TY - JOUR
T1 - Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs)
AU - Nicot, N.
AU - Chiquet, V.
AU - Gandon, B.
AU - Amilhat, L.
AU - Legeai, F.
AU - Leroy, P.
AU - Bernard, M.
AU - Sourdille, P.
PY - 2004/8
Y1 - 2004/8
N2 - The increasing availability of expressed sequence tags (ESTs) in wheat (Triticum aestivum) and related cereals provides a valuable resource of non-anonymous DNA molecular markers. We examined 170,746 wheat ESTs from the public (International Triticeae EST Cooperative) and Génoplante databases, previously clustered in contigs, for the presence of di- to hexanucleotide simple sequence repeats (SSRs). Analysis of 46,510 contigs identified 3,530 SSRs, which represented 7.5% of the total number of contigs. Only 74% of the sequences allowed primer pairs to be designed, 70% led to an amplification product, mainly of a high quality (68%), and 53% exhibited polymorphism for at least one cultivar among the eight tested. Even though dinucleotide SSRs were less represented than trinucleotide SSRs (15.5% versus 66.5%, respectively), the former showed a much higher polymorphism level (83% versus 46%). The effect of the number and type of repeats is also discussed. The development of new EST-SSRs markers will have important implications for the genetic analysis and exploitation of the genetic resources of wheat and related species and will provide a more direct estimate of functional diversity.
AB - The increasing availability of expressed sequence tags (ESTs) in wheat (Triticum aestivum) and related cereals provides a valuable resource of non-anonymous DNA molecular markers. We examined 170,746 wheat ESTs from the public (International Triticeae EST Cooperative) and Génoplante databases, previously clustered in contigs, for the presence of di- to hexanucleotide simple sequence repeats (SSRs). Analysis of 46,510 contigs identified 3,530 SSRs, which represented 7.5% of the total number of contigs. Only 74% of the sequences allowed primer pairs to be designed, 70% led to an amplification product, mainly of a high quality (68%), and 53% exhibited polymorphism for at least one cultivar among the eight tested. Even though dinucleotide SSRs were less represented than trinucleotide SSRs (15.5% versus 66.5%, respectively), the former showed a much higher polymorphism level (83% versus 46%). The effect of the number and type of repeats is also discussed. The development of new EST-SSRs markers will have important implications for the genetic analysis and exploitation of the genetic resources of wheat and related species and will provide a more direct estimate of functional diversity.
UR - http://www.scopus.com/inward/record.url?scp=4544376233&partnerID=8YFLogxK
U2 - 10.1007/s00122-004-1685-x
DO - 10.1007/s00122-004-1685-x
M3 - Article
C2 - 15146317
AN - SCOPUS:4544376233
SN - 0040-5752
VL - 109
SP - 800
EP - 805
JO - Theoretical And Applied Genetics
JF - Theoretical And Applied Genetics
IS - 4
ER -