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Assessment of genetic diversity in Ethiopian field pea (Pisum sativum L.) accessions with newly developed EST-SSR markers.

Teshome A, Bryngelsson T, Dagne K, Geleta M - BMC Genet. (2015)

Bottom Line: These markers have successfully amplified their target loci across seven Pisum sativum subsp. sativum accessions.These newly developed EST-SSR primer-pairs successfully amplified expected loci in P. sativum subsp. sativum as well as in other subspecies of the genus Pisum and related genera.This result implies the potential of the Ethiopian field pea gene pool for improvement of field peas in various desirable traits.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, SE-23053, Alnarp, Sweden. Abel.Teshome@slu.se.

ABSTRACT

Background: Field pea (Pisum sativum L.) is among the prominent crops in the world as food and feed. There are relatively few simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) in P. sativum.

Results: In the present study, 15 new EST-SSR markers were developed from publicly available ESTs. These markers have successfully amplified their target loci across seven Pisum sativum subsp. sativum accessions. Eleven (73%) of these SSRs were trinucleotide repeats, two (13%) dinucleotide and two (13%) were hexanucleotide repeats. Across-taxa transferability of these new markers was also tested on other subspecies of Pisum as well as on P. fulvum, Vicia faba and Lens culinaris. In Pisum sativum subsp. sativum, 13 of the 15 markers were polymorphic and 12 of them subsequently used for genetic diversity analysis. Forty six accessions, of which 43 were from Ethiopia, were subjected to genetic diversity analysis using these newly developed markers. All accessions were represented by 12 individuals except two (NGB103816 and 237508) that were represented by 9 and 11 individuals, respectively. A total of 37 alleles were detected across all accessions. PS10 was the most polymorphic locus with six alleles, and the average number of alleles per locus over the 12 polymorphic loci was 3.1. Several rare and private alleles were also revealed. The most distinct accession (32048) had private alleles at three loci with 100% frequency.

Conclusion: These newly developed EST-SSR primer-pairs successfully amplified expected loci in P. sativum subsp. sativum as well as in other subspecies of the genus Pisum and related genera. High levels of genetic variation were detected in field pea accessions from Ethiopia using these markers. This result implies the potential of the Ethiopian field pea gene pool for improvement of field peas in various desirable traits. In addition, these markers could be a valuable asset in resolving the inconsistency in the taxonomic status of the different subspecies of genus Pisum as well as for characterization of field pea accessions in different gene banks around the world for breeding and conservation purposes.

No MeSH data available.


Related in: MedlinePlus

STRUCTURE analysis at K = 9 for 46 P. sativum accessions. The colors represent different clusters and the colors in each accession represent the average proportion of alleles that placed each accession under two or more clusters. The text above the figure refers to accession names; and the text below the figure refers to different regions within Ethiopia or countries from where the accessions originated. Note: Ethiopia* refers to Ethiopian accessions with unknown site of collection
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Related In: Results  -  Collection


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Fig3: STRUCTURE analysis at K = 9 for 46 P. sativum accessions. The colors represent different clusters and the colors in each accession represent the average proportion of alleles that placed each accession under two or more clusters. The text above the figure refers to accession names; and the text below the figure refers to different regions within Ethiopia or countries from where the accessions originated. Note: Ethiopia* refers to Ethiopian accessions with unknown site of collection

Mentions: Based on the 37 alleles distributed over 12 EST-SSR loci, STRUCTURE software was used to analyze population structure. The structure simulation with STRUCTURE HARVERSTER demonstrated that the K value had the highest peak at K = 9, inferring that nine populations can incorporate all individuals from the 46 accessions with the highest likelihood. The structuring with K = 9 is shown in Fig. 3. The predicted population structure for the accessions displayed partial membership to more than one population, and none of the accessions showed membership to only one population. Several accessions, including the genetically most diverse accession (32713), had partial membership to eight different populations. However, in accessions with no or very low genetic variation, such as the two Norwegian accessions and accession 32048, the vast majority of their alleles came from a single population. Similar to cluster analysis, the distinctness of accession 32048 was depicted in the STRUCTURE analysis (Fig. 3) in that only very few other accessions share partial population membership (at very low proportion) with this accession. Furthermore, the structure analysis corroborates what is shown in the cluster analysis (Fig. 2a) in that there is no clear segregation of accessions based on geographic origin.Fig. 3


Assessment of genetic diversity in Ethiopian field pea (Pisum sativum L.) accessions with newly developed EST-SSR markers.

