Variety classification method for barley or malt using gene diagnosis and the primer used therefor

Abstract: The variety of barley or malt is quickly and conveniently classified by amplifying the genomic DNA by PCR with the primer consisting of the sequence complementary to the gene that is important for brewing and examining the difference in the base sequence of said DNA.

Description: The present invention relates to a method for classifying the variety of malting barley or malt using gene diagnosis and primers used for said method. For variety classification of barley and malt, there has been conventionally used a method for classifying the variety by comparing an SDS polyacrylamide gel electrophoretic pattern of hordein and esterase contained therein. In addition, a classification method using gene diagnosis has recently been developed (e.g., Chee et al., J. Am. Soc. Brew. Chem., 51, 93 (1993)). However, the variety classification method by way of comparing the electrophoretic pattern of hordein and esterase is not necessarily to be an accurate classification method, because the electrophoretic pattern may be modified according to growing conditions of barley or due to the degradation of the hordein and esterase by protease during malting process. Furthermore, since most of classification methods using gene diagnosis use genes from unidentified origin as probe or primer, there has been a problem that results obtained by the method cannot be directly correlated with the effect on the quality of brew, even though mutation of materials or contamination of materials with other varieties are indicated. The present invention has been made considering the problem described above, and aims to provide a more satisfactory method for classifying barley or malt using gene diagnosis from the viewpoint of breeding malting barley or quality control of brewing materials. The solution to this problem is achieved by the provision of the embodiments characterised by the patent claims. In view of the situations described above, through continual ardent studies, the present inventors identified sites wherein the base sequence differs among varieties in genes which are important for brewing, and accomplished the present invention. That is, the present invention provides a variety classification method for barley or malt by performing polymerase chain reaction (PCR) with a set of primers designed to flank the site of a gene which is important for brewing, wherein the base sequence of the gene is different among varieties so as to amplify the genomic DNA of barley or malt, and classifying the variety of barley or malt based on the difference in base sequence of the amplified DNA. In a preferred embodiment of the present invention the gene important for brewing which is used for amplification by PCR is a β-amylase gene, an α-amylase gene, a β-glucanase gene or a gene encoding B1-Hordein. Oligonucleotides useful for the amplification of these genes are depicted in Table 1. According to the invention it is possible to use any primer set alone in order to amplify only one of the genes of interest or to use combinations of the primer sets in order to amplify any possible combination of two or more of the genes of interest. Furthermore, it is possible to use oligonucleotides having sequences complementary to those depicted in Table 1. The present invention also provides primers used for the variety classification method. Primers according to the present invention can be synthesized with a commercial automated DNA synthesizer using the β-cyanoethyl phosphoramidite method or thiophosphite method. More precisely, the present invention provides a variety classification method for barley or malt comprising amplification of the genomic DNA of barley or malt by PCR with the primer having the base sequence complementary to the gene which is important gene in the brewing, and examination of the difference of base sequence of the amplified DNA, The present invention also provides a variety classification method for barley or malt comprising the amplification of genomic DNA of barley or malt by PCR, which is performed with either a set of oligonucleotides consisting of the sequence of (1) 5'-TTCAAAGCAGCAGCAGCG-3' (SEQ ID NO: 1) and (2) 5'-TTCTTCTGGTGCGCTCATC-3' (SEQ ID NO: 2) or a set of oligonucleotides composed of the sequences complementary to the nucleotides as the essential primer, and also a set of oligonucleotides consisting of the sequence of (3) 5'-ATAAGTGGGCATCAATTCGGC-3' (SEQ ID NO: 3) and.