Comparison and Classification of LMW-GS Genes at Glu-3 Loci of Common Wheat
Wheat Research Institute, Henan Academy of Agricultural Sciences (HAAS), Zhengzhou 450002, China
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Author to whom correspondence should be addressed.
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These authors contributed equally to this work.
Genes 2025, 16(1), 90; https://doi.org/10.3390/genes16010090
Submission received: 12 December 2024
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Revised: 31 December 2024
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Accepted: 2 January 2025
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Published: 16 January 2025
(This article belongs to the Section Plant Genetics and Genomics)
Abstract
: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.
1. Introduction
Wheat flour has the distinctive quality properties to form the gluten network, which is suitable to make a lot of foods such as bread, steamed bread, noodles, cake, etc. [1,2]. Osborne first classified the grain proteins of wheat into four types based on their solubility, i.e., albumin dissolving in water or dilute buffer, globulin dissolving in salt solution, prolamin dissolving in 70–90% alcohol, and glutenin dissolving in dilute acid or dilute alkali [3]. The glutenin was further classified into high molecular weight subunits (HMW-GS) and low molecular weight subunits (LMW-GS), which contributed to the fundamental aspects of dough quality, for example, viscoelasticity and extensibility [4,5,6]. The proper viscoelasticity and extensibility were the basis to make good bread; thus, HMW-GS and LMW-GS alleles became the main targets of molecular marker-assisted selection in the quality improvement of wheat variety [7,8]. Because HMW-GS had a low gene copy number and clear resolution by gel electrophoresis, their allelic variation and relationship with wheat quality have been studied extensively [9,10,11], and the molecular markers based on polymerase chain reaction (PCR) were available to distinguish the important Glu-1 alleles [12,13,14]. However, differentiating proteins and scoring alleles by direct analysis of LMW-GS were more difficult due to the larger number of expressed subunits and their overlapping mobility with the abundant gliadin proteins [15,16]. In view of this, the function of individual LMW-GS in the determination of wheat quality was less clear, though some alleles are clearly beneficial or detrimental [17,18,19]. It is very important to characterize LMW-GS genes and design functional markers for identifying different LMW-GS alleles [20].
Most LMW-GS are encoded by the complex Glu-3 loci (Glu-A3, Glu-B3, and Glu-D3) on the short arms of group 1 chromosomes of wheat [21,22]. Gupta and Shepherd detected 20 different banding patterns of LMW-GS in bread wheat cultivars: 6 from Glu-A3, 9 from Glu-B3, and 5 from Glu-D3 [23]. Twenty-six different LMW subunits were identified in one bread wheat cultivar according to the N-terminal amino acid sequences [24]. Based on the first N-terminal amino acid of mature protein, LMW-GS were classified into three types: LMW-m, LMW-s, and LMW-i, corresponding to methionine, serine, and isoleucine, respectively [25,26]. LMW-GS were further divided into 12 groups by Ikeda et al. according to deduced amino acid sequences and, in particular, the number and position of cysteine residues available for inter-molecular disulphide bond formation [27,28]. Long et al. (2005) retrieved 69 known LMW-GS genes from GenBank and classified them into nine groups by the deduced amino acid sequence of the highly conserved N-terminal domain [29]. Zhao et al. identified 6 LMW-GS genes, including 12 haplotypes at the Glu-D3 locus, and made a clear distinction between the subunits, coding genes, alleles, and allelic variants (haplotypes) of LMW proteins for the first time [30,31]. Wang et al. cloned 6 Glu-B3 genes, including 26 allelic variants, and 5 Glu-A3 genes, including 19 allelic variations, respectively [32,33]. In a survey of the LMW-GS genes at NCBI (National Centre for Biotechnology Information, www.ncbi.nlm.nih.gov), a total of 1142 LMW-GS genes and gene fragments (partial genes) were obtained, of which there were 593 Glu-3 genes with complete coding sequences and known loci, including 146 Glu-A3 genes, 136 Glu-B3 genes, and 311 Glu-D3 genes [6,27,34,35,36]. However, the detailed information of Glu-3 genes and their allelic variations was somewhat mixed and confused due to the large number and high homology. In the paper, we try to make a thorough comparison between the Glu-3 genes of common wheat and sort them out according to the similarity of DNA and deduced AA sequences, which will provide a theoretical reference for the quality improvement of wheat breeding.
2. Materials and Methods
The LMW-GS gene sequences used in the paper were all registered in GenBank, which were searched at NCBI (National Centre for Biotechnology Information, www.ncbi.nlm.nih.gov, accessed on 15 July 2024) by means of the Glu-A3 genes, Glu-B3 genes, and Glu-D3 genes. All the 593 Glu-3 gene accessions were listed in Table 1 and Table 2. Sequence analysis and characterization of DNA and deduced amino acids were performed using software DNAman V6.0.3.99 (http://www.lynnon.com).
