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Large-scale development of expressed sequence tag-derived simple sequence repeat markers and diversity analysis in Arachis spp.

Koilkonda P, Sato S, Tabata S, Shirasawa K, Hirakawa H, Sakai H, Sasamoto S, Watanabe A, Wada T, Kishida Y, Tsuruoka H, Fujishiro T, Yamada M, Kohara M, Suzuki S, Hasegawa M, Kiyoshima H, Isobe S - Mol. Breed. (2011)

Bottom Line: The 16 Arachis accessions examined included cultivated peanut varieties as well as diploid species with the A or B genome.Diversity analysis was performed and the genotypes of all 16 Arachis accessions showed similarity coefficients ranging from 0.37 to 0.97.ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9604-8) contains supplementary material, which is available to authorized users.

View Article: PubMed Central - PubMed

ABSTRACT
Large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed in peanut (Arachis hypogaea L.) to obtain more informative genetic markers. A total of 10,102 potential non-redundant EST sequences, including 3,445 contigs and 6,657 singletons, were generated from cDNA libraries of the gynophore, roots, leaves and seedlings. A total of 3,187 primer pairs were designed on flanking regions of SSRs, some of which allowed one and two base mismatches. Among the 3,187 markers generated, 2,540 (80%) were trinucleotide repeats, 302 (9%) were dinucleotide repeats, and 345 (11%) were tetranucleotide repeats. Pre-polymorphic analyses of 24 Arachis accessions were performed using 10% polyacrylamide gels. A total of 1,571 EST-SSR markers showing clear polymorphisms were selected for further polymorphic analysis with a Fluoro-fragment Analyzer. The 16 Arachis accessions examined included cultivated peanut varieties as well as diploid species with the A or B genome. Altogether 1,281 (81.5%) of the 1,571 markers were polymorphic among the 16 accessions, and 366 (23.3%) were polymorphic among the 12 cultivated varieties. Diversity analysis was performed and the genotypes of all 16 Arachis accessions showed similarity coefficients ranging from 0.37 to 0.97. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9604-8) contains supplementary material, which is available to authorized users.

No MeSH data available.


Functional classification of non-redundant peanut EST sequences into eukaryotic clusters of orthologous group (KOG) categories. BLASTX was used to compare non-redundant EST sequences with the KOG sequence set. EST sequences were then classified into the KOG categories according to sequence similarity
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Fig1: Functional classification of non-redundant peanut EST sequences into eukaryotic clusters of orthologous group (KOG) categories. BLASTX was used to compare non-redundant EST sequences with the KOG sequence set. EST sequences were then classified into the KOG categories according to sequence similarity

Mentions: To investigate the functional classification of peanut ESTs, non-redundant EST sequences were compared with KOGs by BLASTX, and classified into KOG categories (Tatusov et al. 2003). Among the 10,102 non-redundant peanut EST sequences, 4,380 showed similarity to KOG sequences with functional classifications, and their distribution into KOG functional categories is shown in Fig. 1. To analyze the expressed gene features at the organ level, KOG classification was carried out against non-redundant EST sequences obtained from the reads of each cDNA library. As a result, the proportion of non-redundant ESTs classified into the metabolism category was slightly higher in the gynophore and root libraries (MOESM6).Fig. 1


Large-scale development of expressed sequence tag-derived simple sequence repeat markers and diversity analysis in Arachis spp.

Koilkonda P, Sato S, Tabata S, Shirasawa K, Hirakawa H, Sakai H, Sasamoto S, Watanabe A, Wada T, Kishida Y, Tsuruoka H, Fujishiro T, Yamada M, Kohara M, Suzuki S, Hasegawa M, Kiyoshima H, Isobe S - Mol. Breed. (2011)

Functional classification of non-redundant peanut EST sequences into eukaryotic clusters of orthologous group (KOG) categories. BLASTX was used to compare non-redundant EST sequences with the KOG sequence set. EST sequences were then classified into the KOG categories according to sequence similarity
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3362703&req=5

Fig1: Functional classification of non-redundant peanut EST sequences into eukaryotic clusters of orthologous group (KOG) categories. BLASTX was used to compare non-redundant EST sequences with the KOG sequence set. EST sequences were then classified into the KOG categories according to sequence similarity
Mentions: To investigate the functional classification of peanut ESTs, non-redundant EST sequences were compared with KOGs by BLASTX, and classified into KOG categories (Tatusov et al. 2003). Among the 10,102 non-redundant peanut EST sequences, 4,380 showed similarity to KOG sequences with functional classifications, and their distribution into KOG functional categories is shown in Fig. 1. To analyze the expressed gene features at the organ level, KOG classification was carried out against non-redundant EST sequences obtained from the reads of each cDNA library. As a result, the proportion of non-redundant ESTs classified into the metabolism category was slightly higher in the gynophore and root libraries (MOESM6).Fig. 1

Bottom Line: The 16 Arachis accessions examined included cultivated peanut varieties as well as diploid species with the A or B genome.Diversity analysis was performed and the genotypes of all 16 Arachis accessions showed similarity coefficients ranging from 0.37 to 0.97.ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9604-8) contains supplementary material, which is available to authorized users.

View Article: PubMed Central - PubMed

ABSTRACT
Large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed in peanut (Arachis hypogaea L.) to obtain more informative genetic markers. A total of 10,102 potential non-redundant EST sequences, including 3,445 contigs and 6,657 singletons, were generated from cDNA libraries of the gynophore, roots, leaves and seedlings. A total of 3,187 primer pairs were designed on flanking regions of SSRs, some of which allowed one and two base mismatches. Among the 3,187 markers generated, 2,540 (80%) were trinucleotide repeats, 302 (9%) were dinucleotide repeats, and 345 (11%) were tetranucleotide repeats. Pre-polymorphic analyses of 24 Arachis accessions were performed using 10% polyacrylamide gels. A total of 1,571 EST-SSR markers showing clear polymorphisms were selected for further polymorphic analysis with a Fluoro-fragment Analyzer. The 16 Arachis accessions examined included cultivated peanut varieties as well as diploid species with the A or B genome. Altogether 1,281 (81.5%) of the 1,571 markers were polymorphic among the 16 accessions, and 366 (23.3%) were polymorphic among the 12 cultivated varieties. Diversity analysis was performed and the genotypes of all 16 Arachis accessions showed similarity coefficients ranging from 0.37 to 0.97. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9604-8) contains supplementary material, which is available to authorized users.

No MeSH data available.