Expressed sequence tag analysis and development of gene associated markers in a near-isogenic plant system of Eragrostis curvula.
Eragrostis curvula (Schrad.) Nees is a forage grass native to the semiarid regions of Southern Africa, which reproduces mainly by pseudogamous diplosporous apomixis. A collection of ESTs was generated from four cDNA libraries, three of them obtained from panicles of near-isogenic lines with different ploidy levels and reproductive modes, and one obtained from 12 days-old plant leaves. A total of 12,295 high-quality ESTs were clustered and assembled, rendering 8,864 unigenes, including 1,490 contigs and 7,394 singletons, with a genome coverage of 22%. A total of 7,029 (79.11%) unigenes were functionally categorized by BLASTX analysis against sequences deposited in public databases, but only 37.80% could be classified according to Gene Ontology. Sequence comparison against the cereals genes indexes (GI) revealed 50% significant hits. A total of 254 EST-SSRs were detected from 219 singletons and 35 from contigs. Di- and tri- motifs were similarly represented with percentages of 38.95 and 40.16%, respectively. In addition, 190 SNPs and Indels were detected in 18 contigs generated from 3 to 4 libraries. The ESTs and the molecular markers obtained in this study will provide valuable resources for a wide range of applications including gene identification, genetic mapping, cultivar identification, analysis of genetic diversity, phenotype mapping and marker assisted selection.
Cervigni
Gerardo D L
GD
Centro de Recursos Naturales Renovables de la Zona Semiárida-CONICET, Camino de La Carrindanga Km 7.0, Bahia Blanca, Argentina.
Paniego
Norma
N
Díaz
Marina
M
Selva
Juan P
JP
Zappacosta
Diego
D
Zanazzi
Darío
D
Landerreche
Iñaki
I
Martelotto
Luciano
L
Felitti
Silvina
S
Pessino
Silvina
S
Spangenberg
Germán
G
Echenique
Viviana
V
D031750:Eragrostis / Q000235:genetics*; D020224:Expressed Sequence Tags; D035264:Flowers / Q000235:genetics; D015723:Gene Library; D005819:Genetic Markers; D018515:Plant Leaves / Q000235:genetics; D011003:Ploidies; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
D005819:Genetic Markers