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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

Accessions of P. sativum subsp. sativum with rare or private alleles or with alleles limited to few accessions at the EST-SSR loci studied. The frequency of each allele for each accession is given on top of each bar
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Related In: Results  -  Collection


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Fig1: Accessions of P. sativum subsp. sativum with rare or private alleles or with alleles limited to few accessions at the EST-SSR loci studied. The frequency of each allele for each accession is given on top of each bar

Mentions: It is interesting to note that only five of the 46 accessions were required to capture all the 37 alleles, namely: 207010, 235897, 32048, 32713 and 32776. The average frequency of each allele across these accessions was more than 1 % (Table 4). Loci like PS04, PS10 and PS21 produced rare allele(s) restricted to one to two accessions with frequencies of less than 20 % and have overall frequencies of less than 1 % across the 46 accessions. Private alleles unique to a single accession were also amplified with 100 % frequency at loci PS08, PS10, and PS34 (Fig. 1). Alleles restricted to 2, 2, 3 and 4 accessions were amplified at loci PS18, PS36, PS21 and PS11, respectively, at frequencies ranging from 8 % to 100 % (Fig. 1). Furthermore, PS15 and PS21 scored alleles in all individuals of an accession from Norway (NGB21659).Table 4


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)

Accessions of P. sativum subsp. sativum with rare or private alleles or with alleles limited to few accessions at the EST-SSR loci studied. The frequency of each allele for each accession is given on top of each bar
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig1: Accessions of P. sativum subsp. sativum with rare or private alleles or with alleles limited to few accessions at the EST-SSR loci studied. The frequency of each allele for each accession is given on top of each bar
Mentions: It is interesting to note that only five of the 46 accessions were required to capture all the 37 alleles, namely: 207010, 235897, 32048, 32713 and 32776. The average frequency of each allele across these accessions was more than 1 % (Table 4). Loci like PS04, PS10 and PS21 produced rare allele(s) restricted to one to two accessions with frequencies of less than 20 % and have overall frequencies of less than 1 % across the 46 accessions. Private alleles unique to a single accession were also amplified with 100 % frequency at loci PS08, PS10, and PS34 (Fig. 1). Alleles restricted to 2, 2, 3 and 4 accessions were amplified at loci PS18, PS36, PS21 and PS11, respectively, at frequencies ranging from 8 % to 100 % (Fig. 1). Furthermore, PS15 and PS21 scored alleles in all individuals of an accession from Norway (NGB21659).Table 4

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