships to other subspecies: Musa laterita, Musa ornata and Musa velutina clustered with M. acuminata var. chinensis, suggesting that they may constitute a secondary gene pool for the improvement of cultivated bananas. Molecular data indicated that Musa tongbiguanensis Chen You & Yao-Ting Wu, which was observed and described by our research group in Yunnan, China, was a distinct, new species.

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Genetic differentiation of Allium sibiricum L. populations in Poland based on their morphological and molecular markers

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.3618 ◽

2019 ◽

Vol 88 (1) ◽

Author(s):

Jacek Urbaniak ◽

Paweł Kwiatkowski ◽

Bartosz Kozak

Keyword(s):

Simple Sequence Repeat ◽

Genetic Similarity ◽

Inter Simple Sequence Repeat ◽

Sequence Repeat ◽

The Carpathians ◽

Repeat Dna ◽

Local Range ◽

High Level ◽

Simple Sequence ◽

Simple Sequence Repeat Dna

Allium sibiricum is one of the rarest plant species in the Sudetes and Carpathians. Inter simple sequence repeat DNA (ISSR) and morphological analyses were conducted to study the biogeographical relationships between geographically disjunctive populations of A. sibiricum in the Carpathians and Sudetes. The results clearly differentiated the Carpathian and Sudetes populations, but also showed a relatively high level of genetic similarity in specimens within certain groups of the Sudetes and Carpathian populations. The plants collected in the Karkonosze probably belong to a mountain form of A. schoenoprasum morphotype C which inhabits natural sites there. In contrast, the study found morphologically and genetically different plants inhabiting Pilsko Mt in the Carpathians. The plants from the Carpathians were present in scattered sites probably due to the activity of Vlach shepherds and the formation of large pastures. The species enlarged its local range due to this type of anthropopressure and likely hybridized with the cultivated Allium plants introduced by the shepherds. This may indicate that the populations on Pilsko Mt are of a partly anthropogenic character.

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Phylogenetic Relationship ofEchinochloaSpecies Based on Simple Sequence Repeat and Phenotypic Marker Analyses

Weed Science ◽

10.1614/ws-d-15-00187.1 ◽

2016 ◽

Vol 64 (3) ◽

pp. 441-454 ◽

Cited By ~ 3

Author(s):

Eun-Jung Lee ◽

Gyoungju Nah ◽

Min-Jung Yook ◽

Soo-Hyun Lim ◽

Tae-Sun Park ◽

...

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Morphological Traits ◽

Reproductive Organs ◽

Sequence Repeat ◽

Phenotypic Marker ◽

Future Studies ◽

High Level ◽

Simple Sequence

Echinochloaspecies are among the most troublesome weeds in rice cultivation, and grow in a broad habitat range in Korea. Although various ecotypes ofEchinochloahave been collected as germplasm for future studies, it has been difficult to classify them due to their high level of morphological similarity. This study was thus conducted to develop and investigate the phylogenetic relationships between 77Echinochloaaccessions with the use of 23 simple sequence repeat (SSR) markers and 24 morphological traits. Of 77Echinochloaaccessions, including 57 accessions from Korea and 5 reference species, late watergrass was clearly clustered as a distinctive group from barnyardgrass and otherEchinochloaspecies. In this analysis, we also identified core genetic and morphological markers that can be used for the future identification and classification ofEchinochloaspecies. Five out of 23 SSR makers produced distinctive bands that discriminate late watergrass from barnyardgrass and otherEchinochloaspecies. Four morphological traits of the reproductive organs were the most influential contributors for classifyingEchinochloaspecies. Although there was no clear consensus generated in this study between SSR markers and morphological trait analyses, our results support the potential use of the selected SSR markers and morphological traits in future studies ofEchinochloa.

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Implementing molecular marker technology in forage improvement

Proceedings of the New Zealand Grassland Association ◽

10.33584/jnzg.2003.65.2498 ◽

2003 ◽

pp. 229-238

Author(s):

M. Faville ◽

B. Barrett ◽

A. Griffiths ◽

M. Schreiber ◽

C. Mercer ◽

...

Keyword(s):

Quantitative Trait Locus ◽

Genetic Variation ◽

White Clover ◽

Simple Sequence Repeat ◽

Sequence Repeat ◽

Linkage Groups ◽

Seedling Vigour ◽

Genome Map ◽

Trait Locus ◽

Simple Sequence

Accelerated improvement of two cornerstones of New Zealand's pastoral industries, per ennial ryegrass (Lolium perenne L.) and white clover (Trifolium repens L.), may be realised through the application of markerassisted selection (MAS) strategies to enhance traditional plant breeding programmes. Genome maps constructed using molecular markers represent the enabling technology for such strategies and we have assembled maps for each species using EST-SSR markers - simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) representing genes. A comprehensive map of the white clover genome has been completed, with 464 EST-SSR and genomic SSR marker loci spanning 1125 cM in total, distributed across 16 linkage groups. These have been further classified into eight pairs of linkage groups, representing contributions from the diploid progenitors of this tetraploid species. In perennial ryegrass a genome map based exclusively on EST-SSR loci was constructed, with 130 loci currently mapped to seven linkage groups and covering a distance of 391 cM. This map continues to be expanded with the addition of ESTSSR loci, and markers are being concurrently transferred to other populations segregating for economically significant traits. We have initiated gene discovery through quantitative trait locus (QTL) analysis in both species, and the efficacy of the white clover map for this purpose was demonstrated with the initial identification of multiple QTL controlling seed yield and seedling vigour. One QTL on linkage group D2 accounts for 25.9% of the genetic variation for seed yield, and a putative QTL accounting for 12.7% of the genetic variation for seedling vigour was detected on linkage group E1. The application of MAS to forage breeding based on recurrent selection is discussed. Keywords: genome map, marker-assisted selection, perennial ryegrass, QTL, quantitative trait locus, SSR, simple sequence repeat, white clover

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