Spatial and temporal genetic variation in Ethiopian barley (Hordeum vulgare L.) landraces as revealed by simple sequence repeat (SSR) markers

Abstract Background Ethiopia is considered as center of diversity for barley (Hordeum vulgare L.) and it is grown across different agro-ecologies of the country. Unraveling population structure and gene flow status on temporal scales assists an evaluation of the consequences of physical, demographic and overall environmental changes on the stability and persistence of populations. This study was to examine spatial and temporal genetic variation within and among barley landrace samples collected over a period of four decades, using simple sequence repeat markers. Results Results from STRUCTURE, neighbor joining tree and discriminant analysis of principal component (DAPC) analysis revealed presence low-to-high genetic diversity among the landraces and grouped the landraces into three clusters. The cluster analysis revealed a close relationship between landraces along geographic proximity with genetic distance increases along with geographic distance. From analysis of molecular variance (AMOVA) in terms of collection year, it was observed that within-population genetic diversity much higher than between population and that the temporal differentiation is considerably smaller. The low-to-high genetic differentiation between landraces could be attributed to gene flow across the region as a consequence of seed exchange among farmers. Conclusion The results demonstrate that this set of SSRs was highly informative and useful in generating a meaningful classification of barley germplasms. Furthermore, results obtained from this study also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change and in situ conservation strategies following adaptation to local environments.

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Development of simple sequence repeat (SSR) markers for the assessment of gene flow and genetic diversity in pigeonpea (Cajanus cajan )

Molecular Ecology Notes ◽

10.1046/j.1471-8278.2001.00109.x ◽

2001 ◽

Vol 1 (4) ◽

pp. 283-285 ◽

Cited By ~ 39

Author(s):

M. J. Burns ◽

K. J. Edwards ◽

H. J. Newbury ◽

B. V. Ford-Lloyd ◽

C. D. Baggott

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Ssr Markers ◽

Cajanus Cajan ◽

Simple Sequence Repeat ◽

Sequence Repeat ◽

Simple Sequence

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Genetic Diversity of Arabica Coffee (Coffea arabicaL.) in Nicaragua as Estimated by Simple Sequence Repeat Markers

The Scientific World JOURNAL ◽

10.1100/2012/939820 ◽

2012 ◽

Vol 2012 ◽

pp. 1-11 ◽

Cited By ~ 11

Author(s):

Mulatu Geleta ◽

Isabel Herrera ◽

Arnulfo Monzón ◽

Tomas Bryngelsson

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Simple Sequence Repeat ◽

Significant Contribution ◽

Gene Diversity ◽

Ex Situ ◽

Sequence Repeat ◽

Breeding Programs ◽

Arabica Coffee ◽

Simple Sequence

Coffea arabicaL. (arabica coffee), the only tetraploid species in the genusCoffea, represents the majority of the world’s coffee production and has a significant contribution to Nicaragua’s economy. The present paper was conducted to determine the genetic diversity of arabica coffee in Nicaragua for its conservation and breeding values. Twenty-six populations that represent eight varieties in Nicaragua were investigated using simple sequence repeat (SSR) markers. A total of 24 alleles were obtained from the 12 loci investigated across 260 individual plants. The total Nei’s gene diversity (HT) and the within-population gene diversity (HS) were 0.35 and 0.29, respectively, which is comparable with that previously reported from other countries and regions. Among the varieties, the highest diversity was recorded in the variety Catimor. Analysis of variance (AMOVA) revealed that about 87% of the total genetic variation was found within populations and the remaining 13% differentiate the populations (FST=0.13;P<0.001). The variation among the varieties was also significant. The genetic variation in Nicaraguan coffee is significant enough to be used in the breeding programs, and most of this variation can be conserved throughex situconservation of a low number of populations from each variety.

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Genetic diversity of Dioscorea japonica germplasm in Taiwan revealed by inter-simple sequence repeat DNA markers

Plant Genetic Resources ◽

10.1017/s147926211500026x ◽

2015 ◽

Vol 14 (3) ◽

pp. 211-218

Author(s):

Tsai-Li Kung ◽

Kuan-Hung Lin ◽

Shun-Fu Lin

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Dna Markers ◽

Simple Sequence Repeat ◽

Germplasm Collection ◽

Inter Simple Sequence Repeat ◽

Northern Region ◽

Sequence Repeat ◽

Dioscorea Japonica ◽

Simple Sequence

There are three native varieties of edible yams (Dioscorea japonica Thunb.) in Taiwan, but germplasm has been collected from only a few. To assess the genetic diversity of 99 accessions collected from four geographically diverse regions, inter-simple sequence repeat (ISSR) DNA markers were analysed, and 90.2% of the polymorphic markers in these accessions were found. Genetic similarity among accessions ranged from 30.8 to 74.4%, averaging 48.4%. Cluster analyses revealed four main clusters plus one outlier (Dioscorea alata L.). The varieties oldhamii and pseudojaponica were separated into different clusters and var. japonica was grouped with both varieties. Since var. japonica was found to be genetically similar to var. oldhamii and var. pseudojaponica, we suggest that var. japonica is a hybrid or intermediate variety between the two varieties. Molecular analysis of variance results indicated that variation within counties (95.94%) was predominantly greater than variation among counties (3.63%) and among regions (0.43%). Overall, gene flow (Nm= 0.970) estimated from genetic differentiation (Gst= 0.340) suggests that gene flow among regions is relatively high. The highest genetic diversity (H= 0.191) and Shannon's index (I= 0.312), and a high gene flow (Nm= 3.926) of germplasm in the northern region suggest that this region is a possible centre of dispersal and domestication of yams in Taiwan. This study provided valuable information for germplasm collection and genetic improvement.

