Phylogenetic relationship of a new class of LMW-GS genes in the M genome of Aegilops comosa

Production and characterization of a disomic 1M/1D Triticum aestivum-Aegilops comosa substitution line

PI 554419, formerly designated as Ae. uniaristata, showed significant difference with other Ae. uniaristata and Ae. comosa accessions in morphological traits at the seedling stage and its leaf color, length, and width behaved as an intermediate type. In this study, we reclassified PI 554419 as Ae. comosa subsp. comosa by comparing the fluorescence in situ hybridization (FISH) signals and the patterns of PCR-based landmark unique gene (PLUG) markers and conserved orthologous set (COS) markers of PI 554419 with other Ae. uniaristata and Ae. comosa accessions as well as the taxonomic character of spike morphology. A disomic 1M/1D substitution line NB 4-8-5-9 derived from PI 554419 was identified from a distant hybridization of Ae. comosa with common wheat (STM 10/CSph1b//CM 39///13 P2-6) by the molecular cytological method. Furthermore, the agronomic and seed morphological traits, as well as the flour processing quality properties of NB 4-8-5-9, were compared with those of its three common wheat parents in two different locations during the 2017-2018 growing seasons. The agronomical traits of NB 4-8-5-9 were similar to or even better than its parents. The seed size-related traits of NB 4-8-5-9 were better than those of all three parents, and the 1000-grain weight and grain width were close to those of Chuanmai 39 (CM 39) and 13 P2-6 and larger than those of CSph1b. The processing quality properties of NB 4-8-5-9 were more similar to those of 13 P2-6 and CSph1b but less similar to those of CM 39. The 1M/1D substitution line NB 4-8-5-9 could further be used for developing translocation lines with 1M segment.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01207-2.

Diploid genome differentiation conferred by RNA sequencing-based survey of genome-wide polymorphisms throughout homoeologous loci in Triticum and Aegilops

Background

Triticum and Aegilops diploid species have morphological and genetic diversity and are crucial genetic resources for wheat breeding. According to the chromosomal pairing-affinity of these species, their genome nomenclatures have been defined. However, evaluations of genome differentiation based on genome-wide nucleotide variations are still limited, especially in the three genomes of the genus Aegilops: Ae. caudata L. (CC genome), Ae. comosa Sibth. et Sm. (MM genome), and Ae. uniaristata Vis. (NN genome). To reveal the genome differentiation of these diploid species, we first performed RNA-seq-based polymorphic analyses for C, M, and N genomes, and then expanded the analysis to include the 12 diploid species of Triticum and Aegilops.

Results

Genetic divergence of the exon regions throughout the entire chromosomes in the M and N genomes was larger than that between A- and A^m-genomes. Ae. caudata had the second highest genetic diversity following Ae. speltoides, the putative B genome donor of common wheat. In the phylogenetic trees derived from the nuclear and chloroplast genome-wide polymorphism data, the C, D, M, N, U, and S genome species were connected with short internal branches, suggesting that these diploid species emerged during a relatively short period in the evolutionary process. The highly consistent nuclear and chloroplast phylogenetic topologies indicated that nuclear and chloroplast genomes of the diploid Triticum and Aegilops species coevolved after their diversification into each genome, accounting for most of the genome differentiation among the diploid species.

Conclusions

RNA-sequencing-based analyses successfully evaluated genome differentiation among the diploid Triticum and Aegilops species and supported the chromosome-pairing-based genome nomenclature system, except for the position of Ae. speltoides. Phylogenomic and epigenetic analyses of intergenic and centromeric regions could be essential for clarifying the mechanisms behind this inconsistency.

Enriching LMW-GS alleles and strengthening gluten properties of common wheat through wide hybridization with wild emmer

