Segregation analysis indicates that Puroindoline b-2 variants 2 and 3 are allelic in Triticum aestivum and that a revision to Puroindoline b-2 gene symbolization is indicated

Genomics-Enabled Analysis of Puroindoline b2 Genes Identifies New Alleles in Wheat and Related Triticeae Species

Kernel hardness is a key trait of wheat seeds, largely controlled by two tightly linked genes Puroindoline a and b (Pina and Pinb). Genes homologous to Pinb, namely Pinb2, have been studied. Whether these genes contribute to kernel hardness and other important seed traits remains inconclusive. Using the high-quality bread wheat reference genome, we show that PINB2 are encoded by three homoeologous loci Pinb2 not syntenic to the Hardness locus, with Pinb2-7A locus containing three tandem copies. PINB2 proteins have several features conserved for the Pin/Pinb2 phylogenetic cluster but lack a structural basis of significant impact on kernel hardness. Pinb2 are seed-specifically expressed with varied expression levels between the homoeologous copies and among wheat varieties. Using the high-quality genome information, we developed new Pinb2 allele specific markers and demonstrated their usefulness by 1) identifying new Pinb2 alleles in Triticeae species; and 2) performing an association analysis of Pinb2 with kernel hardness. The association result suggests that Pinb2 genes may have no substantial contribution to kernel hardness. Our results provide new insights into Pinb2 evolution and expression and the new allele-specific markers are useful to further explore Pinb2's contribution to seed traits in wheat.

Sequence Diversity and Identification of Novel Puroindoline and Grain Softness Protein Alleles in Elymus, Agropyron and Related Species

The puroindoline proteins, PINA and PINB, which are encoded by the Pina and Pinb genes located at the Ha locus on chromosome 5D of bread wheat, are considered to be the most important determinants of grain hardness. However, the recent identification of Pinb-2 genes on group 7 chromosomes has stressed the importance of considering the effects of related genes and proteins. Several species related to wheat (two diploid Agropyron spp., four tetraploid Elymus spp. and five hexaploid Elymus and Agropyron spp.) were therefore analyzed to identify novel variation in Pina, Pinb and Pinb-2 genes which could be exploited for the improvement of cultivated wheat. A novel sequence for the Pina gene was detected in Elymus burchan-buddae, Elymus dahuricus subsp. excelsus and Elymus nutans and novel PINB sequences in Elymus burchan-buddae, Elymus dahuricus subsp. excelsus, and Elymus nutans. A novel PINB-2 variant was also detected in Agropyron repens and Elymus repens. The encoded proteins detected all showed changes in the tryptophan-rich domain as well as changes in and/or deletions of basic and hydrophobic residues. In addition, two new AGP sequences were identified in Elymus nutans and Elymus wawawaiensis. The data presented therefore highlight the sequence diversity in this important gene family and the potential to exploit this diversity to modify grain texture and end-use quality in wheat.

Molecular characterization of the puroindoline-a and b alleles in synthetic hexaploid wheats and in silico functional and structural insights into Pina-D1

Kernel hardness determined by two tightly linked Puroindoline genes, Pina-D1 and Pinb-D1, located on chromosome 5DS define commercially important characteristics, uses, major grades and export markets of wheat. This study was conducted to characterize Pina-D1 and Pinb-D1 alleles, in fifteen synthetic hexaploid wheats (SHWs) and its relation with grain hardness. Additionally, in silico functional analyses of puroindoline-a protein was conducted for better understanding of their putative importance in grain quality. Six different Pina-D1 alleles were identified in the SHWs, of which three i.e. Pina-D1a, Pina-D1c and Pina-D1d were already known whereas the other three had new sequence polymorphisms and were designated as Pina-D1w, Pina-D1x and Pina-D1y. Three different Pinb-D1 alleles were identified which have been reported earlier and no novel sequence polymorphism was detected. It was concluded that despite some primary, secondary and 3D structure variations, ligand binding sites and disulfide bonds discrepancies, the main features of PINA, i.e. the tryptophan-rich domain, the cysteine backbone, the signal peptide and basic identity of the proteins were all conserved. In silico analysis showed that puroindolines having binding capacity with small parts of prolamins causing celiac disease of human, however their potential role is not obvious. Conclusively, the new Pina-D1 alleles with modest effect on grain hardness, and insight into their functional and structural characteristics are important findings and their putative role in celiac disease require further studies to validate.

The house mouse (Mus musculus L.) exerts strong differential grain consumption preferences among hard red and white spring wheat (Triticum aestivum L.) varieties in a single-elimination tournament design

Wheat (Triticum aestivum L.) plays a central role in the health and nutrition of humans. Yet, little is known about possible flavor differences among different varieties. We have developed a model system using the house mouse (Mus musculus L.) to determine feeding preferences as a prelude to extending results to human sensory analysis. Here, we examine the application of a single-elimination tournament design to the analysis of consumption preferences of a set of hard red and hard white spring wheat varieties. A single-elimination tournament design in this case pairs 2 wheat varieties and only 1 of the 2 is advanced to further tests. Preferred varieties were advanced until an overall "winner" was identified; conversely, less desirable varieties were advanced such that an overall "loser" was identified. Hollis and IDO702 were the winner and loser, respectively, for the hard red varieties, and Clear White 515 and WA8123 were the winner and loser, respectively, for the hard white varieties. When using the more powerful protocol of 14 mice and a 4-d trial, differences in mean daily consumption preferences of 2 varieties were separated at P-values as small as 2 × 10(-8) . The single-elimination tournament design is an efficient means of identifying the most and least desirable varieties among a larger set of samples. One application for identifying the 2 extremes in preference within a group of varieties would be to use them as parents of a population to identify quantitative trait loci for preference.