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Development of a gene-centered ssr atlas as a resource for papaya (Carica papaya) marker-assisted selection and population genetic studies.

Vidal NM, Grazziotin AL, Ramos HC, Pereira MG, Venancio TM - PLoS ONE (2014)

Bottom Line: A total of 116,453 (72.6%) of all identified repeats were successfully mapped to one of the nine papaya linkage groups.Primer pairs were designed for markers from 9,594 genes (34.5% of the papaya gene complement).Using papaya-tomato orthology assessments, we assembled a list of 300 genes (comprising 785 SSRs) potentially involved in fruit ripening.

View Article: PubMed Central - PubMed

Affiliation: Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil.

ABSTRACT
Carica papaya (papaya) is an economically important tropical fruit. Molecular marker-assisted selection is an inexpensive and reliable tool that has been widely used to improve fruit quality traits and resistance against diseases. In the present study we report the development and validation of an atlas of papaya simple sequence repeat (SSR) markers. We integrated gene predictions and functional annotations to provide a gene-centered perspective for marker-assisted selection studies. Our atlas comprises 160,318 SSRs, from which 21,231 were located in genic regions (i.e. inside exons, exon-intron junctions or introns). A total of 116,453 (72.6%) of all identified repeats were successfully mapped to one of the nine papaya linkage groups. Primer pairs were designed for markers from 9,594 genes (34.5% of the papaya gene complement). Using papaya-tomato orthology assessments, we assembled a list of 300 genes (comprising 785 SSRs) potentially involved in fruit ripening. We validated our atlas by screening 73 SSR markers (including 25 fruit ripening genes), achieving 100% amplification rate and uncovering 26% polymorphism rate between the parental genotypes (Sekati and JS12). The SSR atlas presented here is the first comprehensive gene-centered collection of annotated and genome positioned papaya SSRs. These features combined with thousands of high-quality primer pairs make the atlas an important resource for the papaya research community.

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Distribution of SSR type according to genomic location.
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pone-0112654-g001: Distribution of SSR type according to genomic location.

Mentions: We detected 160,318 perfectly matching, non-redundant SSRs. After integrating SSRs and gene coordinates, we found that 36% of the papaya genes (9,992/27,769) have at least one SSR. A total of 21,231 SSRs were identified in genic regions, while 139,087 were intergenic (Figure 1). Because UTR annotations are not available for the papaya genome, SSRs located on these regions were not classified as such. As expected, most SSRs are intergenic (86.8%), followed by intronic (9.9%), exonic (3.3%), and only 73 (0.04%) SSRs in exon-intron boundaries (Table 1). Dinucleotide motifs were abundant in intergenic (39.4%) and intronic regions (45.3%), while tri- to hexanucleotides were uniformly distributed in such regions. On the other hand, exons and exon-intron boundaries were enriched in tri- (67.1% and 37%) and hexanucleotides (24.4% and 42.5%), which is expected due to the selective pressure against frameshift mutations in coding regions.


Development of a gene-centered ssr atlas as a resource for papaya (Carica papaya) marker-assisted selection and population genetic studies.

Vidal NM, Grazziotin AL, Ramos HC, Pereira MG, Venancio TM - PLoS ONE (2014)

Distribution of SSR type according to genomic location.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4231050&req=5

pone-0112654-g001: Distribution of SSR type according to genomic location.
Mentions: We detected 160,318 perfectly matching, non-redundant SSRs. After integrating SSRs and gene coordinates, we found that 36% of the papaya genes (9,992/27,769) have at least one SSR. A total of 21,231 SSRs were identified in genic regions, while 139,087 were intergenic (Figure 1). Because UTR annotations are not available for the papaya genome, SSRs located on these regions were not classified as such. As expected, most SSRs are intergenic (86.8%), followed by intronic (9.9%), exonic (3.3%), and only 73 (0.04%) SSRs in exon-intron boundaries (Table 1). Dinucleotide motifs were abundant in intergenic (39.4%) and intronic regions (45.3%), while tri- to hexanucleotides were uniformly distributed in such regions. On the other hand, exons and exon-intron boundaries were enriched in tri- (67.1% and 37%) and hexanucleotides (24.4% and 42.5%), which is expected due to the selective pressure against frameshift mutations in coding regions.

Bottom Line: A total of 116,453 (72.6%) of all identified repeats were successfully mapped to one of the nine papaya linkage groups.Primer pairs were designed for markers from 9,594 genes (34.5% of the papaya gene complement).Using papaya-tomato orthology assessments, we assembled a list of 300 genes (comprising 785 SSRs) potentially involved in fruit ripening.

View Article: PubMed Central - PubMed

Affiliation: Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil.

ABSTRACT
Carica papaya (papaya) is an economically important tropical fruit. Molecular marker-assisted selection is an inexpensive and reliable tool that has been widely used to improve fruit quality traits and resistance against diseases. In the present study we report the development and validation of an atlas of papaya simple sequence repeat (SSR) markers. We integrated gene predictions and functional annotations to provide a gene-centered perspective for marker-assisted selection studies. Our atlas comprises 160,318 SSRs, from which 21,231 were located in genic regions (i.e. inside exons, exon-intron junctions or introns). A total of 116,453 (72.6%) of all identified repeats were successfully mapped to one of the nine papaya linkage groups. Primer pairs were designed for markers from 9,594 genes (34.5% of the papaya gene complement). Using papaya-tomato orthology assessments, we assembled a list of 300 genes (comprising 785 SSRs) potentially involved in fruit ripening. We validated our atlas by screening 73 SSR markers (including 25 fruit ripening genes), achieving 100% amplification rate and uncovering 26% polymorphism rate between the parental genotypes (Sekati and JS12). The SSR atlas presented here is the first comprehensive gene-centered collection of annotated and genome positioned papaya SSRs. These features combined with thousands of high-quality primer pairs make the atlas an important resource for the papaya research community.

Show MeSH
Related in: MedlinePlus