In multiple investigations, conservation in gene order and content were reported among the Poaceae (Goff et al. 2002; Sorrells et al. 2003; Bowers et al. 2005; The Rice Chromosome 3 Sequencing Consortium 2005; Zhu and Buell 2007; Salse et al. 2008).
Genetic maps based on RFLP markers revealed significant macrocollinearity between the cereal genomes (Ahn and Tanksley 1993; Paterson et al. 1995; Devos and Gale 2000; Feuillet and Keller 2002; Devos 2005), and established inter-relationship among the homeologous chromosomes of the Triticeae and their relatives (Naranjo et al. 1987; Chao et al. 1989; Namuth et al. 1994; Devos et al. 1995; Hohmann et al. 1995; Marino et al. 1996; Mickelson-Young et al. 1995; Nelson et al. 1995; Van Deynze et al. 1995; Ming et al. 1998; Paterson et al. 2000, 2004; Salse et al. 2008). Comparative mapping using RFLP markers often probed paralogous rather than orthologous sequences, leading to underestimation of collinearity using these markers.
The availability of genomic resources such as drafts of the rice and sorghum genome sequence and huge collections of ESTs of rice (http://www.gramene.org), sorghum (http://cggc.agtec.uga.edu), wheat (http://www.ncbi.nlm.nih.gov/dbEST), maize (http://www.panzea.org) and many more, has made it possible to compare genome sequences with non-sequenced plant taxa (Ming et al. 2008; Tang et al. 2008a) to refine our understanding of collinearity, genetic diversity and agricultural productivity (Paterson et al. 2003, 2005). For example, the sequences of rice chromosomes 3 and 11 were compared with wheat ESTs (Singh et al. 2004) to increase the resolution of comparative mapping. Maize derived ESTs were compared with the sequence of rice chromosome 3 (Buell et al. 2005), which showed relatively more rearrangements in the cereal genomes.
Whole genome duplication (WGD) occurred before the divergence of cereal genomes (Paterson et al. 2004), supported by RFLP markers in rice (Kishimoto et al. 1994; Nagamura et al. 1995) and sorghum (Chittenden et al. 1994), and the complete genome sequences of the japonica and indica subspecies of rice (Goff et al. 2002; Yu et al. 2002, 2005; Paterson et al. 2003, 2004; Vandepoele et al. 2003; Guyot et al. 2004; International Rice Genome Sequencing Project 2005; Wang et al. 2005).
A large scale comparative genomic analysis of rice with four plant genome sequence data sets including Arabidopsis (The Arabidopsis Genome Initiative 2000), poplar (Tuskan et al. 2006), sorghum (Bedell et al. 2005) and maize (Palmer et al. 2003; Whitelaw et al. 2003), and transcript assemblies from 185 plant species, confirmed 38,109 (89.3%) of the total 42,653 non-transposable element-related genes. Out of these, 7,669 genes are lineage-specific which may have a role in species diversity (Zhu and Buell 2007). The conservation of short intergenic regions in a few genes is attributable to alternative splicing (Wang and Brendel 2006), a common phenomenon in the genome of rice, sorghum and maize. However, its role in biological function is unknown.
In the maize genome, duplications were reported by comparing the orthologous loci between rice, sorghum and maize (Swigonova et al. 2004). In another study, comparison of 2,600 maize mapped sequence markers with the rice genome sequence revealed six duplications between the maize and rice chromosomes (Salse et al. 2008) which has been supplemented by developing a high resolution comparative physical map between rice and maize genomes (Wei et al. 2007). However, the mechanism of duplications, and discovery of the exact number of basic chromosomes of the grass ancestor, is big challenges for researchers. There is inconsistency in the literature about the exact number of ancestral grass chromosomes. Two models have been proposed, exhibiting 5-12 (Gaut 2002; Wei et al. 2007) and five (Salse et al. 2008) chromosomes in the ancestral grass genome.
The sorghum genome has not incurred genome duplication since the pan-cereal event (Paterson et al. 2004), making it an excellent out group for comparison with the duplicated genomes of maize and sugarcane, the worlds leading biofuel crop (Bedell et al. 2005; Bowers et al. 2005). Comparative mapping of Sorghum propin-quum (a closely related species) with sorghum and Oryza longistaminata shed light on genes related to domestication (Paterson et al. 1995; Hu et al. 2003). A comparative physical map of sorghum with rice and maize has identified probable euchro-matic regions in the grass family (Bowers et al. 2005).
A consensus map of Saccharum species and sorghum reveals a high degree of conservativeness between the two genomes, which can be instrumental in translating the genetic information for developing a detailed genetic map (Ming et al.
2002). Complexity and variable chromosome content of the sugarcane genome are major concerns in its whole genome sequencing (Dillon et al. 2007). Comparison of sugarcane genetic maps and EST sequences are the major tools utilized for understanding its genome, and dissecting traits of interest. Out of 237,954 ESTs derived from S. officinarum, two-thirds have recognizable homologs in Arabidopsis, and the remainder appear to be monocot specific or perhaps rapidly-evolving (Vincentz et al. 2004). Additional EST sequences are needed for comparison with the model species to identify genes of potential agronomic value (Vettore et al.
2003) and new EST-SSRs (Cordeiro et al. 2001) will be useful for developing detailed genetic linkage maps.
The Triticeae tribe diverged from rice around 50 mya (Paterson et al. 2004) and contains Triticum aestivum species, one of the most important food crops, which originated around 10,000 years ago through hybridization of diploid ancestors (A, B and D genomes) (Feldman et al. 1995). Over its short evolutionary span, genes remain conserved in comparison with those of T. monococcum (derived from T. urartu, the A genome progenitor of present day wheat), however, the intergenic regions have gone through several changes (Wicker et al. 2003; Isidore et al. 2005; Gu et al. 2006). Extensive conservation in intergenic regions was also discovered between T. aestivum and T. turgidum (spp. durum), which diverged approximately 800,000 years ago (Gu et al. 2006). In another investigation, Pm3 loci isolated from hexaploid wheat (Yahiaoui et al. 2004, 2006), conferring resistance to powdery mildew, have gone through an extremely dynamic evolution which resulted in minimal sequence conservation between the A genome species at three ploidy levels. This wheat locus evolved more rapidly than its homolog in rice (Wicker et al. 2007).
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