Two advanced lines (BAd7-209 and BAd7-213) with identical high-molecular-weight glutenin subunit composition were obtained via wide hybridization between low-gluten cultivar chuannong16 (CN16) and wild emmer D97 (D97). BAd7-209 was better than BAd7-213, and both of them were much better than CN16 in a dough quality test. We found that BAd7-209 had more abundant and higher expression levels of low-molecular-weight glutenin subunit (LMW-GS) proteins than those of BAd7-213. Twenty-nine novel LMW-GS genes at Glu-A3 locus were isolated from BAd7-209, BAd7-213 and their parents. We found that all 29 LMW-GS genes possessed the same primary structure shared by other known LMW-GSs. Twenty-seven genes encode LMW-m-type subunits, and two encode LMW-i-type subunits. BAd7-209 had a higher number of LMW-GS genes than BAd7-213, CN16, and D97. Two wild emmer genes MG574329 and MG574330 were present in the two advanced lines. Most of the LMW-m-type genes showed minor nucleotide variations between wide hybrids and their parents that could be induced through the wide hybridization process. Our results demonstrated that the wild emmer LMW-GS alleles could be feasibly transferred and integrated into common wheat background via wide hybridization and the potential value of the wild emmer LMW-GS alleles in breeding programs designed to improve wheat flour quality.

Potential of Aegilops sp. for Improvement of Grain Processing and Nutritional Quality in Wheat (Triticum aestivum)

Wheat is one of the most important staple crops in the world and good source of calories and nutrition. Its flour and dough have unique physical properties and can be processed to make unique products like bread, cakes, biscuits, pasta, noodles etc., which is not possible from other staple crops. Due to domestication, the genetic variability of the genes coding for different economically important traits in wheat is narrow. This genetic variability can be increased by utilizing its wild relatives. Its closest relative, genus Aegilops can be an important source of new alleles. Aegilops has played a very important role in evolution of tetraploid and hexaploid wheat. It consists of 22 species with C, D, M, N, S, T and U genomes with high allelic diversity relative to wheat. Its utilization for wheat improvement for various abiotic and biotic stresses has been reported by various scientific publications. Here in, for the first time, we review the potential of Aegilops for improvement of processing and nutritional traits in wheat. Among processing quality related gluten proteins; high molecular weight glutenins (HMW GS), being easiest to study have been explored in highest number of accessions or lines i.e., 681 belonging to 13 species and selected ones like Ae. searsii, Ae. geniculata and Ae. longissima have been linked with improved bread making quality of wheat. Gliadins and low molecular weight glutenins (LMW GS) have also been extensively explored for wheat improvement and Ae. umbellulata specific LMW GS have been linked with wheat bread making quality improvement. Aegilops has been explored for seed texture diversity and proteins like puroindolins (Pin) and grain softness proteins (GSP). For nutrition quality improvement, it has been screened for essential micronutrients like Fe, Zn, phytochemicals like carotenoids and dietary fibers like arabinoxylan and β-glucan. Ae. kotschyi and Ae. biuncialis transfer in wheat have been associated with higher Fe, Zn content. In this article we have tried to compile information available on exploration of nutritional and processing quality related traits in Aegilops section and their utilization for wheat improvement by different approaches.

Identification of nicotianamine synthase genes in Triticum monococcum and their expression under different Fe and Zn concentrations

In graminaceous plants, nicotianamine (NA) is an important component of metal acquisition. NA is synthesized from S-adenosyl-l-methionine (SAM) catalyzed by nicotianamine synthase (NAS). Here, eight Triticum monococcum NAS (TmNAS) genes were cloned and characterized. Amino acid sequence analysis showed that TmNAS genes had high sequence identity with those from Triticum aestivum, Zea mays, Oryza sativa and Hordeum vulgare. Phylogenetic analysis showed that NAS genes were classified into two distinct groups, e.g. group I and group II. Expression analysis demonstrated that two of the TmNAS genes in group II were highly expressed in shoot tissues, and the other six TmNAS genes in group I were expressed in root tissues. Further analysis indicated that root-specific TmNAS genes were up-regulated under conditions of Fe- or Zn-deficiency growth, while shoot-specific TmNAS genes were up-regulated under conditions of Fe- or Zn-sufficiency. These results help us understand the NAS genes in T. monococcum and provide novel genetic resources for improving Fe and Zn concentrations in common wheat.

