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A complex recombination pattern in the genome of allotetraploid Brassica napus as revealed by a high-density genetic map.

Cai G, Yang Q, Yi B, Fan C, Edwards D, Batley J, Zhou Y - PLoS ONE (2014)

Bottom Line: A better understanding of the evolutionary relationship between B. napus and B. rapa, B. oleracea, as well as Arabidopsis, which has a common ancestor with these three species, will provide valuable information about the generation and evolution of allopolyploidy.Based on the collinear relationship of B. rapa and B. oleracea in the B. napus genetic map, the B. napus genome was found to consist of 70.1% of the skeleton components of the chromosomes of B. rapa and B. oleracea, with 17.7% of sequences derived from reciprocal translocation between homoeologous chromosomes between the A- and C-genome and 3.6% of sequences derived from reciprocal translocation between non-homologous chromosomes at both intra- and inter-genomic levels.The current study thus provides insights into the formation and evolution of the allotetraploid B. napus genome, which will allow for more accurate transfer of genomic information from B. rapa, B. oleracea and Arabidopsis to B. napus.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, Huazhong Agricultural University, Wuhan, China.

ABSTRACT
Polyploidy plays a crucial role in plant evolution. Brassica napus (2n = 38, AACC), the most important oil crop in the Brassica genus, is an allotetraploid that originated through natural doubling of chromosomes after the hybridization of its progenitor species, B. rapa (2n = 20, AA) and B. oleracea (2n = 18, CC). A better understanding of the evolutionary relationship between B. napus and B. rapa, B. oleracea, as well as Arabidopsis, which has a common ancestor with these three species, will provide valuable information about the generation and evolution of allopolyploidy. Based on a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, we performed a comparative genomic analysis of B. napus with Arabidopsis and its progenitor species B. rapa and B. oleracea. Based on the collinear relationship of B. rapa and B. oleracea in the B. napus genetic map, the B. napus genome was found to consist of 70.1% of the skeleton components of the chromosomes of B. rapa and B. oleracea, with 17.7% of sequences derived from reciprocal translocation between homoeologous chromosomes between the A- and C-genome and 3.6% of sequences derived from reciprocal translocation between non-homologous chromosomes at both intra- and inter-genomic levels. The current study thus provides insights into the formation and evolution of the allotetraploid B. napus genome, which will allow for more accurate transfer of genomic information from B. rapa, B. oleracea and Arabidopsis to B. napus.

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Evolutionary relationship between Brassica napus and its progenitor species B. rapa and B. oleracea.Schematic diagram of the B. napus genome as revealed by a genetic linkage map comprised of simple sequence repeat (SSR) and single nucleotide polymorphisms (SNP) markers and comparative analyses with the B. rapa, B. oleracea and Arabidopsis genomes. The colored blocks at the outermost circle represent the Arabidopsis conserved blocks in the B. napus genome identified with the genetic linkage groups of B. napus, which is represented in the second outer circle (all circles were orientated clockwise). The third circle (from the outermost one) represents the B. napus genome that is reconstructed with 46 homoeologous collinear fragments of B. rapa and B. oleracea. Each homoeologous collinear fragment of B. napus (the third circle) is the same color as the corresponding chromosome of B. rapa and B. oleracea in the inner circle. The ribbons between the third and inner circle depict the origins of the homoeologous collinear fragments from B. rapa and B. oleracea. The inverted homoeologous collinear fragments are indicated with twisted ribbons. The gray ribbons represent the skeletons from the B. rapa and B. oleracea genomes retained in B. napus genome; The green ribbons represent the reciprocal translocations between homoeologous chromosomes from the A and C genomes; The purple ribbons represent the reciprocal translocations between non-homologous chromosomes from the A and C genomes; The yellow ribbon represents the repeat fragment from B. rapa/B. oleracea chromosome. The numbers in the inner circle (under each B. rapa or B. oleracea chromosome) are the percentages of all homoeologous collinear fragments of B. rapa or B. oleracea retained in the B. napus genome relative to the physical length of the corresponding B. rapa (chromosome_v1.5) or B. oleracea (chromosome_v1.0) chromosome.
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pone-0109910-g003: Evolutionary relationship between Brassica napus and its progenitor species B. rapa and B. oleracea.Schematic diagram of the B. napus genome as revealed by a genetic linkage map comprised of simple sequence repeat (SSR) and single nucleotide polymorphisms (SNP) markers and comparative analyses with the B. rapa, B. oleracea and Arabidopsis genomes. The colored blocks at the outermost circle represent the Arabidopsis conserved blocks in the B. napus genome identified with the genetic linkage groups of B. napus, which is represented in the second outer circle (all circles were orientated clockwise). The third circle (from the outermost one) represents the B. napus genome that is reconstructed with 46 homoeologous collinear fragments of B. rapa and B. oleracea. Each homoeologous collinear fragment of B. napus (the third circle) is the same color as the corresponding chromosome of B. rapa and B. oleracea in the inner circle. The ribbons between the third and inner circle depict the origins of the homoeologous collinear fragments from B. rapa and B. oleracea. The inverted homoeologous collinear fragments are indicated with twisted ribbons. The gray ribbons represent the skeletons from the B. rapa and B. oleracea genomes retained in B. napus genome; The green ribbons represent the reciprocal translocations between homoeologous chromosomes from the A and C genomes; The purple ribbons represent the reciprocal translocations between non-homologous chromosomes from the A and C genomes; The yellow ribbon represents the repeat fragment from B. rapa/B. oleracea chromosome. The numbers in the inner circle (under each B. rapa or B. oleracea chromosome) are the percentages of all homoeologous collinear fragments of B. rapa or B. oleracea retained in the B. napus genome relative to the physical length of the corresponding B. rapa (chromosome_v1.5) or B. oleracea (chromosome_v1.0) chromosome.

