Microsatellite analysis in cultivated hexaploid wheat and wild wheat relatives.

Abstract

Analysis of the microsatellite library by restriction digestion indicated that the sizes of clone inserts ranged from 130 to 1000 bp, with an average insert size of 415 bp. Of the 48 sequences analysed, dinucleotides were the most common microsatellite repeat type, with CA then GT occurring most frequently. Compound repeats consisting of 2 or 3 adjacent blocks of different dinucleotide repeats made up of 40% of the dinucleotide repeats. Eleven microsatellite clones of the 48 clones (23%) sequenced were suitable for primer design. Forty percent of inserts which contained microsatellite repeats were unusable because the repeats occurred too near the insert ends, thus leaving insufficient flanking sequence for primer design. Preliminary screening, which involved testing unlabelled primers on six hexaploid wheat cultivars, including Chinese Spring, showed that 6 of the 11 primers gave bands of the expected size on 3.5% agarose gels. The characteristics of the markers, including primer sequence, size of PCR product in reference cultivar, the number of repeat units and a description of the repeat motif are tabulated. Of the 6 primers fluorescently labelled, 5 primers, WMC 144, WMC 141, WMC136, WMC145 and WMC146, were used for subsequent microsatellite analysis. WMC144, WMC141 and WMC146 were polymorphic across the hexaploid wheat cultivars. The wild diploid accessions generally showed a high level of heterozygosity with WMC144 and WMC141, ranging from 60 to 100% in the 9 accessions of each Triticum monococcum, T. speltoides [Aegilops speltoides var. speltoides] and T. tauschii [Aegilops tauschii]. WMC144 amplified 2 alleles across all of the diploid accessions at 137 and 139 bp, which were common to the hexaploid cultivars. WMC141 amplified a wide range of allele sizes in both hexaploid and diploid genotypes. Additionally, the number of alleles observed with WMC141 was not consistent with the primer amplifying a single loci; that is, more than 2 products were amplified in diploids. Examples of this include T. monococcum (accession number 19848), which had an allele at 80, as well as showing heterozygotic alleles of 97 and 101 bp, and T. tauschii (accession number 24226) having alleles at 80 as well as 91 and 93 bp. Some of the fragments amplified by PCR using WMC136 on wild wheat progenitor and cultivated hexaploid wheat are shown in an electropherogram. Microsatellite loci were assigned to chromosomes corresponding to the aneuploid lines for which either no PCR amplification product was obtained, or one of the PCR products was missing, provided that all of the other aneuploid lines gave the relevant PCR product.

Relationships among the A Genomes of Triticum L. Species as Evidenced by SSR Markers, in Iran

“…More than a thousand wheat mapped microsatellite markers are available that are useful tools for genetic analyses. Genomic SSRs have been used in wheat for a variety of purposes including genomic mapping [ 33 , 40 , 62 , 63 ], gene tagging [ 39 , 64 – 66 ] and genetic diversity [ 41 , 67 , 68 ] analyses.…”

Multiplex single nucleotide polymorphism (SNP)‐based genotyping in allohexaploid wheat using padlock probes

“…The increasing world population, issues of food security and the use of wheat as a possible source of bioethanol emphasize the need to grow increased amounts of wheat in the future. However, this new generation of higher yielding, more disease-resistant wheat lines capable of growing in changing conditions will require efficient breeding practises, including the use of marker-assisted selection (McLauchlan et al ., 2001). The use of molecular markers in wheat breeding and diversity studies is increasing, but the allohexaploid nature of bread wheat has limited the development of high-throughput genotyping to a relatively few gene-based markers linked to agronomic traits.…”

Genetic diversity in the USDA Limnanthes germplasm collection assessed by simple sequence repeats

“…In domesticated crops, genetic variation is often subjected to a 'domestication bottleneck' when selection for desirable characteristics results in the loss of diversity. Such loss of variation occurred in maize (Matsuoka et al, 2002) and wheat (McLauchlan et al, 2001), where wild relatives showed greater diversity among SSR markers than did cultivated varieties. Breeding efforts aimed at the development of new cultivars may lead to losses in Limnanthes genetic diversity.…”

“…Simple sequence repeat (SSR) markers were chosen for this work. Due to the wide distribution in the genome and high levels of polymorphism exhibited by SSR markers, they have been successfully employed to determine genetic diversity between accessions in other germplasm collections (Godwin et al, 2001;McLauchlan et al, 2001;Baranger et al, 2004;Dillon et al, 2005). In 2004, Kishore et al…”