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Transcriptome sequencing for SNP discovery across Cucumis melo.

Blanca J, Esteras C, Ziarsolo P, Pérez D, Fernã Ndez-Pedrosa V, Collado C, Rodrã Guez de Pablos R, Ballester A, Roig C, Cañizares J, Picó B - BMC Genomics (2012)

Bottom Line: The number and variability of in silico SNVs differed considerably between pools.This study provides the first comprehensive resequencing data for wild, exotic, and cultivated (landraces and commercial) melon transcriptomes, yielding the largest melon SNP collection available to date and representing a notable sample of the species diversity.This data provides a valuable resource for creating a catalog of allelic variants of melon genes and it will aid in future in-depth studies of population genetics, marker-assisted breeding, and gene identification aimed at developing improved varieties.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.

ABSTRACT

Background: Melon (Cucumis melo L.) is a highly diverse species that is cultivated worldwide. Recent advances in massively parallel sequencing have begun to allow the study of nucleotide diversity in this species. The Sanger method combined with medium-throughput 454 technology were used in a previous study to analyze the genetic diversity of germplasm representing 3 botanical varieties, yielding a collection of about 40,000 SNPs distributed in 14,000 unigenes. However, the usefulness of this resource is limited as the sequenced genotypes do not represent the whole diversity of the species, which is divided into two subspecies with many botanical varieties variable in plant, flowering, and fruit traits, as well as in stress response. As a first step to extensively document levels and patterns of nucleotide variability across the species, we used the high-throughput SOLiD™ system to resequence the transcriptomes of a set of 67 genotypes that had previously been selected from a core collection representing the extant variation of the entire species.

Results: The deep transcriptome resequencing of all of the genotypes, grouped into 8 pools (wild African agrestis, Asian agrestis and acidulus, exotic Far Eastern conomon, Indian momordica and Asian dudaim and flexuosus, commercial cantalupensis, subsp. melo Asian and European landraces, Spanish inodorus landraces, and Piel de Sapo breeding lines) yielded about 300 M reads. Short reads were mapped to the recently generated draft genome assembly of the DHL line Piel de Sapo (inodorus) x Songwhan Charmi (conomon) and to a new version of melon transcriptome. Regions with at least 6X coverage were used in SNV calling, generating a melon collection with 303,883 variants. These SNVs were dispersed across the entire C. melo genome, and distributed in 15,064 annotated genes. The number and variability of in silico SNVs differed considerably between pools. Our finding of higher genomic diversity in wild and exotic agrestis melons from India and Africa as compared to commercial cultivars, cultigens and landraces from Eastern Europe, Western Asia and the Mediterranean basin is consistent with the evolutionary history proposed for the species. Group-specific SNVs that will be useful in introgression programs were also detected. In a sample of 143 selected putative SNPs, we verified 93% of the polymorphisms in a panel of 78 genotypes.

Conclusions: This study provides the first comprehensive resequencing data for wild, exotic, and cultivated (landraces and commercial) melon transcriptomes, yielding the largest melon SNP collection available to date and representing a notable sample of the species diversity. This data provides a valuable resource for creating a catalog of allelic variants of melon genes and it will aid in future in-depth studies of population genetics, marker-assisted breeding, and gene identification aimed at developing improved varieties.

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Degree of shared polymorphism between the momordica group and the 7 pools of both subspecies. Total number of SNPs in each group is indicated in the center of each circle and the number of shared SNPs in the intersection. Numbers in brackets show the percentage of shared SNPs (first number referred to the total number in each group and second number in the momordica).
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Figure 2: Degree of shared polymorphism between the momordica group and the 7 pools of both subspecies. Total number of SNPs in each group is indicated in the center of each circle and the number of shared SNPs in the intersection. Numbers in brackets show the percentage of shared SNPs (first number referred to the total number in each group and second number in the momordica).

Mentions: Only 668 SNPs (0.2%) were shared among all libraries, with only 6 with MAF <0.7, which suggests the existence of differential variation in the different groups. Table3 shows the amount of SNPs shared by every pair of libraries. The momordica group was the group with the highest percentage of SNPs in common with other libraries. Between 16 and 40% of the SNPs found in this group of exotic accessions were also variable in the commercial melons and landraces (Figure2). The percentage of SNPs shared with exotic and wild agrestis was also high, ranging from 29 to 35%. The results are consistent with the intermediate position of the momordica group between both subspecies. The high heterogeneity of this pool might also explain this high level of shared variation with both subspecies, as it includes flexuosus and dudaim genotypes, which are often grouped with agrestis types, even though they have been reported to belong to subsp. melo[2]. Dhillon et al.[48] suggested that snap melon landraces from northern India might represent a central melon origin area from which oriental and occidental melon germplasm developed, a hypothesis that has also been supported by Luan et al.[46]. Momordica is one of the most utilized groups for melon breeding and serves to introgress resistance to pests and diseases and tolerance to abiotic stresses. These introgressions may also account for part of the shared variation.


