Structural variants in the barley gene pool: precision and sensitivity to detect them using short-read sequencing and their association with gene expression and phenotypic variation

Genetic mapping reveals new loci and alleles for flowering time and plant height using the double round-robin population of barley

Flowering time and plant height are two critical determinants of yield potential in barley (Hordeum vulgare). Despite their role in plant physiological regulation, a complete overview of the genetic complexity of flowering time and plant height regulation in barley is still lacking. Using a double round-robin population originated from the crossings of 23 diverse parental inbred lines, we aimed to determine the variance components in the regulation of flowering time and plant height in barley as well as to identify new genetic variants by single and multi-population QTL analyses and allele mining. Despite similar genotypic variance, we observed higher environmental variance components for plant height than flowering time. Furthermore, we detected new QTLs for flowering time and plant height. Finally, we identified a new functional allelic variant of the main regulatory gene Ppd-H1. Our results show that the genetic architecture of flowering time and plant height might be more complex than reported earlier and that a number of undetected, small effect, or low-frequency genetic variants underlie the control of these two traits.

Benchmarking of structural variant detection in the tetraploid potato genome using linked-read sequencing

It has recently been shown that structural variants (SV) can have a higher impact on gene expression variation compared to single nucleotide variants (SNV) in different plant species. Additionally, SV were associated with phenotypic variation in several crops. However, compared to the established SV detection based on short-read sequencing, less approaches were described for linked-read based SV calling. We therefore evaluated the performance of six linked-read SV callers compared to an established short-read SV caller based on simulated linked-reads in tetraploid potato. The objectives of our study were to i) compare the performance of SV callers based on linked-read sequencing to short-read sequencing, ii) examine the influence of SV type, SV length, haplotype incidence (HI), as well as sequencing coverage on the SV calling performance in the tetraploid potato genome, and iii) evaluate the accuracy of detecting insertions by linked-read compared to short-read sequencing. We observed high break point resolutions (BPR) detecting short SV and slightly lower BPR for large SV. Our observations highlighted the importance of short-read signals provided by Manta and LinkedSV to detect short SV. Manta and NAIBR performed well for detecting larger deletions, inversions, and duplications. Detected large SV were weakly influenced by the HI. Furthermore, we illustrated that large insertions can be assembled by Novel-X. Our results suggest the usage of the short-read and linked-read SV callers Manta, NAIBR, LinkedSV, and Novel-X based on at least 90x linked-read sequencing coverage to ensure the detection of a broad range of SV in the tetraploid potato genome.

The double round-robin population unravels the genetic architecture of grain size in barley

Grain number, size and weight primarily determine the yield of barley. Although the genes regulating grain number are well studied in barley, the genetic loci and the causal gene for sink capacity are poorly understood. Therefore, the primary objective of our work was to dissect the genetic architecture of grain size and weight in barley. We used a multi-parent population developed from a genetic cross between 23 diverse barley inbreds in a double round-robin design. Seed size-related parameters such as grain length, grain width, grain area and thousand-grain weight were evaluated in the HvDRR population comprising 45 recombinant inbred line sub-populations. We found significant genotypic variation for all seed size characteristics, and observed 84% or higher heritability across four environments. The quantitative trait locus (QTL) detection results indicate that the genetic architecture of grain size is more complex than previously reported. In addition, both cultivars and landraces contributed positive alleles at grain size QTLs. Candidate genes identified using genome-wide variant calling data for all parental inbred lines indicated overlapping and potential novel regulators of grain size in cereals. Furthermore, our results indicated that sink capacity was the primary determinant of grain weight in barley.