Finding invisible quantitative trait loci with missing data

Gabur, Iulian; Chawla, Harmeet Singh; Liu, Xiwei; Kumar, Vinod; Faure, Sébastien; Tiedemann, Andreas von; Jestin, Christophe; Dryzska, Emmanuelle; Volkmann, Susann; Breuer, Frank; Delourme, Régine; Snowdon, Rod J.; Obermeier, Christian

doi:10.1111/pbi.12942

Cited by 43 publications

(61 citation statements)

References 80 publications

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“…Analysis of raw genotype data from the Brassica 60k SNP array 25,26 for a doubled haploid population ExR53-DH was performed for 244 genotypes. Two genetic maps were produced, one using only SNP markers (the "SNP map") and one using SNP plus SNaP markers 24 (the "SNaP map"), respectively. Comparison of the SNP and SNaP maps revealed that large chromosomal regions were not covered in the SNP map (e.g.…”

Section: Resultsmentioning

confidence: 99%

“…This study focuses exclusively on gene PAV in oilseed rape breeding populations and evaluates the biological relevance and prevalence of gene PAV associated with resistance to a common fungal disease of oilseed rape, Verticillium stem striping caused by Verticillium longisporum. By genetic mapping of genome-wide SNP/ SNaP markers 24 , along with short-read Illumina sequencing in combination with long-range optical mapping, we demonstrate that inclusion of presence-absence polymorphisms in quantitative trait locus (QTL) mapping strategies enables also reliable identification of gene PAV with a putative role in V. longisporum resistance. The results provide a valuable example for the importance of pangenomic gene variation for breeding of a key trait in a major polyploid crop.…”

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Gene presence-absence variation associates with quantitative Verticillium longisporum disease resistance in Brassica napus

Gabur

Chawla

Lopisso

et al. 2020

Sci Rep

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Andreas von tiedemann 2 , Rod J. Snowdon 1 & christian obermeier 1* Although copy number variation (CNV) and presence-absence variation (PAV) have been discovered in selected gene families in most crop species, the global prevalence of these polymorphisms in most complex genomes is still unclear and their influence on quantitatively inherited agronomic traits is still largely unknown. Here we analyze the association of gene PAV with resistance of oilseed rape (Brassica napus) against the important fungal pathogen Verticillium longisporum, as an example for a complex, quantitative disease resistance in the strongly rearranged genome of a recent allopolyploid crop species. Using Single Nucleotide absence Polymorphism (SNaP) markers to efficiently trace PAV in breeding populations, we significantly increased the resolution of loci influencing V. longisporum resistance in biparental and multi-parental mapping populations. Gene PAV, assayed by resequencing mapping parents, was observed in 23-51% of the genes within confidence intervals of quantitative trait loci (QTL) for V. longisporum resistance, and high-priority candidate genes identified within QTL were all affected by PAV. The results demonstrate the prominent role of gene PAV in determining agronomic traits, suggesting that this important class of polymorphism should be exploited more systematically in future plant breeding. Duplication of genes followed by diversification is a common process shaping the evolution of plant species by natural and artificial (breeding) selection 1. Genes can be duplicated by different mechanisms, including tandem duplication, transposon-mediated duplication, segmental duplication, or in the most extreme form by whole-genome duplication (WGD) or polyploidization. WGD is common in the evolutionary history of many wild and cultivated plant species. Different terms have been used frequently to describe short-and long-range genomic duplication and genome structural variation (SV), a term originally defined in reference to insertions, deletions and inversions greater than 1 kb in size 2-4. In contrast to small-scale insertion-deletion (InDel) polymorphisms, which are generally defined as small insertions or deletions of a few nucleotides (up to 50 bp), SV in the size range of genes (up to a few kb) can give rise to copy number variation (CNV) or presence/absence variation (PAV). The latter is an extreme form of CNV where fragments in the size range of genes are missing from the genomes of some investigated genotypes. Genes affected by duplications, InDels, CNVs and PAVs in diploid and polyploid plant species have been linked to local adaptation of wild populations 5 and to important agronomical traits in crops 1,3,6-8 for example flowering time and vernalization requirement in oilseed rape 9,10 and wheat 11 , abiotic stress tolerance in wheat 12,13 and biotic stress tolerance in tobacco 14. However, the strong impact of CNV and other forms of SV in polyploid crop genomes on evolution and trait selection was not recognized until the las...

