Complete switchgrass genetic maps reveal subgenome collinearity, preferential pairing and multilocus interactions
Polyploidy is an important aspect of the evolution of flowering plants. The potential of gene copies to diverge and evolve new functions is influenced by meiotic behavior of chromosomes leading to segregation as a single locus or duplicated loci. Switchgrass (Panicum virgatum) linkage maps were cons...
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| Published in: | Genetics (Austin) Vol. 185; no. 3; pp. 745 - 760 |
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| Format: | Journal Article |
| Language: | English |
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Genetics Society of America
01-07-2010
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| Abstract | Polyploidy is an important aspect of the evolution of flowering plants. The potential of gene copies to diverge and evolve new functions is influenced by meiotic behavior of chromosomes leading to segregation as a single locus or duplicated loci. Switchgrass (Panicum virgatum) linkage maps were constructed using a full-sib population of 238 plants and SSR and STS markers to access the degree of preferential pairing and the structure of the tetraploid genome and as a step toward identification of loci underlying biomass feedstock quality and yield. The male and female framework map lengths were 1645 and 1376 cM with 97% of the genome estimated to be within 10 cM of a mapped marker in both maps. Each map coalesced into 18 linkage groups arranged into nine homeologous pairs. Comparative analysis of each homology group to the diploid sorghum genome identified clear syntenic relationships and collinear tracts. The number of markers with PCR amplicons that mapped across subgenomes was significantly fewer than expected, suggesting substantial subgenome divergence, while both the ratio of coupling to repulsion phase linkages and pattern of marker segregation indicated complete or near complete disomic inheritance. The proportion of transmission ratio distorted markers was relatively low, but the male map was more extensively affected by distorted transmission ratios and multilocus interactions, associated with spurious linkages. |
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| AbstractList | Polyploidy is an important aspect of the evolution of flowering plants. The potential of gene copies to diverge and evolve new functions is influenced by meiotic behavior of chromosomes leading to segregation as a single locus or duplicated loci. Switchgrass (Panicum virgatum) linkage maps were constructed using a full-sib population of 238 plants and SSR and STS markers to access the degree of preferential pairing and the structure of the tetraploid genome and as a step toward identification of loci underlying biomass feedstock quality and yield. The male and female framework map lengths were 1645 and 1376 cM with 97% of the genome estimated to be within 10 cM of a mapped marker in both maps. Each map coalesced into 18 linkage groups arranged into nine homeologous pairs. Comparative analysis of each homology group to the diploid sorghum genome identified clear syntenic relationships and collinear tracts. The number of markers with PCR amplicons that mapped across subgenomes was significantly fewer than expected, suggesting substantial subgenome divergence, while both the ratio of coupling to repulsion phase linkages and pattern of marker segregation indicated complete or near complete disomic inheritance. The proportion of transmission ratio distorted markers was relatively low, but the male map was more extensively affected by distorted transmission ratios and multilocus interactions, associated with spurious linkages. Polyploidy is an important aspect of the evolution of flowering plants. The potential of gene copies to diverge and evolve new functions is influenced by meiotic behavior of chromosomes leading to segregation as a single locus or duplicated loci. Switchgrass (Panicum virgatum) linkage maps were constructed using a full-sib population of 238 plants and SSR and STS markers to access the degree of preferential pairing and the structure of the tetraploid genome and as a step toward identification of loci underlying biomass feedstock quality and yield. The male and female framework map lengths were 1645 and 1376 cM with 97% of the genome estimated to be within 10 cM of a mapped marker in both maps. Each map coalesced into 18 linkage groups arranged into nine homeologous pairs. Comparative analysis of each homology group to the diploid sorghum genome identified clear syntenic relationships and collinear tracts. The number of markers with PCR amplicons that mapped across subgenomes was significantly fewer than expected, suggesting substantial subgenome divergence, while both the ratio of coupling to repulsion phase linkages and pattern of marker segregation indicated complete or near complete disomic inheritance. The proportion of transmission ratio distorted markers was relatively low, but the male map was more extensively affected by distorted transmission ratios and multilocus interactions, associated with spurious linkages. [PUBLICATION ABSTRACT] Polyploidy is an important aspect of the evolution of flowering plants. The potential of gene copies to diverge and evolve new functions is influenced by meiotic behavior of chromosomes leading to segregation as a single locus or duplicated loci. Switchgrass ( Panicum virgatum ) linkage maps were constructed using a full-sib population of 238 plants and SSR and STS markers to access the degree of preferential pairing and the structure of the tetraploid genome and as a step toward identification of loci underlying biomass feedstock quality and yield. The male and female framework map lengths were 1645 and 1376 cM with 97% of the genome estimated to be within 10 cM of a mapped marker in both maps. Each map coalesced into 18 linkage groups arranged into nine homeologous pairs. Comparative analysis of each homology group to the diploid sorghum genome identified clear syntenic relationships and collinear tracts. The number of markers with PCR amplicons that mapped across subgenomes was significantly fewer than expected, suggesting substantial subgenome divergence, while both the ratio of coupling to repulsion phase linkages and pattern of marker segregation indicated complete or near complete disomic inheritance. The proportion of transmission ratio distorted markers was relatively low, but the male map was more extensively affected by distorted transmission ratios and multilocus interactions, associated with spurious linkages. |
| Author | Bouton, Joe Lanzatella, Christina Okada, Miki Tobias, Christian M Saha, Malay C Wu, Rongling |
| AuthorAffiliation | U. S. Department of Agriculture–Agricultural Research Service (USDA–ARS), Genomics and Gene Discovery Research Unit, Western Regional Research Center, Albany, California 94710, † Samuel Roberts Noble Foundation, Inc., Forage Improvement Division, Ardmore, Oklahoma 73401 and ‡ Division of Biostatistics, Pennsylvania State University, Hershey, Pennsylvania 17033 |
| AuthorAffiliation_xml | – name: U. S. Department of Agriculture–Agricultural Research Service (USDA–ARS), Genomics and Gene Discovery Research Unit, Western Regional Research Center, Albany, California 94710, † Samuel Roberts Noble Foundation, Inc., Forage Improvement Division, Ardmore, Oklahoma 73401 and ‡ Division of Biostatistics, Pennsylvania State University, Hershey, Pennsylvania 17033 |
| Author_xml | – sequence: 1 givenname: Miki surname: Okada fullname: Okada, Miki organization: US Department of Agriculture-Agricultural Research Service, Genomics and Gene Discovery Research Unit, Western Regional Research Center, Albany, California 94710, USA – sequence: 2 givenname: Christina surname: Lanzatella fullname: Lanzatella, Christina – sequence: 3 givenname: Malay C surname: Saha fullname: Saha, Malay C – sequence: 4 givenname: Joe surname: Bouton fullname: Bouton, Joe – sequence: 5 givenname: Rongling surname: Wu fullname: Wu, Rongling – sequence: 6 givenname: Christian M surname: Tobias fullname: Tobias, Christian M |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/20407132$$D View this record in MEDLINE/PubMed |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Communicating editor: J. A. Birchler Present address: Department of Plant Sciences, University of California, Davis, CA 95616. Supporting information is available online at http://www.genetics.org/cgi/content/full/genetics.110.113910/DC1. |
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| SubjectTerms | Chromosome Mapping Chromosomes, Plant - genetics Comparative analysis Deoxyribonucleic acid DNA DNA, Plant - genetics Emission standards Genes Genetic Linkage Genetic Markers Genome, Plant Genomics Investigations Panicum - genetics Polyploidy Prairies Rice Studies |
| Title | Complete switchgrass genetic maps reveal subgenome collinearity, preferential pairing and multilocus interactions |
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