Comparative mapping in the Poaceae family reveals translocations in the complex polyploid genome of sugarcane

Abstract

Background: The understanding of sugarcane genetics has lagged behind that of other members of the Poaceae family such as wheat, rice, barley and sorghum mainly due to the complexity, size and polyploidization of the genome. We have used the genetic map of a sugarcane cultivar to generate a consensus genetic map to increase genome coverage for comparison to the sorghum genome. We have utilized the recently developed sugarcane DArT array to increase the marker density within the genetic map. The sequence of these DArT markers plus SNP and EST-SSR markers was then used to form a bridge to the sorghum genomic sequence by BLAST alignment to start to unravel the complex genomic architecture of sugarcane.

Results: Comparative mapping revealed that certain sugarcane chromosomes show greater levels of synteny to sorghum than others. On a macrosyntenic level a good collinearity was observed between sugarcane and sorghum for 4 of the 8 homology groups (HGs). These 4 HGs were syntenic to four sorghum chromosomes with from 98% to 100% of these chromosomes covered by these linked markers. Four major chromosome rearrangements were identified between the other four sugarcane HGs and sorghum, two of which were condensations of chromosomes reducing the basic chromosome number of sugarcane from x = 10 to x = 8. This macro level of synteny was transferred to other members within the Poaceae family such as maize to uncover the important evolutionary relationships that exist between sugarcane and these species.

Conclusions: Comparative mapping of sugarcane to the sorghum genome has revealed new information on the genome structure of sugarcane which will help guide identification of important genes for use in sugarcane breeding. Furthermore of the four major chromosome rearrangements identified in this study, three were common to maize providing some evidence that chromosome reduction from a common paleo-ancestor of both maize and sugarcane was driven by the same translocation events seen in both species.

Figure 1

Global distribution of synteny between the 10 sorghum chromosome sequence (SB1-10) and the 8 composite linkage groups fromSaccharumcultivar Q165. Loci showing homology between the two genomes at P < 1e⁻²⁰ significance threshold are indicated by dots.

Figure 2

Alignment of the composite sugarcane LGs to sorghum, maize and rice genomic sequences (A-D). The bars on the sugarcane LG represent markers from Additional file 1. These are aligned using the BLASTN algorithm (P < e⁻²⁰) and the position indicated by lines to the other chromosomes. The scale of the chromosomes is in bp.

Figure 3

Venn diagram of DArTs with hits against the EST datasets from four species.

Figure 4

Annotations of assembled DArT sequence alignments to different parts of the annotated S . bicolor genome including genes, repeats, the boundary between a repeat and genes and other which are regions that are not annotated.

Figure 5

Categories of repeats in the S. bicolor genome against which assembled DArT sequences aligned.

Figure 6

Ratio of DArT sequences aligning in S. bicolor and Z. mays syntenic to non-syntenic regions.

Figure 7

Ratio of DArT sequences aligning in S. bicolor and O. sativa syntenic to non-syntenic regions.

Figure 8

Model for the structural evolution of the sugarcane monoploid genome (modified from[[26]]). As in [[26]] the ancestral chromosomes are colour coded to represent the original 5 chromosomes (and labelled A1-12) which after a whole genome duplication (~90 MYA) and breakage/fusion formed the 12 ancestral chromosomes of sorghum.