Genetic and environmental factors affecting grain texture in common wheat

Genome-Wide Association Analysis of Grain Hardness in Common Wheat

The grain hardness index (HI) is one of the important reference bases for wheat quality and commodity properties; therefore, it is essential and useful to identify loci associated with the HI in wheat breeding. The grain hardness index of the natural population including 150 common wheat genotypes was measured in this study. The phenotypic data diversity of HI based on four environments and the best linear unbiased prediction (BLUP) was analyzed. The results showed that the grain HI of the natural population ranged from 15.00 to 83.00, the variation range was from 5.10% to 24.44%, and the correlation coefficient was 0.872–0.980. BLUP value was used to grade and assign the grain HI to hard wheat, mixed wheat, and soft wheat, and the assigned phenotypes were used for genome-wide association analysis. Two types of grain hardness index phenotypic values were used for genome-wide association analysis (GWAS) using a 55K SNP array. A total of five significant association loci (p < 0.001) were excavated, among which four loci could be detected in three or more environments. They were distributed on chromosomes 1A and 7D, and the phenotypic contribution rate was 7.52% to 10.66%. A total of 48 sites related to grain hardness were detected by the assignment method, among which five were stable genetic sites, distributed on chromosomes 1A(2), 3B(1), 4B(1), and 7D(1), with phenotypic contribution rates ranging from 7.63% to 11.12%. Of the five loci detected by the assignment method, two stable loci were co-located in the phenotypic mapping results of the hardness index. One of the loci was consistent with previous reports and located on chromosome 1A, and one locus was unreported on chromosome 7D. Therefore, it may be a feasible attempt to use the assignment method to conduct genome-wide association analysis of the grain hardness index. In this study, a total of five genetic loci for grain hardness stability were excavated, and two of the loci were located in the two phenotypic values, two of which were not reported.

Using RT-qPCR, Proteomics, and Microscopy to Unravel the Spatio-Temporal Expression and Subcellular Localization of Hordoindolines Across Development in Barley Endosperm

Hordeum vulgare (barley) hordoindolines (HINs), HINa, HINb1, and HINb2, are orthologous proteins of wheat puroindolines (PINs) that are small, basic, cysteine-rich seed-specific proteins and responsible for grain hardness. Grain hardness is, next to its protein content, a major quality trait. In barley, HINb is most highly expressed in the mid-stage developed endosperm and is associated with both major endosperm texture and grain hardness. However, data required to understand the spatio-temporal dynamics of HIN transcripts and HIN protein regulation during grain filling processes are missing. Using reverse transcription quantitative PCR (RT-qPCR) and proteomics, we analyzed HIN transcript and HIN protein abundance from whole seeds (WSs) at four [6 days after pollination (dap), 10, 12, and ≥20 dap] as well as from aleurone, subaleurone, and starchy endosperm at two (12 and ≥20 dap) developmental stages. At the WS level, results from RT-qPCR, proteomics, and western blot showed a continuous increase of HIN transcript and HIN protein abundance across these four developmental stages. Miroscopic studies revealed HIN localization mainly at the vacuolar membrane in the aleurone, at protein bodies (PBs) in subaleurone and at the periphery of starch granules in the starchy endosperm. Laser microdissetion (LMD) proteomic analyses identified HINb2 as the most prominent HIN protein in starchy endosperm at ≥20 dap. Additionally, our quantification data revealed a poor correlation between transcript and protein levels of HINs in subaleurone during development. Here, we correlated data achieved by RT-qPCR, proteomics, and microscopy that reveal different expression and localization pattern of HINs in each layer during barley endosperm development. This indicates a contribution of each tissue to the regulation of HINs during grain filling. The effect of the high protein abundance of HINs in the starchy endosperm and their localization at the periphery of starch granules at late development stages at the cereal-based end-product quality is discussed. Understanding the spatio-temporal regulated HINs is essential to improve barley quality traits for high end-product quality, as hard texture of the barley grain is regulated by the ratio between HINb/HINa.

Influence of Gene Expression on Hardness in Wheat

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.

Changes in the starch-protein interface depending on common wheat grain hardness revealed using atomic force microscopy

The atomic force microscope tip was used to progressively abrade the surface of non-cut starch granules embedded in the endosperm protein matrix in grain sections from wheat near-isogenic lines differing in the puroindoline b gene and thus, hardness. In the hard near-isogenic wheat lines, starch granules exhibited two distinct profiles corresponding either to abrasion in the surrounding protein layer or the starch granule. An additional profile, only identified in soft lines, revealed a marked stop in the abrasion at the protein-starch transition similar to a lipid interface playing a lubricant role. It was related to the presence of both wild-type puroindolines, already suggested to act at the starch-protein interface through their association with polar lipids. This study revealed, for the first time, in situ differences in the nano-mechanical properties at the starch-protein interface in the endosperm of wheat grains depending on the puroindoline allelic status.

