Utilization of Different <Emphasis Type="Italic">Bmy1</Emphasis> Intron III Alleles for Predicting β-Amylase Activity and Thermostability in Wild and Cultivated Barley

The third intron of barley (Hordeum vulgare L.) β-amylase 1 (Bmy1) is extremely polymorphic. The use of specific insertion/deletions (indels) in the third intron as markers for cultivar development has been recommended based on associations with β-amylase activity and thermostability. The third intron of Bmy1 in 40 barley genotypes was sequenced and aligned with 15 Bmy1 intron III sequences from GenBank and four alleles (Bmy1.a, Bmy1.b, Bmy1.c, and Bmy1.d) were identified based on indels of 126, 38, 11, and 21 bp. β-Amylase activity and thermostability were assayed in 22 North American cultivars and 12 wild barley genotypes. Cultivars carrying the Bmy1.a and Bmy1.b alleles had β-amylase activity ranges calculated on a fresh weight (FW) basis of 1.8- and 1.5-fold, respectively, and thermostability ranges of 8.8- and 1.2-fold, respectively. β-Amylase activity calculated on a protein basis yielded a 2.4- and 1.4-fold range for Bmy1.a and Bmy1.b, respectively. Significantly different activities were observed in cultivars carrying either Bmy1.a or the Bmy1.b allele when calculated on a FW basis and the Bmy1.a allele when calculated on a protein basis. Significantly different thermostabilities were observed in cultivars carrying the Bmy1.a allele. Wild barleys were found to carry Bmy1.a, Bmy1.b, and Bmy1.c alleles with β-amylase activity ranges calculated on a FW basis of 1.7-, 1.7-, and 2.6-fold, respectively, and thermostability ranges of 1.3-, 1.4-, and 2.1-fold, respectively. β-Amylase activity measured on a protein basis identified a 1.3-, 1.4-, and 2.1-fold range for Bmy1.a, Bmy1.b, and Bmy1.c, respectively. Significantly different activities were found in genotypes with any of these three alleles when calculated on a FW basis yet only in those with the Bmy1.c allele when calculated on a protein basis. Significantly different thermostabilities in genotypes carrying either the Bmy1.b or Bmy1.c allele were observed. In the germplasm studied here, the Bmy1 intron III alleles are not reliable predictors of β-amylase activity and thermostability.     

Identification of Ppd-B1 alleles in common wheat cultivars by CAPS marker

Photoperiod response is a major determinant of the duration of growth stages in common wheat. In common wheat, many genes play a role in determining flowering time, but the Ppd genes located on the homoeologous group 2 play a major role. Of these Ppd-B1 is located on the short arm of 2B. In 107 common wheat cultivars grown in Poland and neighboring countries, the identification of Ppd-B1 alleles using in-del analysis by using a CAPS markers was investigated. 87 cultivars were shown to carry dominant Ppd-B1 alleles. This shows that Ppd-B1 alleles is have been widely used in common wheat breeding programme in these countries. Recessive ppd-B1 alleles were found only in 20 cultivars (12 Polish, 5 former Soviet Union, 2 German, 1 Swedish).     

Distribution of the Allelic Variants of Three Hordein-Coding Loci of Spring Barley in Russia

The distribution of alleles of the hordein-coding loci Hrd A, Hrd B, and Hrd Fwas investigated in 101 spring barley cultivars grown in 12 regions of Russia in 1999. It was demonstrated that the genetic structure of populations of these cultivars in the regions studied was affected by climatic factors, such as the average June temperature and average annual rainfall. The distribution patterns of the Hrdalleles in 25 agricultural provinces of the former Soviet Union and 12 regions of Russia were compared. The factor structure of genetic variability in the regions of barley cultivation in the former Soviet Union was found to differ from that in Russia. The change of the factor structure is likely to be related to diminishing the barley-production area under study and to the new administrative subdivision.     

Distribution of β-amylase I haplotypes among European cultivated barleys

The barley β-amylase I (Bmy1) locus encodes a starch breakdown enzyme whose kinetic properties and thermostability are critical during malt production. Studies of allelic variation at the Bmy1 locus have shown that the encoded enzyme can be commonly found in at least three distinct thermostability classes and demonstrated the nucleotide sequence variations responsible for such phenotypic differences. In order to explore the extent of sequence diversity at the Bmy1 locus in cultivated European barley, 464 varieties representing a cross-section of popular varieties grown in western Europe over the past 60 years, were genotyped for three single nucleotide polymorphisms chosen to tag the four common alleles found in the collection. One of these haplotypes, which has not been explicitly recognised in the literature as a distinct allele, was found in 95% of winter varieties in the sample. When release dates of the varieties were considered, the lowest thermostability allele (Bmy1-Sd2L) appeared to decrease in abundance over time, while the highest thermostability allele (Bmy1-Sd2H) was the rarest allele at 5.4% of the sample and was virtually confined to two-row spring varieties. Pedigree analysis was used to track transmission of particular alleles over time and highlighted issues of genetic stratification of the sample.     

