Antibodies to N-terminal Peptides of Low MrSubunits of Wheat Glutenin. II. Detection of Subunits Encoded by Different Loci

A panel of anti-peptide antibodies specific for each of the different N-terminal sequence types of B- and C-low molecular mass glutenin subunits (L M_rGS) were utilised in immunoblotting studies to identify the chromosomal location of genes encoding different sequences and to characterise the allelic variation of the encoding loci. The MET-type sequences were predominantly found among the B- subunits, while the α- and γ- sequences predominated in the C- subunits. The quantitatively major SHIPGLERPS sequence was found in both the B- and C- mobility regions. Using either biotypes in the cultivar, Aroona or genetic lines containing double rye chromosome 1 substitutions and thus expressing only single LM_r GS alleles, the sequences were determined for most of the major polypeptides expressed by each LM_r GS allele. The L M_rGS from different genomes encoded different numbers of each sequence type. Furthermore, different polypeptides within a particular «block» of subunits encoded by a given allele often had differing N-terminal sequences. However, subunits of similar electrophoretic mobilities encoded by different alleles at each locus usually had identical N-terminal sequences, suggesting that they may instead differ in the number of repeats. In Chinese Spring, genes encoding the SHIPGLERPS and METSHIPGL sequence types were predominantly present on chromosomes 1B and 1D, while the related METSRVPGL sequence was only encoded on 1D. In contrast, the METSCIPGL, α- and γ-sequences were encoded on each of chromosomes 1A, 1B and 1D. Several different electrophoretic and immunoblotting approaches using null lines suggested that some of the α-type L M_rGS may also be encoded by group 6 chromosomes, particularly 6D. The anti- SHIPGLERPS antibody also recognised chromosome 1B encoded β-, γ- and ω-gliadins, while the anti-METSRVPGL antibody recognised 1D encoded α- and β-gliadins. The absence of sequences within the major gliadin families that are highly homologous to the latter two N-terminal L M_rGS sequences may suggest that some monomeric L M_rGS could exist within the electrophoretically-resolved gliadins. These antibodies will provide valuable reagents for the study of the roles of particular L M_rGS families in the structure and function of the glutenin macropolymer, the role of different LM_r GS types in determining the influence of allelic variation of L M_rGS composition on dough properties, and potentially in the development of diagnostics for these flour components.     

Characterisation of a ω-gliadin gene in Triticum tauschii

A ω-gliadin gene at the Gli-D^t1 locus of Triticum tauschii accession AUS18913 was isolated using PCR primers, designed from published sequences of ω-gliadin genes of bread wheat cv Cheyenne, and deduced sequences of the N-terminal amino acids of ω-gliadin proteins. Further, the derived protein was isolated from A-PAGE and was sequenced. The protein sequence contained a signal peptide of 19 amino acids followed by a short N-terminal sequence of 11 amino acids, a central repetitive domain that covers approximately 90% of the sequence and a short C-terminal domain of 12 amino acids. The sequence comparison with other ω-gliadins showed a high level of similarities between them. Further analysis of the ω-gliadins using A-PAGE revealed that there are three ω-gliadin proteins in AUS18913 accession. Comparison of N-terminal sequences of these proteins revealed that two of these proteins have very high homologies with ω-gliadins of Cheyenne while the third one was significantly different.     

Molecular characterization and comparative analysis of four new genes from Sec2 locus encoding 75K γ-secalins of rye species

Using a PCR-based strategy, four new 75K γ-secalin genes were isolated from Secale cereale, Secale vavilovii, Secale sylvestre, and Secale strictum in genus Secale (rye). Based on amino acid sequences, the primary structure of the 75K γ-secalin subunits was demonstrated, which was composed of four main structural regions: (a) a conservative 19 amino acids signal peptide, (b) a steady short N-terminal region of 12 amino acids containing a cysteine residue, (c) a repetitive domain, which began with the conservative tetrapeptides PQ₃ and was rich in glutamine and proline. PFPQ₁₋₂(PQQ)₁₋₂ was the core repeat motif in the repetitive region. Besides amino acid substitutions, this region showed variations in length due to the insertion and deletion events. In the repetitive region of EF432549 (Secale strictum), there were two octapeptides (PFPQQPQQ and PVPQQSQQ) insertions. On the contrary, deletion events of two residues (QT) took place in EF432546 (Secale sylvestre). Accounting for the amino acid replacement, an extra cysteine residue appeared in the repetitive region of EF432546, which did not exist in other genes, and (d) a conserved 143 amino acids C-terminal domain including eight cysteine residues. The implications of the results for quality improvement are discussed.     

