Variant Calling Using Whole Genome Resequencing and Sequence Capture for Population and Evolutionary Genomic Inferences in Norway Spruce (Picea Abies)

Bernhardsson, Carolina; Wang, Xi; Eklöf, Helena; Ingvarsson, Pär K.

doi:10.1007/978-3-030-21001-4_2

Cited by 9 publications

(10 citation statements)

References 59 publications

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“…If one allows for 10% or 20% missing data in the GBS results, the size of the regions covered increase to 1.4 Mb and 1.6 Mb, respectively. Repetitive regions are also problematic for downstream genotyping [25], regardless of method and the greater fraction of repetitive regions in the GBS could hence further skew the results from these regions. The overall summary of the data (Table 2) show that the capture probes generates more data both in terms of total size and number of unique scaffolds and also, as expected, contain a greater fraction coding regions.…”

Section: Discussionmentioning

confidence: 99%

“…The sequencing and SNP calling procedures for these samples have previously been described in detail in Bernhardsson et al [25] and Wang et al [24]. Briefly, DNA was extracted with a Qiagen plant mini kit (Qiagen, Hilden, Germany) according to the instructions for the WGS data.…”

Section: Whole-genome Re-sequencing Datamentioning

confidence: 99%

“…Paired-end libraries with an insert size of 500 bp were sequenced using either the Illumina HiSeq 2000 (Pab002-Pab006) or Illumina HiSeq X platforms (Pab007-Pab034). Samples sequenced on both platforms were analysed using the same general bioinformatics pipeline [25]. Raw sequence reads were mapped against the P. abies reference genome v.1.0 [14] using BWA-MEM with default settings.…”

Section: Whole-genome Re-sequencing Datamentioning

confidence: 99%

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Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies

Eklöf

Bernhardsson

Ingvarsson

2020

Forests

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Conifer genomes are characterized by their large size and high abundance of repetitive material, making large-scale genotyping in conifers complicated and expensive. One of the consequences of this is that it has been difficult to generate data on genome-wide levels of genetic variation. To date, researchers have mainly employed various complexity reduction techniques to assess genetic variation across the genome in different conifer species. These methods tend to capture variation in a relatively small subset of a typical conifer genome and it is currently not clear how representative such results are. Here we take advantage of data generated in the first large-scale re-sequencing effort in Norway spruce and assess how well two commonly used complexity reduction methods, targeted capture probes and genotyping by sequencing perform in capturing genome-wide variation in Norway spruce. Our results suggest that both methods perform reasonably well for assessing genetic diversity and population structure in Norway spruce (Picea abies (L.) H. Karst.). Targeted capture probes were slightly more effective than GBS, likely due to them targeting known genomic regions whereas the GBS data contains a substantially greater fraction of repetitive regions, which sometimes can be problematic for assessing genetic diversity. In conclusion, both methods are useful for genotyping large numbers of samples and they greatly reduce the cost involved with genotyping a species with such a complex genome as Norway spruce.

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Section: Discussionmentioning

confidence: 99%

Section: Whole-genome Re-sequencing Datamentioning

confidence: 99%

Section: Whole-genome Re-sequencing Datamentioning

confidence: 99%

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Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies

Eklöf

Bernhardsson

Ingvarsson

2020

Forests

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“…Variants were filtered according to Bernhardsson et al (2020) with minor modifications. Briefly, only biallelic SNPs within the extended probe regions were included with QualbyDepth > 2.0, FisherStrand < 60.0, RMSMappingQuality (MQ) > 40, MappingQualityRankSumTest (MQRankSum) > −12.5, ReadPosRankSumTest (ReadPosRankSum) > –8.0, StrandOddsRatio (SOR) < 3.0 using vcftools (Danecek et al, 2011).…”

Section: Methodsmentioning

confidence: 99%

Killing two enemies with one stone? Genomics of resistance to two sympatric pathogens in Norway spruce

et al. 2021

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Trees must cope with the attack of multiple pathogens, often simultaneously during their long lifespan. Ironically, the genetic and molecular mechanisms controlling this process are poorly understood. The objective of this study was to compare the genetic component of resistance in Norway spruce to Heterobasidion annosum s.s. and its sympatric congener Heterobasidion parviporum. Heterobasidion root‐ and stem‐rot is a major disease of Norway spruce caused by members of the Heterobasidion annosum species complex. Resistance to both pathogens was measured using artificial inoculations in half‐sib families of Norway spruce trees originating from central to northern Europe. The genetic component of resistance was analysed using 63,760 genome‐wide exome‐capture sequenced SNPs and multitrait genome‐wide associations. No correlation was found for resistance to the two pathogens; however, associations were found between genomic variants and resistance traits with synergic or antagonist pleiotropic effects to both pathogens. Additionally, a latitudinal cline in resistance in the bark to H. annosum s.s. was found; trees from southern latitudes, with a later bud‐set and thicker stem diameter, allowed longer lesions, but this was not the case for H. parviporum. In summary, this study detects genomic variants with pleiotropic effects which explain multiple disease resistance from a genic level and could be useful for selection of resistant trees to both pathogens. Furthermore, it highlights the need for additional research to understand the evolution of resistance traits to multiple pathogens in trees.

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“…All sequencing data were aligned to the Saccharum spontaneum reference genome [11] by BWA software (fast and accurate short read alignment with the Burrows-Wheeler Transform) [12] (PCR duplicates reads were further removed by Samtools (v1.3.167, the Sequence Alignment/Map format and SAMtools) [13]. SNPs were identi ed among 216 samples by the HaplotypeCaller module of GATK (v3.868) in GVCF mode (The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data) [14]. Then a joint call was performed using GATK GenotypeGVCFs for all 216 samples.…”

Section: Linkage Disequilibrium Analysismentioning

confidence: 99%

Identification of Genetic Loci for Sugarcane Leaf Angle at Different Developmental Stages by Genome-Wide Association Study

Chen

Huang

Zhang

et al. 2021

Preprint

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Background Sugarcane (Saccharum spp.) is an efficient crop mainly used for sugar and bioethanol production. High yield and high sucrose of sugarcane is always the fundamental demands in sugarcane growth worldwide. Leaf angle and size of sugarcane can be attributed to planting density, which was associated with yield. In this study, we performed Genome-Wide Association Studies (GWAS) in a panel of 216 sugarcane core parents and their derived lines (natural population) to determine the genetic basis of leaf angle and key candidate genes at seedling, elongation and maturity stage. Results A total of 288 significant associated loci of sugarcane leaf angle at different developmental Stages were identified by GWAS. Among them, one key locus and eleven loci was identified in all three stages and two stages, respectively. Overall, 4089 genes were located in the confidence interval of significant loci, among which 3892 genes were functionally annotated. Finally, thirteen core parents and their derivatives tagged with SNPs were selected for Marker-assisted selection (MAS). Conclusion These candidate genes are mainly related to MYB transcription factors, auxin response factors, serine/threonine-protein kinases, etc. The are directly or indirectly associated with leaf angle in sugarcane. This research provided a large number of novel genetic resources for the improvement of leaf angles and simultaneously to high yield and high bioethanol production.

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Variant Calling Using Whole Genome Resequencing and Sequence Capture for Population and Evolutionary Genomic Inferences in Norway Spruce (Picea Abies)

Cited by 9 publications

References 59 publications

Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies

Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies

Killing two enemies with one stone? Genomics of resistance to two sympatric pathogens in Norway spruce

Identification of Genetic Loci for Sugarcane Leaf Angle at Different Developmental Stages by Genome-Wide Association Study

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