Genetic variation of <Emphasis Type="Italic">Bmy1</Emphasis> alleles in barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.) investigated by CAPS analysis

The enzyme beta-amylase is one of the most important hydrolytic enzymes in the grain of malting barley and is encoded by the gene Bmy1. To learn more about its structure and function, a total of 657 barley accessions including 541 Hordeum vulgare ssp. vulgare (HV), and 116 H. vulgare ssp. spontaneum (HS) were selected for the cleaved amplified polymorphic sequence (CAPS) analysis. These materials, covering all the 16 kinds of beta-amylase phenotypes screened from more than 8,500 accessions of the world barley germplasm, were classified into 13 CAPS types in the present study. A combined assay of phenotypes and CAPS types revealed extensive genetic variation at the Bmy1 locus, and in total 23 Bmy1 allele types were identified. The newly identified alleles (A-I-11, A-II-6, A-II-7, A-II-10, B-I-3, B-I-12 and B-I-13) provided us with a novel resource for barley breeding and Bmy1 study. In HV barley, six out of seven major allele types (C-II-1, B-II-2, B-Ia-3, A-II-5, A-II-6, and A-II-7) were shared with HS barley; the B-I-8 allele, which was predominant in north European cultivated barley, was found to be unique. Remarkably, very low Bmy1 genetic variation was detected in Tibetan barleys, which puts the validity of the hypothesis that Tibet is one of the original centers of cultivated barley into question.     

黄淮南片冬麦区主导品种春化基因及冬春性分析

以1950～2007年黄淮南片冬麦区的127个主导小麦品种为材料,利用第5同源群的春化基因分子标记对其进行了春化基因检测,并分析了小麦品种的春化基因与其冬春性的对应关系及黄淮南片冬麦区8次品种更换中春化基因与品种冬春性的演变规律.结果表明,参试品种中没有品种携带显性Vrn-A1基因,7个品种含有Vrn-B1基因(5.5%),2个品种含有Vrn-B1+Vrn-D1基因(1.6%),56个品种含有Vrn-D1基因(44.1%).春化基因类型与品种冬春特性基本相符,春化基因控制着小麦品种的冬春特性.主导品种含春化显性基因频率的变化趋势与冬春性变化规律存在较大差异,与传统方法相比,仅用春化基因来确定品种冬春性存在一定的不完善之处.采用春化基因分子标记与传统的冬春性鉴定方法相结合来认识品种冬春性、预测品种的抗寒性对黄淮南片冬麦区的小麦品种利用更具有指导意义.     

Uniformity of distributing alleleic variants of three hordein-coding loci of spring barley in the Russian Federation]

The distribution of alleles of the hordein-coding loci Hrd A, Hrd B, and Hrd F was investigated in 101 spring barley cutivars grown in 12 regions of Russia in 1999. It was demonstrated that the genetic structure of populations of these cutivars in the regions studied was affected by climatic factors, such as the average June temperature and average annual precipitation. The distribution patterns of the Hrd alleles in 25 agricultural provinces of the former Soviet Union and 12 regions of Russia were compared. The factor structure of genetic variability in the regions of barley cultivation in the former Soviet Union was found to differ from that in Russia. The change of the factor structure is likely to be related to diminishing the barley-production area under study and to the new administrative subdivision.     

Geographical variation of the alleles at the two prolamin loci, Pro1 and Pro2, in foxtail millet, Setaria italica (L.) P. Beauv

Allelic variation at the two prolamin loci (Pro1 and Pro2) and its geographical distribution in 560 local cultivars of foxtail millet (Setaria italica) mainly from Eurasia were studied using SDS-polyacrylamide gel electrophoresis (SDS-PAGE). Genetic analysis of a newly detected polymorphic band, band 6, indicated that it is controlled by an allele at the Pro2 locus, which was designated as Pro2f. Two alleles (Pro1a and Pro1null) at the Pro1 locus and six alleles (Pro2a, Pro2b, Pro2c, Pro2d, Pro2e and Pro2f) at the Pro2 locus were detected among the cultivars examined. Although the frequency of the Pro1a allele varied from 0% in the Nansei islands of Japan and Africa to 66% in Afghanistan, no apparent trend was observed in geographical distribution. In contrast, two common alleles at the Pro2 locus, Pro2b and Pro2f, had clear differential geographical distribution. The Pro2b allele was most frequent in Europe and decreased in frequency eastwards. The Pro2f allele occurred frequently in subtropical and tropical regions including the Nansei islands of Japan, the Philippines, Nepal, India, Pakistan and Africa. All eight alleles at the Pro1 and Pro2 loci occurred in China, suggesting China is a center of diversity. The origin of geographical differentiation of local cultivars into a "tropical group" characterized by the Pro2f allele and other genes was discussed.     

