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

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Abstract

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.

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References

  • Allison MJ, Swanston JS (1974) Relationships between b-amylase polymorphisms in developing, mature and germinating grains of barley. J Inst Brew 80:285–291

    CAS  Google Scholar 

  • Beschreibende Sortenliste. Getreide, Mais, Ölfrüchte, Leguminosen, Hackfrüchte. Bundessortenamt. 1994–2003. Landbuch Verlagsgesellschaft mbH. Hannover

  • Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA (2004) Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 74:106–120

    Article  PubMed  CAS  Google Scholar 

  • Clark SE, Hayes PM, Henson CA (2003) Effects of single nucleotide polymorphisms in β-amylase1 alleles from barley on functional properties of the enzymes. Plant Physiol Biochem 41(9):798–804

    Article  CAS  Google Scholar 

  • Clancey JA, Han F, Ullrich SE (2003) Comparative mapping of β-amylase activity QTLs among three barley crosses. Crop Sci 43:1043–1052

    Article  Google Scholar 

  • Coventry SJ, Collins HM, Barr AR, Jefferies SP, Chalmers KJ, Logue SJ, Langridge P (2003) Use of putative QTLs and structural genes in marker assisted selection for diastatic power in malting barley (Hordeum vulgare L). Aust J Agr Res 54:1241–1250

    Article  CAS  Google Scholar 

  • Dubcovsky J, Chen C, Yan L (2005) Moleculat characterization of the allelic variation at the VRN-H2 vernalization locus in barley. Mol Breeding 15:395–407

    Article  CAS  Google Scholar 

  • Eglinton JK, Langridge P, Evans DE (1998) Thermostability variation in alleles of barley β-amylase. J Cereal Sci 28:301–309

    Article  CAS  Google Scholar 

  • Erkkilä MJ, Ahokas H (2001) Special barley β-amylase allele in a Finnish landrace line HA52 with high grain enzyme activity. Hereditas 134:91–95

    Article  PubMed  Google Scholar 

  • Erkkilä MJ, Leah R, Ahokas H, Cameron-Mills V (1998) Allele-dependent barley grain β-amylase activity. Plant Physiol 117:679–685

    Article  PubMed  Google Scholar 

  • Franckowiak J (1997) Revised linkage maps for morphological markers in barley, Hordeum vulgare. Barley Genetics Newsletter 26:9–21

    Google Scholar 

  • Kaneko T, Kihara M, Ito K (2000) Genetic analysis of β -amylase thermostability to develop a DNA marker for malt fermentability improvement in barley, Hordeum vulgare. Plant Breeding 119:197–201

    Article  CAS  Google Scholar 

  • Kihara M, Kaneko T, Ito K (1998) Genetic variation of β-amylase thermostability among varieties of barley, Hordeum vulgare L., and relation to malting quality. Plant Breeding 117:425–428

    Article  CAS  Google Scholar 

  • Kreis M, Williamson M, Buxton B, Pywell J, Hejgaard J, Svendsen I (1987) Primary structure and differential expression of β-amylase in normal and mutant barley. Eur J Biochem 169:517–525

    Article  PubMed  CAS  Google Scholar 

  • Kreis M, Williamson M, Shewry PR, Sharp P, Gale M (1988) Identification of a 2nd locus encoding β-amylase on chromosome-2 of barley. Genetical Res 51:13–16

    CAS  Google Scholar 

  • Laurie DA, Pratchett N, Bezant JH, Snape JW (1995) RFLP mapping of 5 major genes and 8 quantitative trait loci controlling flowering time in a winter x spring barley (Hordeum vulgare L.) cross. Genome 38(3):575–585

    PubMed  CAS  Google Scholar 

  • Li C, Langridge P, Zhang X, Eckstein PE, Rossnagel BG, Lance RC, Lefol EB, Lu M, Harvey BL, Scoles GJ (2000) Hordeum vulgare cultivar RFLP-Harrington Bmy1 gene for Sd1 beta-amylase, complete cds. Direct submission to GenBank AB048949

  • Lin J-Z, Morell PL, Clegg MT (2002) The influence of linkage and inbreeding on patterns of nucleotide sequence diversity at duplicate alcohol dehydrogenase loci in wild barley (Hordeum vulgare ssp. spontaneum). Genetics 162:2007–2015

    PubMed  CAS  Google Scholar 

  • Ma YF, Evans DE, Logue SJ, Langridge P (2001) Mutations of barley β-amylase that improve substrate-binding affinity and thermostability. Mol Genet Genomics 266:345–52

