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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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PCR products and polymorphic characteristics of four SSR markers across 24Elaeis guineensisaccessions.
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Fig4: PCR products and polymorphic characteristics of four SSR markers across 24Elaeis guineensisaccessions.

Mentions: A total of 442 primer pairs were successfully designed from the flanking sequences of cold-response-associated mono- to hexanucleotide SSR repeats. Primer pairs could not be designed for the remaining SSRs, mainly due to difficulties in obtaining sufficient flanking sequences from either side of the identified microsatellites. Subsequently, the 442 pairs of primer sequences flanking 132 mono-nucleotide repeats, 74 di-nucleotide repeats, 219 tri-nucleotide repeats, 7 tetra-nucleotide repeats, 7 penta-nucleotide repeats and 3 hexa-nucleotide repeats were synthesized to test the extent of polymorphism in the cold-response SSRs across the 24 oil palm lines. In 278 (62.9%) of cases, PCR products could be amplified from genomic DNA. The remaining 164 primer pairs were excluded from further analysis due to lack of PCR products or due to weak amplification. Ninety-one primer pairs amplified monomorphic bands in all lines. In total, 182 (41.2%) polymorphic microsatellite markers were identified (Figure 4), including 50 mono-nucleotide repeats, 22 di-nucleotide repeats, 102 tri-nucleotide repeats, 4 tetra-nucleotide repeats, 2 penta-nucleotide repeats, and 1 hexa-nucleotide repeat. The percentage of polymorphic mono-, di-, tri- and tetra-nucleotide repeats was 38%, 30%, 47% and 57%, respectively. From the 182 loci, 402 microsatellite alleles were identified with an average of 2.2 alleles per locus. Of the 402 alleles, 105 were from mononucleotide motif loci with an average of 2 alleles per locus; 46 were from dinucleotide motif loci with an average of 2 alleles per locus, and 227 were from trinucleotide motif loci with an average of 2.2 alleles per locus. Across the 182 polymorphic markers, PIC values ranged from 0.08 to 0.65 (mean = 0.31 ± 0.12), suggesting the cold-response-associated SSR markers developed had moderate levels of polymorphism (Figure 5). The mean PICs of the 50 mono-nucleotide, 22 di-nucleotide and 102 tri-nucleotide repeats were 0.30, 0.31 and 0.31, respectively. Detailed information for the 182 polymorphic markers is listed in Additional file 1.Figure 4


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)

PCR products and polymorphic characteristics of four SSR markers across 24Elaeis guineensisaccessions.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: PCR products and polymorphic characteristics of four SSR markers across 24Elaeis guineensisaccessions.
Mentions: A total of 442 primer pairs were successfully designed from the flanking sequences of cold-response-associated mono- to hexanucleotide SSR repeats. Primer pairs could not be designed for the remaining SSRs, mainly due to difficulties in obtaining sufficient flanking sequences from either side of the identified microsatellites. Subsequently, the 442 pairs of primer sequences flanking 132 mono-nucleotide repeats, 74 di-nucleotide repeats, 219 tri-nucleotide repeats, 7 tetra-nucleotide repeats, 7 penta-nucleotide repeats and 3 hexa-nucleotide repeats were synthesized to test the extent of polymorphism in the cold-response SSRs across the 24 oil palm lines. In 278 (62.9%) of cases, PCR products could be amplified from genomic DNA. The remaining 164 primer pairs were excluded from further analysis due to lack of PCR products or due to weak amplification. Ninety-one primer pairs amplified monomorphic bands in all lines. In total, 182 (41.2%) polymorphic microsatellite markers were identified (Figure 4), including 50 mono-nucleotide repeats, 22 di-nucleotide repeats, 102 tri-nucleotide repeats, 4 tetra-nucleotide repeats, 2 penta-nucleotide repeats, and 1 hexa-nucleotide repeat. The percentage of polymorphic mono-, di-, tri- and tetra-nucleotide repeats was 38%, 30%, 47% and 57%, respectively. From the 182 loci, 402 microsatellite alleles were identified with an average of 2.2 alleles per locus. Of the 402 alleles, 105 were from mononucleotide motif loci with an average of 2 alleles per locus; 46 were from dinucleotide motif loci with an average of 2 alleles per locus, and 227 were from trinucleotide motif loci with an average of 2.2 alleles per locus. Across the 182 polymorphic markers, PIC values ranged from 0.08 to 0.65 (mean = 0.31 ± 0.12), suggesting the cold-response-associated SSR markers developed had moderate levels of polymorphism (Figure 5). The mean PICs of the 50 mono-nucleotide, 22 di-nucleotide and 102 tri-nucleotide repeats were 0.30, 0.31 and 0.31, respectively. Detailed information for the 182 polymorphic markers is listed in Additional file 1.Figure 4

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