Genetic diversity analysis using simple sequence repeat markers in soybean

To evaluate the genetic diversity (GD) of wild and cultivated soybeans and determine the genetic relationships between them, in this study, 127 wild soybean accessions and 219 cultivated soybean accessions were genotyped using 74 simple sequence repeat (SSR) markers. The results of the study revealed that the GD of the wild soybeans exceeded that of the cultivated soybeans. In all, 924 alleles were detected in the 346 soybean accessions using 74 SSRs, with an average of 12.49 alleles per locus. In the 219 cultivated soybean accessions, 687 alleles were detected, with an average of 9.28 alleles per locus; in the 127 wild soybean accessions, 835 alleles were detected, with an average of 11.28 alleles per locus. We identified 237 wild-soybean-specific alleles and 89 cultivated-soybean-specific alleles in the 346 soybean accessions, and these alleles accounted for 35.28% of all the alleles in the sample. Principal coordinates analysis and phylogenetic analysis based on Nei's genetic distance indicated that all the accessions could be classified into two major clusters, corresponding to wild and cultivated soybeans. These results will increase our understanding of the genetic differences and relationships between wild and cultivated soybeans and provide information to develop future breeding strategies to improve soybean yield.

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Genetic diversity among silkworm (Bombyx mori L., Lep., Bombycidae) germplasms revealed by microsatellites

Genome ◽

10.1139/g05-053 ◽

2005 ◽

Vol 48 (5) ◽

pp. 802-810 ◽

Cited By ~ 30

Author(s):

Muwang Li ◽

Li Shen ◽

Anying Xu ◽

Xuexia Miao ◽

Chengxiang Hou ◽

...

Keyword(s):

Genetic Diversity ◽

Bombyx Mori ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Relationships ◽

Group Method ◽

Sequence Repeat ◽

Bombyx Mori L ◽

Simple Sequence ◽

Silkworm Bombyx Mori

To determine genetic relationships among strains of silkworm, Bombyx mori L., 31 strains with different origins, number of generations per year, number of molts per generation, and morphological characters were studied using simple sequence repeat (SSR) markers. Twenty-six primer pairs flanking microsatellite sequences in the silkworm genome were assayed. All were polymorphic and unambiguously separated silkworm strains from each other. A total of 188 alleles were detected with a mean value of 7.2 alleles/locus (range 2–17). The average heterozygosity value for each SSR locus ranged from 0 to 0.60, and the highest one was 0.96 (Fl0516 in 4013). The mean polymorphism index content (PIC) was 0.66 (range 0.12–0.89). Unweighted pair group method with arithmetic means (UPGMA) cluster analysis of Nei's genetic distance grouped silkworm strains based on their origin. Seven major ecotypic silkworm groups were analyzed. Principal components analysis (PCA) for SSR data support their UPGMA clustering. The results indicated that SSR markers are an efficient tool for fingerprinting cultivars and conducting genetic-diversity studies in the silkworm.Key words: silkworm, Bombyx mori L., microsatellites, simple sequence repeat (SSR), genetic diversity.

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Genetic diversity of Canadian elite summer rape (Brassica napus L.) cultivars from the pre- to post-canola quality era

Canadian Journal of Plant Science ◽

10.4141/cjps09073 ◽

2010 ◽

Vol 90 (1) ◽

pp. 23-33 ◽

Cited By ~ 12

Author(s):

Y -B. Fu ◽

R K Gugel

Keyword(s):

