Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools

Riju, Aikkal; Rajesh, M. K.; Sherin, P. T. P. Fasila; Chandrasekar, A.; Apshara, S. Elain; Arunachalam, V.

doi:10.1007/s12041-009-0030-1

Cited by 8 publications

(5 citation statements)

References 35 publications

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“…The AG/CT dinucleotide repeat motif was consistent with the high frequencies in the genic regions of A. thaliana [72] and rice [73]. Similar patterns were also noted for EST-SSR in peanut [74] and cacao [75]. The CG motif was generally in low abundance in both Elaeis species.…”

Section: Resultssupporting

confidence: 73%

Analyses of Hypomethylated Oil Palm Gene Space

et al. 2014

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Demand for palm oil has been increasing by an average of ∼8% the past decade and currently accounts for about 59% of the world's vegetable oil market. This drives the need to increase palm oil production. Nevertheless, due to the increasing need for sustainable production, it is imperative to increase productivity rather than the area cultivated. Studies on the oil palm genome are essential to help identify genes or markers that are associated with important processes or traits, such as flowering, yield and disease resistance. To achieve this, 294,115 and 150,744 sequences from the hypomethylated or gene-rich regions of Elaeis guineensis and E. oleifera genome were sequenced and assembled into contigs. An additional 16,427 shot-gun sequences and 176 bacterial artificial chromosomes (BAC) were also generated to check the quality of libraries constructed. Comparison of these sequences revealed that although the methylation-filtered libraries were sequenced at low coverage, they still tagged at least 66% of the RefSeq supported genes in the BAC and had a filtration power of at least 2.0. A total 33,752 microsatellites and 40,820 high-quality single nucleotide polymorphism (SNP) markers were identified. These represent the most comprehensive collection of microsatellites and SNPs to date and would be an important resource for genetic mapping and association studies. The gene models predicted from the assembled contigs were mined for genes of interest, and 242, 65 and 14 oil palm transcription factors, resistance genes and miRNAs were identified respectively. Examples of the transcriptional factors tagged include those associated with floral development and tissue culture, such as homeodomain proteins, MADS, Squamosa and Apetala2. The E. guineensis and E. oleifera hypomethylated sequences provide an important resource to understand the molecular mechanisms associated with important agronomic traits in oil palm.

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Section: Resultssupporting

confidence: 73%

Analyses of Hypomethylated Oil Palm Gene Space

et al. 2014

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“…Twelve highly polymorphic SSR markers were used in this test (Lanaud et al, 1999;Riju et al, 2009; Table 2). After evaluating reagent concentration and temperature conditions of several protocols, polymerase chain reaction (PCR) was performed according to Schnell et al (2005) with modifications.…”

Section: Dna Extraction and Ssr Analysismentioning

confidence: 99%

Genetic identification of Theobroma cacao

Vázquez-Ovando¹,

Molina‐Freaner²,

Núñez‐Farfán³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. Criollo-type cacao trees are an important pool of genes with potential to be used in cacao breeding and selection programs. For that reason, we assessed the diversity and population structure of Criollo-type trees (108 cultivars with Criollo phenotypic characteristics and 10 Criollo references) using 12 simple sequence repeat (SSR) markers. Cultivars were selected from 7 demes in the Soconusco region of southern Mexico. SSRs amplified 74 alleles with an average of 3.6 alleles per population. The overall populations showed an average observed heterozygosity of 0.28, indicating heterozygote deficiency (average fixation index F = 0.50). However, moderate allelic diversity was found within populations Genetic identification of high Criollo ancestry cacao trees (Shannon index for all populations I = 0.97). Bayesian method analysis determined 2 genetic clusters (K = 2) within individuals. In concordance, an assignment test grouped 37 multilocus genotypes (including 10 references) into a first cluster (Criollo), 54 into a second (presumably Amelonado), and 27 admixed individuals unassigned at the 90% threshold likely corresponding to the Trinitario genotype. This classification was supported by the principal coordinate analysis and analysis of molecular variance, which showed 12% of variation among populations (F ST = 0.123, P < 0.0001). Sampled demes sites (1-7) in the Soconusco region did not show any evidence of clustering by geographic location, and this was supported by the Mantel test (R xy = 0.54, P = 0.120). Individuals with high Criollo lineage planted in Soconusco farms could be an important reservoir of genes for future breeding programs searching for fine, taste, flavor, and aroma cocoa.

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“…A first set of 34 EST-SSRs was published for cocoa (Borrone et al 2007;Riju et al 2009). These markers were identified in the first ESTs (6581 sequences) from leaf and bean cDNA libraries (Jones et al 2002), and from suppressive subtractive hybridization (SSH) from leaves treated with inducers of the defense response (Verica et al 2004), and shoot tips inoculated with witches' broom caused by Moniliophthora perniciosa (Leal et al 2007).…”

Section: Introductionmentioning

confidence: 99%

Structural characterization and mapping of functional EST-SSR markers in Theobroma cacao

Fouet

Allègre

Argout

et al. 2011

Tree Genetics & Genomes

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Theobroma cacao L. is a major cash crop for tropical countries, providing incomes for 14 million small farmers. Establishing sustainable disease resistance and maintaining cocoa qualities are among the major objectives of breeding programs. To enrich the high-density genetic map, useful for all cocoa genetic studies, with gene-based markers, a recently produced large EST resource was mined to develop expressed sequence tag-based simple sequence repeat markers (EST-SSRs) defined in genes with a putative known function. A set of 174 polymorphic EST-SSRs was identified from a selection of 314 non-redundant EST-SSRs with a putative known function. Of them, 115 loci were mapped on the cocoa reference map. This new map contains 582 codominant markers arranged in ten linkage groups corresponding to the haploid number of chromosomes. An average interval between markers of 1.3 cM was found, with approximately one SSR every 2 cM. This new set of EST-SSRs includes 14 candidate genes for plant resistance or cocoa qualities. The percentage of polymorphic SSRs varied depending on the different gene regions from which they originated, with respectively 54%, 69%, and 82% of polymorphic EST-SSRs originating from coding sequences, and from the non-coding untranslated 5′ UTR and 3′UTR regions. This new map contains a set of 384 SSR markers that are easily transferable across different mapping populations and useful for all genetic analyses in T. cacao. The new set of EST-SSRs will be a useful tool for studying the functional diversity of populations and for carrying out association mapping studies.

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Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools

Cited by 8 publications

References 35 publications

Analyses of Hypomethylated Oil Palm Gene Space

Analyses of Hypomethylated Oil Palm Gene Space

Genetic identification of Theobroma cacao

Structural characterization and mapping of functional EST-SSR markers in Theobroma cacao

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