Puroindoline (Pina and Pinb) genes control grain texture or hardness in wheat. Wild-type/soft alleles lead to softer grain while a mutation in one or both of these genes results in a hard grain. Variation in hardness in genotypes with identical Pin alleles (wild-type or mutant) is known but the molecular basis of this is not known. We now report the identification of wheat genotypes with hard grain texture and wild-type/soft Pin alleles indicating that hardness in wheat may be controlled by factors other than mutations in the coding region of the Pin genes. RNA-Seq analysis was used to determine the variation in the transcriptome of developing grains of thirty three diverse wheat genotypes including hard (mutant Pin) and soft (wild type) and those that were hard without having Pin mutations. This defined the role of pin gene expression and identified other candidate genes associated with hardness. Pina was not expressed in hard wheat with a mutation in the Pina gene. The ratio of Pina to Pinb expression was generally lower in the hard non mutant genotypes. Hardness may be associated with differences in Pin expression and other factors and is not simply associated with mutations in the PIN protein coding sequences.

A large portion of the global wheat crop is milled to produce flour for use in the production of foods such as bread. Pressure to increase food supplies sustainably can be address directly by reducing post-harvest losses during processes such as flour milling. The recovery of flour in the milling of wheat is genetically determined but difficult to assess in wheat breeding due to the requirement for a large sample. Here we report the discovery that human selection for altered expression of putative cell adhesion proteins is associated with wheats that give high yields of flour on milling. Genes encoding fasciclin-like arabinogalactan proteins are expressed at low levels in high milling wheat genotypes at mid grain development. Thirty worldwide wheat genotypes were grouped into good and poor millers based flour yield obtained from laboratory scale milling of mature seeds. Differentially expressed genes were identified by comparing transcript profiles at 14 and 30 days post anthesis obtained from RNA-seq data of all the genotypes. Direct selection for genotypes with appropriate expression of these genes will greatly accelerate wheat breeding and ensure high recoveries of flour from wheat by resulting in grains that break up more easily on milling.

Wheat is the leading crop in the temperate world with its ability to adapt to different environments allowing it to be grown in regions with diverse climatic and environmental conditions. Wheat quality improvement is one of the major objectives of wheat breeding. Breeding for the desired combination of quality attributes is most effective when genes regulating the desired attributes are known. The major objective of this study was to associate gene expression in the developing seed with the quality of wheat: grain hardness, flour yield and the nutritive value of the grain. RNAsequencing data obtained from 35 diverse worldwide wheat genotypes at two stages of seed development, 14 and 30 days post anthesis (DPA), were used in this study. One of the challenges in next generation sequencing (NGS) data analysis, in polyploid plants such as wheat, is the difficulties in accurate identification of the allele-specific gene expression. To overcome this challenge, a protocol was developed to identify allele-specific/sub-genome-specific gene IX Financial support This project was jointly supported by the Department of Agriculture and Fisheries,