Article

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: 1.11). 09/2010; 11(9):702-7. DOI: 10.1631/jzus.B1000004
Source: PubMed

ABSTRACT 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.

0 Bookmarks
 · 
107 Views
  • Source
    [Show abstract] [Hide abstract]
    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.
    AFRICAN JOURNAL OF BIOTECHNOLOGY 10/2012; 11:13546-13559. · 0.57 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The development of expressed sequence tag-derived simple sequence repeats (EST-SSRs) provided a useful tool for investigating plant genetic diversity. In the present study, 22 polymorphic EST-SSRs from grain soybean were identified and used to assess the genetic diversity in 48 vegetable soybean accessions. Among the 22 EST-SSR loci, tri-nucleotides were the most abundant repeats, accounting for 50.00% of the total motifs. GAA was the most common motif among tri-nucleotide repeats, with a frequency of 18.18%. Polymorphic analysis identified a total of 71 alleles, with an average of 3.23 per locus. The polymorphism information content (PIC) values ranged from 0.144 to 0.630, with a mean of 0.386. Observed heterozygosity (Ho) values varied from 0.0196 to 1.0000, with an average of 0.6092, while the expected heterozygosity (He) values ranged from 0.1502 to 0.6840, with a mean value of 0.4616. Principal coordinate analysis and phylogenetic tree analysis indicated that the accessions could be assigned to different groups based to a large extent on their geographic distribution, and most accessions from China were clustered into the same groups. These results suggest that Chinese vegetable soybean accessions have a narrow genetic base. The results of this study indicate that EST-SSRs from grain soybean have high transferability to vegetable soybean, and that these new markers would be helpful in taxonomy, molecular breeding, and comparative mapping studies of vegetable soybean in the future.
    Journal of Zhejiang University SCIENCE B 04/2013; 14(4):279-88. · 1.11 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Flax is an important oilseed crop in North America and is mostly grown as a fibre crop in Europe. As a self-pollinated diploid with a small estimated genome size of ~370 Mb, flax is well suited for fast progress in genomics. In the last few years, important genetic resources have been developed for this crop. Here, we describe the assessment and comparative analyses of 1,506 putative simple sequence repeats (SSRs) of which, 1,164 were derived from BAC-end sequences (BESs) and 342 from expressed sequence tags (ESTs). The SSRs were assessed on a panel of 16 flax accessions with 673 (58 %) and 145 (42 %) primer pairs being polymorphic in the BESs and ESTs, respectively. With 818 novel polymorphic SSR primer pairs reported in this study, the repertoire of available SSRs in flax has more than doubled from the combined total of 508 of all previous reports. Among nucleotide motifs, trinucleotides were the most abundant irrespective of the class, but dinucleotides were the most polymorphic. SSR length was also positively correlated with polymorphism. Two dinucleotide (AT/TA and AG/GA) and two trinucleotide (AAT/ATA/TAA and GAA/AGA/AAG) motifs and their iterations, different from those reported in many other crops, accounted for more than half of all the SSRs and were also more polymorphic (63.4 %) than the rest of the markers (42.7 %). This improved resource promises to be useful in genetic, quantitative trait loci (QTL) and association mapping as well as for anchoring the physical/genetic map with the whole genome shotgun reference sequence of flax.
    Theoretical and Applied Genetics 04/2012; 125(4):685-94. · 3.66 Impact Factor

Full-text

View
2 Downloads
Available from