Molecular characterization of a HMW glutenin subunit allele providing evidence for silencing of x-type gene on Glu-B1

Development of PCR-based markers for identification of wheat HMW glutenin Glu-1Bx and Glu-1By alleles

BACKGROUND

In common wheat (Triticum aestivum L.), allelic variations in the high-molecular-weight glutenin subunits Glu-B1 locus have important effects on grain end-use quality. The Glu-B1 locus consists of two tightly linked genes encoding x- and y-type subunits that exhibit highly variable frequencies. However, studies on the discriminating markers of the alleles that have been reported are limited. Here, we developed 11 agarose gel-based PCR markers for detecting Glu-1Bx and Glu-1By alleles.

RESULTS

By integrating the newly developed markers with previously published PCR markers, nine Glu-1Bx locus alleles (Glu-1Bx6, Glu-1Bx7, Glu-1Bx7*, Glu-1Bx7 OE, Glu-1Bx13, Glu-1Bx14 (-) , Glu-1Bx14 (+)/Bx20, and Glu-1Bx17) and seven Glu-1By locus alleles (Glu-1By8, Glu-1By8*, Glu-1By9, Glu-1By15/By20, Glu-1By16, and Glu-1By18) were distinguished in 25 wheat cultivars. Glu-1Bx6, Glu-1Bx13, Glu-1Bx14 (+)/Bx20, Glu-1By16, and Glu-1By18 were distinguished using the newly developed PCR markers. Additionally, the Glu-1Bx13 and Glu-1Bx14 (+)/Bx20 were distinguished by insertions and deletions in their promoter regions. The Glu-1Bx6, Glu-1Bx7, Glu-1By9, Glu-1Bx14 (-), and Glu-1By15/By20 alleles were distinguished by using insertions and deletions in the gene-coding region. Glu-1By13, Glu-1By16, and Glu-1By18 were dominantly identified in the gene-coding region. We also developed a marker to distinguish between the two Glu-1Bx14 alleles. However, the Glu-1Bx14 (+) + Glu-1By15 and Glu-1Bx20 + Glu-1By20 allele combinations could not be distinguished using PCR markers. The high-molecular-weight glutenin subunits of wheat varieties were analyzed by ultra-performance liquid chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and the findings were compared with the results of PCR analysis.

CONCLUSIONS

Seven Glu-1Bx and four Glu-1By allele detection markers were developed to detect nine Glu-1Bx and seven Glu-1By locus alleles, respectively. Integrating previously reported markers and 11 newly developed PCR markers improves allelic identification of the Glu-B1 locus and facilitates more effective analysis of Glu-B1 alleles molecular variations, which may improve the end-use quality of wheat.

High-throughput analysis of high-molecular weight glutenin subunits in 665 wheat genotypes using an optimized MALDI-TOF-MS method

Gluten protein composition determines the rheological characteristics of wheat dough and is influenced by variable alleles with distinct effects on processing properties. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), we determined the high-molecular weight glutenin subunit (HMW-GS) composition of 665 wheat genotypes employed in breeding programs in South Korea. We identified 22 HMW-GS alleles, including 3 corresponding to the Glu-A1 locus, 14 to Glu-B1, and 5 to Glu-D1. The Glu-1 quality score, which is an important criterion for high-quality wheat development, was found to be 10 for 105/665 (15.79%) of the studied genotypes, and included the following combinations of HMW-GS: 2*, 7 + 8, 5 + 10; 2*, 17 + 18, 5 + 10; 1, 7 + 8, 5 + 10; and 1, 17 + 18, 5 + 10. To select wheat lines with the 1Bx7 overexpression (1Bx7OE) subunit, which is known to have a positive effect on wheat quality, we used a combination of MALDI-TOF-MS and published genotyping markers and identified 6 lines carrying 1Bx7OE out of the 217 showing a molecular weight of 83,400 Da, consistent with 1Bx7G2 and 1Bx7OE. This study demonstrates that the MALDI-TOF-MS method is fast, accurate, reliable, and effective in analyzing large numbers of wheat germplasms or breeding lines in a high-throughput manner.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02637-z.

