Compilation of an informative microsatellite set for genetic characterisation of East African finger millet (Eleusine coracana)

Background Genetic diversity of finger millet (Eleusine coracana), a nutritious neglected staple cereal in Africa and South Asia is largely uncharacterized. This study analysed 82 published SSR markers for finger millet across 10 diverse accessions to compile an informative set for genetic character...

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Autores principales:	De Villiers,Santie M, Michael,Vincent N, Manyasa,Eric O, Saiyiorri,Annis N, Deshpande,Santosh
Lenguaje:	English
Publicado:	Pontificia Universidad Católica de Valparaíso 2015
Materias:	Diversity analysis SSR markers Genotyping
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582015000200003
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spelling	oai:scielo:S0717-345820150002000032015-05-08Compilation of an informative microsatellite set for genetic characterisation of East African finger millet (Eleusine coracana)De Villiers,Santie MMichael,Vincent NManyasa,Eric OSaiyiorri,Annis NDeshpande,Santosh Diversity analysis SSR markers Genotyping Background Genetic diversity of finger millet (Eleusine coracana), a nutritious neglected staple cereal in Africa and South Asia is largely uncharacterized. This study analysed 82 published SSR markers for finger millet across 10 diverse accessions to compile an informative set for genetic characterisation. Extensive optimization compared single samples with bulked leaf or bulked DNA samples for capturing within accession genetic diversity. The markers were evaluated to determine (1) how efficiently they amplified target loci during high-throughput genotyping with a generic PCR protocol, (2) ease of scoring PCR products and (3) polymorphism and ability to discern genetic diversity within the tested finger millet germplasm. Results Across 88 samples, the 52 markers that worked well amplified 274 alleles, ranging from 2 to 14 per locus with a mean of 4.89. Major allele frequency ranged from 0.18 to 0.93 with a mean of 0.57. Polymorphic Information Content (PIC) ranged from 0.13 to 0.88 with a mean of 0.5 and availability varied between 64 and 100% with a mean of 92.8%. Heterozygosity ranged from 0 to 1.0, with a mean of 0.26. Discussion Five individual samples from an accession captured the largest number of alleles per locus compared to the four different bulked sampling strategies but this difference was not significant. The identified set comprised 20 markers: UGEP24, UGEP53, UGEP84, UGEP27, UGEP98, UGEP95, UGEP64, UGEP33, UGEP67, UGEP106, UGEP110, UGEP57, UGEP96, UGEP66, UGEP46, UGEP79, UGEP20, UGEP12, UGEP73 and UGEP5 and was since used to assess East African finger millet genetic diversity in two separate studies.info:eu-repo/semantics/openAccessPontificia Universidad Católica de ValparaísoElectronic Journal of Biotechnology v.18 n.2 20152015-03-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582015000200003en
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	Diversity analysis SSR markers Genotyping
spellingShingle	Diversity analysis SSR markers Genotyping De Villiers,Santie M Michael,Vincent N Manyasa,Eric O Saiyiorri,Annis N Deshpande,Santosh Compilation of an informative microsatellite set for genetic characterisation of East African finger millet (Eleusine coracana)
description	Background Genetic diversity of finger millet (Eleusine coracana), a nutritious neglected staple cereal in Africa and South Asia is largely uncharacterized. This study analysed 82 published SSR markers for finger millet across 10 diverse accessions to compile an informative set for genetic characterisation. Extensive optimization compared single samples with bulked leaf or bulked DNA samples for capturing within accession genetic diversity. The markers were evaluated to determine (1) how efficiently they amplified target loci during high-throughput genotyping with a generic PCR protocol, (2) ease of scoring PCR products and (3) polymorphism and ability to discern genetic diversity within the tested finger millet germplasm. Results Across 88 samples, the 52 markers that worked well amplified 274 alleles, ranging from 2 to 14 per locus with a mean of 4.89. Major allele frequency ranged from 0.18 to 0.93 with a mean of 0.57. Polymorphic Information Content (PIC) ranged from 0.13 to 0.88 with a mean of 0.5 and availability varied between 64 and 100% with a mean of 92.8%. Heterozygosity ranged from 0 to 1.0, with a mean of 0.26. Discussion Five individual samples from an accession captured the largest number of alleles per locus compared to the four different bulked sampling strategies but this difference was not significant. The identified set comprised 20 markers: UGEP24, UGEP53, UGEP84, UGEP27, UGEP98, UGEP95, UGEP64, UGEP33, UGEP67, UGEP106, UGEP110, UGEP57, UGEP96, UGEP66, UGEP46, UGEP79, UGEP20, UGEP12, UGEP73 and UGEP5 and was since used to assess East African finger millet genetic diversity in two separate studies.
author	De Villiers,Santie M Michael,Vincent N Manyasa,Eric O Saiyiorri,Annis N Deshpande,Santosh
author_facet	De Villiers,Santie M Michael,Vincent N Manyasa,Eric O Saiyiorri,Annis N Deshpande,Santosh
author_sort	De Villiers,Santie M
title	Compilation of an informative microsatellite set for genetic characterisation of East African finger millet (Eleusine coracana)
title_short	Compilation of an informative microsatellite set for genetic characterisation of East African finger millet (Eleusine coracana)
title_full	Compilation of an informative microsatellite set for genetic characterisation of East African finger millet (Eleusine coracana)
title_fullStr	Compilation of an informative microsatellite set for genetic characterisation of East African finger millet (Eleusine coracana)
title_full_unstemmed	Compilation of an informative microsatellite set for genetic characterisation of East African finger millet (Eleusine coracana)
title_sort	compilation of an informative microsatellite set for genetic characterisation of east african finger millet (eleusine coracana)
publisher	Pontificia Universidad Católica de Valparaíso
publishDate	2015
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582015000200003
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Compilation of an informative microsatellite set for genetic characterisation of East African finger millet (Eleusine coracana)

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