3. Results
By searching in Genbank, a total of 1142 Glu-3 genes and partial genes were obtained, of which there were 593 Glu-3 genes with complete coding regions and known loci, including 146 Glu-A3 gene sequences, 136 Glu-B3 gene sequences, and 311 Glu-D3 gene sequences. They were compared and grouped, respectively, based on their sequence variations of DNA and deduced amino acids. The results were as follows:
3.1. Composition and Variation of LMW-GS Genes at the Glu-D3 Locus
Glu-D3 genes were first identified and classified systematically by Zhao et al. and a total of 6 Glu-D3 genes with 12 allelic variations were characterized [30,31]. On this basis, the 311 Glu-D3 genes with complete coding sequences from GenBank were compared by means of DNAman and grouped according to their similarity of DNA and deduced AA. The result showed that the Glu-D3 locus contained at least 10 LMW-GS genes, including about 96 allelic variants (Table 1 and Table 2), of which the four newly sorted genes (GluD3-7 to GluD3-10) presented a base similarity of ≤96.0% between each other and with the other six genes. The base similarity between allelic variants of each gene was presented in Table 2. Among the 10 genes, GluD3-2 had the most abundant variations, including 31 at the base level or 25 at the AA level. Then GluD3-1, GluD3-4, and GluD3-6 each had 11, 12, and 14 allelic variations, respectively. GluD3-7 had the least allelic variation, and only one haplotype was found in GenBank. GluD3-7, GluD3-9, and GluD3-10 were all pseudogenes, while GluD3-4, GluD3-6, and GluD3-8 each had one or two pseudogene variants. In addition, a lot of duplicate sequences were found in GenBank, for example, 23 for GluD3-1-1a, 26 for GluD3-2-1a, 43 for GluD3-4-2a, 27 for GluD3-5-1, 30 for GluD3-6-1a, and 32 for GluD3-9-1.
Table 1.
Homology comparison of the representatives of 10 Glu-D3 genes (below diagonal) and their deduced amino acid sequences (above diagonal) (%, irrespective of the sequence length).
Table 1.
Homology comparison of the representatives of 10 Glu-D3 genes (below diagonal) and their deduced amino acid sequences (above diagonal) (%, irrespective of the sequence length).
| Accession | DQ35 7052 | DQ35 7054 | DQ35 7057 | DQ45 7416 | EU18 9096 | DQ45 7420 | EU18 9092 | JQ32 0289 | FJ75 5312 | JF33 9168 |
|---|---|---|---|---|---|---|---|---|---|---|
| DQ357052 | 100 | 78.9 | 78.3 | 82.4 | 77.5 | 78.5 | 77.6 | 78.8 | - | - |
| DQ357054 | 79.9 | 100 | 87.9 | 87.9 | 82.7 | 82.9 | 87.6 | 83.5 | - | - |
| DQ357057 | 78.1 | 88.0 | 100 | 82.7 | 86.7 | 82.2 | 87.6 | 81.8 | - | - |
| DQ457416 | 89.4 | 89.0 | 87.2 | 100 | 82.3 | 85.7 | 84.3 | 86.3 | - | - |
| EU189096 | 80.1 | 80.3 | 81.1 | 83.9 | 100 | 81.8 | 81.9 | 81.1 | - | - |
| DQ457420 | 88.3 | 88.2 | 85.7 | 91.8 | 85.1 | 100 | 92.0 | 92.6 | - | - |
| EU189092 | 84.8 | 93.0 | 91.2 | 89.3 | 81.0 | 93.4 | 100 | 86.7 | - | - |
| JQ320289 | 88.0 | 89.2 | 84.7 | 91.1 | 84.2 | 95.9 | 91.7 | 100 | - | - |
| FJ755312 | 87.3 | 88.3 | 84.3 | 90.7 | 84.1 | 95.0 | 90.5 | 96.0 | 100 | - |
| JF339168 | 82.2 | 838 | 85.4 | 83.7 | 95.1 | 83.7 | 83.4 | 83.4 | 82.9 | 100 |
The representatives are the first allelic variant of each GluD3 gene.
Table 2.
