New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array

Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs we...

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Published inMolecular ecology resources Vol. 16; no. 4; pp. 1023 - 1036
Main Authors Faivre-Rampant, P., Zaina, G., Jorge, V., Giacomello, S., Segura, V., Scalabrin, S., Guérin, V., De Paoli, E., Aluome, C., Viger, M., Cattonaro, F., Payne, A., PaulStephenRaj, P., Le Paslier, M. C., Berard, A., Allwright, M. R., Villar, M., Taylor, G., Bastien, C., Morgante, M.
Format Journal Article
LanguageEnglish
Published England Blackwell Publishing Ltd 01.07.2016
Wiley Subscription Services, Inc
Wiley/Blackwell
Subjects
Biodiversity and Ecology
Environmental Sciences
Europe
Genetic Variation
Genetics, Population - methods
Genome, Plant
Genotyping Techniques - methods
High-Throughput Nucleotide Sequencing
HT-genotyping design
large-scale SNP discovery
Life Sciences
Microarray Analysis - methods
Polymorphism, Single Nucleotide
population genetics
Populus - classification
Populus - genetics
Populus nigra
Sequence Analysis, DNA
Vegetal Biology
population genetics
large-scale SNP discovery
HT-genotyping design
Populus nigra
HT genotyping design
Population genetics
large scale SNP discovery
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Summary:Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water‐use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead‐Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5–7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural‐population based genetic association studies in P. nigra.
Bibliography:istex:4641C09D87806FAB5CCB5E954721598496681FCE
European Commission - No. FP5-QLK5-CT-2002-00953; No. FP6-16322; No. FP7-211868; No. FP7-211917; No. FP7-311929
BBSRC
INRA (AIP Bioresources)
ArticleID:MEN12513
Table S1 SNP-panel discovery and list of genotyped Populus nigra individuals. Table S2 Primer pairs developed within genes for Sanger resequencing and SNP collections. Table S3 List of candidate regions and candidate genes based on the location of QTL hot spots for rust resistance, drought stress, bud phenology, wood composition and transcriptome studies. Table S4 Alignment results of the Poli, BEN3, BDG and 71077-308 short reads onto the Populus nigra reference (389 Mb). Table S5 Origin and number of SNPs included in the 12 000 BeadChip array. Table S6 List of SNPs included in the 12 000 BeadChip array. Table S7 Performance of the BeadChip array. Table S8 Comparison of genotyping data and Sanger data. Table S9 Comparison of genotyping data and NGS data. Table S10 Genomic position and gene assignation of the 8259 useful SNPs. Table S11 List and origin of unexpected replicates. Table S12 Chromosomal distribution of SNP numbers, SNP distances and SNP densities. Table S13 Pairwise Jost's D values for Populus nigra populations.Methods S1 DNA extraction and Sanger sequencing of gene amplicons. Methods S2 Calculation of Illumina sequencing accuracy. Methods S3 Validation and Origin of replicates data with SR genotyping. Fig. S1 Test of SNP segregation conformity within eight progenies belonging to a 3x3 factorial mating design. Fig. S2 Genomic distribution of SNPs detected for the development of the 12k bead-chip array. The coloured bars around the plot represent the 19 Populus chromosomes (unit used is 2 Mb). Fig. S3 Chromosomal distribution of SNP densities and summary of QTL locations for wood composition, bud phenology, water-use efficiency and rust resistance in the poplar genome. Fig. S4 Principal component analysis: The first, second and third axes explain 2.39%, 1.89% and 1.71% of the total variance respectively. Fig. S5 Distribution of Minor Allele Frequencies (MAF) for 7896 SNPs in seven clusters and the association population (706 individuals).
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SourceType-Scholarly Journals-1
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content type line 23
ISSN:1755-098X
1755-0998
DOI:10.1111/1755-0998.12513