Seed dormancy in barley: identifying superior genotypes through incorporating epistatic interactions
Y. Bonnardeaux A B E , C. Li B C D , R. Lance C , X. Q. Zhang B C D , K. Sivasithamparam A and R. Appels B C D EA School of Earth and Geographical Sciences (Soil Science Discipline), Faculty of Natural and Agricultural Sciences, The University of Western Australia, Crawley, WA 6009, Australia.
B Molecular Plant Breeding CRC, Victorian AgriBiosciences Centre, Bundoora, Vic. 3083, Australia.
C Department of Agriculture and Food Western Australia, South Perth, WA 6151, Australia.
D Murdoch University, Murdoch, WA 6150, Australia.
E Corresponding authors. Email: yumiko@ccg.murdoch.edu.au; rapp1495@bigpond.net.au
Australian Journal of Agricultural Research 59(6) 517-526 https://doi.org/10.1071/AR07345
Submitted: 20 September 2007 Accepted: 2 March 2008 Published: 10 June 2008
Abstract
A genetic linkage map of barley with 128 molecular markers was constructed using a doubled haploid (DH) mapping population derived from a cross between barley (Hordeum vulgare) cvv. Stirling and Harrington. Quantitative trait loci controlling seed dormancy were characterised in the population. A major quantitative trait locus (QTL) controlling seed dormancy and accounting for over half the phenotypic variation (52.17%) was identified on the distal end of the long arm of chromosome 5H. Minor QTLs were also detected near the centromeric region of 5H and on chromosomes 1H and 3H. These minor QTLs with additive effects accounted for 7.52% of the phenotypic variance measured. Examination of epistatic interactions further detected additional minor QTLs near the centromere of 2H and on the long arm and short arms of 4H. Combinations of parental alleles at the QTL locations in predictive analyses indicated dramatic differences in germination. These results emphasise the potential differences in dormancy that can be achieved through the use of specific gene combinations and highlights the importance of minor genes and the epistatic interactions that occur between them. This study found that the combination of Stirling alleles at the two QTL locations on the 5H chromosome and Harrington alleles at the 1H and 3H QTL locations significantly produced the greatest dormancy. Uncovering gene complexes controlling the trait may enable breeders to produce superior genotypes with the desirable allele combinations necessary for manipulating seed dormancy in barley.
Additional keywords: pre-harvest sprouting, quantitative trait loci (QTLs), Hordeum vulgare, Stirling, Harrington.
Acknowledgments
This project was supported by the Molecular Plant Breeding CRC (MPBCRC) and marker screening was performed using technology developed by Dr Matthew Hayden from the MPBCRC (Adelaide). The authors thank Ms Fiona Drake-Brockman, Ms Cathy Burchell, and Mike Rosman for technical support. The authors also thank Ms Katia Stefanova and Mr Dean Diepeveen for statistical support and Mr Jian Yang, author of the QTLNetwork software program, for technical assistance with the program. Kirin Australia kindly provided the Stirling/Harrington DH population.
Bailey PC,
McKibbin RS,
Lenton JR,
Holdsworth MJ,
Flintham JE, Gale MD
(1999) Genetic map locations for orthologous Vp1 genes in wheat and rice. Theoretical and Applied Genetics 98, 281–284.
| Crossref |
Barr AR,
Karakousis A,
Lance RCM,
Logue SJ, Manning S , et al.
(2003) Mapping and QTL analysis of the barley population Chebec × Harrington. Australian Journal of Agricultural Research 54, 1125–1130.
| Crossref |
Castor L, Frederiken F
(1977) Seed moulding of grain sorghums caused by Fusarium and Curvularia. Proceedings of Annual Phytopathology Society 4, 151.
Doerge R, Churchill G
(1996) Permutation tests for multiple loci affecting a quantitative character. Genetics 142, 285–294.
| PubMed |
Garlinge J
(2005) The crop variety sowing guide 2005. Department of Agriculture Western Australia Bulletin 4655, 71–97.
Giraudat JB,
Hauge M,
Valon C,
Smalle J,
Parcy F, Goodman HM
(1992) Isolation of the Arabidopsis ABI3 gene by positional cloning. Plant Cell 4, 1251–1261.
| Crossref |
PubMed |
Groos C,
Gay G,
Perretant MR,
Gervais L,
Bernard M,
Dedryver F, Charmet G
(2002) Study of the relationship between pre-harvest sprouting and grain color by quantitative trait loci analysis in a white × red grain bread-wheat cross. Theoretical and Applied Genetics 104, 39–47.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Guberac V,
Martincic J, Maric S
(1998) Influence of seed size on germinability, germ length, rootlet length and grain yield in spring oat. Bodenkultur 49, 13–18.
Han F,
Ullrich SE,
Clancy JA,
Jitkov V,
Kilian A, Romagosa I
(1996) Verification of barley seed dormancy loci via linked molecular markers. Theoretical and Applied Genetics 92, 87–91.
| Crossref | GoogleScholarGoogle Scholar |
Jones HD,
Peters NC, Holdsworth MJ
(1997) Genotype and environment interact to control dormancy and differential expression of the VIVIPAROUS 1 homologue in embryos of Avena fatua. Plant Journal 12, 911–920.
| Crossref |
PubMed |
Karakousis A,
Gustafson JP,
Chalmers KJ,
Barr AR, Langridge P
(2003) A consensus map of barley integrating SSR, RFLP, and AFLP markers. Australian Journal of Agricultural Research 54, 1173–1185.
| Crossref | GoogleScholarGoogle Scholar |
Kato K,
Nakamura W,
Tabiki T,
Miura H, Sawada S
(2001) Detection of loci controlling seed dormancy on group 4 chromosomes of wheat and comparative mapping with rice and barley genomes. Theoretical and Applied Genetics 102, 980–985.
| Crossref | GoogleScholarGoogle Scholar |
Kawade RM,
Ugale SD, Patil RB
(1987) Effect of seed size on germination, seedling vigor and test weight of pearl millet. Seed Research 15, 210–213.