    Article  PubMed  CAS  Google Scholar 

  • Malysheva L, Ganal MW, Röder MS (2004) Evaluation of cultivated barley (Hordeum vulgare L.) germplasm for the presence of thermostable alleles of β-amylase. Plant Breeding 123:128–131

    Article  CAS  Google Scholar 

  • Malysheva-Otto L, Ganal MW, Röder MS (2006) Analysis of molecular diversity, population structure and linkage disequilibrium in worldwide survey of cultivated barley germplasm (Hordeum vulgare L.). BMC. Genetics 7:6

    PubMed  Google Scholar 

  • Massa AN, Morris CF, Gill BS (2004) Sequence diversity of Puroindoline-a, Puroindoline-b, and the grain softness protein genes in Aegilops tauschii Coss. Crop Sci 44:1808–1816

    Article  CAS  Google Scholar 

  • Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76(10):5269–5273

    Article  PubMed  CAS  Google Scholar 

  • Palaisa K, Morgante M, Tingey S, Rafalski A (2004) Long-range pattern of diversity and linkage disequilibrium surrounding the maize gene Y1 gene are indicative of an asymmetric selective sweep. Proc Natl Acad Sci USA 101(26):9885–90

    Article  PubMed  CAS  Google Scholar 

  • Paris M, Jones MGK, Eglinton JK (2002) Genotyping single nucleotide polymorphisms for selection of barley β-amylase alleles. Plant Mol Biol Rep 20:149–159

    Article  CAS  Google Scholar 

  • Plaschke J, Ganal MW, Röder MS (1995) Detection of genetic diversity in closely related bread wheat using microsatellite markers. Theor Appl Genet 91:1001–1007

    Article  CAS  Google Scholar 

  • Polakova K, Laurie D, Vaculova K, Ovesna J (2003) Characterization of β-amylase alleles in 79 barley varieties with Pyrosequencing. Plant Mol Biol Rep 21:439–47

    Article  CAS  Google Scholar 

  • Potokina E, Prasad M, Malysheva L, Röder MS, Graner A (2006) Expression genetics and haplotype analysis reveal cis regulation of serine carboxypeptidase I (Cxp1), a candidate gene for malting quality in barley (Hordeum vulgare L.). Func Integr Genomics 6: 25–35

    Article  CAS  Google Scholar 

  • Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ESIY (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98(20):11479–84

    Article  PubMed  CAS  Google Scholar 

  • Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier M-H, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023

    PubMed  Google Scholar 

  • Rohlf FJ (1998) NTSYS-pc: numerical taxonomy and multivariate analysis system. Applied Biostatistics Inc, New York

    Google Scholar 

  • Sjakste TG, Röder M (2004) Distribution and inheritance of β-amylase alleles in north European barley varieties. Hereditas 141:39–45

    Article  PubMed  Google Scholar 

  • Szalma SJ, Buckler ES IV, Snook ME, McMullen MD (2005) Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks. Theor Appl Genet 110:1324–1333

    Article  PubMed  CAS  Google Scholar 

  • Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielse D, Buckler IV ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nature Genetics 28:286–289

    Article  PubMed  CAS  Google Scholar 

  • von Wettstein-Knowles P (1993) Barley (Hordeum vulgare) 2N = 14. In: Genetic maps: locus maps of complex genomes. Cold Spring Harbor Laboratory Press 1993 Ed. O’Brien SJ

  • Yoshigi N, Okada Y, Sahara H, Koshino S (1994) PCR cloning and sequencing of the beta-amylase cDNA from barley. J Biochem (Tokyo) 115:47–51

    CAS  Google Scholar 

  • Yoshigi N, Okada Y, Sahara H, Tamaki T (1995) A structural gene encoding beta-amylase of barley. Biosci Biotechnol Biochem 10:1991–1993

    Article  Google Scholar 

  • Zhang W, Kaneko T, Ishii M, Takeda K (2004) Differentiation of β-amylase phenotypes in cultivated barley. Crop Sci 44:1608–1614

    Article  CAS  Google Scholar 

Download references

Acknowledgement

We thank Ellen Weiß for excellent technical assistance.

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Authors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Gatersleben, Germany

    L. V. Malysheva-Otto & M. S. Röder

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  1. L. V. Malysheva-Otto
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  2. M. S. Röder
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Correspondence to L. V. Malysheva-Otto.

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Malysheva-Otto, L., Röder, M. Haplotype diversity in the endosperm specific β-amylase gene Bmy1 of cultivated barley (Hordeum vulgare L.). Mol Breeding 18, 143–156 (2006). https://doi.org/10.1007/s11032-006-9023-4

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  • DOI: https://doi.org/10.1007/s11032-006-9023-4

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