Diversity of Bacillus anthracis strains in Georgia and of vaccine strains from the former Soviet Union

Despite the increased number of anthrax outbreaks in Georgia and the other Caucasian republics of the former Soviet Union, no data are available on the diversity of the Bacillus anthracis strains involved. There is also little data available on strains from the former Soviet Union, including the strains previously used for vaccine preparation. In this study we used eight-locus variable-number tandem repeat analyses to genotype 18 strains isolated from infected animals and humans at different sites across Georgia, where anthrax outbreaks have occurred in the last 10 years, and 5 strains widely used for preparation of human and veterinary vaccines in the former Soviet Union. Three different genotypes affiliated with the A3.a cluster were detected for the Georgian isolates. Two genotypes were previously shown to include Turkish isolates, indicating that there is a regional strain pattern in the South Caucasian-Turkish region. Four of the vaccine strains were polymorphic, exhibiting three different patterns of the cluster A1.a genotype and the cluster A3.b genotype. The genotype of vaccine strain 71/12, which is considered an attenuated strain in spite of the presence of both of the virulence pXO plasmids, appeared to be a novel genotype in the A1.a cluster.     

Allelic diversity at gliadin-coding gene loci in cultivars of spring durum wheat (<Emphasis Type="Italic">Triticum durum</Emphasis> Desf.) Bred in Russia and former Soviet republics in the 20th century

Allelic diversity at five gliadin-coding gene loci has been studied in the most important spring durum wheat cultivars released in Russia and former Soviet republics in the 20th century (66 cultivars). Seven, 5, 8, 13, and 2 allelic variants of blocks of gliadin components controlled by the loci Gli-A1 ^d , Gli-B1 ^d , Gli-A2 ^d , Gli-B2 ^d , and Gli-B5 ^d , respectively, have been identified. The allelic diversity did not exhibit a consistent trend during the period studied. Nei’s diversity index (H) was 0.68 in the period from 1929 to 1950, increased to 0.70 in 1951–1980, and decreased to 0.58 after the year 1981. It has been found that the most frequent alleles in this collection are relatively rare in other regions of the world, which suggests unique ways of the formation of the diversity of durum wheat cultivars in the former Soviet Union. The efficiency of electrophoresis of storage proteins as a method for identification of durum wheat cultivars by the gliadin electrophoretic pattern has been estimated.     

Diversity of Bacillus anthracis Strains in Georgia and of Vaccine Strains from the Former Soviet Union

Despite the increased number of anthrax outbreaks in Georgia and the other Caucasian republics of the former Soviet Union, no data are available on the diversity of the Bacillus anthracis strains involved. There is also little data available on strains from the former Soviet Union, including the strains previously used for vaccine preparation. In this study we used eight-locus variable-number tandem repeat analyses to genotype 18 strains isolated from infected animals and humans at different sites across Georgia, where anthrax outbreaks have occurred in the last 10 years, and 5 strains widely used for preparation of human and veterinary vaccines in the former Soviet Union. Three different genotypes affiliated with the A3.a cluster were detected for the Georgian isolates. Two genotypes were previously shown to include Turkish isolates, indicating that there is a regional strain pattern in the South Caucasian-Turkish region. Four of the vaccine strains were polymorphic, exhibiting three different patterns of the cluster A1.a genotype and the cluster A3.b genotype. The genotype of vaccine strain 71/12, which is considered an attenuated strain in spite of the presence of both of the virulence pXO plasmids, appeared to be a novel genotype in the A1.a cluster.     

Dynamics of Genetic Variation at Gliadin-Coding Loci in Saratov Cultivars of Common Wheat Triticum aestivum L. over Eight Decades of Scientific Breeding

Based on analysis of gliadin patterns in common wheat cultivars bred at the Research Institute of Agriculture of the Southeast, allele composition dynamics in gliadin loci has been surveyed for the period of over eight decades. It was shown that long-term breeding of the wheat cultivars involved gradual replacement of alleles characteristic of ancient cultivars for those widely spread in the world, which are probably linked with alleles that currently confer advantage to their carriers. The process of reduction of interpopulation genetic diversity in wheat (with special reference to the allele frequency dynamics at gliadin loci) is discussed. This process is responsible for genetic erosion of the species.     