Classification of 311 Glu-D3 genes from GenBank.
| Gene | Haplotype (Allelic Variation) | Notes | ||
|---|---|---|---|---|
| S/N | GenBank Accessions | DNA | AA | |
| GluD3-1 ≧99.6% | 1a | DQ357052(D3-11); FJ755313; JF339162; JX877785; JX877839; JX877858; JX877874; JX877927; JX877940; JX877958; JX877970; JX877986; JX878002; JX878018; JX878033; JX878065; JX878100; JX878172; JX878184; JX878203; KR612284; MG545991; MH347502; | 23 same | 350 |
| 1b | JX877824; | 1 single | ||
| 2a | DQ357053(D3-12); EU189098; JX877890; JX877907; JX878049; JX878114; JX878126; JX878160; MG545992; | 9 same | 351 | |
| 2b | JX878145; | 1 single | ||
| 3–9 | AB062865; AB062866; AB062867; KR612283; KR612285; KR612286; KR612287; | 7 singles | 321–350 | |
| GluD3-2 ≧99.3% | 1a | DQ357054(D3-21); JX877783; JX877821; JX877838; JX877872; JX877905; JX877955; JX877968; JX877984; JX878000; JX878017; JX878032; JX878047; JX878063; JX878112; JX878124; JX878169; JX878200; KJ152532; KJ152533; KR612292; MH347500; KC222073; KC222075; KC222116; MN744871; | 26 same | 307 |
| 1b–1d | JX877937; KJ152534; KJ152538; | 3 singles | 307 | |
| 2a | DQ357055(D3-22); JF339160; JX877804; JX877888; KC222089; | 5 same | ||
| 2b | KJ152537; | 1 single | ||
| 3a | DQ357056(D3-23); AB062875; FJ755315; FJ755322; JX877856; JX877925; JX878098; JX878181; MG545990; KC222110; KC222119; KC222121; | 12 same | 304 | |
| 3b–3c | AY299485; EU189094; | 2 singles | ||
| 4–24 | AY263369; FJ172533; FJ615309; FJ615310; FJ615311; JQ320291; JQ796685; JQ796686; JQ796688; JQ796690; JX878083; KF020663; KF020664; KF020665; KJ152535; KJ152536; KR612288; KR612289; KR612290; KR612291; MG545996; | 21 singles | 304–308 | |
| 25 | KJ152539; | 1 single | Pseudo | |
| GluD3-3 ≧98.4% | 1 | DQ357057(D3-31); JF339167; JX877790; JX877828; JX877841; JX877878; JX877894; JX877912; JX877944; JX877961; JX877976; JX877989; JX878006; JX878037; JX878069; JX878086; JX878206; KR612295; MG545995; MH347499; HQ619911; HQ619917; | 22 same | 354 |
| 2 | DQ357058(D3-32); FJ755316; JF339182; JF339199; JX877862; JX877929; | 6 same | 354 | |
| 3–7 | EU189095; FJ755323; KR612293; KR612294; MG545994; | 5 singles | 354–383 | |
| GluD3-4 ≧98.2% | 1 | DQ457416(D3-41); JX878122; | 2 same | 304 |
| 2a | DQ457417(D3-42); EU189093; KR612296; JF339158; JX877781; JX877802; JX877819; JX877836; JX877870; JX877886; JX877903; JX877923; JX877935; JX877953; JX877966; JX877982; JX877999; JX878015; JX878030; JX878045; JX878061; JX878081; JX878110; JX878142; JX878157; JX878167; JX878179; JX878198; MH347503; JF339174; MN744843; MN744846; MN744858; MN744861; MN744866; MN744869; MN744875; MN744877; MN744888; MN744895; MN744898; MN744904; MN744908; | 43 same | 303 | |
| 2b–2c | AB062872; MG545989; | 2 singles | ||
| 3–4 | DQ457418(D3-43); JX877854; | 2 singles | Pseudo | |
| 5–10 | FJ755314; HM055909; JQ320290; JQ796689; JX878096; R612297; | 6 singles | 299–303 | |
| GluD3-5 ≧98.4% | 1 | EU189096; FJ755310; JF339165; JX877789; JX877810; JX877827; JX877840; JX877861; JX877877; JX877893; JX877911; JX877943; JX877960; JX877975; JX877988; JX878005; JX878021; JX878036; JX878051; JX878068; JX878104; JX878148; JX878205; MG545993; MH347504; JF339181; JF339197; | 27 same | 365 |
| 2–8 | DQ457419(D3-5); AB062851; EU189097; FJ755317; JX878085; KR612298(97.3%); KR612299; | 7 singles | 345–365 | |
| GluD3-6 ≧98.3% | 1a | DQ457420(D3-6); EU189091; JX877800; JX877816; JX877834; JX877851; JX877868; JX877884; JX877900; JX877920; JX877933; JX877950; JX877964; JX877979; JX877996; JX878012; JX878027; JX878042; JX878058; JX878079; JX878107; JX878119; JX878139; JX878154; JX878164; JX878176; JX878195; KR612300; MH347501; AB062873; | 30 same | 298 |
| 1b | JF339155; JF339172; JF339203; | 3 same | ||
| 1c | KR612306; KR612307; | 2 same | ||
| 1d–1e | KR612302; KR612305; | 2 singles | ||
| 2–8 | EU189090(98.6%); FJ755311; JX878094; KR612301; KR612303; KR612304; MG545988; | 7 singles | ||
| 9–10 | FJ755318; JX877778; | 2 singles | Pseudo | |
| GluD3-7 | 1 | EU189092; | 1 single | 288 |
| GluD3-8 ≧99.0% | 1–2 | JQ320289; JQ796687; | 2 singles | 297 |
| 3 | FJ755319; | 1 single | Pseudo | |