Cloning and expression analysis of kenaf (Hibiscus cannabinus L.) major lignin and cellulose biosynthesis gene sequences and polymer quantification during plant development

In order to apply state-of-the-art molecular breeding techniques in fibre crop it is necessary to have a good knowledge of major polymer biosynthesis gene sequences and their expression pattern. Polymerase chain reaction was employed to isolate sequences of the major genes for lignin and cellulose biosynthesis in a kenaf cultivar. CeSA, 4cl, c4h, cad, and ccr gene primers were designed according to their conservative regions; partial sequences of lignin and cellulose biosynthesis genes were obtained. One actin II gene sequence was also isolated from the kenaf genome as a housekeeping gene to be employed in qPCR analysis. Expression levels of genes c4h, cad and CeSA in bark and core from plants harvested at three different growth stages were evaluated. Using qPCR analyses it was found that the expression levels of the two biosynthesis lignin genes in bark tissues increased during plant growth, while a negative trend was recorded in core tissues. In both bark and core, the quantity of lignin was positively correlated to plant growth while cellulose content decreased.     

玉米耐旱相关基因dbf1的序列变异分析

玉米dbf1 基因在干旱胁迫下的编码产物与DIP₁蛋白相结合,调控植物激素脱落酸（ABA）响应基因rab17 的表达,从而提高耐旱性。以B73的dbf1 基因组序列为模板,对104个玉米自交系的dbf1 基因进行测序,研究玉米dbf1 基因的序列多态性。多态性分析表明,在全长为2 118 bp的序列中共发现48个SNP和12个InDel。尽管大部分变异位点集中在非编码区,但编码区的1个InDel和3个非同义突变位点的变异可以产生氨基酸序列改变。玉米dbf1 基因的全长序列和编码区序列的变异位点可以分别将该基因划分成33和11种单倍型,并且编码7种蛋白质。在供试材料中,dbf1 基因至少经历了9次重组,中性检测表明,该基因的进化没有偏离中性选择。     

Development and characterization of a Triticum aestivum-H. villosa T5VS•5DL translocation line with soft grain texture

The Hardness locus on the short arm of chromosome 5D is the main determinant of grain texture in bread wheat. The Pina and Pinb genes are tightly linked at this locus, and the soft kernel texture phenotype results when both genes are present and encode the wild-type puroindoline proteins PINA and PINB. In this study a compensating T5VS•5DL Triticum aestivum-Haynaldia villosa translocation line, NAU415, was characterized by chromosome C-banding, genomic in situ hybridization and molecular markers. Single Kernel Characterization System (SKCS) analysis and scanning electron microscopy indicated that NAU415 had soft endosperm although it lacked the wheat Pina-D1a and Pinb-D1a genes, suggesting the presence of functional Pin gene orthologs on chromosome 5VS. Using a PCR approach, Pina-related (designated Dina) and Pinb-related (Dinb) genes in H. villosa and NAU415 were identified and sequenced. The nucleotide and predicted amino acid sequences showed close similarities to the wild-type puroindolines of T. aestivum cv. Chinese Spring. The tryptophan-rich regions of both Dina and Dinb showed a sequence change from lysine-42 to arginine, a feature that may have an effect on grain texture. The potential of T5VS•5DL translocation line as a source of genes that may be used for modulation of endosperm texture and other valuable traits in wheat breeding is discussed.     

