2 Calgene, 1920 Fifth Street, Davis, CA, USA, 95616
*corresponding author: ph: (607) 255-4020, Fax: (607) 255-6683, E-mail: firstname.lastname@example.org
Another requirement for comparative mapping is a set of probes that can be used to evaluate homoeology and conservation of linkage groups. In the course of surveying probes from an array of different libraries, many were found to hybridize well to multiple species of grasses. After systematic evaluation of these probes on seven species (rice, wheat, barley, oat, maize, sorghum, and sugarcane), a subset of those that gave good hybridization signal on a majority of species was designated as "anchor probes" for comparative mapping.
Consensus maps can be developed for related species with similar genomes. Such maps are based on conservation of linkage groups composed of homologous and homoeologous chromosomes. These maps merge information about closely related species and are useful for cross-referencing genetic information from more distantly related species. A consensus map has been developed for Triticeae species, based on a common set of markers mapped onto the respective linkage groups of T. aestivum, T. tauschii, and Hordeum species (Nelson et al. 1995ab; Van Deynze et al. 1995ac).
Comparative maps have been constructed for several Gramineae species. Cloned genes, random cDNA's and genomic DNA markers from maize were used to compare the maize and sorghum genomes (Whitkus et al. 1992; Melake Berhan et al. 1993). Substantial conservation of large segments of linkage groups was observed in these two species, with segments of most sorghum linkage groups showing homoeology to two independent segments in the maize genome. A similar study comparing maize, sorghum and sugarcane (Saccharum species) (Grivet et al., 1994), reported that the degree of conservation observed between sorghum and sugarcane was greater than between sorghum and maize, largely because there was less duplication in the sorghum and sugarcane genomes. Devos et al. (1993) demonstrated conservation of the wheat and rye genomes, with a few well-defined rearrangements distinguishing the rye genome.
Comparisons among more distantly related crops require a common set of probes. Probes from rice, oat, and barley cDNA libraries were used to analyze the genetic relationships among rice, wheat, and maize (Ahn and Tanksley 1993; Ahn et al. 1993), and among rice, Triticeae species, maize, and oat (Van Deynze et al. 1995abc). Wheat - rice comparisons using cDNA's (Kurata et al. 1994b), and comparisons between wheat group 7 chromosomes and maize chromosome 9 (Devos et al., 1994) have also been reported. These diverse comparative maps based on probes which hybridize across the cereals provide a basis for combining the genetic information that is available in these crops.
The objective of this study was to identify and characterize a set of DNA probes that would be useful for comparative mapping among several Gramineae species.
The same procedures for RFLP analyses (Heun et al. 1991; Causse et al., 1994) were used for each population. The individual linkage maps were developed by placing markers at a LOD threshold of 2.0 using Mapmaker v3.0 (Lander et al. 1987) with the Kosambi mapping function (Kosambi 1944). The consensus map for wheat, T.tauschii and Hordeum species (Van Deynze et al. 1995c), hereafter referred to as the Triticeae consensus map, was used to make comparisons among these species and rice, maize and oat.
Figure 1. Autoradiogram of CDO460 hybridized to rice (IR36), oat (Ogle), barley (SE16), wheat (Chinese spring), sugarcane (SES208), sorghum (BTx406) and maize (CO159) digested with EcoRI in lanes 2-8, respectively; lane 1 lambda/HindIII size marker.
This data was complemented by the results obtained on mapping filters, and is summarized in Tables 1 and 2. The proportion of probes in the current anchor set giving good hybridization signals for rice and maize is biased upward because a large proportion of these clones had been previously mapped on these species.
More than 75% of oat cDNAs produced strong hybridization signals in the 7 species tested (Fig.2).
Figure 2. Proportion of clones providing good hybridization signal (stringency = 0.5X SSC at 65C) for selected barley (BCD), oat (CDO) and rice (RZ) cDNA clones.
For barley cDNAs, 100% hybridized to barley, wheat, oat and maize, about 90% to rice, 82% to sorghum, and only 58% to sugarcane. Rice cDNAs hybridized 100% to rice, 78-90% to the tropical crops, maize, sorghum and sugarcane, and 48-55% to wheat, barley, and oat genomic DNA.
