Background: The low molecular weight glutenin subunits (LMW-GS) of wheat have great effects on food processing quality, but the resolution of LMW-GS and the scoring of their alleles by direct analysis of proteins are difficult due to the larger number of expressed subunits and high similarity of DNA sequences. It is important to identify and classify the LMW-GS genes in order to recognize the LMW-GS alleles clearly and develop the functional markers. Methods: The LMW-GS genes registered in GenBank were searched at NCBI, and 593 Glu-3 genes with complete coding sequences were obtained, including 146 Glu-A3, 136 Glu-B3, and 311 Glu-D3. Sequence analysis and characterization of DNA and deduced amino acids were performed using the software DNAman. Results: The alignment and classification showed that there were at least 9 genes with 69 allelic variants at the Glu-A3 locus, 11 genes with 64 allelic variants at the Glu-B3 locus, and 10 genes with 96 variants at the Glu-D3 locus, respectively. Furthermore, the specificity of some Glu-3 genes and their variations was analyzed. Conclusions: The results were beneficial to understanding the LMW-GS genes fully and to developing the functional markers and will provide a theoretical reference for the quality improvement of wheat variety.

Low Molecular Weight Glutenin Subunits (LMW-GS) proteins have great effects on the end-use quality of bread wheat and are difficult to differentiate directly. It is very important to characterize and classify LMW-GS genes systematically. In this paper, 692 complete Glu-3 gene sequences were retrieved from GenBank and were grouped based on their sequence characters and variations. Based on the characters of their N-terminal sequences, these genes were classified into two types, LMW-m and LMW-i, of which LMW-m genes were further classified into three sub-types based on their first amino acid (AA) (LMW-M, LMW-V and LMW-I). Based on the first seven or eight AA variations in the N-terminal sequence, LMW-GS Glu-3 genes were classified into 16 types, namely LMW-N1 to LMW-N16. Based on the last 10 AA variations in the C-terminal, the Glu-3 genes were classified into 22 types, designated as LMW-C1 to LMW-C22. Based on the number and distribution of cysteines, the Glu-3 genes classified into 22 types included 7 conventional types with eight cysteines and 15 variant types with seven or nine cysteines. In addition, two new Glu-A3 genes (GluA-10 and GluA-11) were identified based on their sequence homology, and the connection between different classification methods was analyzed briefly. The results provide insight into the nature of the Glu-3 gene family and are valuable for molecular marker-assisted selection of end-use quality traits in wheat improvement.

Background: Grain length is a key determinant of yield and quality in barley (Hordeum vulgare L.) and is typically governed by complex quantitative traits. Methods: In this study, a diverse natural population comprising 198 barley accessions was evaluated across two years to investigate the genetic basis of grain length. Results: Phenotypic analysis revealed continuous variation with near-normal distribution, indicating polygenic control. Genome-wide association study (GWAS) identified 84 stable single nucleotide polymorphism (SNP) loci significantly associated with grain length, predominantly enriched on chromosome 7. RNA sequencing (RNA-seq) was conducted using two contrasting genotypes at four developmental stages. Differentially expressed genes (DEGs) were mainly enriched in structural constituent of chromatin, protein heterodimerization activity, and the starch and sucrose metabolism. Integration of GWAS and RNA-seq identified 7 key candidate genes seven key candidate genes, including LOC123412467, LOC123408579, LOC123407599, LOC123410619, LOC123410954, LOC123411868, and LOC123426274. Sequence variation analysis further revealed functional polymorphisms, including non-synonymous mutations. The sequencing results show that LOC123412467 and LOC123410619 exhibited consistent allelic variation between long-grain and short-grain accessions, while LOC123426274 displayed stable differential expression across developmental stages, indicating their potential roles as key genes controlling grain length. Conclusions: Collectively, these findings suggest that chromosome 7 contains major regulatory loci controlling barley grain length and demonstrate that integrative multi-omics analysis is an effective strategy for identifying high-confidence candidate genes associated with complex agronomic traits. This study provides valuable insights into the genetic basis of grain length and offers key candidate genes for barley molecular breeding.

Leaf length is an important component of barley plant architecture, but its genetic basis remains incompletely understood. Here, we integrated genome-wide association study (GWAS), RNA sequencing (RNA-seq), and sequence variation analyses to investigate the genetic and transcriptional basis of barley leaf-length variation. A panel of 198 barley accessions was evaluated across two growing seasons, and contrasting long- and short-leaf accessions were subjected to RNA-seq. GWAS identified a major association signal on chromosome 4H, with a core interval of approximately 941.73 kb defined by local linkage disequilibrium analysis. RNA-seq identified 3507 and 3878 differentially expressed genes (DEGs) in flag leaves and second leaves below the flag leaf, respectively, including 2648 shared DEGs. Functional enrichment and gene set enrichment analyses indicated differences in developmental, signaling, metabolic, and temperature-responsive processes. Integration of GWAS and RNA-seq data prioritized three candidate genes, LOC123447426, LOC123449930, and LOC123450878, with different levels of supporting evidence. LOC123447426 and LOC123450878 were located within the core association interval, whereas LOC123449930 was located in the extended candidate-screening region, approximately 2.2 Mb from the lead SNP. LOC123447426 showed the strongest integrated support, with evidence from GWAS and differential expression in both leaf positions. Sequence variation, and qRT-PCR analyses provided further support for these candidates. Overall, this study prioritizes a major chromosome 4H region and three candidate genes associated with barley leaf-length variation, providing a basis for further investigation of their potential roles in leaf development. However, the current evidence does not establish causal relationships between these genes and leaf-length variation, and their biological functions remain to be experimentally verified.