| GluD3-9 ≧99.0% | 1 | FJ755312; KR612309; MG545941; JX877801; JX877818; JX877835; JX877853; JX877869; JX877885; JX877902; JX877922; JX877934; JX877952; JX877965; JX877981; JX877998; JX878014; JX878029; JX878044; JX878060; JX878080; JX878095; JX878109; JX878121; JX878141; JX878156; JX878166; JX878178; JX878197; JF339173; JF339188; JX828371; | 32 same | Pseudo |
| 2–4 | JF339157; JX877780; KR612310; | 3 singles | ||
| GluD3-10 100% | 1 | JF339168; JX877812; JX877843; JX877864; JX877990; JX878087; MG545944; | 7 same | Pseudo |
| 2 | JX877829; JX877879; JX877896; JX877913; JX877930; JX877946; JX877962; JX878008; JX878023; JX878039; JX878070; MG545943; | 12 same | ||
| 3 | JX878053; JX878128; MG545945; | 3 same | ||
| 4 | JX878116; JX878151; MG545946; | 3 same | ||
| 5 | MG545942; JX877792; | 2 same | ||
The framed were genes located in the study by alignment.
3.2. Composition and Variation of LMW-GS Genes at the Glu-B3 Locus
The 136 Glu-B3 genes from GenBank were aligned by DNAman and classified based on the study of Wand et al. [32]. In addition to the 7 LMW-GS genes with 26 variants known, another 4 genes (GluB3-8 to GluB3-11) were grouped, which presented the similarity of ≤96.6% between each other and with others (Table 3 and Table 4). The base similarity between allelic variants of each gene was presented in Table 4.
Among the 11 genes, GluB3-4 had the most abundant allelic variants, including 20 at the base level or 17 at the AA level. On the contrary, GluB3-7 had the least, and only one pseudogene was found in GenBank. The very high similarities were found between GluB3-1 and GluB3-5 (99.7%) and between GluB3-3 and GluB3-6 (99.8%). It was interesting that 24 duplicate sequences of the GluB3-7 haplotype were found in GenBank, the most for Glu-B3 genes, suggesting that GluB3-7 was more stable.
3.3. Composition and Variation of LMW-GS Genes at the Glu-A3 Locus
The 146 Glu-A3 genes with complete coding sequences from GenBank were also compared with each other and were grouped based on the study of Wang et al. [33], who identified 5 Glu-A3 genes with 19 allelic variations. The result showed that the Glu-A3 locus contained at least 9 LMW-GS genes, including about 69 allelic variants, of which the four newly sorted genes (GluA3-6 to GluA3-9) showed a base similarity of ≤96.8% (Table 5 and Table 6). The base similarity between allelic variants of each gene was ≧98.9% for GluA3-1, ≧98.2% for GluA3-2, ≧99.6% for GluA3-3, ≧99.2% for GluA3-4, ≧99.8% for GluA3-6, and ≧98.6% for GluA3-8.
Among the 9 genes, GluA3-1 had the most abundant variations, including 22 at the base level or 20 at the AA level. GluA3-2 also had 13 allelic variations, including three pseudogene variations. GluA3-3 had six allelic variants, but all were pseudogenes. GluA3-5, GluA3-7, and GluA3-9 presented the least allelic variation.
4. Discussion
4.1. Characteristics of LMW-GS Genes and Their Deduced AA Sequences
LMW-GS accounts for about one third of the seed storage proteins and has great effects on the end-use quality of wheat [7,8]. Thus, they have received considerable attention from wheat researchers all the time [37]. The sequence analysis showed that the coding regions of LMW-GS genes were not interrupted by introns and were highly conserved at 5′- and 3′-terminal sequences [31]. Each haplotype encoded a highly conserved signal peptide of 20 amino acids and a short N-terminal conserved region with 13 amino acids, followed by an N-terminal repetitive domain and then a C-terminal conserved domain involving three sub-regions of cysteine-rich, glutamine-rich, and final conserved domain. The longest and the shortest LMW glutenin subunits at the Glu-A3, Glu-B3, and Glu-D3 loci were 391/212, 393/257, and 383/288 amino acids, respectively, indicating that the length change of Glu-D3 genes was relatively small. All the deduced LMW-GS showed a typical eight conserved cysteine residues except for a few mutations [38], which were the same as the B-hordeins of barley [39]. It is very useful to characterize the LMW-GS genes because of the difficulties in differentiating the proteins by SDS-PAGE [20].
