Wheat pre-harvest sprouting (PHS) is a precocious germination of seed in the head when there are prolonged wet conditions occurs during the harvest period. Recent damage caused by PHS occurred in 2008, 2009 and 2011, resulting in severe losses to the Michigan wheat industry. Direct annual losses caused by PHS worldwide can reach up to US $1 billion. Breeding for PHS resistant wheat cultivars is critical for securing soft white wheat production and reducing the economic loss to Michigan farmers, food processors and millers. In general, white wheat is more susceptible to PHS in comparison to red wheat. However, the underlying mechanism connecting seed coat color and PHS resistance has not been clearly described. In this study, a recombinant inbred line population segregating for seed coat color alleles was evaluated for seed coat color and alpha-amylase activity in three years with two treatments. The genotyping results enabled us to group individuals by the specific red allele combinations and allowed us to examine the allelic contribution of each color loci to both seed coat color and alpha-amylase activity. A high-density genetic map based upon Infinium 9K SNP array was generated to locate QTL in relatively narrow regions. A total of 38 Quantitative Trait Loci (QTL) for seed coat color and alpha-amylase activity were identified from this population and mapped on eleven chromosomes (1B, 2A, 2B, 3A, 3B, 3D, 4B, 5A, 5D, 6B and 7B) from three years and two post-harvest treatments. Most QTL explained 6-15% of the phenotypic variance while a major QTL on chromosome 2B explained up to 37.6% of phenotypic variance of alpha-amylase activity in 2012 non-mist condition. Significant QTL × QTL interactions were also found between and within color and enzyme related traits. Next generation sequencing (NGS) technology was used in current study to generate wheat transcriptome using Trinity with two methods: de novo assembly and Genome Guided assembly. Quality assessment of the two assemblies was conducted based on their concordance, completeness and contiguity. Three assembly scenarios were evaluated in order to find a balance between sample specificity and transcriptome completeness. Red wheat and white wheat lines from previous QTL population were collected under mist and non-mist conditions and their expression profiles were compared to identify differentially expressed (DE) genes. At non-mist condition, only around 1% of the genes were differentially expressed between physiologically matured red wheat and white wheat while the rate had a 10-fold increase after 48 hr misting treatment. Annotation of the DE genes showed signature genes involved in germination process, such as late embryogenesis abundant protein, peroxidase, hydrolase, and several transcription factors. They can be potential key players involved in the underlying genetic networks related to the PHS induction process. Gene Ontology (GO) terms enriched in DE genes were also summarized for each comparison and germination related molecular function and biological process were retrieved.In conclusion, with the population segregating for seed coat color loci, the relationship between seed coat color and alpha-amylase activity were examined using biochemical methods, QTL analysis, and transcriptome profiling. The variation of seed coat color do closely linked with PHS resistance level at all three levels. DE genes and enriched GO terms identified were discussed for their potential role in bridging the gap between seed coat color and PHS resistance.
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