Comparative Studies of High MrSubunits of Rye and Wheat. II. Partial Amino Acid Sequences

A panel of anti-peptide antibodies specific for each of the different N-terminal sequence types of B- and C-low molecular mass glutenin subunits (L M_rGS) were utilised in immunoblotting studies to identify the chromosomal location of genes encoding different sequences and to characterise the allelic variation of the encoding loci. The MET-type sequences were predominantly found among the B- subunits, while the α- and γ- sequences predominated in the C- subunits. The quantitatively major SHIPGLERPS sequence was found in both the B- and C- mobility regions. Using either biotypes in the cultivar, Aroona or genetic lines containing double rye chromosome 1 substitutions and thus expressing only single LM_r GS alleles, the sequences were determined for most of the major polypeptides expressed by each LM_r GS allele. The L M_rGS from different genomes encoded different numbers of each sequence type. Furthermore, different polypeptides within a particular «block» of subunits encoded by a given allele often had differing N-terminal sequences. However, subunits of similar electrophoretic mobilities encoded by different alleles at each locus usually had identical N-terminal sequences, suggesting that they may instead differ in the number of repeats. In Chinese Spring, genes encoding the SHIPGLERPS and METSHIPGL sequence types were predominantly present on chromosomes 1B and 1D, while the related METSRVPGL sequence was only encoded on 1D. In contrast, the METSCIPGL, α- and γ-sequences were encoded on each of chromosomes 1A, 1B and 1D. Several different electrophoretic and immunoblotting approaches using null lines suggested that some of the α-type L M_rGS may also be encoded by group 6 chromosomes, particularly 6D. The anti- SHIPGLERPS antibody also recognised chromosome 1B encoded β-, γ- and ω-gliadins, while the anti-METSRVPGL antibody recognised 1D encoded α- and β-gliadins. The absence of sequences within the major gliadin families that are highly homologous to the latter two N-terminal L M_rGS sequences may suggest that some monomeric L M_rGS could exist within the electrophoretically-resolved gliadins. These antibodies will provide valuable reagents for the study of the roles of particular L M_rGS families in the structure and function of the glutenin macropolymer, the role of different LM_r GS types in determining the influence of allelic variation of L M_rGS composition on dough properties, and potentially in the development of diagnostics for these flour components.     

Promoter Trapping in Microalgae Using the Antibiotic Paromomycin as Selective Agent

The lack of highly active endogenous promoters to drive the expression of transgenes is one of the main drawbacks to achieving efficient transformation of many microalgal species. Using the model chlorophyte Chlamydomonas reinhardtii and the paromomycin resistance APHVIII gene from Streptomyces rimosus as a marker, we have demonstrated that random insertion of the promoterless marker gene and subsequent isolation of the most robust transformants allows for the identification of novel strong promoter sequences in microalgae. Digestion of the genomic DNA with an enzyme that has a unique restriction site inside the marker gene and a high number of target sites in the genome of the microalga, followed by inverse PCR, allows for easy determination of the genomic region, which precedes the APHVIII marker gene. In most of the transformants analyzed, the marker gene is inserted in intragenic regions and its expression relies on its adequate insertion in frame with native genes. As an example, one of the new promoters identified was used to direct the expression of the APHVIII marker gene in C. reinhardtii, showing high transformation efficiencies.     

Genetic characterization of kernel polyphenol oxidases in wheat and related species

Polyphenol oxidase (PPO) activity causes undesirable darkening of raw Asian noodles and other wheat products. In this study we investigate the genetic origins and diversity of wheat kernel PPO. PPO was characterized via activity assays, antigenic staining, and Southern blots in Triticum aestivum, Triticum dicoccoides, Triticum durum, Triticum dicoccum, Triticum monococcum, Triticum urartu, Aegilops speltoides, and Aegilops tauschii. Among these species, PPO activity was well-correlated with antigenic staining intensity toward a wheat kernel-type PPO antibody. High PPO activity was observed in all three T. monococcum accessions (A^m genome), one Ae. speltoides accession, one T. durum accession, and two hexaploid wheat cultivars. Southern blots suggested the presence of two or more kernel-type PPO genes in diploid progenitors of the hexaploid A, B, and D genomes. Whole-kernel PPO activity was evaluated in disomic substitution lines derived from three T. dicoccoides accessions in the background of T. durum ‘Langdon’. PPO activity was primarily associated with chromosome 2A and to a much lower degree with chromosome 2B. DNA sequence comparisons showed that the intron associated with the high PPO allele on chromosome 2AL of hexaploid wheat had 94% nucleotide identity with the homeologous intron found in T. monococcum, a species with high kernel PPO activity. This implies that the ancestral PPO allele on the A genome is one of the high activity, and the low PPO allele found in hexaploid wheat represents a relatively recent genetic alteration. Results confirm the presence of multiple kernel-type PPO genes in the diploid and tetraploid progenitors and relatives of hexaploid wheat. However, it is likely that relatively few of the many kernel-type PPO genes present in wheat contribute substantially to kernel PPO activity. A single genetic locus on homeologous group 2 chromosomes may be the primary cause of high PPO activity in wheat kernels.     