The set of anchor probes represents a collaborative effort between researchers studying rice, wheat, barley and oat with probes derived from each of these species. This set of probes provides good coverage of the linkage maps of rice, maize and oat. Linkage data is not available for 84 of the 153 probes for Triticeae species, mainly due to the low polymorphism in cultivated wheat (Figure 6-See end of document), but this is more than compensated by the use of aneuploid stocks that provide arm locations for nearly all hybridizing fragments (Table 2). For example, loci detected with CDO122 map to the same relative positions in homoeologous segments of rice chromosome 3, maize 1 and 5, and oat E (Figures 3 to 5-See end of document). If the positions of orthologous loci detected with this probe were conserved relative to Triticeae species, the distal portion of Triticeae chromosome 4S would be better represented (Van Deynze et al.1995c). The positions of these markers must be confirmed by mapping in additional populations of Triticeae species or by using the deletion stocks developed by Werner et al. (1992). Additional probes mapping to poorly represented regions in the Triticeae from other DNA libraries must be screened to meet the criteria and added to this set of anchor probes in the future.
The probes in our current anchor marker set are being end-sequenced (W. Park, Biochemistry Dept., Texas A&M, College Station, USA; and J. Bennett, Division of Plant Breeding, Genetics and Biochemistry , IRRI, Los Banos, Philippines, personal communication), and plans to construct specific primers for them are underway.
The use of anchor probes for comparative mapping is an efficient way of establishing genetic relationships for comparisons among all the species being studied (Ahn and Tanksley 1993; Ahn et al. 1993; Van Deynze et al. 1995abc). Collaboration among research groups involved in mapping of related Gramineae species will contribute to extending the set of anchor markers. As the development of comparative maps is a dynamic process, we envision the expansion of this set of clones to include 1) cDNA clones from a wider array of species and libraries, 2) cDNA clones of known gene function which are of agronomic importance, and 3) clones from poorly represented regions of specific genomes that give single copy hybridization signal across a majority of Gramineae species tested.
All materials and information relating to this work are available to other researchers. The anchor probes described in this report are available from Susan McCouch (email: email@example.com) and Mark Sorrells (email: firstname.lastname@example.org), Department of Plant Breeding and Biometry, Cornell University, Ithaca, NY, USA, 14853-1901). The data, images of screening filters and linkage maps developed using the anchor probes are continuously being updated and are available on the World Wide Web [http://greengenes.cit.cornell.edu/anchors/].
Ahn S, Anderson JA, Sorrells ME, Tanksley SD (1993) Homoeologous relationships of rice, wheat and maize chromosomes. Mol. Gen. Genet. 241:483-490
Arumunagathan K, and Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol. Bio. Reporter 9: 208-218
Burr B, Burr FA (1991) Recombinant inbreds for molecular mapping in maize. Trends in Genet. 7:55-60
Causse M, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu K, Xiao J, Yu Z, Ronald PC, Harrington SB, Second GA, McCouch SR, Tanksley SD (1994) Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138:1251-1274
Chao S, Sharp PJ, Worland AJ, Warham EJ, Koebner RMD, Gale MD (1989) RFLP-based genetic maps of wheat homoeologous group 7 chromosomes. Theor. Appl. Genet. 78:495-504
Chittenden LM, Schertz KF, Lin YR, Wing RA and Paterson AH (1994) A detailed RFLP map of Sorghum bicolor x S. propinquum suitable for high-density mapping suggests ancestral duplication of Sorghum chromosomes or chromosomal segments. Theor Appl Genet 87:925-933
Da SiIva JAG, Sorrells ME, Burnquist WL, and Tanksley SD (1993) RFLP linkage map and genome analysis of Saccharum spontaneum. Genome 36(4):782-791
Devos KM, Atkinson MD, Chinoy CN, Liu CJ, Gale MD (1992) RFLP-based genetic map of the homoeologous group 3 chromosomes of wheat and rye. Theor. Appl. Genet. 83:931-939
