Development, characterization and use of genomic SSR markers for assessment of genetic diversity in some Saudi date palm (Phoenix dactylifera L.) cultivars

Background: The present study was undertaken towards the development of SSR markers and assessing genetic relationships among 32 date palm (Phoenix dactylifera L.) representing common cultivars grown in different geographical regions in Saudi Arabia. Results: Ninety-three novel simple sequence repea...

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Autores principales:	Al-Faifi,Sulieman A, Migdadi,Hussein M, Algamdi,Salem S, Altaf Khan,Mohammad, Ammar,Megahed H, Al-Obeed,Rashid S, I. Al-Thamra,Mohammad, EL-Harty,Ehab H, Jakse,Jerenj
Lenguaje:	English
Publicado:	Pontificia Universidad Católica de Valparaíso 2016
Materias:	Expected and observed heterozygosity Microsatellite markers Polymorphic information content Polymorphism Primer discrimination power
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000300002
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spelling	oai:scielo:S0717-345820160003000022016-07-06Development, characterization and use of genomic SSR markers for assessment of genetic diversity in some Saudi date palm (Phoenix dactylifera L.) cultivarsAl-Faifi,Sulieman AMigdadi,Hussein MAlgamdi,Salem SAltaf Khan,MohammadAmmar,Megahed HAl-Obeed,Rashid SI. Al-Thamra,MohammadEL-Harty,Ehab HJakse,Jerenj Expected and observed heterozygosity Microsatellite markers Polymorphic information content Polymorphism Primer discrimination power Background: The present study was undertaken towards the development of SSR markers and assessing genetic relationships among 32 date palm (Phoenix dactylifera L.) representing common cultivars grown in different geographical regions in Saudi Arabia. Results: Ninety-three novel simple sequence repeat markers were developed and screened for their ability to detect polymorphism in date palm. Around 71% of genomic SSRs were dinucleotide, 25% tri, 3% tetra and 1% penta nucleotide motives. Twenty-two primers generated a total of 91 alleles with a mean of 4.14 alleles per locus and 100% polymorphism percentage. A 0.595 average polymorphic information content and 0.662 primer discrimination power values were recorded. The expected and observed heterozygosities were 0.676 and 0.763 respectively. Pair-wise similarity values ranged from 0.06 to 0.89 and the overall cultivars averaged 0.41. The UPGMA cluster analysis recovered by principal coordinate analysis illustrated that cultivars tend to group according to their class of maturity, region of cultivation, and fruit color. Analysis of molecular variations (AMOVA) revealed that genetic variation among and within cultivars were 27% and 73%, respectively according to geographical distribution of cultivars. Conclusions: The developed microsatellite markers are additional values to date palm characterization tools that can be used by researchers in population genetics, cultivar identification as well as genetic resource exploration and management. The tested cultivars exhibited a significant amount of genetic diversity and could be suitable for successful breeding program. Genomic sequences generated from this study are available at the National Center for Biotechnology Information (NCBI), Sequence Read Archive (Accession numbers. LIBGSS_039019).info:eu-repo/semantics/openAccessPontificia Universidad Católica de ValparaísoElectronic Journal of Biotechnology v.19 n.3 20162016-05-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000300002en10.1016/j.ejbt.2016.01.006
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	Expected and observed heterozygosity Microsatellite markers Polymorphic information content Polymorphism Primer discrimination power
spellingShingle	Expected and observed heterozygosity Microsatellite markers Polymorphic information content Polymorphism Primer discrimination power Al-Faifi,Sulieman A Migdadi,Hussein M Algamdi,Salem S Altaf Khan,Mohammad Ammar,Megahed H Al-Obeed,Rashid S I. Al-Thamra,Mohammad EL-Harty,Ehab H Jakse,Jerenj Development, characterization and use of genomic SSR markers for assessment of genetic diversity in some Saudi date palm (Phoenix dactylifera L.) cultivars
description	Background: The present study was undertaken towards the development of SSR markers and assessing genetic relationships among 32 date palm (Phoenix dactylifera L.) representing common cultivars grown in different geographical regions in Saudi Arabia. Results: Ninety-three novel simple sequence repeat markers were developed and screened for their ability to detect polymorphism in date palm. Around 71% of genomic SSRs were dinucleotide, 25% tri, 3% tetra and 1% penta nucleotide motives. Twenty-two primers generated a total of 91 alleles with a mean of 4.14 alleles per locus and 100% polymorphism percentage. A 0.595 average polymorphic information content and 0.662 primer discrimination power values were recorded. The expected and observed heterozygosities were 0.676 and 0.763 respectively. Pair-wise similarity values ranged from 0.06 to 0.89 and the overall cultivars averaged 0.41. The UPGMA cluster analysis recovered by principal coordinate analysis illustrated that cultivars tend to group according to their class of maturity, region of cultivation, and fruit color. Analysis of molecular variations (AMOVA) revealed that genetic variation among and within cultivars were 27% and 73%, respectively according to geographical distribution of cultivars. Conclusions: The developed microsatellite markers are additional values to date palm characterization tools that can be used by researchers in population genetics, cultivar identification as well as genetic resource exploration and management. The tested cultivars exhibited a significant amount of genetic diversity and could be suitable for successful breeding program. Genomic sequences generated from this study are available at the National Center for Biotechnology Information (NCBI), Sequence Read Archive (Accession numbers. LIBGSS_039019).
author	Al-Faifi,Sulieman A Migdadi,Hussein M Algamdi,Salem S Altaf Khan,Mohammad Ammar,Megahed H Al-Obeed,Rashid S I. Al-Thamra,Mohammad EL-Harty,Ehab H Jakse,Jerenj
author_facet	Al-Faifi,Sulieman A Migdadi,Hussein M Algamdi,Salem S Altaf Khan,Mohammad Ammar,Megahed H Al-Obeed,Rashid S I. Al-Thamra,Mohammad EL-Harty,Ehab H Jakse,Jerenj
author_sort	Al-Faifi,Sulieman A
title	Development, characterization and use of genomic SSR markers for assessment of genetic diversity in some Saudi date palm (Phoenix dactylifera L.) cultivars
title_short	Development, characterization and use of genomic SSR markers for assessment of genetic diversity in some Saudi date palm (Phoenix dactylifera L.) cultivars
title_full	Development, characterization and use of genomic SSR markers for assessment of genetic diversity in some Saudi date palm (Phoenix dactylifera L.) cultivars
title_fullStr	Development, characterization and use of genomic SSR markers for assessment of genetic diversity in some Saudi date palm (Phoenix dactylifera L.) cultivars
title_full_unstemmed	Development, characterization and use of genomic SSR markers for assessment of genetic diversity in some Saudi date palm (Phoenix dactylifera L.) cultivars
title_sort	development, characterization and use of genomic ssr markers for assessment of genetic diversity in some saudi date palm (phoenix dactylifera l.) cultivars
publisher	Pontificia Universidad Católica de Valparaíso
publishDate	2016
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000300002
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Development, characterization and use of genomic SSR markers for assessment of genetic diversity in some Saudi date palm (Phoenix dactylifera L.) cultivars

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