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Means of minimum (blue line) and maximum (red line) temperatures and cumulated rainfall (blue bars) during the months of the growth cycle for both trials. (PDF 95 kb)

(a) Summary of the mixed model analysis performed for the grain number components studied comprising 553 NILs carrying the Avalon or Cadenza alleles in the introgressed region in 2013. (b) Average values for the two groups (carrying the Avalon or Cadenza alleles in the QTL region) based on the chromosome and background in 2013. Significant difference between Avalon and Cadenza alleles are highlighted in bold (spikes/m2 (S), spikelet/spike (s/S) and grains/spikelet (G/S). (PDF 111 kb)

Difference between Avalon and Cadenza alleles for the ratio between the lenghts of each PH component and the total PH for the chromosome that showed significant differences for plant height (values above zero indicates that the Avalon allele increased height whereas below zero the Cadenza allele reduced height; ear length (EL), peduncle (PL) and internode lengths (from the first to the fifth counted from the top, abbreviated as 1stITL, 2ndITL, 3rdITL, 4thITL, 5thITL); * P-value

Comparions between the magnitude of the effects of the A × C DH population (red) and the NILs for heading date (a) and plant heigth (b) (2013 and 2014 are indicated in bakc and grey color, respectively; the Avalon background is showed in dashed line whereas the Cadenza background is showed in straigth line). (PDF 91 kb)

International audience; To understand the population genetics of structural variants and their effects on phenotypes, we developed an approach to mapping structural variants that segregate in a population sequenced at low coverage. We avoid calling structural variants directly. Instead, the evidence for a potential structural variant at a locus is indicated by variation in the counts of short-reads that map anomalously to that locus. These structural variant traits are treated as quantitative traits and mapped genetically, analogously to a gene expression study. Association between a structural variant trait at one locus, and genotypes at a distant locus indicate the origin and target of a transposition. Using ultra-low-coverage (0.3x) population sequence data from 488 recombinant inbred Arabidopsis thaliana genomes, we identified 6502 segregating structural variants. Remarkably, 25% of these were transpositions. While many structural variants cannot be delineated precisely, we validated 83% of 44 predicted transposition breakpoints by polymerase chain reaction. We show that specific structural variants may be causative for quantitative trait loci for germination and resistance to infection by the fungus Albugo laibachii, isolate Nc14. Further we show that the phenotypic heritability attributable to read-mapping anomalies differs from, and, in the case of time to germination and bolting, exceeds that due to standard genetic variation. Genes within structural variants are also more likely to be silenced or dysregulated. This approach complements the prevalent strategy of structural variant discovery in fewer individuals sequenced at high coverage. It is generally applicable to large populations sequenced at low-coverage, and is particularly suited to mapping transpositions.

(a) Summary of the mixed model analysis performed for the grain number components studied comprising 553 NILs carrying the Avalon or Cadenza alleles in the introgressed region in 2013. (b) Average values for the two groups (carrying the Avalon or Cadenza alleles in the QTL region) based on the chromosome and background in 2013. Significant difference between Avalon and Cadenza alleles are highlighted in bold (spikes/m2 (S), spikelet/spike (s/S) and grains/spikelet (G/S). (PDF 111Â kb)

Means of minimum (blue line) and maximum (red line) temperatures and cumulated rainfall (blue bars) during the months of the growth cycle for both trials. (PDF 95Â kb)

Difference between Avalon and Cadenza alleles for the ratio between the lenghts of each PH component and the total PH for the chromosome that showed significant differences for plant height (values above zero indicates that the Avalon allele increased height whereas below zero the Cadenza allele reduced height; ear length (EL), peduncle (PL) and internode lengths (from the first to the fifth counted from the top, abbreviated as 1stITL, 2ndITL, 3rdITL, 4thITL, 5thITL); * P-value

To understand the population genetics of structural variants and their effects on phenotypes, we developed an approach to mapping structural variants that segregate in a population sequenced at low coverage. We avoid calling structural variants directly. Instead, the evidence for a potential structural variant at a locus is indicated by variation in the counts of short-reads that map anomalously to that locus. These structural variant traits are treated as quantitative traits and mapped genetically, analogously to a gene expression study. Association between a structural variant trait at one locus, and genotypes at a distant locus indicate the origin and target of a transposition. Using ultra-low-coverage (0.3×) population sequence data from 488 recombinant inbred Arabidopsis thaliana genomes, we identified 6502 segregating structural variants. Remarkably, 25% of these were transpositions. While many structural variants cannot be delineated precisely, we validated 83% of 44 predicted transposition breakpoints by polymerase chain reaction. We show that specific structural variants may be causative for quantitative trait loci for germination and resistance to infection by the fungus Albugo laibachii, isolate Nc14. Further we show that the phenotypic heritability attributable to read-mapping anomalies differs from, and, in the case of time to germination and bolting, exceeds that due to standard genetic variation. Genes within structural variants are also more likely to be silenced or dysregulated. This approach complements the prevalent strategy of structural variant discovery in fewer individuals sequenced at high coverage. It is generally applicable to large populations sequenced at low-coverage, and is particularly suited to mapping transpositions., Genetics, 205 (4), ISSN:1943-2631