Developing new SSR markers from ESTs of pea (Pisum sativum L.)

Institute of Vegetables, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China.
Journal of Zhejiang University SCIENCE B (Impact Factor: 1.28). 09/2010; 11(9):702-7. DOI: 10.1631/jzus.B1000004
Source: PubMed


The development of expressed sequence tags (ESTs) from pea has provided a useful source for mining novel simple sequence repeat (SSR) markers. In the present research, in order to find EST-derived SSR markers, 18 552 pea ESTs from the National Center for Biotechnology Information (NCBI) database were downloaded and assembled into 10 086 unigenes. A total of 586 microsatellites in 530 unigenes were identified, indicating that merely 5.25% of sequences contained SSRs. The most abundant SSRs within pea were tri-nucleotide repeat motifs, and among all the tri-nucleotide repeats, the motif GAA was the most abundant type. In total, 49 SSRs were used for primer design. EST-SSR loci were subsequently screened on 10 widely adapted varieties in China. Of these, nine loci showed polymorphic profiles that revealed two to three alleles per locus. The polymorphism information content value ranged from 0.18 to 0.58 with an average of 0.41. Furthermore, transferable analysis revealed that some of these loci showed transferability to faba bean. Because of their polymorphism and transferability, these nine novel EST-SSRs will be valuable tools for marker-assisted breeding and comparative mapping of pea in the future.

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    • "However, since they are usually not part of the expressed portion of the genome, they are likely to provide, at most, indirect information on functional genes (van Treuren and van Hintum 2009). Therefore , attempts have been made to generate genic molecular markers in pea such as eST-PCr based (ellis and Poyser 2002; Miesel et al. 2005; Aubert et al. 2006; Bordat et al. 2011), eST-derived SSr (Burstin et al. 2001; Smýkal et al. 2008; Gong et al. 2010; De Caire et al. 2011), and intron targeted markers (Brauner et al. 2002) for the construction of genetic maps. Since transcriptomic markers are derived from gene sequences, they are also useful for establishing syntenic relationships with related crop species. "
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    ABSTRACT: Key message Gene-based SNPs were identified and mapped in pea using five recombinant inbred line populations segregating for traits of agronomic importance. Abstract Pea (Pisum sativum L.) is one of the world’s oldest domesticated crops and has been a model system in plant biology and genetics since the work of Gregor Mendel. Pea is the second most widely grown pulse crop in the world following common bean. The importance of pea as a food crop is growing due to its combination of moderate protein concentration, slowly digestible starch, high dietary fiber concentration, and its richness in micronutrients; however, pea has lagged behind other major crops in harnessing recent advances in molecular biology, genomics and bioinformatics, partly due to its large genome size with a large proportion of repetitive sequence, and to the relatively limited investment in research in this crop globally. The objective of this research was the development of a genome-wide transcriptome-based pea single-nucleotide polymorphism (SNP) marker platform using next-generation sequencing technology. A total of 1,536 polymorphic SNP loci selected from over 20,000 non-redundant SNPs identified using deep transcriptome sequencing of eight diverse Pisum accessions were used for genotyping in five RIL populations using an Illumina GoldenGate assay. The first high-density pea SNP map defining all seven linkage groups was generated by integrating with previously published anchor markers. Syntenic relationships of this map with the model legume Medicago truncatula and lentil (Lens culinaris Medik.) maps were established. The genic SNP map establishes a foundation for future molecular breeding efforts by enabling both the identification and tracking of introgression of genomic regions harbouring QTLs related to agronomic and seed quality traits.
    Full-text · Article · Aug 2014 · Theoretical and Applied Genetics
    • ") produced by traditional Sanger sequencing have proven extremely useful for research. The development of expressed sequence tags (ESTs) from pea has provided a source for mining novel simple sequence repeats (SSR) markers, valuable resources for gene discovery, expression analysis, and genome annotation (Kaur et al. 2012 ; Gong et al. 2010 ). Pea 6 k oligo-array (Ps6kOLI1) developed from diverse sources of genomic sequence, especially seed EST libraries, have been performed for several transcriptome analyses. "
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    ABSTRACT: Pea (Pisum sativum L.) is important temperate region pulse, with feed, fodder and vegetable uses. Pea was the model organism for Mendel´s discovery of the laws of inheritance, making it the foundation of modern genetics. However, subsequent progress in pea genomics has lagged behind many other plant species, largely as a consequence of its genome size (4.45 Gbp), consisting to large part (75–97 %) of repetitive sequences and its relatively low economic significance (compare to cereals or soybean). There is a long history of genetic mapping studies in pea leading to seven linkage groups definition as well as subsequent marker/trait association. The availability of the genome sequences of three phylogenetically related legume species (Medicago truncatula, Lotus japonicus and Glycine max) has offered opportunities for genome wide comparison. Combination of a candidate gene and colinearity approach has allowed the identification of genes underlying agronomicaly important traits. The progress in the understanding of genes and functional association to traits in the model legume species has been accompanied by gene-based marker development in pea. This together with enhanced computational power and access to diverse germplasm collections, led to association mapping application to identify genetic variation related to desirable agronomic traits. Some of this knowledge has already been applied to marker assisted selection (MAS) programs, increasing the precision and shortening the breeding cycle. Comprehensive pea genomic resources already exist and include several types of molecular marker sets as well as both transcriptome and proteome datasets. Various available marker types have been used for assessment of genetic diversity and mapping of agronomicaly important Quantitative Trait Loci (QTL). Fast neutron and TILLING pea mutant populations are available for reverse genetics approaches, BAC libraries for positional gene cloning as well as transgenic and in vitro regeneration for proof of function or novel gene incorporation. Current genomic knowledge and technologies can facilitate the allele mining for novel traits and incorporation from wild Pisum sp. into elite domestic backgrounds. The availability of high throughput sequencing, genotyping and the -omics methodologies, these hold great promise for the development of novel, highly accurate selective breeding tools for improved pea genotypes suitable for various climates and farming systems.
    No preview · Chapter · Jan 2014
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    • "Trinucleotide repeats were the most abundant. Similar observation was reported by Gong et al. (2010) and Mishra et al. (2011). "
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    ABSTRACT: Maintaining identity of clones is essential in breeding programs. New EST-SSR markers have been developed for banana and used to screen a diploid population for clonal identity. A total of 410 primer pairs were designed from an EST database, validated using polyacrylamide gel electrophoresis (PAGE) and a subset was optimized for accurate genotyping on a capillary genetic analyzer. Combining PAGE and capillary electrophoresis, about 44% of the designed primers were informative in the diploid population. The majority of markers produced two alleles as expected in a diploid population. However, some showed three to four alleles, possibly indicating closely-related members of gene families. Screening of field samples using SSR markers revealed genotype identity issues in the target population. The present study demonstrates the applicability of SSRs in the establishment of parentage and relatedness between accessions. The newly-developed SSRs will be valuable tools in the understanding of Musa genetics, in marker-trait associations, thereby enhancing the effectiveness of breeding programs.
    Full-text · Article · Oct 2012 · AFRICAN JOURNAL OF BIOTECHNOLOGY
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