Transcriptome sequencing for SNP discovery across Cucumis melo.

Blanca J, Esteras C, Ziarsolo P, Pérez D, Fernã Ndez-Pedrosa V, Collado C, Rodrã Guez de Pablos R, Ballester A, Roig C, Cañizares J, Picó B - BMC Genomics (2012)

Degree of shared polymorphism between the momordica group and the 7 pools of both subspecies. Total number of SNPs in each group is indicated in the center of each circle and the number of shared SNPs in the intersection. Numbers in brackets show the percentage of shared SNPs (first number referred to the total number in each group and second number in the momordica).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3473316&req=5

Figure 2: Degree of shared polymorphism between the momordica group and the 7 pools of both subspecies. Total number of SNPs in each group is indicated in the center of each circle and the number of shared SNPs in the intersection. Numbers in brackets show the percentage of shared SNPs (first number referred to the total number in each group and second number in the momordica).
Mentions: Only 668 SNPs (0.2%) were shared among all libraries, with only 6 with MAF <0.7, which suggests the existence of differential variation in the different groups. Table3 shows the amount of SNPs shared by every pair of libraries. The momordica group was the group with the highest percentage of SNPs in common with other libraries. Between 16 and 40% of the SNPs found in this group of exotic accessions were also variable in the commercial melons and landraces (Figure2). The percentage of SNPs shared with exotic and wild agrestis was also high, ranging from 29 to 35%. The results are consistent with the intermediate position of the momordica group between both subspecies. The high heterogeneity of this pool might also explain this high level of shared variation with both subspecies, as it includes flexuosus and dudaim genotypes, which are often grouped with agrestis types, even though they have been reported to belong to subsp. melo[2]. Dhillon et al.[48] suggested that snap melon landraces from northern India might represent a central melon origin area from which oriental and occidental melon germplasm developed, a hypothesis that has also been supported by Luan et al.[46]. Momordica is one of the most utilized groups for melon breeding and serves to introgress resistance to pests and diseases and tolerance to abiotic stresses. These introgressions may also account for part of the shared variation.

Bottom Line: The number and variability of in silico SNVs differed considerably between pools.This study provides the first comprehensive resequencing data for wild, exotic, and cultivated (landraces and commercial) melon transcriptomes, yielding the largest melon SNP collection available to date and representing a notable sample of the species diversity.This data provides a valuable resource for creating a catalog of allelic variants of melon genes and it will aid in future in-depth studies of population genetics, marker-assisted breeding, and gene identification aimed at developing improved varieties.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.

ABSTRACT

Background: Melon (Cucumis melo L.) is a highly diverse species that is cultivated worldwide. Recent advances in massively parallel sequencing have begun to allow the study of nucleotide diversity in this species. The Sanger method combined with medium-throughput 454 technology were used in a previous study to analyze the genetic diversity of germplasm representing 3 botanical varieties, yielding a collection of about 40,000 SNPs distributed in 14,000 unigenes. However, the usefulness of this resource is limited as the sequenced genotypes do not represent the whole diversity of the species, which is divided into two subspecies with many botanical varieties variable in plant, flowering, and fruit traits, as well as in stress response. As a first step to extensively document levels and patterns of nucleotide variability across the species, we used the high-throughput SOLiD™ system to resequence the transcriptomes of a set of 67 genotypes that had previously been selected from a core collection representing the extant variation of the entire species.

Results: The deep transcriptome resequencing of all of the genotypes, grouped into 8 pools (wild African agrestis, Asian agrestis and acidulus, exotic Far Eastern conomon, Indian momordica and Asian dudaim and flexuosus, commercial cantalupensis, subsp. melo Asian and European landraces, Spanish inodorus landraces, and Piel de Sapo breeding lines) yielded about 300 M reads. Short reads were mapped to the recently generated draft genome assembly of the DHL line Piel de Sapo (inodorus) x Songwhan Charmi (conomon) and to a new version of melon transcriptome. Regions with at least 6X coverage were used in SNV calling, generating a melon collection with 303,883 variants. These SNVs were dispersed across the entire C. melo genome, and distributed in 15,064 annotated genes. The number and variability of in silico SNVs differed considerably between pools. Our finding of higher genomic diversity in wild and exotic agrestis melons from India and Africa as compared to commercial cultivars, cultigens and landraces from Eastern Europe, Western Asia and the Mediterranean basin is consistent with the evolutionary history proposed for the species. Group-specific SNVs that will be useful in introgression programs were also detected. In a sample of 143 selected putative SNPs, we verified 93% of the polymorphisms in a panel of 78 genotypes.

Conclusions: This study provides the first comprehensive resequencing data for wild, exotic, and cultivated (landraces and commercial) melon transcriptomes, yielding the largest melon SNP collection available to date and representing a notable sample of the species diversity. This data provides a valuable resource for creating a catalog of allelic variants of melon genes and it will aid in future in-depth studies of population genetics, marker-assisted breeding, and gene identification aimed at developing improved varieties.

Show MeSH
Related in: MedlinePlus