Nutritional Genomic Approach for Improving Grain Protein Content in Wheat

Abstract

Grain protein content (GPC) is a key aspect of grain quality, a major determinant of the flour functional properties and grain nutritional value of bread wheat. Exploiting diverse germplasms to identify genes for improving crop performance and grain nutritional quality is needed to enhance food security. Here, we evaluated GPC in a panel of 255 Triticum aestivum L. accessions from 27 countries. GPC determined in seeds from three consecutive crop seasons varied from 8.6 to 16.4% (11.3% on average). Significant natural phenotypic variation in GPC among genotypes and seasons was detected. The population was evaluated for the presence of the trait-linked single nucleotide polymorphism (SNP) markers via a genome-wide association study (GWAS). GWAS analysis conducted with calculated best linear unbiased estimates (BLUEs) of phenotypic data and 90 K SNP array using the fixed and random model circulating probability unification (FarmCPU) model identified seven significant genomic regions harboring GPC-associated markers on chromosomes 1D, 3A, 3B, 3D, 4B and 5A, of which those on 3A and 3B shared associated SNPs with at least one crop season. The verified SNP–GPC associations provide new promising genomic signals on 3A (SNPs: Excalibur_c13709_2568 and wsnp_Ku_c7811_13387117) and 3B (SNP: BS00062734_51) underlying protein improvement in wheat. Based on the linkage disequilibrium for significant SNPs, the most relevant candidate genes within a 4 Mbp-window included genes encoding a subtilisin-like serine protease; amino acid transporters; transcription factors; proteins with post-translational regulatory functions; metabolic proteins involved in the starch, cellulose and fatty acid biosynthesis; protective and structural proteins, and proteins associated with metal ions transport or homeostasis. The availability of molecular markers within or adjacent to the sequences of the detected candidate genes might assist a breeding strategy based on functional markers to improve genetic gains for GPC and nutritional quality in wheat.

GWAS in a Collection of Bulgarian Old and Modern Bread Wheat Accessions Uncovers Novel Genomic Loci for Grain Protein Content and Thousand Kernel Weight

“…The observed moderate to high values of broad-sense heritability and the consistency of trait records evidenced by the significant correlations between the crop seasons suggest that a considerable part of the variation is due to inherent genetic differences among the accessions. These results agree with similar findings in bread and durum wheat for GPC [ 19 , 25 , 27 , 40 ], and TKW [ 13 , 41 ]. Given that the panel contains historical and contemporary varieties released or collected between 1925 and 2010, it is possible that the recorded genetic variance—especially for TKW—is inflated.…”

“…This study shows that a large proportion (89%) of the accessions have protein above 12%, and are suitable for preparing leavened breads [ 2 ]. The average grain protein values (13.4%) are similar to or higher than the reported information on protein contents in other bread wheat collections [ 19 , 27 , 28 , 31 , 34 ]. Additional research revealed that some accession sets had greater protein values (up to 20%), demonstrating the impact of genotype-by-environment interactions [ 22 , 23 , 33 ].…”

“…The idea that the older germplasm had superior yield-related metrics than the more recent varieties was also not supported by the observed variability in mean TKW values of SP2-accessions across the growing seasons. One likely reason is that a lot of contemporary Bulgarian varieties are either descended from old accessions, or have highly productive and high-protein Russian and Serbian ancestors in their pedigrees as Table S1 and the research by Kartseva et al [ 27 ] show. These results suggest that wheat breeders have managed to construct improved varieties in terms of the studied traits.…”

“…Identifying marker-trait associations (MTAs) or quantitative trait nucleotides (QTNs) can make it easier for breeders to choose the best genotypes, reduce the breeding cycle, and achieve higher genetic gains. A number of recent GWAS studies reported genomic regions associated with GPC and yield components [ 14 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 ].…”

“…The association panels employed in these studies varied in terms of diversity level, genetic relatedness, and the nature of accessions. For instance, Kartseva et al [ 27 ] used a diverse population of 255 accessions from 27 countries on five continents, and revealed novel stable genomic regions harboring GPC-associated markers on chromosomes 3A and 3B. QTL hotspots containing 165 significant MTAs for quality and agronomic traits were mapped on almost all chromosomes in an association panel of 170 diverse landraces from the Mediterranean region [ 31 ].…”