Molecular characterisation of indigenous Swedish apple cultivars based on SSR and S-allele analysis

Trees of 68 apple cultivars, aimed for preservation by the 'National Program for diversity of cultivated plants' as mandate cultivars, were analysed using a set of 10 SSR (simple sequence repeat) primer pairs and the self-incompatibility (S-)locus to evaluate genetic diversity and reveal inter-cultivar relationships. The 12 polymorphic SSR loci exhibited 2 to 15 alleles, with expected heterozygozity (H(e)) ranging from 0.36 to 0.88 and a mean of 0.74. Numerous alleles were classified as rare or unique (35% and 18% respectively). For the S-locus, a total of 14 alleles were identified in this study. Five alleles, S1-S3, S5 and S7 had frequencies ranging from 11 to 18%, whereas the remaining 9 alleles were below 6%. All sexually obtained cultivars could be distinguished with the set of SSR loci. Sports were identical with their progenitors in two cases, but differed in one SSR allele in a third case. An SSR-based dendrogram, based on Roger's genetic distances, did not reveal any clear pattern of clustering. The genetic distances were, however, correlated with a corresponding matrix obtained in a previously conducted RAPD-based study of the same cultivars. Non-mandate parents of Swedish mandate cultivars together with some other reference cultivars were included in this study to check the accuracy of allele scoring, verify parentage and compare the results of this study with those presented in previously published studies. Some discrepancies in allele sizing were revealed and the possibilities of avoiding this problem are discussed.     

Genetic differentiation of common wheat cultivars using multiple alleles of gliadin-coding loci

The alleles of gliadin-coding loci have been identified in 105 spring common wheat cultivars bred in Omsk and Saratov by polyacrylamide gel electrophoresis. It has been shown that 49% of the Omsk cultivars and 40% of the Saratov cultivars are heterogeneous, i.e., composed of several biotypes that differ in alleles of the gliadin-coding loci. A total of 278 genotypes have been determined (170 in the Saratov cultivars and 112 in the Omsk cultivars); in these two groups of cultivars, four genotypes are identical. Due to this heterogeneity, the cultivars bred in Omsk and Saratov can be differentiated in a statistically significant manner despite their close kinship, which allows them to be ascribed an accession to a particular breeding center based on the gliadin pattern and the number or frequency of biotypes, as well as to determine its species affiliation with a 95% probability. Close relations prevent 5% of the Saratov cultivars and 4.4% of the Omsk cultivars from being distinguished within populations, since they have identical alleles of gliadin-coding loci.     

Genotyping of Yersinia pestis: variability of locus (CAAA)n in natural strains isolated in territory of former SSSR

Genome polymorphism by the locus (CAAA)n was studied in 69 strains of Yersinia pestis isolated from natural foci of the former Soviet Union. The polymorphism was found to be represented by ten alleles in chromosomes, which could be regarded as evidence of variability of this VNTR-locus (diversity index, DI = 0.86). The value of DI was found to vary substantially: from 0.24 in a group of vole strains from seven isolates from the Transcaucasian highlands to 0.77 in nine strains from the Central Asia desert focus. The allele polymorphism of the variable locus (CAAA)n in natural strains of Y. pestis was suggested to be used as a possible genetic marker of the strain. It was concluded that the oligonucleotide primers used in polymerase chain reaction should be upgraded to the genotyping accuracy.     

Haplotype diversity in the endosperm specific β-amylase gene Bmy1 of cultivated barley (Hordeum vulgare L.)

Five single nucleotide polymorphism (SNP) sites corresponding to substitutions in the protein sequence of the β-amylase gene Bmy1 at amino acid (AA) positions 115, 165, 233, 347 and 430 were genotyped in 493 cultivated barley accessions by Pyrosequencing and a CAPS assay. A total of 6 different haplotypes for the Bmy1 gene were discovered of which 4 haplotypes were identified as previously described alleles Bmy1-Sd1, Bmy1-Sd2L, Bmy1-Sd2H and Bmy1-Sd3, while 2 haplotypes were new. A broad spectrum of haplotypes was found in spring barleys, while the winter barleys were dominated by the newly described haplotype Bmy1-Sd4. Individual haplotype frequencies varied between the geographic regions.Three pairs of SNP loci within the gene showed highly significant (P<0.0001) elevated values of linkage disequilibrium (LD) with r ² > 0.6. In the European and Asian subpopulations different loci were in linkage disequilibrium due to the differences in haplotype frequency distributions. By applying LD data to select haplotype tagging SNPs, three SNP sites corresponding to AA positions 115, 233 and 347 were identified that allowed to discriminate 4 haplotypes and to capture 91.6% of the available diversity by distinguishing 452 out of 493 accessions. In a subset of 2-rowed German spring barley varieties 4 SNPs and 2 haplotypes had a significant association with the malting quality parameter final attenuation limit which is related to the total amylolytic enzymatic activity.     