Relationships between wheat grain physical characteristics studied through near-isogenic lines with distinct puroindoline-b allele

Genetic (different forms of puroindoline-b) and environment (through variations in vitreousness), have important effects on wheat grain mechanical properties. The two methods of hardness measurements (NIRS, SKCS) do not give the same information. Bread wheat near-isogenic lines differing in hardness, due to distinct puroindoline-b alleles (the wild type, Pinb-D1a, or the mutated forms, Pinb-D1b or Pinb-D1d), were grown for three years in seven sites and under two nitrogen fertilization levels, to study genetic and environmental effects on grain mechanical properties. Two methods, Near-Infrared Reflectance Spectroscopy (NIRS) and Single Kernel Characterization System (SKCS), currently used for grain hardness characterization, were carried out. Grain vitreousness, which is known to affect the grain mechanical behavior but is generally not studied, was also measured, as well as three other characters (Thousand Grain Weight, Test Weight and protein content). The relationships between the different characters were studied. Results revealed a clear effect of the different Pinb-D1 alleles on NIRS hardness, and a marked impact of the environmental conditions on vitreousness. SKCS hardness was influenced by both Pinb-D1 alleles and environmental conditions. The relationship between SKCS and NIRS hardness was strong when considering together soft and hard genotypes, but moderate within a class of genetical hardness. Vitreousness had only a weak effect on NIRS hardness, whereas vitreousness and SKCS values were strongly correlated, with two distinct regressions for soft and hard genotypes. Vitreousness was positively related to protein content, especially in the case of hard genotypes, which were able to reach high vitreousness values never observed for soft genotypes.

Chromosome 5H of Hordeum species involved in reduction in grain hardness in wheat genetic background

Grain hardness is an important factor affecting end-use quality in wheat. Mutations of the puroindoline genes, which are located on chromosome 5DS, control a majority of grain texture variations. Hordoindoline genes, which are the puroindoline gene homologs in barley, are located on chromosome 5HS and are also responsible for grain texture variation. In this study, we used three types of wheat-barley species (Hordeum vulgare, H. vulgare ssp. spontaneum, and H. chilense) chromosome addition lines and studied the effect of chromosome 5H of these species on wheat grain characteristics. The 5H chromosome addition lines showed significantly lower grain hardness and higher grain weight than the corresponding wheat parents. The effect of enhancing grain softness was largest in the wheat-H. chilense line regardless of having an increase in grain weight similar to those in the wheat-H. vulgare and wheat-H. spontaneum lines. Our results indicated that chromosome 5H of the Hordeum species plays a role in enhancing grain softness and increasing grain weight in the wheat genetic background, and the extent of effect on grain hardness depends on the type of Hordeum species. Protein analysis of hordoindolines indicated that profiles of 2D-electrophoresis of hordoindolines were different among Hordeum species and hordoindolines in the addition lines appeared to be most abundant in wheat-H. chilense line. The differences in enhancing grain softness among the Hordeum species might be attributed to the quantity of hordoindolines expressed in the 5H chromosome addition lines. These results suggested that the barley hordoindolines located on chromosome 5HS play a role in reducing grain hardness in the wheat genetic background.

Chromosomal loci associated with endosperm hardness in a malting barley cross

A breeding objective for the malting barley industry is to produce lines with softer, plumper grain containing moderate protein content (9-12%) as they are more likely to imbibe water readily and contain more starch per grain, which in turn produces higher levels of malt extract. In a malting barley mapping population, 'Arapiles' × 'Franklin', the most significant and robust quantitative trait locus (QTL) for endosperm hardness was observed on the short arm of chromosome 1H, across three environments over two growing seasons. This accounted for 22.6% (Horsham 2000), 26.8% (Esperance 2001), and 12.0% (Tarranyurk 2001) of the genetic variance and significantly increased endosperm hardness by 2.06-3.03 SKCS hardness units. Interestingly, Arapiles and Franklin do not vary in Ha locus alleles. Therefore, this region, near the centromere on chromosome 1H, may be of great importance when aiming to manipulate endosperm hardness and malting quality. Interestingly, this region, close to the centromere on chromosome 1H, in our study, aligns with the region of the genome that includes the HvCslF9 and the HvGlb1 genes. Potentially, one or both of these genes could be considered to be candidate genes that influence endosperm hardness in the barley grain. Additional QTLs for endosperm hardness were detected on chromosomes 2H, 3H, 6H and 7H, confirming that the hardness trait in barley is complex and multigenic, similar to many malting quality traits of interest.

