Exploiting a wheat EST database to assess genetic diversity

Abstract

Expressed sequence tag (EST) markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum). In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F2 individuals derived from cultivar crosses were screened for resistance to yellow rust at the seedling stage in greenhouses and adult stage in the field to identify DNA markers genetically linked to resistance. Five hundred and sixty ESTs were assembled into 136 contigs and 989 singletons. BlastX search results showed that 39 (29%) contigs and 96 (10%) singletons were homologous to wheat genes. The database-matched contigs and singletons were assigned to eight functional groups related to protein synthesis, photosynthesis, metabolism and energy, stress proteins, transporter proteins, protein breakdown and recycling, cell growth and division and reactive oxygen scavengers. PCR analyses with primers based on the contigs and singletons showed that the most polymorphic functional categories were photosynthesis (contigs) and metabolism and energy (singletons). EST analysis revealed considerable genetic variability among the Turkish wheat cultivars resistant and susceptible to yellow rust disease and allowed calculation of the mean genetic distance between cultivars, with the greatest similarity (0.725) being between Harmankaya99 and Sönmez2001, and the lowest (0.622) between Aytin98 and Izgi01.

Molecular characterization of genetic diversity in some durum wheat (Triticum durum Desf.) in Palestine

“…Molecular markers have been used thoroughly to study the genetics and genome organization of wheat (Akfirat-Senturk et al, 2010;Ercan et al, 2010;Karakas et al, 2010). It have been widely used in genetic analysis, breeding studies and assessments of genetic diversity and the relationship between cultivated species and their wild relatives, because they have numerous advantages as compared to morphological markers, including high polymorphism and independence on effects related to environmental conditions and the physiological stage of the plant (Bertini et al, 2006).…”

“…Polymerase chain reactions (PCR) have become a basic and essential tool for detecting genetic variation and elucidating unknown DNA sequences (Newton and Graham, 1994). Microsatellites (simple sequence repeats, SSRs) (Nawaz et al, 2009), restriction fragment length polymorphism (PCR-RFLP) (Carvalho et al, 2009(Carvalho et al, , 2011, amplified fragment length polymorphism (AFLP) (Gulbitti-Onarici et al, 2007), selective amplification of microsatellite polymorphic loci (SAMPL) (Altintas et al, 2008), expressed sequence tag (EST)-derived contigs and singletons (Karakas et al, 2010) have been widely used to characterize genetic diversity in wheat accessions, and random amplified polymorphic DNA (RAPD) (Asif et al, 2005). RAPD has been used widely because it requires no DNA probe and no sequence information for the design of specific primers.…”

Discrimination Capacity of RAPD, ISSR and SSR Markers and of their Effectiveness in Establishing Genetic Relationship and Diversity among Egyptian and Saudi Wheat Cultivars

“…Molecular markers provide a direct measure and go beyond indirect diversity measures based on agronomic traits or geographic origin. Applying molecular markers and recognition of polymorphic nucleotide sequences dispersed throughout the genome have provided new possibility for evaluating genetic diversity and determining of interand intra-species genetic relationships (Gostimsky et al, 2005;Karakas et al, 2010). Several PCR based molecular markers are available for investigation of genetic diversity such as Simple Sequence Repeat (SSR) (Tautz, 1989), Random Amplified polymorphic DNA (RAPD) (Okumus, 2007;Rahman et al, 2006;Williams et al, 1990), Amplified Fragment Length Polymorphism (AFLP) (Vos et al, 1995), Inter-Simple Sequence Repeat polymorphic DNA (ISSR) (Zietkiewicz et al, 1994), Sequence Tagged Sites (STS), Random Amplified Microsatellite Polymorphism (RAMP) and so on (Altintas et al, 2008;Ercan et al, 2010).…”

Assessment of genetic diversity of wheat genotypes by resistance gene analog-EST markers

“…The allohexaploid wheat genome (2n = 6x = 42) is one of the largest among crop species with a haploid size of 16 billion bp (Bennett and Leitch, 1995), and wheat genetics and genome organization have been extensively studied by molecular markers (Ercan et al, 2010;Akfirat-Senturk et al, 2010;Karakas et al, 2010). Molecular markers have been widely used in genetic analyses, breeding studies and investigations of genetic diversity and the relationship between cultivated species and their wild parents, because they have several advantages as compared with morphological markers, including high polymorphism and independence from effects related to environmental conditions and the physiological stage of the plant (Bertini et al, 2006).…”

“…Microsatellites (SSRs: simple sequence repeats) (Plaschke et al, 1995), restriction fragment length polymorphism (RFLP) (Nagaoka and Ogihara, 1997), amplified fragment length polymorphism (AFLP) (Gulbitti-Onarici et al, 2007), selective amplification of microsatellite polymorphic loci (SAMPL) (Altintas et al, 2008), random amplified polymorphic DNA (RAPD) (Asif et al, 2005), and expressed sequence tag (EST)-derived contigs and singletons (Karakas et al, 2010) have been widely used to characterize genetic diversity in wheat accessions. Besides these marker types, the resistance gene-analog polymorphism (RGAP) approach (Chen et al, 1998), which utilizes high-resolution electrophoresis and sensitive detection of PCR products amplified with primers based on conserved domains of plant resistance genes, has been used to identify molecular markers tightly linked to or co-segregating with disease resistance genes and also genetic diversity (Shi et al, 2001;Yan et al, 2003).…”