Dynamics of genetic variation of Sartov cultivars of common wheat Triticum aestivum L. (from the gliadin-coding locus) after a an 80-year period of scientific selection

Based on analysis of gliadin patterns in common wheat cultivars developed at the Research Institute of Agriculture of the Southeast, profile dynamics in gliadin loci has been surveyed for the period of over eight decades. It was shown that long-term breeding of the wheat cultivars involved gradual replacement of alleles characteristic of ancient cultivars for those widely spread in the world, which are probably linked with alleles that currently confer advantage to their carriers. The process of reduction of inter-population genetic diversity in wheat (with special reference to the allele frequency dynamics at gliadin loci) is discussed. This process is responsible for genetic erosion of the species.     

Molecular characterization of vernalization response genes in Canadian spring wheat.

Vernalization response (Vrn) genes play a major role in determining the flowering/maturity times of spring-sown wheat. We characterized a representative set of 40 western Canadian adapted spring wheat cultivars/lines for 3 Vrn loci. The 40 genotypes were screened, along with 4 genotypes of known Vrn genes, using previously published genome-specific polymerase chain reaction primers designed for detecting the presence or absence of dominant or recessive alleles of the major Vrn loci: Vrn-A1, Vrn-B1, and Vrn-D1. The dominant promoter duplication allele Vrn-A1a was present in 34 of 40 cultivars/lines, whereas the promoter deletion allele Vrn-A1b was present in only 1 of the western Canadian cultivars (Triticum aestivum L. 'Rescue') and 2 of its derivative chromosomal substitution lines. The intron deletion allele Vrn-A1c was not present in any line tested. Only 4 of the western Canadian spring wheat cultivars tested here carry the recessive vrn-A1 allele. The dominant allele of Vrn-B1 was detected in 20 cultivars/lines. Fourteen cultivars/lines had dominant alleles of Vrn-A1a and Vrn-B1 in combination. All cultivars/lines carried the recessive allele for Vrn-D1. The predominance of the dominant allele Vrn-A1a in Canadian spring wheat appears to be due to the allele's vernalization insensitivity, which confers earliness under nonvernalizing growing conditions. Wheat breeders in western Canada have incorporated the Vrn-A1a allele into spring wheats mainly by selecting for early genotypes for a short growing season, thereby avoiding early and late season frosts. For the development of early maturing cultivars with high yield potential, different combinations of Vrn alleles may be incorporated into spring wheat breeding programs in western Canada.     

The frequency and distribution of thiopurine S-methyltransferase alleles in south Iranian population

Thiopurine methyltransferase (TPMT) catalyzes the S-methylation of thiopurine drugs such as 6-mercaptopurine, 6-thioguanine, and azathiopurine. Variability in TPMT activity is mainly due to genetic polymorphism. The frequency of the four allelic variants of the TPMT gene, TPMT*2 (G238C), TPMT*3A (G460A and A719G), TPMT*3B (G460A) and TPMT*3C (A719G) were determined in an Iranian population from south of Iran (n = 500), using polymerase chain reaction (PCR)-RFLP and allele-specific PCR-based assays. Four hundred seventy four persons (94.8%) were homozygous for the wild type allele (TPMT*1/*1) and twenty five people were TPMT*1/*3C (5%). One patient was found to be heterozygous in terms TPMT*1 and *2 alleles with genotype of TPMT*1/*2 (0.2%). None of the participants had both defective alleles. The TPMT*3C and *2 were the only variant alleles observed in this population. The total frequency of variant alleles was 2.6% and the wild type allele frequency was 97.4%. The TPMT*3B and *3A alleles were not detected. Distributions of TPMT genotype and allele frequency in Iranian populations are different from the genetic profile found among Caucasian or Asian populations. Our findings also revealed inter-ethnic differences in TPMT frequencies between different parts of Iran. This view may help clinicians to choose an appropriate strategy for thiopurine drugs and reduce adverse drug reactions such as bone marrow suppression.