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Exploiting transcriptome data for the development and characterization of gene-based SSR markers related to cold tolerance in oil palm (Elaeis guineensis).

Xiao Y, Zhou L, Xia W, Mason AS, Yang Y, Ma Z, Peng M - BMC Plant Biol. (2014)

Bottom Line: Interestingly, 5' untranslated region of both Unigene21287 (ICE1) and CL2628.Contig1 (NAC) both contained an SSR markers.These EST-SSR markers would be particularly useful for gene mapping and population structure analysis in Elaeis guineensis.Meanwhile, the EST-SSR loci were inducible expressed in response to low temperature, which may have potential application in identifying trait-associated markers in oil palm in the future.

View Article: PubMed Central - PubMed

ABSTRACT

Background: The oil palm (Elaeis guineensis, 2n = 32) has the highest oil yield of any crop species, as well as comprising the richest dietary source of provitamin A. For the tropical species, the best mean growth temperature is about 27°C, with a minimal growth temperature of 15°C. Hence, the plantation area is limited into the geographical ranges of 10°N to 10°S. Enhancing cold tolerance capability will increase the total cultivation area and subsequently oil productivity of this tropical species. Developing molecular markers related to cold tolerance would be helpful for molecular breeding of cold tolerant Elaeis guineensis.

Results: In total, 5791 gene-based SSRs were identified in 51,452 expressed sequences from Elaeis guineensis transcriptome data: approximately one SSR was detected per 10 expressed sequences. Of these 5791 gene-based SSRs, 916 were derived from expressed sequences up- or down-regulated at least two-fold in response to cold stress. A total of 182 polymorphic markers were developed and characterized from 442 primer pairs flanking these cold-responsive SSR repeats. The polymorphic information content (PIC) of these polymorphic SSR markers across 24 lines of Elaeis guineensis varied from 0.08 to 0.65 (mean = 0.31 ± 0.12). Using in-silico mapping, 137 (75.3%) of the 182 polymorphic SSR markers were located onto the 16 Elaeis guineensis chromosomes. Total coverage of 473 Mbp was achieved, with an average physical distance of 3.4 Mbp between adjacent markers (range 96 bp - 20.8 Mbp). Meanwhile, Comparative analysis of transcriptome under cold stress revealed that one ICE1 putative ortholog, five CBF putative orthologs, 19 NAC transcription factors and four cold-induced orhologs were up-regulated at least two fold in response to cold stress. Interestingly, 5' untranslated region of both Unigene21287 (ICE1) and CL2628.Contig1 (NAC) both contained an SSR markers.

Conclusions: In the present study, a series of SSR markers were developed based on sequences differentially expressed in response to cold stress. These EST-SSR markers would be particularly useful for gene mapping and population structure analysis in Elaeis guineensis. Meanwhile, the EST-SSR loci were inducible expressed in response to low temperature, which may have potential application in identifying trait-associated markers in oil palm in the future.

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The distribution of the motif repeats of mono to hexa-nucleotide microsatellites based on all transcript sequences and transcript sequences differentially expressed in response to cold treatment.
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Fig1: The distribution of the motif repeats of mono to hexa-nucleotide microsatellites based on all transcript sequences and transcript sequences differentially expressed in response to cold treatment.

Mentions: Of the 51,452 transcripts, 10,973 were up-regulated or down-regulated at least two-fold in response to cold stress. The 10,973 transcripts contained 916 identified SSR loci. Identical distribution with respect to microsatellite motif type was observed between all SSR loci identified in the 51,452 transcripts and the 916 SSR loci associated with response to cold stress (Figure 1). Of the SSR loci associated with response to cold stress, tri-nucleotide motif types were the most abundant (42.58%), followed by mono-nucleotide (34.61%) and di-nucleotide (20.52%) motif types.Figure 1


Exploiting transcriptome data for the development and characterization of gene-based SSR markers related to cold tolerance in oil palm (Elaeis guineensis).

Xiao Y, Zhou L, Xia W, Mason AS, Yang Y, Ma Z, Peng M - BMC Plant Biol. (2014)

The distribution of the motif repeats of mono to hexa-nucleotide microsatellites based on all transcript sequences and transcript sequences differentially expressed in response to cold treatment.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4279980&req=5

Fig1: The distribution of the motif repeats of mono to hexa-nucleotide microsatellites based on all transcript sequences and transcript sequences differentially expressed in response to cold treatment.
Mentions: Of the 51,452 transcripts, 10,973 were up-regulated or down-regulated at least two-fold in response to cold stress. The 10,973 transcripts contained 916 identified SSR loci. Identical distribution with respect to microsatellite motif type was observed between all SSR loci identified in the 51,452 transcripts and the 916 SSR loci associated with response to cold stress (Figure 1). Of the SSR loci associated with response to cold stress, tri-nucleotide motif types were the most abundant (42.58%), followed by mono-nucleotide (34.61%) and di-nucleotide (20.52%) motif types.Figure 1

Bottom Line: Interestingly, 5' untranslated region of both Unigene21287 (ICE1) and CL2628.Contig1 (NAC) both contained an SSR markers.These EST-SSR markers would be particularly useful for gene mapping and population structure analysis in Elaeis guineensis.Meanwhile, the EST-SSR loci were inducible expressed in response to low temperature, which may have potential application in identifying trait-associated markers in oil palm in the future.

View Article: PubMed Central - PubMed

ABSTRACT

Background: The oil palm (Elaeis guineensis, 2n = 32) has the highest oil yield of any crop species, as well as comprising the richest dietary source of provitamin A. For the tropical species, the best mean growth temperature is about 27°C, with a minimal growth temperature of 15°C. Hence, the plantation area is limited into the geographical ranges of 10°N to 10°S. Enhancing cold tolerance capability will increase the total cultivation area and subsequently oil productivity of this tropical species. Developing molecular markers related to cold tolerance would be helpful for molecular breeding of cold tolerant Elaeis guineensis.

Results: In total, 5791 gene-based SSRs were identified in 51,452 expressed sequences from Elaeis guineensis transcriptome data: approximately one SSR was detected per 10 expressed sequences. Of these 5791 gene-based SSRs, 916 were derived from expressed sequences up- or down-regulated at least two-fold in response to cold stress. A total of 182 polymorphic markers were developed and characterized from 442 primer pairs flanking these cold-responsive SSR repeats. The polymorphic information content (PIC) of these polymorphic SSR markers across 24 lines of Elaeis guineensis varied from 0.08 to 0.65 (mean = 0.31 ± 0.12). Using in-silico mapping, 137 (75.3%) of the 182 polymorphic SSR markers were located onto the 16 Elaeis guineensis chromosomes. Total coverage of 473 Mbp was achieved, with an average physical distance of 3.4 Mbp between adjacent markers (range 96 bp - 20.8 Mbp). Meanwhile, Comparative analysis of transcriptome under cold stress revealed that one ICE1 putative ortholog, five CBF putative orthologs, 19 NAC transcription factors and four cold-induced orhologs were up-regulated at least two fold in response to cold stress. Interestingly, 5' untranslated region of both Unigene21287 (ICE1) and CL2628.Contig1 (NAC) both contained an SSR markers.

Conclusions: In the present study, a series of SSR markers were developed based on sequences differentially expressed in response to cold stress. These EST-SSR markers would be particularly useful for gene mapping and population structure analysis in Elaeis guineensis. Meanwhile, the EST-SSR loci were inducible expressed in response to low temperature, which may have potential application in identifying trait-associated markers in oil palm in the future.

Show MeSH
Related in: MedlinePlus