4.2. Classification and Specificity of LMW-GS Genes at Three Glu-3 Loci
A lot of LMW-GS genes have been cloned and registered in GenBank [34,35,36], but the relationship of them with each other was not very clear. In view of this, 593 Glu-3 genes with complete coding sequences (some with partial or without signal peptide) were obtained from GenBank and compared by means of DNAman, of which the 146 Glu-A3 genes were classified into 9 groups with 69 variations, the 136 Glu-B3 genes were classified into 11 groups with 64 variations, while the 311 Glu-D3 genes were classified into 10 groups with 96 variations. In addition, 47 LMW-GS gene sequences, which loci were unknown before, were newly located in the study, including 7 Glu-A3, 5 Glu-B3, and 35 Glu-D3 genes, because they had 100% base similarity with the related genes (Table 2, Table 4 and Table 6, framed). Obviously, the Glu-D3 locus had the most abundant LMW-GS haplotypes and allelic variations [26]. The similarities of genes were higher between the allelic variants of each gene and relatively lower between the classified groups, but some exceptions were found in the study. For example, there was 99.7% similarity between GluB3-1 (EU369699) and GluB3-5 (EU369706) haplotypes and 99.8% between GluB3-3 (EU369715) and GluB3-6 (EU369711) haplotypes (Table 3), respectively, which were previously classified by Wang et al. [32], indicating that they might have the same origin, no matter at the gene level or variant level. The results indicated that the LMW-GS genes were more complicated than expected and worthy of being studied further.
4.3. Comparison of LMW-GS Genes Between Glu-A3, Glu-B3, and Glu-D3 Loci
Most of the LMW-GS genes were jointly encoded by the Glu-A3, Glu-B3, and Glu-D3 loci, which were located on the short arms of the A1, B1, and D1 wheat chromosomes, respectively [21,22,40]. However, the relationships of LMW-GS genes between the three Glu-3 loci were not very clear, so we carried out a horizontal comparison between Glu-A3, Glu-B3, and Glu-D3 genes. In most cases, the base similarities were lower than 90% between the Glu-A3, Glu-B3, and Glu-D3 genes, but there were some exceptions in the study. For example, the base similarity between GluA3-7, GluB3-8, and GluD3-1 reached 99.1%, 99.2%, and 99.7%, respectively (Supplementary Tables S1–S3), while the similarity of GluA3-6 with GluD3-2 reached 100%. The results interpreted why it was difficult to differentiate the three Glu-3 proteins by SDS-PAGE [15,16] and also presented the importance of characterizing the LMW-GS genes and their allelic variations [20].
5. Conclusions
In summary, 593 complete LMW-GS genes at Glu-3 loci were obtained from GenBank. They were compared systematically by means of DNAman and classified based on their similarities of base and AA sequences. It was found that there were at least 9 genes with 69 allelic variants, 11 genes with 64 allelic variants, and 10 genes with 96 variants, respectively, at the Glu-A3, Glu-B3, and Glu-D3 loci. The base similarities between the Glu-3 genes were generally less than 90%, although the highest could reach to over 99.8%, presenting the specificity and complexity of Glu-3 gene composition. The results are beneficial to understanding the Glu-3 genes comprehensively and will provide a theoretical basis for developing functional markers of LMW-GS genes and for characterizing the LMW-GS genes of wheat-related species such as Triticum monococcum, Triticum dicoccum, Aegilops tauschii, etc.
Supplementary Materials
The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/genes16010090/s1, Table S1: Homology comparison of the representatives of LMW-GS genes between Glu-A3 and Glu-B3 loci (%, irrespective of the sequence length); Table S2: Homology comparison of the representatives of LMW-GS genes between Glu-A3 and Glu-D3 loci (%, irrespective of the sequence length); Table S3: Homology comparison of the representatives of LMW-GS genes between Glu-A3 and Glu-D3 loci (%, irrespective of the sequence length).
Author Contributions
Conceptualization, Y.Z. and X.Z.; methodology, X.Z. and Z.X.; validation, Y.Z. and X.Z.; investigation, Y.Z., X.Z., Z.X., D.Z., and H.Y.; resources, Y.Z. and X.Z.; writing—original draft preparation, Y.Z. and X.Z.; writing—review and editing, Y.Z. and X.Z.; supervision, Y.Z. and Z.X.; project administration, Y.Z. and Y.Z.; funding acquisition, Y.Z. and X.Z. All authors have read and agreed to the published version of the manuscript.