Development of Molecular Tools for Distinguishing Between the Highly Similar Rx1 and Rx2 PVX Extreme Resistance Genes in Tetraploid Potato

The Rx1 and Rx2 are extreme resistance genes, which have been introgressed from different species into potato cultivars and breeding lines. These two genes have a 98% and 96% sequence similarity at the nucleotide as well as at the amino acid level, respectively. Except one extra amino acid in the Rx2 gene, the high variations of the amino acid chain are due to single and double nucleotide variations, which are scattered throughout the coding regions. The high level of sequence similarity makes it complicated to identify these genes and to distinguish them from other highly similar genes, like the Gpa2 or from paralogous sequences by a single polymerase chain reaction (PCR). Here, we report the development of markers for the simple and rapid identification of the Rx1 as well as the Rx2 gene. Further, a multiplex PCR reaction is recommended for the simultaneous detection of both genes in a single reaction. Since these genes reside on different chromosomes, following their inheritance by the multiplex PCR method could help the easy incorporation of both genes into breeding lines. The detection method shown here could be routinely used in marker-assisted selection for Potato virus X extreme resistance and could enhance the effectiveness of potato breeding programs. Besides potato breeding, this method could also be effectively applied to mapping experiments as well as in research studies of resistance.     

Isolation and characterisation of friabilin genes in rye

The Hardness locus on chromosome 5D is the main determinant of grain texture in hexaploid wheat. Puroindoline-a (pin-a), puroindoline-b (pin-b) and Grain Softness Protein (GSP) genes are tightly linked at this locus and their products are the predominant components of friabilin, a 15 kDa endosperm protein complex. Differences in grain texture are mainly caused by specific puroindoline genes mutations and are known to play a large impact on the end-product quality of wheat, contributing to the distinction of well-suited market classes for specific end-uses. We investigated friabilin genes in rye (Secale cereale L.), aiming at an increase information on the friabilin molecular system in cereals and to further investigate their potential use for the genetic improvement of this crop. Using a PCR approach, puroindoline-b and GSP-like sequences were identified for the first time in several rye and triticale cultivars, sequenced and located on specific chromosomal arms. The primary structures of deduced proteins were determined and compared with those from other cereal species. In contrast with data from previous studies, secaloindoline-a was not found. Our results introduce new evidence for a discrete allelic variation at the secaloindoline loci in rye, indicating that future larger screenings may facilitate preliminary selection of germplasm for rye breeding purposes and triticale production.     

Rice Germin-Like Proteins: Allelic Diversity and Relationships to Early Stress Responses

Germin-like protein (GLP) markers were associated with quantitative trait loci (QTL) for resistance to the rice blast pathogen, Magnaporthe oryzae in multiple rice (Oryza sativa) mapping populations. Twelve paralogous OsGLP gene family members are located within the physical QTL region on chromosome 8, and gene silencing studies suggest that they contribute collectively to the resistance phenotype. We compared sequence and expression profiles of OsGLP alleles in two resistant and two susceptible parental rice lines to find functional polymorphisms that correlated with the resistant phenotype. Based on coding and promoter sequences, the genes belong to two germin subfamily groups (GER3 and GER4). OsGLP members from both subfamilies were constitutively expressed and developmentally regulated in all cultivars. Transient induction above constitutive levels was observed for some OsGLPs, especially GER4 subfamily members, at early time points after M. oryzae infection and mechanical wounding. Varying 5′ regulatory regions and differential expression of some family members between resistant and susceptible cultivars corresponded with differential hydrogen peroxide (H₂O₂) accumulation after the same stimuli. OsGLP of both GER subfamilies localized to the plant cell wall. The protein location and early gene induction suggest that OsGLPs protect rice leaves at early stages of infection before fungal penetration and subsequent ingress. Our data suggest that regulation of OsGLP genes defines resistant versus susceptible phenotypes.     