Mentions: Based on the above analysis, we further identified homoeologous collinear fragments of B. rapa and B. oleracea in the B. napus genome using a similar method described by Parkin et al. [18]. Homoeologous collinear fragments of B. rapa/B. oleracea in B. napus were defined as DNA sequences that included at least four molecular markers in every 5 cM of the map, and simultaneously contained at least one homoeologous locus in a 2.5 Mb region of the corresponding B. rapa/B. oleracea genomes. Using this criterion, 22 homoeologous collinear fragments of B. rapa and 24 of B. oleracea were identified in B. napus (Figure 2, Table 3 and Table S1), which corresponded to 1,309 loci (Table 1, Table S1) and covered 2,237.1 cM (90.3%) of the whole B. napus genome (Table 3, Figure 2). Except for a 2.74 Mb fragment in chromosome A07 of B. rapa (BrA07) that had one duplicated copy located on BnC06 (yellow ribbon in Figure 3, Table 3), the rest of the 21 B. rapa fragments and 24 B. oleracea fragments appeared only once on each of the 19 LGs/chromosomes of B. napus (Table 3). These homoeologous collinear fragments of B. rapa and B. oleracea identified in B. napus genome accounted for 90.3% and 71.4% of the total length of the B. rapa and B. oleracea genomes, respectively, based on the known physical lengths of the two species (Figure 2, Table 3 and Table S1).


A complex recombination pattern in the genome of allotetraploid Brassica napus as revealed by a high-density genetic map.

Cai G, Yang Q, Yi B, Fan C, Edwards D, Batley J, Zhou Y - PLoS ONE (2014)

