Dataset Information

Design and evaluation of a sequence capture system for genome-wide SNP genotyping in highly heterozygous plant genomes: a case study with a keystone Neotropical hardwood tree genome.

ABSTRACT: Targeted sequence capture coupled to high-throughput sequencing has become a powerful method for the study of genome-wide sequence variation. Following our recent development of a genome assembly for the Pink Ipê tree (Handroanthus impetiginosus), a widely distributed Neotropical timber species, we now report the development of a set of 24,751 capture probes for single-nucleotide polymorphisms (SNPs) characterization and genotyping across 18,216 distinct loci, sampling more than 10 Mbp of the species genome. This system identifies nearly 200,000 SNPs located inside or in close proximity to almost 14,000 annotated protein-coding genes, generating quality genotypic data in populations spanning wide geographic distances across the species native range. To provide recommendations for future developments of similar systems for highly heterozygous plant genomes we investigated issues such as probe design, sequencing coverage and bioinformatics, including the evaluation of the capture efficiency and a reassessment of the technical reproducibility of the assay for SNPs recall and genotyping precision. Our results highlight the value of a detailed probe screening on a preliminary genome assembly to produce reliable data for downstream genetic studies. This work should inspire and assist the development of similar genomic resources for other orphan crops and forest trees with highly heterozygous genomes.

SUBMITTER: Silva-Junior OB

PROVIDER: S-EPMC6191306 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Design and evaluation of a sequence capture system for genome-wide SNP genotyping in highly heterozygous plant genomes: a case study with a keystone Neotropical hardwood tree genome.

Silva-Junior Orzenil Bonfim OB Grattapaglia Dario D Novaes Evandro E Collevatti Rosane G RG

DNA research : an international journal for rapid publication of reports on genes and genomes 20181001 5

Targeted sequence capture coupled to high-throughput sequencing has become a powerful method for the study of genome-wide sequence variation. Following our recent development of a genome assembly for the Pink Ipê tree (Handroanthus impetiginosus), a widely distributed Neotropical timber species, we now report the development of a set of 24,751 capture probes for single-nucleotide polymorphisms (SNPs) characterization and genotyping across 18,216 distinct loci, sampling more than 10 Mbp of the sp ...[more]

PMID: 30020434

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Project description:BACKGROUND: High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high, a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology (GGGT). This issue becomes exacerbated when attempting to transfer SNPs across species, a scarcely explored topic in plants, and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera. RESULTS: We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of Eucalyptus from a mixed Sanger/454 database with 1,164,695 ESTs and the preliminary 4.5X draft genome sequence for E. grandis. A systematic assessment of in silico SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous in silico constraints; 93% of them provided high quality genotype calls and 71% of them were polymorphic in a diverse panel of 96 individuals of five different species.SNP reliability was high across nine Eucalyptus species belonging to three sections within subgenus Symphomyrtus and still satisfactory across species of two additional subgenera, although polymorphism declined as phylogenetic distance increased. CONCLUSIONS: This study indicates that the GGGT performs well both within and across species of Eucalyptus notwithstanding its nucleotide diversity ? 2%. The development of a much larger array of informative SNPs across multiple Eucalyptus species is feasible, although strongly dependent on having a representative and sufficiently deep collection of sequences from many individuals of each target species. A higher density SNP platform will be instrumental to undertake genome-wide phylogenetic and population genomics studies and to implement molecular breeding by Genomic Selection in Eucalyptus.

Project description:Genotyping-by-sequencing (GBS) represents a highly cost-effective high-throughput genotyping approach. By nature, however, GBS is subject to generating sizeable amounts of missing data and these will need to be imputed for many downstream analyses. The extent to which such missing data can be tolerated in calling SNPs has not been explored widely. In this work, we first explore the use of imputation to fill in missing genotypes in GBS datasets. Importantly, we use whole genome resequencing data to assess the accuracy of the imputed data. Using a panel of 301 soybean accessions, we show that over 62,000 SNPs could be called when tolerating up to 80% missing data, a five-fold increase over the number called when tolerating up to 20% missing data. At all levels of missing data examined (between 20% and 80%), the resulting SNP datasets were of uniformly high accuracy (96-98%). We then used imputation to combine complementary SNP datasets derived from GBS and a SNP array (SoySNP50K). We thus produced an enhanced dataset of >100,000 SNPs and the genotypes at the previously untyped loci were again imputed with a high level of accuracy (95%). Of the >4,000,000 SNPs identified through resequencing 23 accessions (among the 301 used in the GBS analysis), 1.4 million tag SNPs were used as a reference to impute this large set of SNPs on the entire panel of 301 accessions. These previously untyped loci could be imputed with around 90% accuracy. Finally, we used the 100K SNP dataset (GBS + SoySNP50K) to perform a GWAS on seed oil content within this collection of soybean accessions. Both the number of significant marker-trait associations and the peak significance levels were improved considerably using this enhanced catalog of SNPs relative to a smaller catalog resulting from GBS alone at ?20% missing data. Our results demonstrate that imputation can be used to fill in both missing genotypes and untyped loci with very high accuracy and that this leads to more powerful genetic analyses.

Project description:Tropical forests in the Americas are undergoing rapid conversion to commercial agriculture, and many migratory bird species that use these forests have experienced corresponding populations declines. Conservation research for migratory birds in the tropics has focused overwhelmingly on shade coffee plantations and adjacent forest, but both cover types are now in decline, creating an urgent need to evaluate conservation opportunities in other agricultural systems. Here we compare how a community of 42 Neotropical migratory bird species and a subset of five conservation-priority species differ in usage and habitat associations among a secondary forest baseline and four expanding commercial plantation systems in Guatemala: African oil palm, teak, rubber, and mixed-native hardwoods. We found that mixed-native hardwood plantations supported the highest richness and diversity of all migrants and that the three hardwood plantation types generally outperformed oil palm in richness and diversity metrics. Despite this, oil palm supported high abundance of several common and widespread species also experiencing range-wide population declines and may therefore play an important role in conserving common species. Mature secondary forest hosted low abundance and diversity of the full migratory community, but high abundance and richness of conservation priority migrants along with native hardwood and teak plantations. Likewise, the percentage of forest cover on the landscape was positively associated with priority migrant abundance and richness but negatively associated with the abundance of migrants in general, highlighting how individual species within the broad group of Neotropical migratory landbirds respond differently to anthropogenic changes in land use. Across all cover types, the retention of tall overstory trees increased the abundance, richness, and diversity of all migrants, which indicates that vertical structural diversity and remnant trees are important habitat features for birds in agricultural landscapes. Our findings show that conservation opportunities exist in hardwood and oil palm plantations, though the species likely to benefit from conservation action will vary among plantation types. For the subset of conservation priority migrants, our results suggest that conservation efforts should combine strategies that retain and restore secondary forest, promote the adoption of native hardwood and teak plantations, and promote the retention of tall, remnant trees in agricultural landscapes.

Dataset Information

Design and evaluation of a sequence capture system for genome-wide SNP genotyping in highly heterozygous plant genomes: a case study with a keystone Neotropical hardwood tree genome.

Publications

Design and evaluation of a sequence capture system for genome-wide SNP genotyping in highly heterozygous plant genomes: a case study with a keystone Neotropical hardwood tree genome.

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