Kosambi DD
(1944) The estimation of map distance from recombination values. Annals of Eugenics 12, 172–175.
Kulwal PL,
Singh R,
Balyan HS, Gupta PK
(2004) Genetic basis of pre-harvest sprouting tolerance using single-locus and two-locus QTL analysis in bread wheat. Functional & Integrative Genomics 4, 94–101.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Lafond GP, Baker RJ
(1986) Effects of temperature, moisture stress and seed size on germination of nine spring wheat cultivars. Crop Science 26, 563–567.
Larsen SU, Andreasen C
(2004) Light and heavy seeds differ in germination percentage and mean germination thermal time. Crop Science 44, 1710–1720.
Li C,
Ni P,
Francki M,
Hunter A, Zhang Y , et al.
(2004) Genes controlling seed dormancy and pre-harvest sprouting in a rice–wheat–barley comparison. Functional & Integrative Genomics 4, 84–93.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Li CD,
Tarr A,
Lance RCM,
Harasymow S, Uhlmann J , et al.
(2003) A major QTL controlling seed dormancy and pre-harvest sprouting/grain α-amylase in two-rowed barley (Hordeum vulgare L.). Australian Journal of Agricultural Research 54, 1303–1313.
| Crossref | GoogleScholarGoogle Scholar |
Marquez-Cedillo LA,
Hayes PM,
Jones BL,
Kleinhofs A,
Legge WG,
Rossnagel BG,
Sato K,
Ullrich E, Wesenberg DM
(2000) QTL analysis of malting quality in barley based on the doubled-haploid progeny of two elite North American varieties representing different germplasm groups. Theoretical and Applied Genetics 101, 173–184.
| Crossref | GoogleScholarGoogle Scholar |
Mather DE,
Tinker NA,
LaBerge DE,
Edney M, Jones BL , et al.
(1997) Regions of genome that affect grain and malt quality in a North American two-row barley cross. Crop Science 37, 544.
Mathur PN,
Sinha NC, Singh RP
(1982) Effect of seed size on germination and seed vigour in oat (Avena sativa L.). Seed Research 10, 109–113.
McCarty DR,
Hattori T,
Carson CB,
Vasil V,
Lazar M, Vasil IK
(1991) The Viviparous-1 developmental gene of maize encodes a novel transcriptional activator. Cell 66, 895–905.
| Crossref |
PubMed |
Prada D,
Ullrich SE,
Molina-Cano JL,
Cistue L,
Clancy JA, Romagosa I
(2004) Genetic control of dormancy in a Triumph/Morex cross in barley. Theoretical and Applied Genetics 109, 62–70.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Rogowsky PM,
Gtuidet FLY,
Langridge P,
Shepherd KW, Koebner RMD
(1991) Isolation and characterization of wheat-rye recombinants involving chromosome arm 1DS of wheat. Theoretical and Applied Genetics 82, 537–544.
| Crossref | GoogleScholarGoogle Scholar |
Romagosa I,
Han H,
Clancy JA, Ullrich SE
(1999) Individual locus effects on dormancy during seed development and after ripening in barley. Crop Science 39, 74–79.
Roy SKS,
Hamid A,
Giashuddin Miah M, Hashem A
(1996) Seed size variation and its effects on germination and seedling vigour in rice. Journal of Agronomy & Crop Science 176, 79–82.
| Crossref | GoogleScholarGoogle Scholar |
Thomas WTB,
Powell W,
Swanston JS,
Ellis RP, Chalmers KJ , et al.
(1996) Quantitative trait loci for germination and malting quality characters in a spring barley cross. Crop Science 36, 265–273.
van Der Schaar W,
Alonso-Blanco C,
Leon-Kloosterziel KM,
Jansen RC,
van Ooijen JW, Koornneef M
(1997) QTL analysis of seed dormancy in Arabidopsis using recombinant inbred lines and MQM mapping. Heredity 79, 190–200.
| PubMed |
Van Os H,
Stam P,
Visser RGF, Van Eck HJ
(2005) RECORD: a novel method for ordering loci on a genetic linkage map. Theoretical and Applied Genetics 112, 30–40.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Varshney RK,
Marcel TC,
Ramsay L,
Russell J,
Röder MS,
Stein N,
Waugh R,
Langridge P,
Niks RE, Graner A
(2007) A high density barley microsatellite consensus map with 775 SSR loci. Theoretical and Applied Genetics 114, 1091–1103.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Willenborg CJ,
Wilderman JC,
Miller AK,
Rossnagel BG, Shirtliffe SJ
(2005) Oat germination characteristics differ among genotypes, seed sizes and osmotic potentials. Crop Science 45, 2023–2029.
| Crossref | GoogleScholarGoogle Scholar |
Zanetti S,
Winzeler M,
Keller M,
Keller B, Messmer M
(2000) Genetic analysis of pre-harvest sprouting resistance in a wheat × spelt cross. Crop Science 40, 1406–1417.
Zhang F,
Chen G,
Huang Q,
Orion O,
Krugman T,
Fahima T,
Korol AB,
Nevo E, Gutterman Y
(2005) Genetic basis of barley caryopsis dormancy and seedling desiccation tolerance at the germination stage. Theoretical and Applied Genetics 110, 445–453.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
