Development of 1000 microsatellite markers across the date palm (Phoenix dactylifera L.) genome

A. Hamwieh, J. Farah, S. Moussally, K. Al-Sham'Aa, K. Almer, H. Khierallah, S. Udupa, S. Lababidi, Joel Malek, M. Aaouine, M. Baum

Research output: Chapter in Book/Report/Conference proceedingConference contribution

12 Citations (Scopus)

Abstract

Date Palm is a major environmental and economic factor in arid climates in many countries around the world. Microsatellite markers have been proven to be very powerful in plant genome analysis because they are locus-specific, codominant, highly polymorphic and highly reproducible. In date palm only few microsatellite markers have been developed so far. Recently, the Cornell Medical College in Qatar issued a draft assembly of the date palm genome ('Khalas') generated by whole genome shotgun next generation DNA sequencing. In this paper, we analyzed the microsatellite motifs across the date palm genome. The results indicated that the most abundant type of microsatellite repeats are dinucleotide repeats (52442 motifs) followed by trinucleotide (28503 motifs) and pentanucleotide repeats (12873 motifs). The frequencies of tetra-nucleotide and hexa-nucleotide repeats were less across the genome (5555 and 5810 motifs, respectively). The most common type of dinucleotide repeat was GA (48.7%) followed by AT (37%). Out of 28645 trinucleotide repeats, TAA and GAA repeats were the most abundant repeats (28.1 and 27.1%) respectively. More than 1090 new microsatellite markers could be designed. The primary test for 50 primer pairs revealed that 28 (56%) were functional and 19 (38%) yielded polymorphic PCR products. We wish that the results of our study will be a starting point for researchers making use of the markers for genetic mapping and diversity analysis of date palm.

Original languageEnglish
Title of host publicationIV International Date Palm Conference
Pages269-277
Number of pages9
Volume882
Publication statusPublished - 3 Dec 2010

Publication series

NameActa Horticulturae
Volume882
ISSN (Print)05677572

Fingerprint

Phoenix dactylifera
microsatellite repeats
genome
nucleotides
Qatar
economic factors
arid zones
chromosome mapping
sequence analysis
researchers
genetic variation
loci
environmental factors

Keywords

  • Adh gene
  • Microsatellite marker
  • P. dactylifera
  • Simple sequence repeats

ASJC Scopus subject areas

  • Horticulture

Cite this

Hamwieh, A., Farah, J., Moussally, S., Al-Sham'Aa, K., Almer, K., Khierallah, H., ... Baum, M. (2010). Development of 1000 microsatellite markers across the date palm (Phoenix dactylifera L.) genome. In IV International Date Palm Conference (Vol. 882, pp. 269-277). (Acta Horticulturae; Vol. 882).

Development of 1000 microsatellite markers across the date palm (Phoenix dactylifera L.) genome. / Hamwieh, A.; Farah, J.; Moussally, S.; Al-Sham'Aa, K.; Almer, K.; Khierallah, H.; Udupa, S.; Lababidi, S.; Malek, Joel; Aaouine, M.; Baum, M.

IV International Date Palm Conference. Vol. 882 2010. p. 269-277 (Acta Horticulturae; Vol. 882).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Hamwieh, A, Farah, J, Moussally, S, Al-Sham'Aa, K, Almer, K, Khierallah, H, Udupa, S, Lababidi, S, Malek, J, Aaouine, M & Baum, M 2010, Development of 1000 microsatellite markers across the date palm (Phoenix dactylifera L.) genome. in IV International Date Palm Conference. vol. 882, Acta Horticulturae, vol. 882, pp. 269-277.
Hamwieh A, Farah J, Moussally S, Al-Sham'Aa K, Almer K, Khierallah H et al. Development of 1000 microsatellite markers across the date palm (Phoenix dactylifera L.) genome. In IV International Date Palm Conference. Vol. 882. 2010. p. 269-277. (Acta Horticulturae).
Hamwieh, A. ; Farah, J. ; Moussally, S. ; Al-Sham'Aa, K. ; Almer, K. ; Khierallah, H. ; Udupa, S. ; Lababidi, S. ; Malek, Joel ; Aaouine, M. ; Baum, M. / Development of 1000 microsatellite markers across the date palm (Phoenix dactylifera L.) genome. IV International Date Palm Conference. Vol. 882 2010. pp. 269-277 (Acta Horticulturae).
@inproceedings{f9f303bf3386444583ea31c57d24749d,
title = "Development of 1000 microsatellite markers across the date palm (Phoenix dactylifera L.) genome",
abstract = "Date Palm is a major environmental and economic factor in arid climates in many countries around the world. Microsatellite markers have been proven to be very powerful in plant genome analysis because they are locus-specific, codominant, highly polymorphic and highly reproducible. In date palm only few microsatellite markers have been developed so far. Recently, the Cornell Medical College in Qatar issued a draft assembly of the date palm genome ('Khalas') generated by whole genome shotgun next generation DNA sequencing. In this paper, we analyzed the microsatellite motifs across the date palm genome. The results indicated that the most abundant type of microsatellite repeats are dinucleotide repeats (52442 motifs) followed by trinucleotide (28503 motifs) and pentanucleotide repeats (12873 motifs). The frequencies of tetra-nucleotide and hexa-nucleotide repeats were less across the genome (5555 and 5810 motifs, respectively). The most common type of dinucleotide repeat was GA (48.7{\%}) followed by AT (37{\%}). Out of 28645 trinucleotide repeats, TAA and GAA repeats were the most abundant repeats (28.1 and 27.1{\%}) respectively. More than 1090 new microsatellite markers could be designed. The primary test for 50 primer pairs revealed that 28 (56{\%}) were functional and 19 (38{\%}) yielded polymorphic PCR products. We wish that the results of our study will be a starting point for researchers making use of the markers for genetic mapping and diversity analysis of date palm.",
keywords = "Adh gene, Microsatellite marker, P. dactylifera, Simple sequence repeats",
author = "A. Hamwieh and J. Farah and S. Moussally and K. Al-Sham'Aa and K. Almer and H. Khierallah and S. Udupa and S. Lababidi and Joel Malek and M. Aaouine and M. Baum",
year = "2010",
month = "12",
day = "3",
language = "English",
isbn = "9789066056336",
volume = "882",
series = "Acta Horticulturae",
pages = "269--277",
booktitle = "IV International Date Palm Conference",