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KEANEKARAGAMAN GENETIK KAPULASAN [NEPHELIUM RAMBOUTAN-AKE (LABILL.) LEENH.] DI JAWA BERDASARKAN MARKA SSR DAN ISSR

Floribunda ◽

10.32556/floribunda.v6i4.2020.300 ◽

2020 ◽

Vol 6 (4) ◽

Author(s):

Nina Ratna Djuita ◽

Alex Hartana ◽

Tatik Chikmawati ◽

Dorly

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Genomic Dna ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Sequence Repeat ◽

Polymorphic Bands ◽

Simple Sequence

Nina Ratna Djuita, Alex Hartana, Tatik Chikmawati, Dorly. 2020. Genetic Diversity of Pulasan [Nephelium ramboutan-ake (Labill.) Leenh.] of Java Based on SSR and ISSR Markers. Floribunda 6(4): 117–126. — Pulasan is one of the potential local fruits to be developed. This study aimed to analyze the genetic diversity of pulasan of Java using Simple Sequence Repeat (SSR) and Inter Simple Sequence Repeat (ISSR) markers and to obtain information whether primers of the markers could be used to distinguish male and her-maphrodite plants. The results showed that two primers in the SSR markers and seven primers in the ISSR markers produced polymorphic bands. The genomic DNA of the pulasan amplified with SSR markers produced bands 140–500 bp, while those from the ISSR markers were 150–1500 bp. The population of pulasan in Babakan Madang has the highest genetic diversity, while that of Patean is the lowest. Genetic variation of pulasan based on SSR and ISSR markers in the population and among populations have different compositions. Variation in the population is 72% while among the population is 28%. Primers of LML Y6 and LML Y12 from SSR markers and primers of ISSR 2, 3, 4, 5, 6, 8, 9 cannot be used to distinguish male and hermaphrodite pulasan plants. Nina Ratna Djuita, Alex Hartana, Tatik Chikmawati, Dorly. 2020. Keanekaragaman Genetik Kapulasan [Nephelium ramboutan-ake (Labill.) Leenh.] di Jawa Berdasarkan Marka SSR dan ISSR. Floribunda 6(4): 117–126. — Kapulasan merupakan salah satu buah lokal yang potensial untuk dikembangkan. Penelitian ini bertujuan untuk menganalisis keanekaragaman genetik kapulasan di Jawa dengan menggunakan marka Simple Sequence Repeat (SSR) dan Inter Simple Sequence Repeat (ISSR) serta untuk mendapatkan informasi apakah primer dari marka tersebut dapat dipakai untuk membedakan tumbuhan jantan dan hermafrodit. Hasil penelitian menunjukkan bahwa dua primer pada marka SSR dan tujuh primer pada marka ISSR menghasilkan pita polimorfik. DNA genom kapulasan yang diamplifikasi dengan marka SSR menghasilkan pita-pita dengan ukuran 110–500 bp, sedangkan dari marka ISSR berukuran 150–1500 bp. Populasi kapulasan di Babakan Madang mempunyai keanekaragaman genetik paling tinggi, sedangkan populasi di Patean paling rendah. Variasi genetik kapulasan berdasarkan marka SSR dan ISSR di dalam populasi dan di antara populasi mempunyai komposisi yang berbeda. Variasi di dalam populasi sebesar 72 % sedangkan di antara populasi sebesar 28%. Primer LML Y6 dan LML Y12 dari marka SSR dan primer ISSR 2, 3, 4, 5, 6, 8, 9 tidak dapat digunakan untuk membedakan tumbuhan kapulasan jantan dan hermafrodit.

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Molecular characterization of wild grapes from northeastern part of Turkey

Genetika ◽

10.2298/gensr2101093k ◽

2021 ◽

Vol 53 (1) ◽

pp. 93-102

Author(s):

Muhammed Kupe ◽

Sezai Ercisli ◽

Tatjana Jovanovic-Cvetkovic ◽

Sadiye Eyduran ◽

Rayda Ayed

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Simple Sequence Repeat ◽

Group Method ◽

Gene Pools ◽

Sequence Repeat ◽

Natural Habitats ◽

Wild Grape ◽

Wild Grapevine ◽

Simple Sequence

Progress in grape breeding requires the exploitation of genetic variation among market classes, races and gene pools. Wild grapevines (Vitis vinifera ssp. sylvestris) are being endangered in their natural habitats and high priorities should be given to the wild germplasm. Turkey is one of the richest sources of wild grapevine and they mostly grown on forest trees on river basin. The present study was carried out to determine the amount of genetic variation and the degree of relatedness among 23 wild grape genotypes using 17 simple-sequence-repeat markers (SSR). Two international grape cultivars, Cabernet Sauvignon and Merlot are also included study. Number of alleles per locus of the 17 Simple Sequence Repeat (SSR) markers ranged from 3.0 to 14.0 and a total of 162 alleles with an average of 9.53 alleles per locus. The average expected and observed heterozygosity values were 0.773 and 0.781, respectively, which exhibited high level of genetic diversity in the wild grape germplasm. The unweighted pair group method with arithmetic mean analysis revealed three main genetic clusters that partially separated wild grape genotypes each other and. The international cultivars formed a out group. The high genetic diversity among native wild grapes from Coruh valley is suggesting that this area could be one of the centre of diversity of the specie. The results indicate a substantial genetic diversity in V. vinifera ssp. sylvestris and the need of exploring a wider area to increase the chance of finding a particular genotype.

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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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