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

Aitken KS, McNeil MD, Berkman PJ, Hermann S, Kilian A, Bundock PC, Li J - BMC Plant Biol. (2014)

Bottom Line: Comparative mapping revealed that certain sugarcane chromosomes show greater levels of synteny to sorghum than others.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane 4067, QLD, Australia. Karen.Aitken@csiro.au.

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.

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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.
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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.

Mentions: Four major rearrangements were identified from syntenic analysis between the sugarcane genetic map and the sorghum genome (Figure 2A-D). Two of these account for the reduction in basic chromosome number from x = 10 in sorghum and S. officinarum to x = 8 in S. spontaneum. The complicated nature of the hybrid sugarcane genome means that only a few of the LGs within a HG have the translocation, for example in HG2, 7 of the LGs display the translocation, the other LGs align only to one of the two chromosomes (Additional file 1). This recombination results in the two sorghum chromosomes combining into one sugarcane HG. This translocation event reduces the basic chromosome number of sugarcane (Figure 2A). The other translocation event is in HG8 which aligns to Sb8 and Sb2 and again reduces the chromosome number to its final basic chromosome number of x = 8 (Figure 2B). The other major rearrangements had no effect on basic chromosome number but involved rearrangements between chromosomes. HG6 aligns in the main to Sb9 but one LG contains a significant translocation from Sb3 covering approximately 50% of Sb3 (Table 3, Figure 2C) The last rearrangement is in HG5 which aligns to Sb7 and Sb5 (Figure 2D); this appears to be a simple translocation between Sb7 and half of Sb5 and is present in 5 LGs within this HG (Additional file 1).


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

Aitken KS, McNeil MD, Berkman PJ, Hermann S, Kilian A, Bundock PC, Li J - BMC Plant Biol. (2014)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4222257&req=5

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.
Mentions: Four major rearrangements were identified from syntenic analysis between the sugarcane genetic map and the sorghum genome (Figure 2A-D). Two of these account for the reduction in basic chromosome number from x = 10 in sorghum and S. officinarum to x = 8 in S. spontaneum. The complicated nature of the hybrid sugarcane genome means that only a few of the LGs within a HG have the translocation, for example in HG2, 7 of the LGs display the translocation, the other LGs align only to one of the two chromosomes (Additional file 1). This recombination results in the two sorghum chromosomes combining into one sugarcane HG. This translocation event reduces the basic chromosome number of sugarcane (Figure 2A). The other translocation event is in HG8 which aligns to Sb8 and Sb2 and again reduces the chromosome number to its final basic chromosome number of x = 8 (Figure 2B). The other major rearrangements had no effect on basic chromosome number but involved rearrangements between chromosomes. HG6 aligns in the main to Sb9 but one LG contains a significant translocation from Sb3 covering approximately 50% of Sb3 (Table 3, Figure 2C) The last rearrangement is in HG5 which aligns to Sb7 and Sb5 (Figure 2D); this appears to be a simple translocation between Sb7 and half of Sb5 and is present in 5 LGs within this HG (Additional file 1).

Bottom Line: Comparative mapping revealed that certain sugarcane chromosomes show greater levels of synteny to sorghum than others.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane 4067, QLD, Australia. Karen.Aitken@csiro.au.

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.

Show MeSH
Related in: MedlinePlus