Devos KM, Millan T, Gale MD (1993) Comparative RFLP maps of homoeologous group 2 chromosomes of wheat, rye and barley. Theor. Appl. Genet. 85:784-792
Devos KM, Chao S, Li QY, Simonetti MC, Gale M (1994) Relationship between chromosome 9 of maize and wheat homoeologous group 7 chromosomes. Genetics 138:1287-1292
Gardiner JM, Coe EH, Melia-Hancock S, Hoisington DA, Chao, S (1993) Development of a core RFLP map using an immortalized F2 population. Genetics 134:917-930
Graner A, Jahoor A, Schondelmaier J, Siedler H, Pillen K, Fischbeck G, Wenzel G, Herrmann RG (1991) Construction of an RFLP map of barley. Theor. Appl. Genet. 83:250-256
Graner A, Bauer E, Kellermann A, Kirchner S, Muraya JK, Jahoor A, Wenzel G (1994) Progress of RFLP map construction in winter barley. Barley Genetics Newsletter 23:53-61
Grivet L, D'Hont A, Dufour P, Hamon P, Roques D, Glaszmann JC (1994) Comparative mapping of sugar cane with other species within the Andropogoneae tribe. Heredity 73:500-508
Heun M, Kennedy AE, Anderson JA, Lapitan NLV, Sorrells ME, Tanksley SD (1991) Construction of a restriction fragment length polymorphism map for barley (Hordeum vulgare). Genome 34:437-447
Kleinhofs A, Kilian A, Saghai-Maroof MA, Biyashev RM, Hayes P, Chen FQ, Lapitan N, Fenwick A, Blake TK, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp SJ, Liu B, Sorrells M, Heun M, Franckowiak JD, Hoffman D, Skadsen R, Steffenson BJ (1993) A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome. Theor. Appl. Genet. 86:705-712
Kosambi DD (1944) The estimation of map distances from recombination values. Ann. Eugen. 12:172-175
Kurata N, Nagumara Y, Yamamoto K, Harushima Y, Sue N, Wu J, Antonio BA, Shomura A, Shimuzu T, Lin S-Y, Inoue T, Fukuda A, Shimano T, Kuboki Y, Toyama T, Miyamoto Y, Kirihara T, Hayasaka K, Miyao A, Monna L. Zhong HS, Tamura Y, Wang Z-X, Momma T, Umehara Y, Yano M, Sasaki T, Minobe Y (1994a) A 300 kilobase interval genetic map of rice including 883 expressed sequences. Nature Genetics 8:365-372
Kurata N, Moore G, Nagumara Y, Foote T, Yano M, Minobe Y, Gale M (1994b) Conservation of genome structure between rice and wheat. Bio/technology 12:276-278
Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg I (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174-181
Liu YG, and Tsunewaki K (1991) Restriction fragment length polymorphism analysis of wheat. II. Linkage maps of the RFLP sites in common wheat. Jap. J. Genet. 66:617-633
McCouch, S. R., G. Kochert, Z. H. Yu, Z. Y. Wang, G. S. Khush, W. R. Coffman, and S. D. Tanksley, 1988 Molecular mapping of rice chromosomes. Theor. Appl. Genet. 76: 815-829
Melake Berhan A, Hulbert SH, Butler LG, and Bennetzen JL (1993) Structure and evolution of the genomes of Sorghum bicolor and Zea mays Theor Appl Genet 86:598-604
Naranjo T, Roca P, Goicoechea PG, Giraldez R (1987) Arm homoeology of wheat and rye chromosomes. Genome 29:873-882
Nelson JC, Van Deynze AE, Autrique E, Sorrells ME, Lu YH, Merlino M, Atkinson M, Leroy P (1995a) Molecular mapping of wheat. Homoeologous group 2. Genome 38:517-524
Nelson JC, Van Deynze AE, Autrique E, Sorrells ME, Lu YH, Negre S, Bernard M, Leroy P (1995b) Molecular mapping of wheat. Homoeologous group 3. Genome 38:525-533
Nelson JC, Sorrells ME, Van Deynze AE, Lu YH, Atkinson M Bernard M, Leroy P, Faris J, Anderson J (1995c) Molecular mapping of wheat. Major genes and rearrangements in homoeologous groups 4, 5, and 7. Genetics 141:721-731
O'Donoughue LS, Wang Z, Ršder M, Kneen B, Leggett M, Sorrells ME, Tanksley SD (1992) An RFLP-based map of oat on a cross between two diploid taxa (Avena atlantica x A. hirtula). Genome 35:765-771
O'Donoughue LS, Kianian SF, Rayapati PJ, Penner GA, Sorrells ME, Tanksley SD, Phillips RL, Rines HW, Lee M, Fedak G, Molnar SJ, Hoffman D, Salas CA, Wu B, Autrique E, Van Deynze A (1995) A molecular map of cultivated oat. Genome 38:368-380
Rayapati PJ, Gregory JW, Lee M, Wise RP (1995) A linkage map of diploid oat Avena based on RFLP loci and a locus conferring resistance to Puccinia coronata var. avenae. Theor. Appl. Genet. 89:831
Sears ER (1966) Nullisomic-tetrasomic combinations in hexaploid wheat In R. Riley and K.R. Lewis (eds) Chromosome manipulation and plant genetics. Oliver and Boyd, Edinburgh. pp. 29-45.
