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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: firstname.lastname@example.org) and Mark Sorrells (email: email@example.com), 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/].
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