Diversity of sequences encoded by the Gsp-1 genes in wheat and other grass species

The Gsp-1 genes of wheat encode two components, the “grain softness protein” (whose role in determining texture has not been substantiated) and a 15 residue arabinogalactan peptide (AGP) sequence which is O-glycosylated and is also of unknown function. We have determined genomic Gsp-1 sequences from 29 species within the Triticeae tribe and an additional 12 species from the major subfamilies of the Poaceae (Anomochlooideae, Bambusoideae, Ehrhartoideae, Chloridoideae and Panicoideae). Twelve new AGP sequence types were identified with forms present in Agropyron mongolicum, Secale cereale, Oryza sativa subsp. japonica and Sorghum bicolor containing an extra ten amino acids within the AGP sequence. Phylogenetic analysis showed distinct groupings of AGP/GSP sequence types which had no apparent relationship to the species or even the genus. However, individual forms of AGP forms were associated with specific groups of GSP sequences, providing no evidence that the AGP and GSP-1 parts of the protein have diverged at different rates or in different ways.     

PCR-based markers for identification of HMW-GS at Glu-B1x loci in common wheat

The bread wheat elasticity, which is very important for bread-making quality, is largely determined by the composition of high-molecular-weight glutenin subunits (HMW-GS). The HMW-GS encoded by Glu-B1 loci are highly polymorphic and the combinations 17+18 and 14+15 are good for bread making. Thus it is very important to identify the alleles at Glu-B1 loci for wheat quality improvement. In this study, the five common HMW-GS types encoded by Glu-B1x locus carried by 18 Chinese bread wheat cultivars (or lines) were analyzed by SDS-PAGE. Two pairs of PCR primers which could distinguish the Glu-Blx alleles of the five common HMW-GS types were designed based on the Glu-B1x gene sequences (Reddy and Appels, 1993; Genbank accession: X13927; Genbank accession:AY367771). 22 recombinant inbred lines (RILs) derived from Jing711 (contains 17 subunit on Glu-B1x) and Pm97034 (contains 14 subunit on Glu-B1x) were used to validate the accuracy of the primers, which showed that the two specific markers could be used together to distinguish alleles at Glu-B1x locus and accelerate wheat quality breeding by marker assisted selection.     

Comparative Analysis of Glycoside Hydrolases Activities from Phylogenetically Diverse Marine Bacteria of the Genus Arenibacter

A total of 16 marine strains belonging to the genus Arenibacter, recovered from diverse microbial communities associated with various marine habitats and collected from different locations, were evaluated in degradation of natural polysaccharides and chromogenic glycosides. Most strains were affiliated with five recognized species, and some presented three new species within the genus Arenibacter. No strains contained enzymes depolymerizing polysaccharides, but synthesized a wide spectrum of glycosidases. Highly active β-N-acetylglucosaminidases and α-N-acetylgalactosaminidases were the main glycosidases for all Arenibacter. The genes, encoding two new members of glycoside hydrolyses (GH) families, 20 and 109, were isolated and characterized from the genomes of Arenibacter latericius. Molecular genetic analysis using glycosidase-specific primers shows the absence of GH27 and GH36 genes. A sequence comparison with functionally-characterized GH20 and GH109 enzymes shows that both sequences are closest to the enzymes of chitinolytic bacteria Vibrio furnissii and Cellulomonas fimi of marine and terrestrial origin, as well as human pathogen Elisabethkingia meningoseptica and simbionts Akkermansia muciniphila, gut and non-gut Bacteroides, respectively. These results revealed that the genus Arenibacter is a highly taxonomic diverse group of microorganisms, which can participate in degradation of natural polymers in marine environments depending on their niche and habitat adaptations. They are new prospective candidates for biotechnological applications due to their production of unique glycosidases.     