Funding
This research was funded by the Emerging Subject Project of HAAS (2023XK02) and Henan Province Joint Fund (232301420107).
Institutional Review Board Statement
Not applicable.
Informed Consent Statement
Not applicable.
Data Availability Statement
The original contributions presented in this study are included in the article/Supplementary Materials. Further inquiries can be directed to the corresponding author.
Acknowledgments
We would like to thank funders and people for contributing to this study.
Conflicts of Interest
The authors declare no conflicts of interest.
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Table 3.
Homology comparison of the representatives of 11 Glu-B3 genes (below diagonal) and their deduced amino acid sequences (above diagonal) (%, irrespective of the sequence length).
Table 3.
Homology comparison of the representatives of 11 Glu-B3 genes (below diagonal) and their deduced amino acid sequences (above diagonal) (%, irrespective of the sequence length).
| Accession | EU36 9699 | EU36 9704 | EU36 9715 | EU36 9724 | EU36 9706 | EU36 9711 | EU36 9731 | DQ63 0441 | KF02 0660 | JF33 9166 | JX87 7826 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| EU369699 | 100 | 93.8 | 93.9 | 85.3 | 100 | 93.9 | - | 77.9 | 75.5 | - | 83.4 |
| EU369704 | 95.0 | 100 | 92.1 | 84.2 | 93.8 | 92.1 | - | 78.2 | 75.9 | - | 82.7 |
| EU369715 | 94.6 | 94.5 | 100 | 84.9 | 93.9 | 100 | - | 77.0 | 75.9 | - | 83.1 |
| EU369724 | 887 | 88.9 | 89.5 | 100 | 85.3 | 84.9 | - | 79.0 | 75.4 | - | 94.9 |
| EU369706 | 99.7 | 95.2 | 94.8 | 88.4 | 100 | 93.9 | - | 77.9 | 75.5 | - | 83.4 |
| EU369711 | 94.8 | 94.3 | 99.8 | 89.0 | 95.2 | 100 | - | 77.0 | 75.9 | - | 83.1 |
| EU369731 | 88.2 | 89.2 | 89.1 | 95.2 | 88.1 | 88.9 | 100 | - | - | - | - |
| DQ630441 | 82.7 | 83.3 | 82.2 | 84.0 | 82.5 | 82.0 | 83.6 | 100 | 90.8 | - | 77.7 |
| KF020660 | 82.3 | 83.1 | 81.8 | 82.8 | 82.1 | 81.6 | 82.1 | 95.4 | 100 | - | 74.8 |
| JF339166 | 95.5 | 95.1 | 96.0 | 89.1 | 95.8 | 96.0 | 88.9 | 81.9 | 81.2 | 100 | - |
| JX877826 | 87.9 | 89.0 | 89.0 | 96.6 | 88.0 | 89.0 | 95.8 | 83.3 | 82.0 | 89.4 | 100 |
The representatives are the first allelic variant of each GluB3 gene.
Table 4.
Classification of 136 Glu-B3 genes from GenBank.
| Gene | Haplotype (Allelic Variation) | Notes | ||
|---|---|---|---|---|
| S/N | GenBank Accessions | DNA | AA | |
| GluB3-1 ≧99.2% | 1–6 | EU369699(B3-11); EU369700(B3-12); EU369701(B3-13); EU369702(B3-14); EU369703(B3-15); MH347497; | 6 singles | 343–365 |
| GluB3-2 ≧99.4% | 1 | EU369704(B3-21); MH347496; | 2 same | 370 |
| 2 | EU369721(B3-22); EU369722; EU369723; | 3 same | 369 | |
| 3–5 | EU369705(B3-23); JX163861, JX163862, | 3 singles | 369 | |
| GluB3-3 ≧99.6% | 1 | EU369717(B3-33); AB119006; | 2 same | 392 |
| 2–6 | EU369715(B3-31); EU369716(B3-32); EU369718(B3-34), FJ755309; KR612277; | 5 singles | 392 | |
| GluB3-4 ≧98.9% | 1 | EU369724(B3-41); EU369725; EU369726; JF339163; JX877971; JX878003; JX878019; JX878034; JX878050; JX878066; JX878101; JX878146; MH347498; JF339194; | 14 same | 350 |