Cloning and characterization of special HMW glutenin subunit genes from Aegilops longissima L. and their potential for wheat quality improvement

Identification and cloning of new glutenin genes from wheat-related species can provide candidate gene resources for quality improvement of wheat. In this study, ten special high-molecular-weight glutenin subunits (HMW-GS), including five x-type (1Sl2x, 1Sl16x, 1Sl17x, 1Sl23x, and 1Sl25x) and five y-type (1Sl2y, 1Sl6y1, 1Sl16y, 1Sl17y, and 1Sl23y) from Aegilops longissima L. (SlSl, 2n = 2x = 14) were identified, and their complete encoding genes were cloned by allelic-specific polymerase chain reaction (AS-PCR). The deduced amino acid (aa) residues of the x-type subunit genes ranged from 821 aa (2469 bp) to 941 aa (2829 bp), while those of the y-type subunit genes varied from 749 aa (2250 bp) to 771 aa (2361 bp). These special HMW-GS had a longer central repetitive domain with more glutamine repeats and glutamine residues compared to the previously characterized HMW-GS in common wheat, which provided a structural basis for superior gluten quality formation. The authenticity of the four cloned genes were verified by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF-MS). Abundant single-nucleotide polymorphism (SNP) and insertion/deletion (InDel) variations among these genes were identified, which would benefit for developing specific molecular markers used for wheat gluten quality improvement. Phylogenetic analysis revealed that the 1Sl-encoded HMW-GS had close relationships with those from bread wheat, which were divergent from Triticum species at 2.10-10.00 million years ago. Our results indicate that the 1Sl genome contains superior candidate glutenin genes that have potential application values for the improvement of wheat bread making quality.

Expression of wheat high molecular weight glutenin subunit 1Bx is affected by large insertions and deletions located in the upstream flanking sequences

To better understand the transcriptional regulation of high molecular weight glutenin subunit (HMW-GS) expression, we isolated four Glu-1Bx promoters from six wheat cultivars exhibiting diverse protein expression levels. The activities of the diverse Glu-1Bx promoters were tested and compared with β-glucuronidase (GUS) reporter fusions. Although all the full-length Glu-1Bx promoters showed endosperm-specific activities, the strongest GUS activity was observed with the 1Bx7OE promoter in both transient expression assays and stable transgenic rice lines. A 43 bp insertion in the 1Bx7OE promoter, which is absent in the 1Bx7 promoter, led to enhanced expression. Analysis of promoter deletion constructs confirmed that a 185 bp MITE (miniature inverted-repeat transposable element) in the 1Bx14 promoter had a weak positive effect on Glu-1Bx expression, and a 54 bp deletion in the 1Bx13 promoter reduced endosperm-specific activity. To investigate the effect of the 43 bp insertion in the 1Bx7OE promoter, a functional marker was developed to screen 505 Chinese varieties and 160 European varieties, and only 1Bx7-type varieties harboring the 43 bp insertion in their promoters showed similar overexpression patterns. Hence, the 1Bx7OE promoter should be important tool in crop genetic engineering as well as in molecular assisted breeding.

Molecular characterization of two silenced y-type genes for Glu-B1 in Triticum aestivum ssp. yunnanese and ssp. tibetanum

The high molecular weight glutenin subunits (HMW-GSs) are a major class of common wheat storage proteins. The bread-making quality of common wheat flour is influenced by the composition of HMW-GSs. In the present study, two unexpressed 1By genes from Triticum aesitvum L.ssp.yunnanese AS332 and T. aesitvum ssp.tibetanum AS908 were respectively cloned and characterized. The results indicated that both of the silenced 1By genes in AS332 and AS908 were 1By9. In contrast to previously reported mechanisms for silenced genes 1Ax and 1Ay, which was due to the insertion of transposon elements or the presence of premature stop codon via base substitution of C-->T transition in trinucleotides CAA or CAG, the silence of 1By9 genes was caused by premature stop codons via the deletion of base A in trinucleotide CAA, which lead to frameshift mutation and indirectly produced several premature stop codons (TAG) downstream of the coding sequence.