(4) 5'-GTGTGTCTGGCCAGGTAT-3' (SEQ ID NO: 4) or a set of oligonucleotides composed of the sequence complementary to them as the selective essential primer, and using either one of the two sets of essential primers and either one of the two sets of selective essential primers or either one primer thereof, and the classification based on the difference in the base sequence of said DNA. Furthermore, the present invention provides a variety classification method for barley or malt comprising the amplification of the genomic DNA of barley or malt by PCR, which is performed with oligonucleotides consisting of the sequence of (5) 5'-CGTGAAAAAACCGCCGCCGA-3' (SEQ ID NO: 5), (6) 5'-CTTTCTCTCTCTAGCTGCGT-3' (SEQ ID NO: 6), (7) 5'-CCACCATGAAGACCTTCCTC-3' (SEQ ID NO: 7) and (8) 5'-TCGCAGGATCCTGTACAACG-3' (SEQ ID NO: 8) or oligonucleotides composed of the sequence complementary to them as a group of selective primers and further using, in addition to the essential primers and the selective essantial primers, a combination of at least any one or any two primers from the group of selective primers, and the classification of a variety of barley or malt based on the difference in the base sequence of the amplified DNA. Furthermore, the present invention provides oligonucleotides useful as PCR primers comprising nucleotide sequences as depicted in any one of the sequence listings SEQ ID NO:1 to 8 or sequences complementary to these nucleotide sequences. The present invention also relates to the use of the oligonucleotides according to the invention as PCR primers. According to the present invention, the genomic DNA is first extracted from the sample of barley or malt. Extraction of the genomic DNA may be carried out, for example, by a CTAB method (Nucleic Acids Res., 8, 4321 (1980)). Then, a portion of the targeted gene is amplified by applying the primers of the present invention to the genomic DNA. The partial amplification of the genomic DNA may be carried out, for example, by PCR (Science, 230, 1350 (1985)). Then, the variety of barley or malt is classified either by the base sequence determination of amplified DNA thus obtained or based on the difference in the base sequence detected by electrophoresis on denatured gradient gel or temperature gradient gel, or on the restriction enzyme cleavage pattern. Since the method of the present invention aims to target the gene which is important for brewing, it is highly possible that results obtained may directly influence the quality of brew. Therefore, the method may become a satisfactory variety classification method from the viewpoint of breeding of brewer's barley or the quality control of brewing material. Fig. 1 is a photograph of the polyacrylamide gel electrophoretic pattern of DNAs which were amplified by PCR with primers (1) and (2), and then treated with restriction enzymes NcoI and EcoT22I. In the figure, 1 to 10 correspond to the variety of barley, A, B, B', C, and C' denote the type of electrophoretic pattern, and M is DNA MW marker 9 (Nippon Gene). Fig. 2 is a photograph of the polyacrylamide gel electrophoretic pattern of DNAs which were amplified by PCR with primers (3) and (4), and then treated with restriction enzyme TaqI. In the figure, A, B and C denote the type of electrophoretic pattern and M is DNA MW marker 9 (Nippon Gene). Fig. 3 is a photograph of polyacrylamide gel electrophoretic pattern of DNAs which were amplified by PCR with primers (5) and (6), and then treated with restriction enzyme HaeIII. In the figure, A and B denote the type of electrophoretic pattern and M is DNA MW marker 9 (Nippon Gene). Fig. 4 is a photography of polyacrylamide gel electrophoretic pattern of DNAs which are amplified by PCR with primers (7) and (8) (left half, A to E) and those which were then treated with restriction enzyme HaeIII (right half, A to E). In the figure, A, B, C, D and E denote the type of polyacrylamide gel electrophoretic pattern, and M is DNA MW marker 9 (Nippon Gene) and M' DNA MW marker 2 (Nippon Gene). The invention will now be described with reference to specific examples, however, it should understood that the technical scope of the invention is not to be construed as being limited to them in any way. Example 1 Extraction of the Genomic DNA In this embodiment, as the variety of barley or malt, Amagi Nijo (called Variety No. 1 hereinafter), Haruna Nijo (called Variety No. 2 hereinafter), Misato Golden (Variety No. 3 hereinafter), Clipper (called Variety No. 4 hereinafter), Schooner (called Variety No. 5 hereinafter), Stirling (called Variety No. 6 hereinafter), Harrington (called Variety No. 7 hereinafter), Manley (called Variety No. 8 hereinafter), Ellice (called Variety No. 9 hereinafter) and Alexis (called Variety No. 10 hereinafter) were used. Embryos of barley or leaf buds of malt were taken out and the genomic DNA was extracted from them using "Plant Genome Extraction Kit" (Clontech). Example 2 Design and synthesis of primers Various primers were designed from known base sequences of the barley genes important for brewing, including those of β-amylase (J. Biochem., 115, 47 (1994)), α-amylase (Plant Mol. Biol., 12, 119 (1989)), β-glucanase (Eur. J. Biochem., 194, 831 (1990)), and B1-hordein (Nucleic Acid Res., 13, 7327 (1985)). PCR was performed with these primers, and DNAs thus amplified were examined for the difference in the base sequence among varieties using temperature gradient gel electrophoresis or based on the base sequence determination. As a result, it became clear that, using the primer (1) to (8), the DNA region wherein the base sequence is different among varieties can be amplified, and utilizing the restriction enzyme site in that region, the variety classification of barley or malt may become possible. Synthesis and purification of primers were entrusted to Sawady Technology Co. Ltd. Example 3 Variety classification method using primers (1) and (2) A PCR mixture (100 µ l) which contained the genomic DNA (100 ng) extracted from 10 barley grains of each variety, dNTPs (20 nmol each), primers (1) and (2) (10 pmol each) and Taq DNA polymerase (2.5 U) was subjected to 33 cycles of reaction wherein each cycle consisted of incubating the mixture in sequence at 94°C for 1 min, 55°C for 2 min, and 72°C for 1 min, and then finally treated at 72°C for 5 min. After the completion of the PCR, restriction enzymes NcoI and EcoT22I (5 U each) and a buffer for the enzymatic reaction were added to the reaction mixture (8 µ l), and the mixture was incubated at 37°C for 1 h. This reaction mixture was electrophoresed on 5% polyacrylamide gel. After the electrophoresis, the gel was stained with ethidium bromide, and then the DNA were made visible by UV exposure. Results are shown in Fig. 1. As shown in this figure, from the electrophoretic pattern of the fragments of DNAs obtained by digestion with restriction enzymes NcoI and EcoT22I, 10 varieties of barley could be classified into 5 types (A, B, B', C and C'). Furthermore, based on results of analyses on single grains, Variety Nos 5 and 10 were found to be a mixed type consisting of either C and C' or B and C, therefore denoted as C/C' and B/C respectively. Example 4 Variety classification method using primers (3) and (4) Analysis was performed under similar conditions to those described for Example 3, except that PCR was performed with the primer sequences (3) and (4) instead of (1) and (2) and subjected to 30 cycles instead of 33, and the restriction enzyme digestion was carried out with TaqI at 65°C instead of NcoI and EcoT22I at 37°C. As a result, as shown in Fig. 2, the electrophoretic pattern could be classified into 3 types (A, B and C). Example 5 Variety classification method using primers (5) and (6) Analysis was performed under similar conditions to the described for Example 3, except that PCR was performed with the primer sequences (5) and (6) instead of (1) and (2) and subjected to 30 cycles instead of 33, and restriction enzyme digestion was carried out with HaeIII instead of NcoI and EcoT22I. As a result, as shown in Fig. 3, the electrophoretic pattern could be classified into 2 types (A and B). Example 6 Variety classification method using primers (7) and (8) PCR was performed under similar conditions to those described for Example 3, except for using the primer sequences (7) and (8), subjected to 30 cycles instead of 33, and annealing at 57°C instead of 55°C. A portion of the PCR products were electrophresed and the result was as shown on the left half of Fig. 4. Then, the PCR products were digested with the restriction enzyme HaeIII under the similar conditions to those described for Example 3, and electrophoresed. The fragment patterns were as shown on the right half of Fig. 4. By comparing the results from intact and digested PCR products, as shown in Fig. 4, the electrophoresis pattern could be classified into 5 types (A, B, C, D and E). Example 7 Variety classification method by overall evaluation Results of the type classification performed in Examples 3 to 6 are summarized in Table 2. These results show that it is possible to classify all of the 10 varieties by using the overall evaluation. Example 8 Purity test of variety Out of barley or malt purchased, 100 grains or 100 leaf buds as one sample lot were subjected to analysis of type classification described above in Examples 3 to 6. As a result, DNA fragments corresponding to the type of variety indicated at the time of purchase were identified, and the purity of variety could be determined by examining whether DNA fragments were contaminated with different types derived from other varieties. When contamination with other varieties is expected, the purity of the sample can be estimated to a certain extent by quantifying the intensity of an electrophoretic band with an image analyzer. Furthermore, when each single grain or leaf bud is subjected to similar analysis, the