| 2a | EU369719(B3-42); JX877806; JX877845; JX877875; JX877908; JX877928; JX878127; KR612281; HQ619905; JF339179; | 10 same | 350 | |
| 2b | EU369727(B3-43); EU369728; | 2 same | ||
| 3a | EU369729(B3-44); EU369730; JX877786; JX877859; JX878134; JX878161; | 6 same | 350 | |
| 3b | EU189089; | 1 single | ||
| 4a | JX878115; | 1 single | 350 | |
| 4b | JX878212; | 1 single | ||
| 5 | JX877823; JX877939; JX877957; JX878091; JX878171; JX878183; JX878191; JX878202; | 8 same | 343 | |
| 6–17 | EU369720(B3-45); AB062852; FJ755306; FJ876823; FJ876824; JX877891; FJ876825; FJ972196; KR612278; KR612279; KR612280; KR612282; | 12 singles | 269–350 | |
| GluB3-5 ≧99.6% | 1–4 | EU369706(B3-51); EU369707(B3-52); EU369708(B3-53); EU369709(B3-54); | 4 singles | 360–365 |
| 5 | EU369710(B3-55); EU189088; AB262661; | 3 same | 343 | |
| GluB3-6 ≧99.2% | 1–6 | EU369711(B3-61); EU369712(B3-62); EU369713(B3-63); EU369714(B3-64); JX877832; JX878089; | 6 singles | 392–393 |
| GluB3-7 ≧99.7% | 1 | EU369731(GluB3-71); EU369732; EU369733; EU369734; EU369735; EU369736; JF339164; JX877788; JX877807; JX877825; JX877860; JX877876; JX877892; JX877909; JX877941; JX878004; JX878020; JX878035; JX878067; JX878084; JX878147; JF339180; JF339196; JF271919; | 24 same | Pseudo |
| 2–3 | JX877972; JX878204; | 2 singles | ||
| GluB3-8 ≧99.9% | 1 | DQ630441; KJ152530; | 2 same | 349 257–350 Pseudo |
| 2–6 | DQ630442; KF020661; KF020662; KJ152528; KJ152531; | 5 singles | ||
| 7 | KJ152529; | 1 single | ||
| GluB3-9 | 1 | KF020660; | 1 single | 350 |
| GluB3-10 ≧99.8% | 1 | JF339166; JX877811; JX877842; JX877895; JX877945; JX878007; JX878022; JX878038; JX878052; JX878135; JX878149; | 11 same | Pseudo |
| 2 | JF339198; JX877791; JX877863; JX878213; | 4 same | ||
| 3 | JX878173; | 1 single | ||
| GluB3-11 | 1a | JX877826; JX877959; | 1 same | 364 |
| 1b | JX877942; | 1 single | ||
The framed were genes located in the study by alignment.
Table 5.
Homology comparison of the representatives of eight Glu-A3 genes (below diagonal) and their deduced amino acid sequences (above diagonal) (%, irrespective of the sequence length).
Table 5.
Homology comparison of the representatives of eight Glu-A3 genes (below diagonal) and their deduced amino acid sequences (above diagonal) (%, irrespective of the sequence length).
| Accession | FJ54 9928 | FJ54 9937 | FJ54 9939 | FJ54 9945 | FJ54 9946 | MG57 4323 | DQ63 0440 | JF33 9156 | FJ75 5305 |
|---|---|---|---|---|---|---|---|---|---|
| FJ549928 | 100 | 71.2 | - | 96.2 | 72.3 | 74.3 | 68.8 | - | - |
| FJ549937 | 83.5 | 100 | - | 69.1 | 97.7 | 88.2 | 82.2 | - | - |
| FJ549939 | 93.2 | 84.3 | 100 | - | - | - | - | - | - |
| FJ549945 | 94.0 | 82.9 | 93.2 | 100 | 70.8 | 72.2 | 68.4 | - | - |
| FJ549946 | 83.6 | 98.7 | 84.5 | 82.9 | 100 | 87.2 | 83.1 | - | - |
| MG574323 | 84.5 | 91.2 | 84.7 | 83.4 | 90.6 | 100 | 80.3 | - | - |
| DQ630440 | 82.3 | 88.4 | 83.3 | 82.0 | 87.7 | 96.2 | 100 | - | - |
| JF339156 | 84.0 | 94.3 | 84.2 | 82.8 | 93.9 | 91.8 | 88.4 | 100 | - |
| FJ755305 | 94.7 | 82.4 | 93.6 | 96.8 | 82.2 | 84.7 | 81.3 | 82.9 | 100 |
The representatives are the first allelic variant of each GluA3 gene.
Table 6.