Teshome A, Bryngelsson T, Dagne K, Geleta M - BMC Genet. (2015)

STRUCTURE analysis at K = 9 for 46 P. sativum accessions. The colors represent different clusters and the colors in each accession represent the average proportion of alleles that placed each accession under two or more clusters. The text above the figure refers to accession names; and the text below the figure refers to different regions within Ethiopia or countries from where the accessions originated. Note: Ethiopia* refers to Ethiopian accessions with unknown site of collection
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4541747&req=5

Fig3: STRUCTURE analysis at K = 9 for 46 P. sativum accessions. The colors represent different clusters and the colors in each accession represent the average proportion of alleles that placed each accession under two or more clusters. The text above the figure refers to accession names; and the text below the figure refers to different regions within Ethiopia or countries from where the accessions originated. Note: Ethiopia* refers to Ethiopian accessions with unknown site of collection
Mentions: Based on the 37 alleles distributed over 12 EST-SSR loci, STRUCTURE software was used to analyze population structure. The structure simulation with STRUCTURE HARVERSTER demonstrated that the K value had the highest peak at K = 9, inferring that nine populations can incorporate all individuals from the 46 accessions with the highest likelihood. The structuring with K = 9 is shown in Fig. 3. The predicted population structure for the accessions displayed partial membership to more than one population, and none of the accessions showed membership to only one population. Several accessions, including the genetically most diverse accession (32713), had partial membership to eight different populations. However, in accessions with no or very low genetic variation, such as the two Norwegian accessions and accession 32048, the vast majority of their alleles came from a single population. Similar to cluster analysis, the distinctness of accession 32048 was depicted in the STRUCTURE analysis (Fig. 3) in that only very few other accessions share partial population membership (at very low proportion) with this accession. Furthermore, the structure analysis corroborates what is shown in the cluster analysis (Fig. 2a) in that there is no clear segregation of accessions based on geographic origin.Fig. 3

Bottom Line: These markers have successfully amplified their target loci across seven Pisum sativum subsp. sativum accessions.These newly developed EST-SSR primer-pairs successfully amplified expected loci in P. sativum subsp. sativum as well as in other subspecies of the genus Pisum and related genera.This result implies the potential of the Ethiopian field pea gene pool for improvement of field peas in various desirable traits.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, SE-23053, Alnarp, Sweden. Abel.Teshome@slu.se.

ABSTRACT

Background: Field pea (Pisum sativum L.) is among the prominent crops in the world as food and feed. There are relatively few simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) in P. sativum.

Results: In the present study, 15 new EST-SSR markers were developed from publicly available ESTs. These markers have successfully amplified their target loci across seven Pisum sativum subsp. sativum accessions. Eleven (73%) of these SSRs were trinucleotide repeats, two (13%) dinucleotide and two (13%) were hexanucleotide repeats. Across-taxa transferability of these new markers was also tested on other subspecies of Pisum as well as on P. fulvum, Vicia faba and Lens culinaris. In Pisum sativum subsp. sativum, 13 of the 15 markers were polymorphic and 12 of them subsequently used for genetic diversity analysis. Forty six accessions, of which 43 were from Ethiopia, were subjected to genetic diversity analysis using these newly developed markers. All accessions were represented by 12 individuals except two (NGB103816 and 237508) that were represented by 9 and 11 individuals, respectively. A total of 37 alleles were detected across all accessions. PS10 was the most polymorphic locus with six alleles, and the average number of alleles per locus over the 12 polymorphic loci was 3.1. Several rare and private alleles were also revealed. The most distinct accession (32048) had private alleles at three loci with 100% frequency.

Conclusion: These newly developed EST-SSR primer-pairs successfully amplified expected loci in P. sativum subsp. sativum as well as in other subspecies of the genus Pisum and related genera. High levels of genetic variation were detected in field pea accessions from Ethiopia using these markers. This result implies the potential of the Ethiopian field pea gene pool for improvement of field peas in various desirable traits. In addition, these markers could be a valuable asset in resolving the inconsistency in the taxonomic status of the different subspecies of genus Pisum as well as for characterization of field pea accessions in different gene banks around the world for breeding and conservation purposes.

No MeSH data available.


Related in: MedlinePlus