}

TY - GEN

T1 - Development of 1000 microsatellite markers across the date palm (Phoenix dactylifera L.) genome

AU - Hamwieh, A.

AU - Farah, J.

AU - Moussally, S.

AU - Al-Sham'Aa, K.

AU - Almer, K.

AU - Khierallah, H.

AU - Udupa, S.

AU - Lababidi, S.

AU - Malek, Joel

AU - Aaouine, M.

AU - Baum, M.

PY - 2010/12/3

Y1 - 2010/12/3

N2 - Date Palm is a major environmental and economic factor in arid climates in many countries around the world. Microsatellite markers have been proven to be very powerful in plant genome analysis because they are locus-specific, codominant, highly polymorphic and highly reproducible. In date palm only few microsatellite markers have been developed so far. Recently, the Cornell Medical College in Qatar issued a draft assembly of the date palm genome ('Khalas') generated by whole genome shotgun next generation DNA sequencing. In this paper, we analyzed the microsatellite motifs across the date palm genome. The results indicated that the most abundant type of microsatellite repeats are dinucleotide repeats (52442 motifs) followed by trinucleotide (28503 motifs) and pentanucleotide repeats (12873 motifs). The frequencies of tetra-nucleotide and hexa-nucleotide repeats were less across the genome (5555 and 5810 motifs, respectively). The most common type of dinucleotide repeat was GA (48.7%) followed by AT (37%). Out of 28645 trinucleotide repeats, TAA and GAA repeats were the most abundant repeats (28.1 and 27.1%) respectively. More than 1090 new microsatellite markers could be designed. The primary test for 50 primer pairs revealed that 28 (56%) were functional and 19 (38%) yielded polymorphic PCR products. We wish that the results of our study will be a starting point for researchers making use of the markers for genetic mapping and diversity analysis of date palm.

AB - Date Palm is a major environmental and economic factor in arid climates in many countries around the world. Microsatellite markers have been proven to be very powerful in plant genome analysis because they are locus-specific, codominant, highly polymorphic and highly reproducible. In date palm only few microsatellite markers have been developed so far. Recently, the Cornell Medical College in Qatar issued a draft assembly of the date palm genome ('Khalas') generated by whole genome shotgun next generation DNA sequencing. In this paper, we analyzed the microsatellite motifs across the date palm genome. The results indicated that the most abundant type of microsatellite repeats are dinucleotide repeats (52442 motifs) followed by trinucleotide (28503 motifs) and pentanucleotide repeats (12873 motifs). The frequencies of tetra-nucleotide and hexa-nucleotide repeats were less across the genome (5555 and 5810 motifs, respectively). The most common type of dinucleotide repeat was GA (48.7%) followed by AT (37%). Out of 28645 trinucleotide repeats, TAA and GAA repeats were the most abundant repeats (28.1 and 27.1%) respectively. More than 1090 new microsatellite markers could be designed. The primary test for 50 primer pairs revealed that 28 (56%) were functional and 19 (38%) yielded polymorphic PCR products. We wish that the results of our study will be a starting point for researchers making use of the markers for genetic mapping and diversity analysis of date palm.

KW - Adh gene

KW - Microsatellite marker

KW - P. dactylifera

KW - Simple sequence repeats

UR - http://www.scopus.com/inward/record.url?scp=79961186596&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79961186596&partnerID=8YFLogxK

M3 - Conference contribution

SN - 9789066056336

VL - 882

T3 - Acta Horticulturae

SP - 269

EP - 277

BT - IV International Date Palm Conference

ER -