Polyploidy Evolution of New Genomes

Polyploidy has contributed significantly to enhancing the productivity of plant taxa such as cotton, wheat, sugarcane, oat, soybean, peanut, canola, tobacco, coffee, and banana. The increase in genomic content of nuclei either brought about through whole genome duplication or polyploidy (uniting of two genomes in one nucleus), followed by extensive chromosome restructuring (Brubaker et al. 1999) possibly through retrotransposon activity (Zhao et al. 1998), is one of the major causes of deviating from the arithmetic sums of the sizes of the parental genomes (Chen 2007). Presently, all the diploids including rice and Arabidopsis are apparently ancient polyploids (Bowers et al. 2003b). In ancient polyploids, domesticated forms evolve through tinkering with genes in their wild relatives (Doebley 2006). However, in recent allopolyploid species such as wheat, a null mutation of the GPC-B1 gene in the B genome, greatly facilitated by repetitive elements in the wheat genome (Flavell et al. 1974), caused a few days difference in the maturity (Slade et al. 2005). In the success of polyploids, the role of repetitive elements in impacting gene content still needs research and development efforts.

The reactivation of mobile elements (Kashkush et al. 2003; Madlung et al. 2005) resulting in chromosomal abnormalities, deletions, pollen sterility, and other problems may limit the chances of evolving successful synthetic allopoly-ploids such as allotetraploid Arabidopsis (Madlung et al. 2005) and wheat (Shaked et al. 2001). The process of accumulating chromosomal changes, especially deletions, is not sudden but is slow in examples such as the D genome of T. aestivum (Dvorak et al. 2004).

Cultivated cotton species G. hirsutum and G. barbadense evolved from a common paleopolyploid ancestor that formed about 1-2 mya by hybridization of an A genome species resembling G. herbaceum and a D genome species resembling G. raimondii. The two progenitors of tetraploid cottons are themselves thought to have shared a common ancestor about 6-11 mya (Wendel and Cronn 2003). The genus Gossypium is especially well suited to investigating the evolutionary consequences of polyploidy, as both the progenitor genomes of the allotetraploids are known and remain extant. The Dt genome (version of the D genome present in the allotetraploid) remains largely unchanged from that of its diploid progenitor, while two reciprocal translocations along with several inversions distinguish A from At chromosomes. While the diploid D-genome species does not produce spinnable fiber, it imparts important genes or regulators involved in fiber morphogenesis and its properties (Jiang et al. 1998; Paterson et al. 2003; Ulloa et al. 2005; Rong et al. 2007). Conversely, A-genome progenitor diploid species are extremely resistant to cotton leaf curl disease, while its derived tetraploid cotton species are susceptible (Rahman et al. 2005). Indeed, the A-genome species is more tolerant to many biotic and abiotic stress than AD-tetraploids. The loss of either A or D subgenome genes in subsequent generations by the AD-tetraploids, a phenomenon that is nearly ubiquitous among paleopolyploids but has only been studied to a limited degree in cotton, needs further investigation.

Most if not all Poaceae shared a common genome duplication (Paterson et al. 2004), with additional subsequent duplications in some lineages such as maize, wheat, and sugarcane. Despite this variation in ploidy and also substantial variation in genome size, chromosome number has remained more stable (Bennett and Smith 1991). Indeed, some polyploidizations have most probably been followed by a substantial degree of chromosome condensation, uniting two chromosomes into one. For example Z. mays has been through one whole genome duplication (Swigonova et al. 2004) since the divergence of the Zea and Sorghum lineages -however, Z. mays contains the same chromosome number (n = 10) as S. bicolor, although the latter has not incurred genome duplication since the event shared by all cereals (Paterson et al. 2004). Likewise, some members of the Sorghum genus appear to have condensed from n = 10 to n = 5. Condensation of maize chromosomes would be consistent with the observation that single arms of several maize chromosomes correspond with entire sorghum chromosomes (Whitkus et al. 1992; Bowers et al. 2003a).

Building on a growing understanding of ancestral genome duplications and polyploidization events in the present day diploid cereals, low copy RFLP markers permitted the construction of a consensus grass map of low resolution based on 25 rice linkage blocks (Feuillet and Keller 2002). More recently, comparison of the rice genome sequence with wheat and maize cytological maps, have shown more chromosomal rearrangements between the genomes of rice, maize and wheat species, and also revealed evidence of ancestral genome duplications occurred between 53 and 94 mya (Paterson et al. 2003, 2004; Buell et al. 2005; Yu et al. 2005; Singh et al. 2007). All this information led to models proposing the basic chromosome number of the grass ancestor, ranging from n = 5 to 12 (Wei et al. 2007), and more recently n = 5 has gained support (Salse et al. 2008).

The basic chromosome set of wheat, barley and oat is x = 7, and one chromosome corresponds to the rice linkage groups 5 and 10 and another corresponds to a novel combination of parts of rice chromosomes 4 and 7 (Kellogg 1998). The members of tribe Bambuseae are polyploid except Chusquea talamancensis and possibly C. subtesselata (Judziewicz et al. 1999), and vary substantially in morphology perhaps in part due to passing through major genomic changes both in structure and function following polyploidy. It is hypothesized that the woody bamboos have two full copies of a rice-like genome which needs further investigation. Zizania aquatica, a wild relative of rice, has 15 chromosomes, with 14 that are clearly collinear with 11 of the 12 rice chromosomes. Moreover, three chromosomes seems to be duplicates of rice chromosomes 1, 4 and 9 (Kennard et al. 1999).

Sugarcane, an important biofuel crop, has undergone at least two genome duplications since its divergence from sorghum 8-9 mya (Jannoo et al. 2007). Polyploidy further added to the complexity of its genome (n = 18-85 versus n = 10 for sorghum) which not only impedes breeding progress but also makes challenging the job of understanding the sugarcane genome or its transmission genetics (Ming et al. 2005). Comparative genome mapping studies suggest a high degree of collinearity between the gene order of sugarcane and sorghum genomes (Ming et al. 2002).

In the Brassicaceae, three rounds of ancestral genome duplications (Vision et al. 2000; Bowers et al. 2003b) coupled with the polyploid origin of 37% of species playing a decisive role in the evolution of different plant taxa in this family (Warwick et al. 2006). Several comparative mapping studies between the A. thaliana and Brassica species have shown the footprints of triplication in numerous homeologous regions within Brassica (Lagercrantz 1998), complemented by sequencing (Town et al. 2006; Yang et al. 2006) and cytogenetic approaches

(Lysak et al. 2006; Ziolkowski et al. 2006), cumulatively supporting the possibility of having a common hexaploid ancestor in the ancestry of Brassica and the tribe Brassiceae which needs further investigations (Lukens et al. 2004).

Like other crop plants, the genome of Glycine max L. Merr. (n = 20) has also evolved from an ancestral genome karyotype (n = 11) that lost one chromosome to make n = 10 followed by diploidization (n = 20, Singh and Hymowitz 1988). The soybean genome might have gone through two or more duplications (Blanc and Wolfe 2004; Van et al. 2008) followed by genomic rearrangements (Yan et al. 2003). The whole genome sequence of soybean is underway, and will help in establishing the relationship with legumes and members of other plant families to understand the evolutionary history comprehensively (Schlueter et al. 2008).

In Solanaceae, potato and tomato genomes can be differentiated by few paracentric inversions. Moreover, evidence of translocations and inversions have also been reported in tomato, eggplant and pepper (Zygier et al. 2005).

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