Genetic Diversity ◽

Brassica Napus ◽

Erucic Acid ◽

Simple Sequence Repeat ◽

Genetic Relationships ◽

Gene Pools ◽

Sequence Repeat ◽

Low Erucic Acid ◽

Simple Sequence ◽

Canola Quality

The development of canola quality Brassica napus oilseed cultivars was a major achievement of Canadian public oilseed breeding programs. Simple sequence repeat (SSR) markers were applied to assess the genetic diversity of 300 plants representing one landrace introduced from Argentina in 1943, seven Canadian elite cultivars developed and released by Agriculture and Agri-Food Canada since 1954, and two European cultivars that were the source of the low erucic acid and low glucosinolate traits that define canola quality. Application of 22 SSR primer pairs from eight linkage groups detected 88 polymorphic alleles from 33 likely loci. The allelic frequencies in 300 samples ranged from 0.003 to 0.993 and averaged 0.388. The estimates of mean heterozygosity for these cultivars ranged from 0.055 to 0.203 and averaged 0.139. The most SSR variation was detected in the cultivars Argentine, Golden and Oro. A trend of decline in SSR variation was observed over the years of breeding effort. The proportion of total SSR variation residing among the cultivars was 51.4%; between high vs. low erucic acid cultivars 15% and between high vs. low glucosinolate cultivars 21.2%. Pairwise genetic differentiations among these cultivars ranged from 0.140 to 0.819 and averaged 0.500. Cluster analysis revealed that the genetic relationships of these cultivars were consistent with their known pedigrees. These findings are useful for broadening the genetic base of improved B. napus gene pools, selecting genetically diverse genotypes for hybrid combinations, and conserving summer rape germplasm.Key words: Simple sequence repeat, summer rape, Brassica napus, genetic diversity, genetic relationship, genetic structure

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Genetic relatedness among cultivated and wild mulberry (Moraceae: Morus) as revealed by inter-simple sequence repeat analysis in China

Canadian Journal of Plant Science ◽

10.4141/p04-110 ◽

2006 ◽

Vol 86 (1) ◽

pp. 251-257 ◽

Cited By ~ 16

Author(s):

Zhao Weiguo ◽

Zhou Zhihua ◽

Miao Xuexia ◽

Wang Sibao ◽

Zhang Lin ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Genetic Relatedness ◽

Genetic Relationships ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Group Method ◽

Sequence Repeat ◽

Pair Group ◽

Simple Sequence

The genetic diversity of 27 mulberry (Morus spp.) genotypes mainly from China was investigated using inter-simple sequence repeat (ISSR) markers to assist in addressing breeding objectives and conserving existing genetic resources. Of the 22 primers screened, 15 produced highly reproducible ISSR bands. Using these 15 primers, 138 discernible DNA fragments were generated with 126 (91.3%) being polymorphic, indicating considerable genetic variation among the mulberry genotypes studied. Genetic similarity ranged from 0.6014 between Yu 2 and Yu 711 to 0.9493 between Cuizhisang and Dejiang 10. The phenetic dendrogram based on ISSR data generated by the unweighed pair group method with arithmetical averages (UPGMA) method grouped the 27 accessions into two major clusters: cluster I, cultivated mulberry species (M. multicaulis Perr., M. alba Linn., M. atropurpurea oxb., M. bombycis Kiodz., M. australis Poir., M. rotundiloba Kiodz., M. alba var. pendula Dipp., M. alba var. macrophylla Loud., and M. alba var. venose Delile.); and cluster II, wild mulberry species (M. cathayana Hemsl., M. laevigata Wall., M. wittiorum Hand-Mazz., M. nigra Linn., and M. mongolica Schneid.). Our molecular analyses agree with the existing morphological classification of Morus and clarify the genetic relationships among mulberry species. Key words: Morus L., genetic diversity, inter-simple sequence repeat, relatedness

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Genetic diversity analysis of yam cultivars (Dioscorea rotundata Poir.) in Benin using simple sequence repeat (SSR) markers

Plant Genetic Resources ◽

10.1017/s1479262107672323 ◽

2007 ◽

Vol 5 (02) ◽

pp. 71-81 ◽

Cited By ~ 23

Author(s):

Serge Tostain ◽

Clément Agbangla ◽

Nora Scarcelli ◽

Cédric Mariac ◽

Ogoubi Daïnou ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Management Practices ◽

Genetic Relationships ◽

Sequence Repeat ◽

Dioscorea Rotundata ◽

Tuber Crop ◽

The Mean ◽

Simple Sequence

Guinea yam (Dioscorea rotundataPoir.) is a dioecious vegetatively propagated tuber crop. It is widely cultivated by traditional techniques in West Africa, its area of origin. The genetic diversity of 146 accessions from Benin was analysed using 10 polymorphic simple sequence repeat (SSR) nuclear markers and agromorphological traits. An average of 8.4 alleles per locus was detected. The mean heterozygosity was 0.57 and the mean polymorphism information content (PIC) for polymorphic markers was 0.51. Some cultivars (23%) were found to have an identical genotype for the 10 markers. The structure of the genetic diversity observed in Benin is the result of farmers' crop management practices and their know-how. The cultivar diversity had a geographical component. We also noted major differentiation between early and late cultivars, with higher diversity in the early ones. Cultivars from northern Benin and early cultivars had the greatest allelic richness. SSR markers proved to be powerful tools for fingerprinting each cultivar and analysing their genetic relationships. The results of this study could be useful for defining a strategy for the conservation of genetic diversity in yams.