Sears ER and Sears LMS (1978) The telocentric chromosomes of common wheat. In: S. Ramanujam (ed) Proc. 5th Int. Wheat Genet. Symp. Indian Soc. Genet. Plant Breed, New Delhi, pp. 389-407
Song W-Y, Wang G-L, Chen L, Kim H-S, Wang B.,Holsten T, Zhai W-X, Zhu L-H, Fauquet C, Ronald P. 1995. The rice disease resistance gene Xa21 encodes a receptor kinase-like protein. Science 270:1804-1806
Umehara Y, Inagaki A, Tanoue H, Yasukochi T, Nagamura Y, Saji S, Otsuki Y, Fujimura T, Kurata N, and Minobe Y (1994) Construction and characterization of rice YAC libraries for physical mapping. Molecular Breeding 1:79-89
Van Deynze AE, Dubcovsky J, Gill KS, Nelson JC, Sorrells ME, Dvorak J, Gill BS, Lagudah ES, McCouch SR, Appels R (1995a) Molecular-genetic maps for chromosome 1 in Triticeae species and their relation to chromosomes in rice and oats. Genome 38:45-59
Van Deynze AE, Nelson JC, O'Donoughue LS, Ahn SN, Siripoonwiwat W, Harrington SE, Yglesias ES, Braga DP, McCouch SR, Sorrells ME (1995b) Comparative mapping in grasses. Oat relationships. Mol. Gen. Genet. 249:in press
Van Deynze AE, Nelson JC, Yglesias ES, Harrington SE, Braga DP, McCouch SR, and Sorrells ME (1995c) Comparative mapping in grasses. Wheat relationships. Mol. Gen. Genet. 248:744-754
Van Houten W, Kurata N, Umehara Y, Sasaki T, and Minobe Y (1996) Generation of a YAC contig encompassing the extra glume gene, eg, in rice. Mol. Gen. Genet.: in press
Wang GL, Holsten TE, Song WY, Wang HP, and Ronald PC (1995) Construction of a rice bacterial artificial chromosome library and identification of clones linked to the Xa-21 disease resistance locus. The Plant Journal 5:525
Werner JE, TR Endo and BS Gill (1992) Toward a cytogenetically based physical map of the wheat genome. Proc. Natl. Acad. Sci. 89:11307-11311
Whitkus R, Doebley J, Lee M (1992) Comparative genome mapping of sorghum and maize. Genetics 132:119-1130
Xie DX, Devos KM, Moore G, Gale MD (1993) RFLP-based maps of the homoeologous group 5 chromosomes of bread wheat (Triticum aestivum L.). Theor. Appl. Genet. 87:70-74
Zhang, H.B., S.D. Choi, S.S. Woo, Z.K. Li, and R.A. Wing. 1996. Construction and characterization of two rice bacterial artificial chromosome libraries from the parents of a permanent recombinant inbred mapping population. Molecular Breeding: in press