Characterization of novel LMW glutenin subunit genes at the Glu-M3 locus from Aegilops comosa

We report the characterization of seven novel low-molecular-weight glutenin subunit (LMW-GS) genes from Aegilops comosa (2n = 2x = 14, MM). We found that all seven LMW-GS genes possessed the same primary structure shared by other known LMW-GSs. Three genes (comosa-M1, comosa-M2, and comosa-M3) encode LMW-m-type subunits, two (comosa-I1 and comosa-I2) encode LWM-i-type subunits, and two (comosa-L1 and comosa-L2) encode LWM-l-type subunits. The comosa-M1 possessed seven cysteine residues, which resulted from a single-nucleotide polymorphism (SNP) of the G-A transition in the fifth position of the N-terminal sequence. Two l-type subunits, comosa-L1 and comosa-L2, contained nine cysteine residues with an extra cysteine residue located in the signal peptide and repetitive domain. In addition, a long insertion of 13 residues (LGQQPQ8/LVQQPQ8) was present in the end of the C-terminal II. Phylogenetic analysis implied that the comosa-L2 may be the intermediate type during the evolution of LMW-l and LMW-i-type genes. Our results demonstrated that the novel LMW-GSs, such as comosa-M1, comosa-L1, and comosa-L2, may have positive effects on dough properties.

Low-molecular-weight glutenin subunits from the 1U genome of Aegilops umbellulata confer superior dough rheological properties and improve breadmaking quality of bread wheat

BACKGROUND

Wheat-related genomes may carry new glutenin genes with the potential for quality improvement of breadmaking. In this study, we estimated the gluten quality properties of the wheat line CNU609 derived from crossing between Chinese Spring (CS, Triticum aestivum L., 2n = 6x = 42, AABBDD) and the wheat Aegilops umbellulata (2n = 2x = 14, UU) 1U(1B) substitution line, and investigated the function of 1U-encoded low-molecular-weight glutenin subunits (LMW-GS).

RESULTS

The main quality parameters of CNU609 were significantly improved due to introgression of the 1U genome, including dough development time, stability time, farinograph quality number, gluten index, loaf size and inner structure. Glutenin analysis showed that CNU609 and CS had the same high-molecular-weight glutenin subunit (HMW-GS) composition, but CNU609 carried eight specific 1U genome-encoded LMW-GS. The introgression of the 1U-encoded LMW-GS led to more and larger protein body formation in the CNU609 endosperm. Two new LMW-m type genes from the 1U genome, designated Glu-U3a and Glu-U3b, were cloned and characterized. Secondary structure prediction implied that both Glu-U3a and Glu-U3b encode subunits with high α-helix and β-strand content that could benefit the formation of superior gluten structure.

CONCLUSION

Our results indicate that the 1U genome has superior LMW-GS that can be used as new gene resources for wheat gluten quality improvement. © 2017 Society of Chemical Industry.

Low molecular weight glutenin subunit gene Glu-B3h confers superior dough strength and breadmaking quality in wheat (Triticum aestivum L.)

Low molecular weight glutenin subunit is one of the important quality elements in wheat (Triticum aestivum L.). Although considerable allelic variation has been identified, the functional properties of individual alleles at Glu-3 loci are less studied. In this work, we performed the first comprehensive study on the molecular characteristics and functional properties of the Glu-B3h gene using the wheat cultivar CB037B and its Glu-B3 deletion line CB037C. The results showed that the Glu-B3h deletion had no significant effects on plant morphological or yield traits, but resulted in a clear reduction in protein body number and size and main quality parameters, including inferior mixing property, dough strength, loaf volume, and score. Molecular characterization showed that the Glu-B3h gene consists of 1179 bp, and its encoded B-subunit has a longer repetitive domain and an increased number of α-helices, as well as higher expression, which could contribute to superior flour quality. The SNP-based allele-specific PCR markers designed for the Glu-B3h gene were developed and validated with bread wheat holding various alleles at Glu-B3 locus, which could effectively distinguish the Glu-B3h gene from others at the Glu-B3 locus, and have potential applications for wheat quality improvement through marker-assisted selection.

Deletion of the low-molecular-weight glutenin subunit allele Glu-A3a of wheat (Triticum aestivum L.) significantly reduces dough strength and breadmaking quality

BACKGROUND

Low-molecular-weight glutenin subunits (LMW-GS), encoded by Glu-3 complex loci in hexaploid wheat, play important roles in the processing quality of wheat flour. To date, the molecular characteristics and effects on dough quality of individual Glu-3 alleles and their encoding proteins have been poorly studied. We used a Glu-A3 deletion line of the Chinese Spring (CS-n) wheat variety to conduct the first comprehensive study on the molecular characteristics and functional properties of the LMW-GS allele Glu-A3a.