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Simple Sequence Repeat Marker Analysis of Genetic Relationships within Hydrangea macrophylla

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.132.3.341 ◽

2007 ◽

Vol 132 (3) ◽

pp. 341-351 ◽

Cited By ~ 12

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.

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Genetic diversity in wild Lens spp. using inter simple sequence repeat (ISSR) marker

Legume Research - An International Journal ◽

10.18805/lr.v38i5.5932 ◽

2015 ◽

Vol 38 (5) ◽

Author(s):

Padmavati G. Gore ◽

M. K. Rana ◽

Kuldeep Tripathi ◽

Mohar Singh ◽

I. S. Bisht ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Molecular Diversity ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Sequence Repeat ◽

Principal Coordinates ◽

Cultivated Species ◽

Simple Sequence ◽

Issr Primers

Genetic diversity was assessed in 50 accessions of seven <italic>Lens</italic> species using ISSR markers. The collection included accessions of the cultivated species <italic>L. culinaris</italic> and six wild species, <italic>viz</italic>., <italic>L. culinaris</italic> ssp. <italic>odemensis, L. culinaris</italic> ssp. <italic>orientalis</italic>, <italic>L.</italic> <italic>orientalis, L. nigricans, L. lamottei</italic> and <italic>L. ervoides.</italic> The 23 ISSR primers amplified a total of 368 bands with an average of 16 bands per primer. Maximum number of 20 bands was amplified using each of the primers ISSR-34 and ISSR-835. All the primers were found to be polymorphic. PIC values ranged from 0.02 to 0.80. The primers ISSR-807, ISSR- 809, ISSR- 827, ISSR- 847, ISSR-28 and ISSR- 37 were found to be very useful for analyzing the molecular diversity of the genus <italic>Lens</italic>. Cluster Analysis and Principal Coordinates Analyses placed the 50 accessions into two groups and complemented each other.

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Genetic diversity in Vicia faba L. populations cultivated in Tunisia revealed by simple sequence repeat analysis

Plant Genetic Resources ◽

10.1017/s1479262114000021 ◽

2014 ◽

Vol 12 (3) ◽

pp. 278-285 ◽

Cited By ~ 4

Author(s):

Yassine Yahia ◽

Hédia Hannachi ◽

Antonio Jose Monforte ◽

James Cockram ◽

Mohamed Loumerem ◽

...

Keyword(s):

Genetic Diversity ◽

Vicia Faba ◽

Faba Bean ◽

Simple Sequence Repeat ◽

Variance Component ◽

Genetic Relationships ◽

Factorial Correspondence Analysis ◽

Sequence Repeat ◽

Breeding Programmes ◽

Simple Sequence

Faba bean (Vicia faba L.) is one of the most important legumes in the world. Little is known about the genetic resources of faba bean in Southern Tunisia. In the present study, genetic diversity within Tunisian faba bean germplasms was investigated using 16 simple sequence repeat markers. In total, 50 alleles were detected. The number of alleles per marker ranged from 2 to 6, with an average of 3. Genetic diversity and polymorphism information content values averaged, respectively, 0.43 (range 0.34–0.51) and 0.36 (range 0.28–0.43). The mean heterozygosity value was 0.27. A model-based structure analysis based on neighbour-joining tree and factorial correspondence analysis revealed the presence of two subpopulations, consistent with the clustering based on genetic distance (GD). The overall Fis value was 0.36, indicating the importance of selfing in these populations. Analysis of molecular variance revealed that the within-population genetic variance component was much higher than the between-population or between-subpopulation variance component. The genetic relationships based on Nei's GD revealed that AGD (Aguadulce) and SAG (Super Aguadulce) and TF1 and TF2 (Tafartassa-Gafsa) were the most closely related populations. Assessment of genetic variation within faba bean populations will be informative for the conservation of germplasms and the implementation of effective breeding programmes in Tunisia.

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