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Single nucleotide polymorphism, haplotype diversity and recombination in the Isa gene of barley

Abstract

The Isa gene from barley—an intronless gene expressed in maternal tissues of the seed—has a likely role in defence against pathogens. The protein product—bi-functional α-amylase/subtilisin inhibitor—inhibits the seed’s own amylase in addition to the bacterial protease subtilisin and fungal xylanase. Sixteen barley genotypes were targeted to amplify and sequence the Isa gene region to detect sequence polymorphisms, since little is known about genetic diversity at this locus. A total of 80 single nucleotide polymorphisms (SNPs) and 23 indels were detected in 2,164 bp of sequence containing the Isa transcript, promoter and 3′ non-transcribed region (overall one SNP per 27 bp and one indel per 94 bp), with eight sequence-based haplotypes distinguishable amongst the 16 varieties. Sequencing a polymorphic region in the promoter in an additional 27 barley genotypes increased the number of sequence-based haplotypes discovered to 11. However there is low haplotype diversity amongst the cultivated barley varieties sampled, with most varieties represented by a single haplotype. There was minor amino acid diversity in the protein, with five out of ten SNP sites in the coding region predicted to produce amino acid substitutions. SNP analysis indicated a history of recombination events—a minimum of seven based on the initial eight haplotypes from the whole sequenced region. Most of the recombination events occurred in the highly polymorphic regions, the 3′ non-transcribed region and sequences flanking a microsatellite in the Isa promoter.

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References

  1. Abe J, Sidenius U, Svensson B (1993) Arginine is essential for the α-amylase inhibitory activity of the α-amylase/subtilisin inhibitor (BASI) from barley seeds. Biochem J 293:151−155

  2. de Barros G, Tingey S, Rafalski JA (2000) Sequence characterisation of hypervariable regions in the soyabean genome: leucine-rich repeats and simple sequence repeats. Genet Mol Biol 23:411–415

  3. Bhattramakki D, Dolan M, Hanafey M, Wineland R, Vaske D, Register JC, Tingey SV, Rafalski A (2002) Insertion–deletion polymorphisms in 3′ regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Mol Biol 48:539–547

  4. Brown AHD, Zohary D, Nevo E (1978) Outcrossing rates and heterozygosity in natural populations of Hordeum spontaneum Koch in Israel. Heredity 41:49–62

  5. Collins NC, Lahaye T, Peterhansel C, Freialdenhoven A, Corbitt M, Schulze-Lefert P (2001) Sequence haplotypes revealed by sequence-tagged site fine mapping of the Ror1 gene in the centromeric region of barley chromosome 1H. Plant Physiol 125:1236–1247

  6. Cummings MP, Clegg MT (1998) Nucleotide sequence diversity at the alcohol dehydrogenase 1 locus in wild barley (Hordeum vulgare ssp. spontaneum): an evaluation of the background selection hypothesis. Proc Natl Acad Sci USA 95:5637–5642

  7. Daly MJ, Rioux JD, Schaffner SE, Hudson TJ, Lander ES (2001) High-resolution haplotype structure in the human genome. Nat Genet 29:229–232

  8. Furtado A, Henry RJ, Scott KJ, Meech S (2003) The promoter of the Isa gene directs expression in the maternal tissues of the seed in transgenic barley. Plant Mol Biol 52:787–799

  9. Hejgaard J, Bjorn SE, Nielsen G (1984) Localization to chromosomes of structural genes for the major protease inhibitors of barley grains. Theor Appl Genet 68:127–130

  10. Henry RJ, Battershell VG, Brennan PS, Oono K (1992) Control of wheat α-amylase using inhibitors from cereals. J Sci Food Agric 58:281–284

  11. Hudson RR, Kaplan NL (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111:147–164

  12. Jarrett SJ, Marschke RJ, Symons MH, Gibson CE, Henry RJ, Fox GP (1997) α-amylase/subtilisin inhibitor levels in Australian barleys. J Cereal Sci 25:261–266

  13. Kota R, Varshney RK, Thiel T, Dehmer KJ, Graner A (2001) Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.). Hereditas 135:145–151

  14. Kuittinen H, Aguade M (2000) Nucleotide variation at the chalcone isomerase locus in Arabidopsis thaliana. Genetics 155:863–872

  15. Leah R, Mundy J (1989) The bifunctional α-amylase/subtilisin inhibitor of barley: nucleotide sequence and patterns of seed-specific expression. Plant Mol Biol 12:673–682

  16. Lichten M, Goldman ASH (1995) Meiotic recombination hotspots. Annu Rev Genet 29:423–444

  17. Lin JZ, Brown AHD, Clegg MT (2001) Heterogeneous geographic patterns of nucleotide sequence diversity between two alcohol dehydrogenase genes in wild barley (Hordeum vulgare subspecies spontaneum). Proc Natl Acad Sci USA 98:531–536

  18. Lin JZ, Morrell 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

  19. Mogg R, Batley J, Hanley S, Edwards D, O’Sullivan H, Edwards KJ (2002) Characterization of the flanking regions of Zea mays microsatellites reveals a large number of useful sequence polymorphisms. Theor Appl Genet 105:532–543

  20. Mundy J, Svendsen I, Hejgaard J (1983) Barley α-amylase/subtilisin inhibitor. I. Isolation and characterisation. Carlsberg Res Commun 48:81–90

  21. Myers SR, Griffiths RC (2003) Bounds on the minimum number of recombination events in a sample history. Genetics 163:375–394

  22. Patil N, Berno AJ, Hinds DA, Barrett WA, Doshi JM, Hacker CR, Kautzer CR, Lee DH, Marjoribanks C, McDonough DP, et al (2001) Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294:1719–1723

  23. Rodenburg KW, Vallee F, Juge N, Aghajari N, Guo XJ, Haser R, Svensson B (2000) Specific inhibition of barley α-amylase 2 by barley α-amylase/subtilisin inhibitor depends on charge interactions and can be conferred to isozyme 1 by mutation. Eur J Biochem 267:1019–1029

  24. Sancho AI, Faulds CB, Svensson B, Bartolme B, Williamson G, Juge N (2003) Cross-inhibitory activity of cereal protein inhibitors against α-amylases and xylanases. Biochim Biophys Acta 1650:136–144

  25. Vallee F, Kadziola A, Bourne Y, Juy M, Rodenburg KW, Svensson B, Haser R (1998) Barley α-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 angstrom resolution. Struct Fold Des 6:649–659

  26. Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–1134

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Acknowledgements

We would like to acknowledge the contribution of Linh Nguyen for carrying out sequencing and allele sizing of the microsatellite region and Giovani Cordeiro for running RecMin.

Author information

Correspondence to P. C. Bundock.

Additional information

Communicated by P. Langridge

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Bundock, P.C., Henry, R.J. Single nucleotide polymorphism, haplotype diversity and recombination in the Isa gene of barley. Theor Appl Genet 109, 543–551 (2004). https://doi.org/10.1007/s00122-004-1675-z

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Keywords

  • Recombination Event
  • Wild Barley
  • Barley Variety
  • Single Nucleotide Polymorphism Site
  • Endosperm Transfer Cell