A microcolinearity study at the earliness per se gene Eps-Am1 region reveals an ancient duplication that preceded the wheat–rice divergence
Wheat flowering is controlled by numerous genes, which respond to environmental signals such as photoperiod and vernalization. Earliness per se (Eps) genes control flowering time independently of these environmental cues and are responsible for the fine tuning of flowering time. We recently mapped the Eps-Am1 gene on the end of Triticum monococcum chromosome arm 1AmL. As a part of our efforts to clone Eps-Am1 we developed PCR markers flanking this gene within a 2.7 cM interval. We screened more than one thousand gametes with these markers and identified 27 lines with recombination between them. Recombinant lines were used to generate a high-density map and to investigate the microcolinearity between wheat and rice in this region. We mapped ten genes from a 149 kb region located at the distal part of rice chromosome 5 (cdo393 – Ndk3) on a 3.7 cM region on wheat chromosome one. This region is part of an ancient duplication between rice chromosomes 5 and 1. Genes present in both rice chromosomes were less similar to each other than to the closest wheat orthologues, suggesting that this duplication preceded the divergence between wheat and rice. This hypothesis was supported by the presence of 18 loci duplicated both in rice chromosomes 5 and 1 and in the colinear wheat chromosomes from homoeologous groups 1 and 3. Independent gene deletions in wheat and rice lineages explain the alternations of colinearity between rice chromosome 5 and wheat chromosomes 1 and 3. Colinearity between the end of rice chromosome 5 and wheat chromosome 1 was also interrupted by a small inversion, and several non-colinear genes. These results suggest that the distal region of the long arm of wheat chromosome 1 was involved in numerous changes that differentiated wheat and rice genomes. This comparative study provided sufficient markers to saturate the Eps-Am1 gene region and to precisely map this gene within a 0.9 cM interval flanked by the VatpC and Smp loci.
KeywordsFlowering time Earliness per se Wheat Rice Duplication Microcolinearity
- Akhunov ED, Akhunova AR, Linkiewicz AM, Dubcovsky J, Hummel D, Lazo G, Chao SM, Anderson OD, David J, Qi LL, Echalier B, Gill BS, Miftahudin, Gustafson JP, La Rota M, Sorrells ME, Zhang DS, Nguyen HT, Kalavacharla V, Hossain K, Kianian SF, Peng JH, Lapitan NLV, Wennerlind EJ, Nduati V, Anderson JA, Sidhu D, Gill KS, McGuire PE, Qualset CO, Dvorak J, (2003a) Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates along chromosome arms. Proc Natl Acad Sci USA 100:10836–10841CrossRefGoogle Scholar
- Akhunov ED, Goodyear AW, Geng S, Qi LL, Echalier B, Gill BS, Miftahudin, Gustafson JP, Lazo G, Chao SM, Anderson OD, Linkiewicz AM, Dubcovsky J, La Rota M, Sorrells ME, Zhang DS, Nguyen HT, Kalavacharla V, Hossain K, Kianian SF, Peng JH, Lapitan NLV, Gonzalez-Hernandeiz JL, Anderson JA, Choi DW, Close TJ, Dilbirligi M, Gill KS, Walker-Simmons MK, Steber C, McGuire PE, Qualset CO, Dvorak J, (2003b) The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms. Genome Res13:753–763Google Scholar
- Dvorak J, McGuire PE, Cassidy B, (1988) Apparent sources of the A genomes of wheats inferred from the polymorphism in abundance and restriction fragment length of repeated nucleotide sequences. Genome 30:680–689Google Scholar
- Huang S, Sirikhachornkit A, Su X, Faris JD, Gill BS, Haselkorn R, Gornicki P, (2002) Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proc Natl Acad Sci USA 99: 8133–8138CrossRefPubMedGoogle Scholar
- Islam-Faridi MN, Worland AJ, Law CN, (1996) Inhibition of ear-emergence time and sensitivity to day-length determined by the group 6 chromosomes of wheat. Heredity 77:572–580Google Scholar
- McIntosh RA, Yamazaki Y, Devos KM, Dubcovsky J, Rogers WJ, Appels R, (2003) Catalogue of Gene Symbols for Wheat. In: Pogna NE, Romano M, Pogna E, Galterio G (eds) Proceedings of 10th international wheat genetic symposium. Instituto Sperimentale per la Cerealicoltura, Rome, Paestum, Italy, http://www.wheat.pw.usda.gov/ggpages/wgc/2000upd.html.
- Peng JH, Zadeh H, Lazo G, Gustafson JP, Chao S, Anderson OD, Qi LL, Echalier B, Gill BS, Dilbirligi M, Sandhu D, Gill KS, Greene RA, Sorrells ME, Akhunov ED, Dvorak J, Linkiewicz AM, Dubcovsky J, Hossain K, Kianian SF, Mohmand A, Miftahudin, Wennerlind E, Anderson JA, Pathan MS, Nguyen HT, McGuire PE, Qualset CO, Lapitan NLV, (2004) Chromosome bin map of expressed sequence tags in homoeologous group 1 of hexaploid wheat and homoeology with rice and Arabidopsis. Genetics 168:609–623CrossRefPubMedGoogle Scholar
- Qi LL, Echalier B, Chao S, Lazo GR, Butler GE, Anderson OD, Akhunov ED, Dvorak J, Linkiewicz AM, Ratnasiri A, Dubcovsky J, Bermudez-Kandianis CE, Greene RA, Kantety R, La Rota CM, Munkvold JD, Sorrells SF, Sorrells ME, Dilbirligi M, Sidhu D, Erayman M, Randhawa HS, Sandhu D, Bondareva SN, Gill KS, Mahmoud AA, Ma XF, Miftahudin, Gustafson JP, Conley EJ, Nduati V, Gonzalez-Hernandez JL, Anderson JA, Peng JH, Lapitan NLV, Hossain KG, Kalavacharla V, Kianian SF, Pathan MS, Zhang DS, Nguyen HT, Choi DW, Fenton RD, Close TJ, McGuire PE, Qualset CO, Gill BS, (2004) A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 168:701–712CrossRefPubMedGoogle Scholar
- Scarth R, Law CN, (1984) The control of the day-length response in wheat by the Group-2 chromosomes. Plant Breed 92:140–150Google Scholar
- Sorrells ME, La Rota CM, Bermudez-Kandianis CE, Greene RA, Kantety R, Munkvold JD, Miftahudin, Mahmoud A, Gustafson PP, Qi LL, Echalier BE, Gill BS, Matthews DE, Lazo GR, Chao S, Anderson OD, Edwards H, Linkiewicz AM, Dubcovsky J, Akhunov ED, Dvorak J, Zhang D, Nguyen HT, Peng J, Lapitan NLV, Gonzalez-Hernandez JL, Anderson JA, Hossain KG, Kalavacharla V, Kianian SF, Choi DW, Close TJ, Dilbirligi M, Gill KS, Steber C, Walker-Simmons MK, McGuire PE, Qualset CO, (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13:1818–1827PubMedGoogle Scholar
- Worland AJ, Law CN, (1986) Genetic analysis of chromosome 2D of wheat. I. The location of genes affecting height, day-length insensitivity, hybrid dwarfism and yellow-rust resistance. Plant Breed 96:331–345Google Scholar