Evolutionary relationship between Brassica napus and its progenitor species B. rapa and B. oleracea.Schematic diagram of the B. napus genome as revealed by a genetic linkage map comprised of simple sequence repeat (SSR) and single nucleotide polymorphisms (SNP) markers and comparative analyses with the B. rapa, B. oleracea and Arabidopsis genomes. The colored blocks at the outermost circle represent the Arabidopsis conserved blocks in the B. napus genome identified with the genetic linkage groups of B. napus, which is represented in the second outer circle (all circles were orientated clockwise). The third circle (from the outermost one) represents the B. napus genome that is reconstructed with 46 homoeologous collinear fragments of B. rapa and B. oleracea. Each homoeologous collinear fragment of B. napus (the third circle) is the same color as the corresponding chromosome of B. rapa and B. oleracea in the inner circle. The ribbons between the third and inner circle depict the origins of the homoeologous collinear fragments from B. rapa and B. oleracea. The inverted homoeologous collinear fragments are indicated with twisted ribbons. The gray ribbons represent the skeletons from the B. rapa and B. oleracea genomes retained in B. napus genome; The green ribbons represent the reciprocal translocations between homoeologous chromosomes from the A and C genomes; The purple ribbons represent the reciprocal translocations between non-homologous chromosomes from the A and C genomes; The yellow ribbon represents the repeat fragment from B. rapa/B. oleracea chromosome. The numbers in the inner circle (under each B. rapa or B. oleracea chromosome) are the percentages of all homoeologous collinear fragments of B. rapa or B. oleracea retained in the B. napus genome relative to the physical length of the corresponding B. rapa (chromosome_v1.5) or B. oleracea (chromosome_v1.0) chromosome.
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pone-0109910-g003: Evolutionary relationship between Brassica napus and its progenitor species B. rapa and B. oleracea.Schematic diagram of the B. napus genome as revealed by a genetic linkage map comprised of simple sequence repeat (SSR) and single nucleotide polymorphisms (SNP) markers and comparative analyses with the B. rapa, B. oleracea and Arabidopsis genomes. The colored blocks at the outermost circle represent the Arabidopsis conserved blocks in the B. napus genome identified with the genetic linkage groups of B. napus, which is represented in the second outer circle (all circles were orientated clockwise). The third circle (from the outermost one) represents the B. napus genome that is reconstructed with 46 homoeologous collinear fragments of B. rapa and B. oleracea. Each homoeologous collinear fragment of B. napus (the third circle) is the same color as the corresponding chromosome of B. rapa and B. oleracea in the inner circle. The ribbons between the third and inner circle depict the origins of the homoeologous collinear fragments from B. rapa and B. oleracea. The inverted homoeologous collinear fragments are indicated with twisted ribbons. The gray ribbons represent the skeletons from the B. rapa and B. oleracea genomes retained in B. napus genome; The green ribbons represent the reciprocal translocations between homoeologous chromosomes from the A and C genomes; The purple ribbons represent the reciprocal translocations between non-homologous chromosomes from the A and C genomes; The yellow ribbon represents the repeat fragment from B. rapa/B. oleracea chromosome. The numbers in the inner circle (under each B. rapa or B. oleracea chromosome) are the percentages of all homoeologous collinear fragments of B. rapa or B. oleracea retained in the B. napus genome relative to the physical length of the corresponding B. rapa (chromosome_v1.5) or B. oleracea (chromosome_v1.0) chromosome.
Mentions: Based on the above analysis, we further identified homoeologous collinear fragments of B. rapa and B. oleracea in the B. napus genome using a similar method described by Parkin et al. [18]. Homoeologous collinear fragments of B. rapa/B. oleracea in B. napus were defined as DNA sequences that included at least four molecular markers in every 5 cM of the map, and simultaneously contained at least one homoeologous locus in a 2.5 Mb region of the corresponding B. rapa/B. oleracea genomes. Using this criterion, 22 homoeologous collinear fragments of B. rapa and 24 of B. oleracea were identified in B. napus (Figure 2, Table 3 and Table S1), which corresponded to 1,309 loci (Table 1, Table S1) and covered 2,237.1 cM (90.3%) of the whole B. napus genome (Table 3, Figure 2). Except for a 2.74 Mb fragment in chromosome A07 of B. rapa (BrA07) that had one duplicated copy located on BnC06 (yellow ribbon in Figure 3, Table 3), the rest of the 21 B. rapa fragments and 24 B. oleracea fragments appeared only once on each of the 19 LGs/chromosomes of B. napus (Table 3). These homoeologous collinear fragments of B. rapa and B. oleracea identified in B. napus genome accounted for 90.3% and 71.4% of the total length of the B. rapa and B. oleracea genomes, respectively, based on the known physical lengths of the two species (Figure 2, Table 3 and Table S1).

Bottom Line: A better understanding of the evolutionary relationship between B. napus and B. rapa, B. oleracea, as well as Arabidopsis, which has a common ancestor with these three species, will provide valuable information about the generation and evolution of allopolyploidy.Based on the collinear relationship of B. rapa and B. oleracea in the B. napus genetic map, the B. napus genome was found to consist of 70.1% of the skeleton components of the chromosomes of B. rapa and B. oleracea, with 17.7% of sequences derived from reciprocal translocation between homoeologous chromosomes between the A- and C-genome and 3.6% of sequences derived from reciprocal translocation between non-homologous chromosomes at both intra- and inter-genomic levels.The current study thus provides insights into the formation and evolution of the allotetraploid B. napus genome, which will allow for more accurate transfer of genomic information from B. rapa, B. oleracea and Arabidopsis to B. napus.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, Huazhong Agricultural University, Wuhan, China.

ABSTRACT
Polyploidy plays a crucial role in plant evolution. Brassica napus (2n = 38, AACC), the most important oil crop in the Brassica genus, is an allotetraploid that originated through natural doubling of chromosomes after the hybridization of its progenitor species, B. rapa (2n = 20, AA) and B. oleracea (2n = 18, CC). A better understanding of the evolutionary relationship between B. napus and B. rapa, B. oleracea, as well as Arabidopsis, which has a common ancestor with these three species, will provide valuable information about the generation and evolution of allopolyploidy. Based on a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, we performed a comparative genomic analysis of B. napus with Arabidopsis and its progenitor species B. rapa and B. oleracea. Based on the collinear relationship of B. rapa and B. oleracea in the B. napus genetic map, the B. napus genome was found to consist of 70.1% of the skeleton components of the chromosomes of B. rapa and B. oleracea, with 17.7% of sequences derived from reciprocal translocation between homoeologous chromosomes between the A- and C-genome and 3.6% of sequences derived from reciprocal translocation between non-homologous chromosomes at both intra- and inter-genomic levels. The current study thus provides insights into the formation and evolution of the allotetraploid B. napus genome, which will allow for more accurate transfer of genomic information from B. rapa, B. oleracea and Arabidopsis to B. napus.

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