RESULTS

The Glu-A3a allele at the Glu-A3 locus in CS and its deletion in CS-n were identified and characterized by proteome and molecular marker methods. The deletion of Glu-A3a had no significant influence on plant morphological and yield traits, but significantly reduced the dough strength and breadmaking quality compared to CS. The complete sequence of the Glu-A3a allele was cloned and characterized, which was found to encode a B-subunit with longer repetitive domains and an increased number of α-helices. The Glu-A3a-encoded B-subunit showed a higher expression level and accumulation rate during grain development. These characteristics of the Glu-A3a allele could contribute to achieving superior gluten quality and demonstrate its potential application to wheat quality improvement. Furthermore, an allele-specific polymerase chain reaction (AS-PCR) marker for the Glu-A3a allele was developed and validated using different bread wheat cultivars, including near-isogenic lines (NILs) and recombinant inbred lines (RILs), which could be used as an effective molecular marker for gluten quality improvement through marker-assisted selection.

CONCLUSIONS

This work demonstrated that the LMW-GS allele Glu-A3a encodes a specific LMW-i type B-subunit that significantly affects wheat dough strength and breadmaking quality. The Glu-A3a-encoded B-subunit has a long repetitive domain and more α-helix structures as well as a higher expression level and accumulation rate during grain development, which could facilitate the formation of wheat with a stronger dough structure and superior breadmaking quality.

Variations and classification of toxic epitopes related to celiac disease among α-gliadin genes from four Aegilops genomes

The α-gliadins are associated with human celiac disease. A total of 23 noninterrupted full open reading frame α-gliadin genes and 19 pseudogenes were cloned and sequenced from C, M, N, and U genomes of four diploid Aegilops species. Sequence comparison of α-gliadin genes from Aegilops and Triticum species demonstrated an existence of extensive allelic variations in Gli-2 loci of the four Aegilops genomes. Specific structural features were found including the compositions and variations of two polyglutamine domains (QI and QII) and four T cell stimulatory toxic epitopes. The mean numbers of glutamine residues in the QI domain in C and N genomes and the QII domain in C, N, and U genomes were much higher than those in Triticum genomes, and the QI domain in C and N genomes and the QII domain in C, M, N, and U genomes displayed greater length variations. Interestingly, the types and numbers of four T cell stimulatory toxic epitopes in α-gliadins from the four Aegilops genomes were significantly less than those from Triticum A, B, D, and their progenitor genomes. Relationships between the structural variations of the two polyglutamine domains and the distributions of four T cell stimulatory toxic epitopes were found, resulting in the α-gliadin genes from the Aegilops and Triticum genomes to be classified into three groups.

PCR-based isolation and identification of full-length low-molecular-weight glutenin subunit genes in bread wheat (Triticum aestivum L.)

Low-molecular-weight glutenin subunits (LMW-GSs) are encoded by a multi-gene family and are essential for determining the quality of wheat flour products, such as bread and noodles. However, the exact role or contribution of individual LMW-GS genes to wheat quality remains unclear. This is, at least in part, due to the difficulty in characterizing complete sequences of all LMW-GS gene family members in bread wheat. To identify full-length LMW-GS genes, a polymerase chain reaction (PCR)-based method was established, consisting of newly designed conserved primers and the previously developed LMW-GS gene molecular marker system. Using the PCR-based method, 17 LMW-GS genes were identified and characterized in Xiaoyan 54, of which 12 contained full-length sequences. Sequence alignments showed that 13 LMW-GS genes were identical to those found in Xiaoyan 54 using the genomic DNA library screening, and the other four full-length LMW-GS genes were first isolated from Xiaoyan 54. In Chinese Spring, 16 unique LMW-GS genes were isolated, and 13 of them contained full-length coding sequences. Additionally, 16 and 17 LMW-GS genes in Dongnong 101 and Lvhan 328 (chosen from the micro-core collections of Chinese germplasm), respectively, were also identified. Sequence alignments revealed that at least 15 LMW-GS genes were common in the four wheat varieties, and allelic variants of each gene shared high sequence identities (>95%) but exhibited length polymorphism in repetitive regions. This study provides a PCR-based method for efficiently identifying LMW-GS genes in bread wheat, which will improve the characterization of complex members of the LMW-GS gene family and facilitate the understanding of their contributions to wheat quality.