Advertisement

Molecular Breeding

, Volume 27, Issue 1, pp 1–9 | Cite as

Dissecting the telomere region of barley chromosome 5HL using rice genomic sequences as references: new markers for tracking a complex region in breeding

  • Xiao-Qi Zhang
  • Chengdao LiEmail author
  • Joe Panozzo
  • Sharon Westcott
  • Guoping Zhang
  • Amy Tay
  • Rudi Appels
  • Mike Jones
  • Reg Lance
Article

Abstract

The terminal region of barley chromosome 5HL controls malt extract, diastatic power, free amino acid nitrogen, alpha-amylase activity, seed dormancy and pre-harvest sprouting. Comparative analysis of the barley and rice maps has established that the terminal region of barley chromosome 5HL is syntenic to rice chromosome 3L near the telomere end. The rice BAC (Bacterial Artificial Chromosome) sequences covering the region of chromosome 3L were used to search barley expressed sequenced tags database. Thirty-three genes were amplified by PCR (polymerase chain reaction) with the primers designed from barley ESTs (expressed sequence tag). Comparison of the sequences of the PCR generated DNA fragments revealed polymorphisms including single nucleotide polymorphism (SNP), insertions or deletions between the barley varieties. Seven new PCR based molecular markers were developed and mapped within 10 cM in three doubled haploid barley populations (Stirling × Harrington, Baudin × AC Metcalfe and Chebec × Harrington). The mapped genes maintain the micro-syntenic relationship between barley and rice. These gene specific markers provide simple and efficient tools for germplasm characterization and marker-assisted selection for barley malting quality, and ultimately lead to isolation and identification of the major gene(s) controlling multiple quality traits on barley chromosome 5HL.

Keywords

Malting quality Comparative mapping Micro-synteny Rice Hordeum vulgare Marker-assisted selection 

Notes

Acknowledgments

This research was supported by Molecular Plant Breeding CRC, Australian Grain Research and Development Corporation and Natural Science Foundation of China (30828023).