Grain hardness: a major determinant of wheat quality

Wheat quality, a complex term, depends upon intentional use for unambiguous products. The foremost determinants of wheat quality are endosperm texture (grain hardness), protein content and gluten strength. Endosperm texture in wheat is the single most important and defining quality characteristic, as it facilitates wheat classification and affects milling, baking and end-use quality. Various techniques used for grain hardness measurement are classified into diverse groups according to grinding, crushing and abrasion. The most extensively used methods for texture measurement are PSI, NIR hardness, SKCS, pearling index, SDS-PAGE and PCR markers. Friabilin is a 15 kDa endosperm specific protein associated with starch granules of wheat grain and is unswervingly related to grain softness. Chemically, it is a concoction of different polypeptides, primarily puroindolines; Pin a and Pin b. Hardness (Ha) locus of chromosome 5DS makes the distinction between soft and hard classes of wheat. Some additional modifying genes are also present which contribute to the disparity within wheat classes. Numerous allelic mutations in Pin have been reported and their relation to end product quality has been established. This treatise elaborates the consequence of grain hardness in wheat eminence.

The determinants of grain texture in cereals

Kernel hardness is an important agronomic trait that influences end-product properties. In wheat cultivars, this trait is determined by the Puroindoline a (Pina) and Puroindoline b (Pinb) genes, located in the Hardness locus (Ha) on chromosome 5DS of the D genome. Wild type alleles code puroindoline a (PINA) and puroindoline b (PINB) proteins, which form a 15-kDa friabilin present on the surface of water-washed starch granules. Both the proteins are accumulated in the starch endosperm cells and aleurone of the mature kernels. Puroindoline-like genes coding puroindoline-like proteins in the starch endosperm occur in some of the genomes of Triticeae and Aveneae cereals. Orthologs are present in barley, rye and oats. However, some genomes of these diploid and polyploid cereals, like that of Triticum turgidum var. durum (AABB) lack the puroindoline genes, having a very hard kernel texture. The two wild type alleles in opposition (dominant loci) control the soft phenotype. Mutation either in Pina or Pinb or in both leads to a medium-hard or hard kernel texture. The most frequent types of Pin mutations are point mutations within the coding sequence resulting in the substitution of a single amino acid or a null allele. The latter is the result of a frame shift determined by base deletion or insertion or a one-point mutation to the stop codon. The lipid-binding properties of the puroindolines affect not only the dough quality but also the plants' resistance to pathogens. Genetic modification of cereals with Puroindoline genes and/or their promoters enable more detailed functional analyses and the production of plants with the desired characteristics.

Starch-bound 2S proteins and kernel texture in einkorn, Triticum monococcum ssp monococcum

The starch granule proteins from 113 einkorn wheat (Triticum monococcum ssp monococcum) accessions were analyzed by acidic, polyacrylamide gel electrophoresis (A-PAGE), and two-dimensional A-PAGE x SDS-PAGE. All accessions were confirmed to contain equal amounts of two polypeptide chains corresponding to puroindoline B (Pin-B), as well as a prominent component plus a faint band corresponding to puroindoline A (Pin-A). When compared with soft-textured common wheat, "monococcum" accessions showed an increase of 3.2- and 2.7-fold in Pin-A and Pin-B levels on the starch granules, respectively. In addition, all accessions contained a novel component of the 2S super-family of seed proteins named Einkorn Trypsin Inhibitor (ETI), which was found to be encoded as a pre-protein 148 residues long. Wild-type ETI encoded by allele Eti-A(m) 1a and "valine-type" ETI encoded by allele Eti-A(m) 1b, which occurred in 107 and six einkorn accessions, respectively, were found to accumulate on starch granules as a mature protein of 121 amino acids with a hydrophobic central domain. The einkorn accessions exhibited an average SKCS index as low as -2.05 +/- 11.4, which is typical of extra-soft kernels. The total surface area of starch granules in "monococcum" wheat, as determined by visual assessments in counting chambers, was estimated at 764 mm(2)/mg of starch, and was about 1.5 times higher than that for common wheat. The results are discussed in relation to the identification of factors that cause the extra-soft texture of einkorn kernels.