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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

Rogers genetic distance-based UPGMA phenograms for (a) 46 accessions of P. sativum subsp. sativum (sub-region or country of origin of each accession is given in front of the accession name); (b) 18 groups of accessions after grouping Ethiopian accessions into sub-region of origin; (c) seven groups of the accessions after grouping Ethiopian accessions into their regions of origin. Sub-regions in “B” that belong to the same region are connected to each other and to their corresponding region in “C” with arrows. The two Ethiopian accessions with unknown site of collections (32048 and 32776) were excluded in the case of “B” and “C”. Numbers in front of the branches are bootstrap values (only bootstrap values more than 50 % are shown)
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Fig2: Rogers genetic distance-based UPGMA phenograms for (a) 46 accessions of P. sativum subsp. sativum (sub-region or country of origin of each accession is given in front of the accession name); (b) 18 groups of accessions after grouping Ethiopian accessions into sub-region of origin; (c) seven groups of the accessions after grouping Ethiopian accessions into their regions of origin. Sub-regions in “B” that belong to the same region are connected to each other and to their corresponding region in “C” with arrows. The two Ethiopian accessions with unknown site of collections (32048 and 32776) were excluded in the case of “B” and “C”. Numbers in front of the branches are bootstrap values (only bootstrap values more than 50 % are shown)

Mentions: Cluster analysis based on Rogers genetic distance coefficient was done for accessions, sub-regions and regions (Fig. 2). First, accession 32048 was separated from the rest of the accessions with 100 % bootstrap support, and was followed by accession NGB21659 from Norway, also with 100 % bootstrap support. Three accessions from southeastern and eastern Ethiopia (230864, 230048 and 2330858) formed a cluster with 92 % bootstrap support. The other major clusters in Fig. 2a were not supported by high bootstrap values. Accessions NGB103816 (USA) and NGB7131 (Norway) were not separated from Ethiopian accessions. At sub-region level Bale and Harerge formed a separate cluster with 100 % bootstrap support (Fig. 2b). At region level, Amhara region clustered with SNNP with 58 % bootstrap support (Fig. 2c).Fig. 2


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)

Rogers genetic distance-based UPGMA phenograms for (a) 46 accessions of P. sativum subsp. sativum (sub-region or country of origin of each accession is given in front of the accession name); (b) 18 groups of accessions after grouping Ethiopian accessions into sub-region of origin; (c) seven groups of the accessions after grouping Ethiopian accessions into their regions of origin. Sub-regions in “B” that belong to the same region are connected to each other and to their corresponding region in “C” with arrows. The two Ethiopian accessions with unknown site of collections (32048 and 32776) were excluded in the case of “B” and “C”. Numbers in front of the branches are bootstrap values (only bootstrap values more than 50 % are shown)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Rogers genetic distance-based UPGMA phenograms for (a) 46 accessions of P. sativum subsp. sativum (sub-region or country of origin of each accession is given in front of the accession name); (b) 18 groups of accessions after grouping Ethiopian accessions into sub-region of origin; (c) seven groups of the accessions after grouping Ethiopian accessions into their regions of origin. Sub-regions in “B” that belong to the same region are connected to each other and to their corresponding region in “C” with arrows. The two Ethiopian accessions with unknown site of collections (32048 and 32776) were excluded in the case of “B” and “C”. Numbers in front of the branches are bootstrap values (only bootstrap values more than 50 % are shown)
Mentions: Cluster analysis based on Rogers genetic distance coefficient was done for accessions, sub-regions and regions (Fig. 2). First, accession 32048 was separated from the rest of the accessions with 100 % bootstrap support, and was followed by accession NGB21659 from Norway, also with 100 % bootstrap support. Three accessions from southeastern and eastern Ethiopia (230864, 230048 and 2330858) formed a cluster with 92 % bootstrap support. The other major clusters in Fig. 2a were not supported by high bootstrap values. Accessions NGB103816 (USA) and NGB7131 (Norway) were not separated from Ethiopian accessions. At sub-region level Bale and Harerge formed a separate cluster with 100 % bootstrap support (Fig. 2b). At region level, Amhara region clustered with SNNP with 58 % bootstrap support (Fig. 2c).Fig. 2

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