Classification of 146 Glu-A3 Genes from GenBank.
| Gene | Haplotype (Allelic Variation) | Notes | ||
|---|---|---|---|---|
| S/N | GenBank Accessions | DNA | AA | |
| GluA3-1 ≧98.9% | 1 | FJ549928(A3-11); AY453154; JF339169; JX878117; MH347495; | 5 same | 376 |
| 2 | FJ549929(A3-12); AY453155; | 2 same | 384 | |
| 3a | FJ549930(A3-13); AY453156; JX877793; JX877830; JX877865; JX877963; JX878075; JX878152; JX878174; JX878207; JX878214; JF339201; | 12 same | 376 | |
| 3b | KJ152523; | 1 single | ||
| 4–6 | FJ549931(A3-14); FJ549932(A3-15); FJ549933(A3-16); | 3 singles | 356 | |
| 7a | FJ549934(A3-17); EU189087; | 2 same | 388 | |
| 7b | AY453160; | 1 single | ||
| 8–20 | AB062876; AY453157; AY453158; AY453159; EU871816; FJ755304; FJ876819; FJ876820; FJ876821; FJ876822; KR612275; KR612276; KC136287 | 13 singles | 212–388 | |
| GluA3-2 ≧98.2% | 1–3 | FJ549935(A3-21); FJ549936(A3-22); KR612308; | 3 singles | Pseudo |
| 4 | FJ549937(A3-23); JX877803; JX878097; | 3 same | 304 | |
| 5 | FJ549938(A3-24); JX877837; JX877871; JX877887; JX877936; JX877967; JX878218; | 7 same | 306 | |
| 6 | JX877782; JX877855; JX877904; JX877924; JX878016; JX878031; JX878046; JX878062; JX878123; JX878143; JX878168; JX878180; JX878210; JX878221; | 14 same | Pseudo | |
| 7 | X877820; X877983; X878224; | 3 same | Pseudo | |
| 8 | JX878082; JX878132; JX878189; | 3 same | 307 | |
| 9–15 | AB062868; AB062869; AB062870; AB062871; FJ755302; JQ320288; JQ320292; | 7 singles | 279–304 | |
| GluA3-3 ≧99.6% | 1 | FJ549939(A3-31); JF339161; JX877784; JX877956; JX878113; JX878144; JX878159; | 7 same | Pseudo |
| 2 | FJ549940(A3-32); JX877994; | 2 same | ||
| 3–4 | FJ549941(A3-33); FJ549944(A3-36); | 2 singles | ||
| 5 | FJ549942(A3-34); JX878125; JX878133; | 3 same | ||
| 6 | FJ549943(A3-35); JX877906; JX878182; | 3 same | ||
| 7 | JX877822; JX878170; JX878201; JX878211; | 4 same | ||
| GluA3-4 ≧99.2% | 1a | FJ549945(A3-4); | 1 single | 390 |
| 1b | FJ755303; JX877815; JX877850; | 3 same | ||
| 2–9 | AB062877; AB062878; DQ630443; JX877798; JX877977; JX878105; KC136285; KC136286; | 8 singles | 389–391 | |
| GluA3-5 | 1 | FJ549946(A3-5); | 1 single | 301 |
| GluA3-6 ≧99.8% | 1a | MG574323; MN744845; MN744855; MN744864; MN744897; | 5 same | 307 |
| 1b | MG574327; | 1 single | ||
| 2–6 | MG574321; MG574322; MG574324; MG574325; MG574326; | 5 singles | ||
| GluA3-7 | 1–2 | DQ630440; MG574328; | 2 singles | 350 |
| GluA3-8 ≧98.6% | 1 | JF339156; JX877817; JX877852; JX877921; JX877951; JX877980; JX877997; JX878013; JX878028; JX878043; JX878059; X878108; JX878120; JX878140; JX878155; JX878165; JX878177; X878196; | 18 same | pseudo |
| 2 | JX877799; JX878093 | 2 same | ||
| 3 | JX877833; JX877867; JX877883 | 3 same | ||
| 4 | JX877901 | 1 single | ||
| GluA3-9 | 1 | FJ755305; | 1 single | pseudo |
The framed were located in the study by alignment.
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Zhao, Y.; Zhao, X.; Xiang, Z.; Zhang, D.; Yang, H. Comparison and Classification of LMW-GS Genes at Glu-3 Loci of Common Wheat. Genes 2025, 16, 90. https://doi.org/10.3390/genes16010090
AMA Style
Zhao Y, Zhao X, Xiang Z, Zhang D, Yang H. Comparison and Classification of LMW-GS Genes at Glu-3 Loci of Common Wheat. Genes. 2025; 16(1):90. https://doi.org/10.3390/genes16010090
Chicago/Turabian StyleZhao, Yongying, Xianlin Zhao, Zhiguo Xiang, Dan Zhang, and Hongshan Yang. 2025. "Comparison and Classification of LMW-GS Genes at Glu-3 Loci of Common Wheat" Genes 16, no. 1: 90. https://doi.org/10.3390/genes16010090
APA StyleZhao, Y., Zhao, X., Xiang, Z., Zhang, D., & Yang, H. (2025). Comparison and Classification of LMW-GS Genes at Glu-3 Loci of Common Wheat. Genes, 16(1), 90. https://doi.org/10.3390/genes16010090
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