Complete switchgrass genetic maps reveal subgenome collinearity, preferential pairing and multilocus interactions

Miki Okada, Christina Lanzatella, Malay C. Saha, Joe Bouton, Rongling Wu, Christian M. Tobias

Research output: Contribution to journalArticle

98 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)745-760
Number of pages16
JournalGenetics
Volume185
Issue number3
DOIs
StatePublished - Jul 1 2010

Fingerprint

Panicum
Genome
Polyploidy
Sorghum
Tetraploidy
Diploidy
Biomass
Chromosomes
Polymerase Chain Reaction
Population
Genes

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Okada, Miki ; Lanzatella, Christina ; Saha, Malay C. ; Bouton, Joe ; Wu, Rongling ; Tobias, Christian M. / Complete switchgrass genetic maps reveal subgenome collinearity, preferential pairing and multilocus interactions. In: Genetics. 2010 ; Vol. 185, No. 3. pp. 745-760.
@article{16e74d25a97743d2a8ddd13ec549b70d,
title = "Complete switchgrass genetic maps reveal subgenome collinearity, preferential pairing and multilocus interactions",
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 = "Miki Okada and Christina Lanzatella and Saha, {Malay C.} and Joe Bouton and Rongling Wu and Tobias, {Christian M.}",
year = "2010",
month = "7",
day = "1",
doi = "10.1534/genetics.110.113910",
language = "English (US)",
volume = "185",
pages = "745--760",
journal = "Genetics",
issn = "0016-6731",
publisher = "Genetics Society of America",
number = "3",

}

Complete switchgrass genetic maps reveal subgenome collinearity, preferential pairing and multilocus interactions. / Okada, Miki; Lanzatella, Christina; Saha, Malay C.; Bouton, Joe; Wu, Rongling; Tobias, Christian M.

In: Genetics, Vol. 185, No. 3, 01.07.2010, p. 745-760.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Complete switchgrass genetic maps reveal subgenome collinearity, preferential pairing and multilocus interactions

AU - Okada, Miki

AU - Lanzatella, Christina

AU - Saha, Malay C.

AU - Bouton, Joe

AU - Wu, Rongling

AU - Tobias, Christian M.

PY - 2010/7/1

Y1 - 2010/7/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=78349233134&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=78349233134&partnerID=8YFLogxK

U2 - 10.1534/genetics.110.113910

DO - 10.1534/genetics.110.113910

M3 - Article

C2 - 20407132

AN - SCOPUS:78349233134

VL - 185

SP - 745

EP - 760

JO - Genetics

JF - Genetics

SN - 0016-6731

IS - 3

ER -