Isolation and Analysis of the Cppsy Gene and Promoter from Chlorella protothecoides CS-41

Phytoene synthase (PSY) catalyzes the condensation of two molecules of geranylgeranyl pyrophosphate to form phytoene, the first colorless carotene in the carotenoid biosynthesis pathway. So it is regarded as the crucial enzyme for carotenoid production, and has unsurprisingly been involved in genetic engineering studies of carotenoid production. In this study, the psy gene from Chlorella protothecoides CS-41, designated Cppsy, was cloned using rapid amplification of cDNA ends. The full-length DNA was 2488 bp, and the corresponding cDNA was 1143 bp, which encoded 380 amino acids. Computational analysis suggested that this protein belongs to the Isoprenoid_Biosyn_C1 superfamily. It contained the consensus sequence, including three predicted substrate-Mg²⁺ binding sites. The Cppsy gene promoter was also cloned and characterized. Analysis revealed several candidate motifs for the promoter, which exhibited light- and methyl jasmonate (MeJA)-responsive characteristics, as well as some typical domains universally discovered in promoter sequences, such as the TATA-box and CAAT-box. Light- and MeJA treatment showed that the Cppsy expression level was significantly enhanced by light and MeJA. These results provide a basis for genetically modifying the carotenoid biosynthesis pathway in C. protothecoides.     

玉米耐盐基因ZmHKT1的序列变异分析

HKT(High-affinity potassium transporter,高亲和性钾转运蛋白)基因所编码的蛋白能起到维持植物体内的Na+/K+平衡的作用。在作物中HKT蛋白主要通过排出叶片中的Na+,从而提高植物耐盐性。对54份玉米自交系材料的Zm HKT1基因及上游序列进行多态性分析。结果表明,在3 784 bp的序列中,共有194个SNP和32个In Del。大部分变异集中在基因上游序列和内含子区,编码区的变异相对较少,说明编码区在进化和人工选择中承受了更大的选择压力。根据序列变异情况可将54份玉米自交系材料划分为15个单倍型,上游序列主要存在3种单倍型,而基因序列存在9种单倍型。遗传重组和连锁不平衡分析发现,全长序列只有3次重组事件发生,上游序列存在着非常强的连锁不平衡。     

黑麦基因组DNA甲基化修饰位点的MSAP分析

为了获得黑麦基因组DNA甲基化修饰水平、模式及位点等表观遗传信息,采用EcoR Ⅰ和Hpa Ⅱ / Msp Ⅰ双酶切建立适合于黑麦基因组的"甲基化敏感扩增多态性"(Methylation sensitive amplification polymorphism,MSAP)分析体系,在全基因组水平检测黑麦DNA甲基化修饰位点.以12对MSAP引物进行选择性扩增,共检测到甲基化修饰位点226个,"CCGG/GGCC"位点甲基化修饰比例为51.72%.对部分黑麦基因组甲基化修饰位点进行回收,最终分离了22条存在甲基化修饰的基因组DNA序列.BLAST比对分析结果表明,黑麦基因组中包括转座子序列、散在重复序列以及单拷贝蛋白质编码序列在内的多种类型DNA序列中均存在DNA甲基化修饰现象.同时发现,在甲基化检出序列中都存在明显的"CpG"二核苷酸成簇富集现象,这些区域分布与MSAP分析结果相一致.在此基础上,对应用MSAP技术分离黑麦基因组DNA甲基化修饰位点的有效性以及黑麦基因组序列中DNA甲基化修饰潜在位点分布特征和生物意义进行了讨论.     

Puroindoline genes and proteins in tetraploid and hexaploid species of Triticum

Six tetraploid (5 Triticum turgidum and 1 Triticum timopheevii) and four hexaploid (three Triticum aestivum and one Triticum kiharae) taxa of Triticum were studied in order to identify novel variation in Pin genes and proteins which can be exploited in the improvement of cultivated wheat. Western blotting with a highly specific antibody showed that puroindoline proteins were present in all of the hexaploid lines but were absent from the tetraploids. The immunoreactive bands differed slightly in their relative mobilities and their relative amounts, which could have resulted from variation in the allelic forms of Pin a and Pin b. This was supported by HPLC analyses which showed differences in the retention times and peaks heights of the putative puroindoline components in T. kiharae and T. timopheevii. Sequence analyses of cDNAs also showed variation in the sequences of expressed puroindoline genes. In particular, a sequence encoding a new form of Pin b was present in T. aestivum ssp. macha.