References

  1. Barr A, Karakousis A, Lance RCM, Logue SJ, Manning S, Chalmers K, Kretschmer J, Boyd WJR, Collins H, Roumeliotis S, Coventry S, Moody D, Read B, Poulsen D, Li CD, Platz G, Inkerman A, Panozzo J, Cullis B, Smith A, Lim P, Langridge P (2003) Mapping and QTL analysis of the barley population Chebec × Harrington. Aust J Agric Res 54:1125–1130CrossRefGoogle Scholar
  2. Bonnardeaux Y, Li C, Lance R, Zhang XQ, Sivasithamparam K, Appels R (2008) Seed dormancy in barley: identifying superior genotypes through incorporating epistatic interactions. Aust J Agric Res 59:517–526CrossRefGoogle Scholar
  3. Cattley S, Arthur JW (2007) BioManager: the use of a bioinformatics web application as a teaching tool in undergraduate bioinformatics training. Brief Bioinform 8:457–465CrossRefPubMedGoogle Scholar
  4. Collins HM, Panozzo JF, Logue SJ, Jefferies SP, Barr AR (2003) Mapping and validation of chromosome regions associated with high malt extract in barley (Hordeum vulgare L.). Aust J Agric Res 54:1223–1240CrossRefGoogle Scholar
  5. Coventry SJ, Barr AR, Eglinton JK, McDonald GK (2003) The determinants and genome locations influencing grain weight and size in barley (Hordeum vulgare L.). Aust J Agric Res 54:1103–1115CrossRefGoogle Scholar
  6. Emebiri LC, Michael P, Moody DB, Ogbonnaya FC, Black C (2009) Pyramiding QTLs to improve malting quality in barley: gains in phenotype and genetic diversity. Mol Breeding 23:219–228CrossRefGoogle Scholar
  7. Fox G, Panozzo JF, Li CD, Lance RCM, Inkerman A, Henry RJ (2003) Molecular basis of barley quality. Aust J Agric Res 54:1081–1101CrossRefGoogle Scholar
  8. Gao W, Clancy JA, Han F, Prada D, Kleinhofs A, Ullrich SE, NABGMP (2003) Molecular dissection of a dormancy QTL region near the chromosome 7 (5H) L telomere in barley. Theor Appl Genet 107:552–559CrossRefPubMedGoogle Scholar
  9. Han F, Ullrich SE, Clancy JA, Jitkov V, Kilian A, Romagosa I (1996) Verification of barley seed dormancy loci via linked molecular markers. Theor Appl Genet 92:87–91CrossRefGoogle Scholar
  10. Hayden MJ, Nguyen TM, Waterman A, Chalmers KJ (2008) Multiplex-Ready PCR: a new method for multiplexed SSR and SNP genotyping. BMC Genomics 9:80CrossRefPubMedGoogle Scholar
  11. Hayes PM, Liu BH, Knapp SJ, Chen F, Jones B, Blake T, Franckowiack JD, Rassmusson D, Sorells M, Ullrich SE, Wesenberg D, Kleinhofs A (1993) Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm. Theor Appl Genet 87:392–401CrossRefGoogle Scholar
  12. Hayes PM, Castro A, Marquez-Cedillo L, Corey A, Henson C, Jones BL, Kling J, Mather D, Matus I, Rossi C, Sato K (2003) Genetic diversity for quantitatively inherited agronomic and malting quality traits. In: von Bothmer R, Van Hintum T, Knupffer H, Sato K (eds) Diversity in barley (Hordeum vulgare). Elsevier Science B.V, Amsterdam, pp 201–226CrossRefGoogle Scholar
  13. Kleinhofs A, Han F (2002) Molecular mapping of the barley genome. In: Slafer GA, Molina-Cano JL, Savin R, Araus JL, Romagosa I (eds) Barley science recent advances from molecular biology to agronomy of yield and quality. Food Products Press, New York, pp 31–63Google Scholar
  14. Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175Google Scholar
  15. Li CD, Tarr A, Lance RCM, Harasymow S, Uhlmann J, Westcot S, Young K, Grime C, Cakir M, Broughton S, Appels R (2003) A major QTL controlling seed dormancy and pre-harvest sprouting/grain alpha-amylase in two-rowed barley (Hordeum vulgare L.). Aust J Agric Res 54:1303–1313CrossRefGoogle Scholar
  16. Li C, Ni P, Francki M, Hunter A, Zhang Y, Schibeci D, Li H, Tarr A, Wang J, Cakir M, Yu J, Bellgard M, Lance R, Appels R (2004) Genes controlling seed dormancy and pre-harvest sprouting in a rice–wheat–barley comparison. Funct Integr Genomics 4:84–93CrossRefPubMedGoogle Scholar
  17. Li JZ, Huang XQ, Heinrichs F, Ganal MW, Röder MS (2005) Analysis of QTLs for yield, yield components, and malting quality in a BC3-DH population of spring barley. Theor Appl Genet 110:356–363CrossRefPubMedGoogle Scholar
  18. Li C, Cakir M, Lance R (2009) Genetic improvement of malting quality through conventional breeding and marker-assisted selection. In: Zhang GP, Li CD (eds) Genetics and improvement of barley malting quality. The Springer, Berlin, pp 260–292CrossRefGoogle Scholar
  19. Manly KF, Cudmore RH Jr, Meer JM (2001) Map Manager QTX, cross-platform software for genetic mapping. Mamm Genome 12:930–932CrossRefPubMedGoogle Scholar
  20. Marquez-Cedillo LA, Hayes PM, Jones BL, Kleinhofs A, Legge WG, Rossnagel BG, Sato K, Ullrich SE, Wesenberg DM (2000) QTL analysis of malting quality in barley based on the double-haploid progeny of two elite North American varieties representing different germplasm groups. Theor Appl Genet 101:173–184CrossRefGoogle Scholar
  21. Mather DE, Tinker NA, LaBerge DE, Edney M, Jones BL, Rossnagel BG, Legge WG, Briggs KG, Irvine RB, Falk DE, Kasha KJ (1997) Regions of the genome that affect grain and malt quality in a North American two-row barley cross. Crop Sci 37:544–554CrossRefGoogle Scholar
  22. Panozzo JF, Eckermann PJ, Mather DE, Moody DB, Black CK, Collins HM, Barr AR, Lim P, Cullis BR (2007) QTL analysis of malting quality traits in two barley populations. Aust J Agric Res 58:858–866CrossRefGoogle Scholar
  23. Ullrich SE, Han F, Blake TK, Oberthur LE, Dyer WE, Clancy JA (1996) Seed dormancy in barley. Genetic resolution and relationship to other traits. In: Noda K, Mares D (eds) Pre-harvest sprouting in cereals 1995. Centre for Academic Societies, Osaka, pp 157–163Google Scholar
  24. Van Os H, Stam P, Visser RGF, Van Eck HJ (2005) RECORD: a novel method for ordering loci on a genetic linkage map. Theor Appl Genet 112:30–40CrossRefPubMedGoogle Scholar
  25. Von Korff M, Grando S, Del Greco A, This D, Baum M, Ceccarelli S (2008) Quantitative trait loci associated with adaptation to Mediterranean dryland conditions in barley. Theor Appl Genet 117:653–669CrossRefPubMedGoogle Scholar
  26. Zhang XQ, Li CD, Tay A, Lance R, Mares D, Cheong J, Cakir M, Ma J, Appels R (2008) A new PCR-based marker on chromosome 4AL for resistance to pre-harvest sprouting in wheat (Triticum aestivum L.). Mol Breed 22:227–236CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Xiao-Qi Zhang
    • 1
  • Chengdao Li
    • 1
    • 2
    Email author
  • Joe Panozzo
    • 3
  • Sharon Westcott
    • 2
  • Guoping Zhang
    • 4
  • Amy Tay
    • 2
  • Rudi Appels
    • 5
  • Mike Jones
    • 1
  • Reg Lance
    • 2
  1. 1.State Agricultural Biotechnology CenterMurdoch UniversityPerthAustralia
  2. 2.Department of Agriculture and Food, Western AustraliaSouth PerthAustralia
  3. 3.Department of Primary IndustryDPI Horsham CentreHorshamAustralia
  4. 4.Department of AgronomyZhejiang UniversityHangzhouChina
  5. 5.Centre of Comparative GenomicsMurdoch UniversityPerthAustralia

Personalised recommendations