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Section: Resultsmentioning

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Gene presence-absence variation associates with quantitative Verticillium longisporum disease resistance in Brassica napus

Gabur

Chawla

Lopisso

et al. 2020

Sci Rep

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“…Examples demonstrating the contribution of such SV towards 37 eco-geographical adaptation and disease resistance in oilseed rape suggest that revisiting 38 complex plant genomes using medium-coverage, long-read sequencing might reveal 39 unexpected levels of functional gene variation, with major implications for trait regulation 40 and crop improvement. 41 visualization based on mRNAseq data (He et al, 2017) or deletion calling from SNP array 55 data (Gabur et al, 2018;Grandke et al, 2016). Critically, numerous examples have 56 connected genome SV in B. napus to important agronomic traits (Gabur et al, 2018; Gabur et 57 al., 2019;Liu et al, 2012;Stein et al, 2017).…”

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“…41 visualization based on mRNAseq data (He et al, 2017) or deletion calling from SNP array 55 data (Gabur et al, 2018;Grandke et al, 2016). Critically, numerous examples have 56 connected genome SV in B. napus to important agronomic traits (Gabur et al, 2018; Gabur et 57 al., 2019;Liu et al, 2012;Stein et al, 2017). These studies revealed the important role of SV 58 in the creation of de novo variation for adaptation and breeding, however the methods used 59were not yet capable of resolving SV at gene scale.…”

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Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant

Chawla

Lee

Gabur

et al. 2020

Preprint

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Phone: +49 641 9937420 20 21 22 highly-duplicated nature of plant genomes, which makes them difficult to assess using high-31throughput genome screening methods. Here we describe how long-read sequencing 32 technologies can overcome this problem, revealing a surprisingly high level of widespread, 33 small to mid-scale SV in a major allopolyploid crop species, Brassica napus. We found that 34 up to 10% of all genes were affected by small to mid-scale SV events. Nearly half of these 35 SV events ranged between 100 bp to 1000 bp, which makes them challenging to detect using 36 short read Illumina sequencing. Examples demonstrating the contribution of such SV towards 37 eco-geographical adaptation and disease resistance in oilseed rape suggest that revisiting 38 complex plant genomes using medium-coverage, long-read sequencing might reveal 39 unexpected levels of functional gene variation, with major implications for trait regulation 40 and crop improvement. 41 visualization based on mRNAseq data (He et al., 2017) or deletion calling from SNP array 55 data (Gabur et al., 2018;Grandke et al., 2016). Critically, numerous examples have 56 connected genome SV in B. napus to important agronomic traits (Gabur et al., 2018; Gabur et 57 al., 2019;Liu et al., 2012;Stein et al., 2017). These studies revealed the important role of SV 58 in the creation of de novo variation for adaptation and breeding, however the methods used 59were not yet capable of resolving SV at gene scale. 60 A first example of intragenic SV impacting quantitatively inherited traits in B. napus was 61 reported by Qian et al. (2016), who demonstrated that deletion of exons 2 and 3 from a B. 62 napus orthologue of Mendel's "Green Cotyledon" gene (the Staygreen gene NON-63 YELLOWING 1; NYE1) associated with quantitative variation for chlorophyll and oil content. 64 Unfortunately, such small deletions are challenging to reliably detect using short-read 65 sequencing or low-cost marker arrays, so that their genome-wide extent could not yet be 66 investigated in detail. In this study, using B. napus as an example for a plant genome with 67 widespread structural variation, we demonstrate the power of whole-genome long-read 68 sequencing for high-resolution detection of intragenic SV. The results reveal widespread 69 functional variation on a completely unexpected scale, suggesting that small to mid-scale SV 70 may be a major driver of functional gene diversity in this recent polyploid crop. With the 71 growing accessibility, accuracy and cost-effectiveness of long-read sequencing, our results 72 suggest that there could be enormous promise in revisiting complex crop genomes to discover 73 potentially novel functional SV which has previously been overlooked. 74 75 Results and discussions 76 Long read sequencing reveal novel SV diversity in B. napus 77 We sequenced 4 B. napus accessions with long reads using the Oxford Nanopore Technology 78 (ONT) an 8 further accessions using the Pacific Biosciences (PacBio) platform (obtained 79 from Song et al. (2020)). The ...

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“…Enhancing the opportunities to mine genome sequence data for previously invisible diversity (Gabur et al, 2018a) prolific Gabur et al, 2018b). For example, there is growing evidence that novel genome structural variants in B. napus are created even during self-pollination of homozygous cultivars or during generation of doubled haploid lines (He et al, 2017).…”

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