Novel Informatic Tools to Support Functional Annotation of the Durum Wheat Genome.

Seed mutagenesis is one strategy to create a population with thousands of useful mutations for the direct selection of desirable traits, to introduce diversity into varietal improvement programs, or to generate a mutant collection to support gene functional analysis. However, phenotyping such large collections, where each individual may carry many mutations, is a bottleneck for downstream analysis. Targeting Induced Local Lesions in Genomes (TILLinG), when coupled with next-generation sequencing allows high-throughput mutation discovery and selection by genotyping. We mutagenized an advanced durum breeding line, UAD0951096_F2:5 and performed short-read (2x125 bp) Illumina sequencing of the exome of 100 lines using an available exome capture platform. To improve variant calling, we generated a consolidated exome reference using the recently available genome sequences of the cultivars Svevo and Kronos to facilitate the alignment of reads from the UAD0951096_F2:5 derived mutants. The resulting exome reference was 484.4 Mbp. We also developed a user-friendly, searchable database and bioinformatic analysis pipeline that allowed us to predict zygosity of the mutations discovered and extracts flanking sequences for rapid marker development. Here, we present these tools with the aim of allowing researchers fast and accurate downstream selection of mutations discovered by TILLinG by sequencing to support functional annotation of the durum wheat genome.

A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes.

BACKGROUND: Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. RESULTS: A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies. CONCLUSIONS: Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets.