Abstract
Recent updates in comparative genomics among cereals have provided the opportunity to identify conserved orthologous set (COS) DNA sequences for cross-genome map-based cloning of candidate genes underpinning quantitative traits. New tools are described that are applicable to any cereal genome of interest, namely, alignment criterion for orthologous couples identification, as well as the Intron Spanning Marker software to automatically select intron-spanning primer pairs. In order to test the software, it was applied to the bread wheat genome, and 695 COS markers were assigned to 1,535 wheat loci (on average one marker/2.6 cM) based on 827 robust rice–wheat orthologs. Furthermore, 31 of the 695 COS markers were selected to fine map a pentosan viscosity quantitative trait loci (QTL) on wheat chromosome 7A. Among the 31 COS markers, 14 (45%) were polymorphic between the parental lines and 12 were mapped within the QTL confidence interval with one marker every 0.6 cM defining candidate genes among the rice orthologous region.
Similar content being viewed by others
References
Asnaghi C, Roques D, Ruffel S, Kaye C, Hoarau JY, Telismart H, Girard JC, Raboin LM, Risterucci AM, Grivet L, D'Hont A (2004) Targeted mapping of a sugarcane rust resistance gene (Bru1) using bulked segregant analysis and AFLP markers. Theor Appl Genet 108:759–764
Bailey PC, McKibbin RS, Lenton JR, Holdsworth MJ, Flintham JE, Gale MD (1999) Genetic map locations for orthologous Vp1 genes in wheat and rice. Theor Appl Genet 98:281–284
Bertin I, Zhu JH, Gale MD (2005) SSCP-SNP in pearl millet-a new marker system for comparative genetics. Theor Appl Genet 110:1467–1472
Bolot S, Abrouk M, Masood-Quraishi U, Stein N, Messing J, Feuillet C, Salse J (2009) Curr Opin Plant Biol 12(2):1–7
Brueggeman R, Rostoks N, Kudrna D, Kilian A, Han F, Chen J, Druka A, Steffenson B, Kleinhofs A (2002) The barley stem rust-resistance gene Rpg1 is a novel disease-resistance gene with homology to receptor kinases. Proc Natl Acad Sci U S A 99:9328–9333
Brunner S, Keller B, Feuillet C (2003) A large rearrangement involving genes and low copy DNA interrupts the microcolinearity between rice and barley at the Rph7 locus. Genetics 164:673–683
Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH (2004) An SNP resource for rice genetics and breeding based on subspecies Indica and Japonica genome alignments. Genome Res 14:1812–1819
Feltus FA, Singh HP, Lohithaswa HC, Schulze SR, Silva TD, Paterson AH (2006) A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops. Plant Physiol 140(4):1183–1191
Fulton TM, Van der Hoeven R, Eannetta NT, Tanksley SD (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14(7):1457–1467
Gupta PK, Rustgi S (2004) Molecular markers from the transcribed/expressed region of the genome in higher plants. Funct Integr Genomics 4(3):139–162
Groos C, Robert N, Bervas E, Charmet G (2003) Genetic analysis of grain protein content, grain yield and thousand kernel weight in bread wheat. Theor Appl Genet 106:1032–1040
Hampson S, McLysaght A, Gaut B, Baldi P (2003) LineUp: statistical detection of chromosomal homology with application to plant comparative genomics. Genome Res 13:1–12
Hampson SE, Gaut BS, Baldi P (2005) Statistical detection of chromosomal homology using shared-gene density alone. Bioinformatics. 21:1339–1348
Hyne V, Kearsey MJ (1995) QTL analysis: further uses of ‘marker’ regression. Theor Appl Genet 91:471–476
Ishikawa G, Yonemaru J, Saito M, Nakamura T (2007) PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes. BMC Genomics 30(8):135
Kearsey MJ, Hyne V (1994) QTL analysis: a simple ‘marker-regression’ approach. Theor Appl Genet 89:698–702
Kim S, Misra A (2007) SNP genotyping: technologies and biomedical applications. Annu Rev Biomed Eng 9:289–320
Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175
Lander ES, Green P (1987) Construction of multilocus genetic linkage maps in humans. Proc Natl Acad Sci U S A 84:2363–2367
La Rota M, Sorrells ME (2004) Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat. Funct Integr Genomics 4:34–46
Leister D, Kurth J, Laurie DA, Yano M, Sasaki T, Devos K, Graner A, Schulze-Lefert P (1998) Rapid reorganization of resistance gene homologues in cereal genomes. Proc Natl Acad Sci U S A 95:370–375
Lin YR, Schertz KF, Paterson AH (1995) Comparative analysis of QTLs affecting plant height and maturity across the poaceae, in reference to an interspecific sorghum population. Genetics 141:391–411
Martinant JP, Billot A, Bouguennec A, Charmet G, Saulnier L, Branlard G (1999) Genetic and environmental variations in water-extractable arabinoxylans content and flour extract viscosity. J Cereal Sci 30:45–48
Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, Maehara Y, Tanji M, Sato M, Nasu S, Minobe Y (2002) Positional cloning of rice semi-dwarfing gene, sd-1: rice ‘green revolution gene’ encodes a mutant enzyme involved in gibberellin synthesis. DNA Res 9:11–17
Panjabi P, Jagannath A, Bisht NC, Padmaja KL, Sharma S, Gupta V, Pradhan AK, Pental D (2008) Comparative mapping of Brassica juncea and Arabidopsis thaliana using intron polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genome. BMC Genomics 9:113
Paterson AH, Lin YR, Li ZK, Schertz KF, Doebley JF, Pinson SRM, Liu SC, Stansel JW, Irvine JE (1995) Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science 269:1714–1718
Peng JR, Richards DE, Hartley NM, Murphy GP, Devos KM, Flintham JE, Beales J, Fish LJ, Worland AJ, Pelica F, Sudhakar D, Christou P, Snape JW, Gale MD, Harberd NP (1999) ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature 400:256–261
Qi LL, Echalier B, Chao S, Lazo GR, Butler GE, Anderson OD, Akhunov ED, Dvorák 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 GJP, Conley EJ, Nduati V, Gonzalez-Hernandez JL, Anderson JA, Peng JH, Lapitan NL, 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 168:701–712
Röder MS, Korsun V, Gill BS, Ganal MW (1998a) The physical mapping of microsatellite markers in wheat. Genome 41:278–283
Röder MS, Korsun V, Wendehake K, Plaschke J, Tixier MH, Leroy P, Ganal MW (1998b) A microsatellite map of the wheat genome. Genetics 149:2007–2023
Salse J, Feuillet C (2007) Comparative genomics of cereals. Chapter 18 in Genomics-assisted crop improvement; published by Springer, pp 177–205
Salse J, Piegu B, Cooke R, Delseny M (2004) New in silico insight into the synteny between rice (Oryza sativa L.) and maize (Zea mays L.) highlights reshuffling and identifies new duplications in the rice genome. Plant J 38:396–409
Salse J, Bolot S, Throude T, Jouffe V, Piegu B, Masood Quraishi U, Calcagno C, Cooke C, Delseny M, Feuillet C (2008a) Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell 20(1):11–24
Salse J, Chagué V, Bolot S, Magdelenat G, Huneau C, Pont C, Belcram H, Couloux A, Gardais S, Evrard A, Segurens B, Charles M, Ravel C, Samain S, Charmet G, Boudet N, Chalhoub B (2008b) New insights into the origin of the B genome of hexaploid wheat: evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides. BMC Genomics 9:555
Saulnier L, Sado PE, Branlard G, Charmet G, Guillon F (2007) Wheat arabinoxylans: exploiting variation in amount and composition to develop enhanced varieties. J Cereal Sci 46:261–281
Singh NK, Dalal V, Batra K, Singh BK, Chitra G, Singh A, Ghazi IA, Yadav M, Pandit A, Dixit R, Singh PK, Singh H, Koundal KR, Gaikwad K, Mohapatra T, Sharma TR (2007) Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes. Funct Integr Genomics 7(1):17–35
Sorrells ME, La Rota M, Bermudez-Kandianis CE, Greene RA, Kantety R, Munkvold JD, Miftahudin MA, Ma X, Gustafson PJ, Qi LL, Echalier B, 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 NL, Gonzalez-Hernandez JL, Anderson JA, Hossain K, 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 13:1818–1827
Turner A, Beales J, Faure S, Dunford RP, Laurie DA (2005) The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley. Science 310:1031–1034
Visscher PM, Haley CS, Thompson R (1996) Marker-assisted introgression in backcross breeding programs. Genetics 144:1923–1932
Wei F, Coe E, Nelson W, Bharti AK, Engler F, Butler E, Kim H, Goicoechea JL, Chen M, Lee S, Fuks G, Sanchez-Villeda H, Schroeder S, Fang Z, McMullen M, Davis G, Bowers JE, Paterson AH, Schaeffer M, Gardiner J, Cone K, Messing J, Soderlund C, Wing RA (2007) Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet 3(7):e123
Wu F, Mueller LA, Crouzillat D, Pétiard V, Tanksley SD (2006) Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics 174(3):1407–1420
Yan L, Loukoiannov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J (2003) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci U S A 100:6263–6268
Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, Li R, Xu Z, Li S, Li X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Wang J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren X, Wang J, Wang X, Li D, Liu D, Zhang X, Ji Z, Zhao W, Sun Y, Zhang Z, Bao J, Han Y, Dong L, Ji J, Chen P, Wu S, Liu J, Xiao Y, Bu D, Tan J, Yang L, Ye C, Zhang J, Xu J, Zhou Y, Yu Y, Zhang B, Zhuang S, Wei H, Liu B, Lei M, Yu H, Li Y, Xu H, Wei S, He X, Fang L, Zhang Z, Zhang Y, Huang X, Su Z, Tong W, Li J, Tong Z, Li S, Ye J, Wang L, Fang L, Lei T, Chen C, Chen H, Xu Z, Li H, Huang H, Zhang F, Xu H, Li N, Zhao C, Li S, Dong L, Huang Y, Li L, Xi Y, Qi Q, Li W, Zhang B, Hu W, Zhang Y, Tian X, Jiao Y, Liang X, Jin J, Gao L, Zheng W, Hao B, Liu S, Wang W, Yuan L, Cao M, McDermott J, Samudrala R, Wang J, Wong GK, Yang H (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biology 3(2):e38
Acknowledgements
Data included in the current article including COS genotyping data as well as QTL analysis in the Renan × Recital INRA genetic population were generated within programs partially funded by GENOPLANTE and HEALTH GRAIN (FP6 EU). We would like also to thank Richard Cooke (Laboratoire Génome et Développement des Plantes, Perpignan University, France) for fruitful discussions during the article preparation.
Author information
Authors and Affiliations
Corresponding author
Additional information
Umar Masood Quraishi and Michael Abrouk contributed equally to this work.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Supplementary material S1
List of 827 orthologous gene pairs between rice and wheat. Detailed features for the 13 orthologous regions identified between rice and wheat. For each of the 827 orthologous wheat and rice gene pairs are mentioned the GenBank accession name, position, chromosome number, sequence, as well as the sequence alignment criterion (CIP, CALP). (XLS 619 kb)
Supplementary material S2
List of 695 COS markers. Detailed features for the 695 orthologous wheat and rice gene pairs associated with COS primers. For each COS marker are mentioned wheat and rice orthologous genes with their Genbank accession name, position, chromosome number, sequence, the sequence alignment criterion (CIP, CALP); as well as the intron-spanning primers (number of intron, forward and reverse primer, amplicon size). (XLS 591 kb)
Supplementary material S3
List of 31 COS markers for fine mapping of PV QTL in Renan × Recital. Detailed features for the 31 orthologous wheat and rice gene pairs associated with COS primers involved in PV QTL fine mapping. For each COS marker are mentioned the wheat and rice orthologous genes with their GenBank accession name, position, chromosome number, sequence, the intron-spanning primers (number of intron, forward and reverse primer, amplicon size); as well as the polymorphism data (NP for No Polymorphism; P for Polymorphism) and mapping data (chromosome 7A, 7B or NA when the mapping information is not available). (XLS 40.5 kb)
Supplementary material S4
List of 124 rice candidate genes for PV QTL in Renan × Recital. The rice annotated gene within the orthologous region of the PV QTL are detailed through the chromosome number, LOC name, gene start/end positions, GenBank accession number, function. (XLS 81 kb)
Rights and permissions
About this article
Cite this article
Quraishi, U.M., Abrouk, M., Bolot, S. et al. Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection. Funct Integr Genomics 9, 473–484 (2009). https://doi.org/10.1007/s10142-009-0129-8
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10142-009-0129-8