extent of contamination and type of contaminating variety may be possibly determined qualitatively as well as quantitatively. Since primers according to the present invention are prepared to target the gene which is important for brewing, it is highly possible that results obtained by this invention will directly affect the quality of brewing products. Therefore, using the variety classification method with such primers, a satisfactory variety classification can be carried out from the viewpoint of breeding of barley for brewing and the quality control of materials used for brewing. SEQUENCE LISTING (1) GENERAL INFORMATION: (i) APPLICANT: (A) NAME: Sapporo Breweries, Ltd. (B) STREET: 20-1, Ebisu 4-chome, Shibuya-ku (C) CITY: Tokyo (E) COUNTRY: Japan (F) POSTAL CODE (ZIP): 150 (ii) TITLE OF INVENTION: Variety classification method for barley or malt using gene diagnosis and the primer used therefor (iii) NUMBER OF SEQUENCES: 8 (iv) COMPUTER READABLE FORM: (A) MEDIUM TYPE: Floppy disk (B) COMPUTER: IBM PC compatible (C) OPERATING SYSTEM: PC-DOS/MS-DOS (D) SOFTWARE: Patent In Release #1.0, Version #1.30 (EPO) (v) CURRENT APPLICATION DATA: APPLICATION NUMBER: EP 95 11 5438.4 (vi) PRIOR APPLICATION DATA: (A) APPLICATION NUMBER: JP Hei 6-261286 (B) FILING DATE: 29-SEP-1994 (2) INFORMATION FOR SEQ ID NO: 1: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 18 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: other nucleic acid (A) DESCRIPTION: /desc = "oligonucleotide" (xi) SEQUENCE DESCRIPTION: SEO ID NO: 1: (2) INFORMATION FOR SEQ ID NO: 2: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 19 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: other nucleic acid (A) DESCRIPTION: /desc = "oligonucleotide" (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 2: (2) INFORMATION FOR SEQ ID NO: 3: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 21 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: other nucleic acid (A) DESCRIPTION: /desc = "oligonucleotide" (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 3: (2) INFORMATION FOR SEQ ID NO: 4: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 18 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: other nucleic acid (A) DESCRIPTION: /desc = "oligonucleotide" (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 4: (2) INFORMATION FOR SEQ ID NO: 5: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 20 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: other nucleic acid (A) DESCRIPTION: /desc = "oligonucleotide" (xi) SEQUENCE DESCRIPTION: SEO ID NO: 5: (2) INFORMATION FOR SEQ ID NO: 6: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 20 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: other nucleic acid (A) DESCRIPTION: /desc = "oligonucleotide" (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 6: (2) INFORMATION FOR SEQ ID NO: 7: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 20 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: other nucleic acid (A) DESCRIPTION: /desc = "oligonucleotide" (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 7: (2) INFORMATION FOR SEQ ID NO: 8: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 20 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: other nucleic acid (A) DESCRIPTION: /desc = "oligonucleotide" (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 8:

Claims: A method for classifying a variety of barley or malt by amplifying genomic DNA of barley or malt by PCR with one or more pairs of primers comprising nucleotide sequences complementary to one or more genes important for brewing, and examining differences in the nucleotide sequence of the amplified DNA, wherein the primer pair(s) is (are) selected from the group consisting of (i) and respectively, or nucleotide sequences complementary to these sequences: (ii) and respectively, or nucleotide sequences complementary to these sequences; and (iii) and respectively, or nucleotide sequences complementary to these sequences. The method of claim 1, wherein the genomic DNA of barley or malt is further amplified by PCR with another pair of oligonucleotides as primers which comprise the nucleotide sequence (iv) and respectively, or nucleotide sequences complementary to these sequences. An oligonucleotide comprising a nucleotide sequence as depicted in any one of the sequence listings SEQ NO:1 to 6 or a nucleotide sequence complementary to any one of these sequences. Use of an oligonucleotide of claim 3 as a PCR primer.

Inventors: ARAKI SHIGEKI, TSUCHIYA YOUICHI, ARAKI, SHIGEKI, TSUCHIYA, YOUICHI, Araki, Shigeki, c/o Sapporo Breweries Ltd., Tsuchiya, Youichi, c/o Sapporo Breweries Ltd.
Applicants: SAPPORO BREWERIES, SAPPORO BREWERIES LTD.
Application year: 1995
Main classification: C12Q1
IPC codes: C07H21, C12Q1, G01N33, C12C1, C12N15