Contrasting geographic patterns of genetic variation for molecular markers vs. phenotypic traits in the energy grass Miscanthus sinensis

Gancho Slavov; Paul Robson; Elaine Jensen; Edward Hodgson; Kerrie Farrar; Gordon Allison; Sarah Hawkins; Sian  Thomas-Jones; Xue-Feng Ma; Lin Huang; Timothy Swaller; Richard Flavell; John Clifton-Brown; Iain Donnison

doi:10.1111/gcbb.12025

Contrasting geographic patterns of genetic variation for molecular markers vs. phenotypic traits in the energy grass Miscanthus sinensis

Standard

Contrasting geographic patterns of genetic variation for molecular markers vs. phenotypic traits in the energy grass Miscanthus sinensis. / Slavov, Gancho ; Robson, Paul ; Jensen, Elaine et al.

In: GCB Bioenergy, Vol. 5, No. 5, 09.2013, p. 562-571.

Research output: Contribution to journal › Article › peer-review

Bibtex - Download

@article{ef07b0ce86f346c8b7e9e5b6e30b1d3e,

title = "Contrasting geographic patterns of genetic variation for molecular markers vs. phenotypic traits in the energy grass Miscanthus sinensis",

abstract = "Species and hybrids of Miscanthus are a promising energy crop, but their outcrossing mating systems and perennial life cycles are serious challenges for breeding programs. One approach to accelerating the domestication of Miscanthus is to harness the tremendous genetic variation that is present within this genus using phenotypic data from extensive field trials, high-density genotyping and sequencing technologies, and rapidly developing statistical methods of relating phenotype to genotype. The success of this approach, however, hinges on detailed knowledge about the population genetic structure of the germplasm used in the breeding program. We therefore used data for 120 single-nucleotide polymorphism and 52 simple sequence repeat markers to depict patterns of putatively neutral population structure among 244 Miscanthus genotypes grown in a field trial near Aberystwyth (UK) and delineate a population of 145 M. sinensis genotypes that will be used for association mapping and genomic selection. Comparative multivariate analyses of molecular marker and phenotypic data for 17 traits related to phenology, morphology/biomass, and cell wall composition revealed significant geographic patterns in this population. A longitudinal cline accounted for a substantial proportion of molecular marker variation (R2 = 0.60, P = 3.4 × 10−15). In contrast, genetic variation for phenotypic traits tended to follow latitudinal and altitudinal gradients, with several traits appearing to have been affected by divergent selection (i.e., QST >> FST). These contrasting geographic trends are unusual relative to other plants and provide opportunities for powerful studies of phenotype–genotype associations and the evolutionary history of M. sinensis.",

keywords = "biomass, cell wall composition, divergent selection, Miscanthus sinensis, molecular markers, morphology, phenology, population genetic structure",

author = "Gancho Slavov and Paul Robson and Elaine Jensen and Edward Hodgson and Kerrie Farrar and Gordon Allison and Sarah Hawkins and Sian Thomas-Jones and Xue-Feng Ma and Lin Huang and Timothy Swaller and Richard Flavell and John Clifton-Brown and Iain Donnison",

note = "RONO: Grant Reference: BBSRC BBSEG00003134 (PR, GA, ID); BB/E014933/1 (EJ); BB/E024319/2 (KF); NF0426 (JCB)",

year = "2013",

month = sep,

doi = "10.1111/gcbb.12025",

language = "English",

volume = "5",

pages = "562--571",

journal = "GCB Bioenergy",

issn = "1757-1693",

publisher = "Wiley",

number = "5",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Contrasting geographic patterns of genetic variation for molecular markers vs. phenotypic traits in the energy grass Miscanthus sinensis

AU - Slavov, Gancho

AU - Robson, Paul

AU - Jensen, Elaine

AU - Hodgson, Edward

AU - Farrar, Kerrie

AU - Allison, Gordon

AU - Hawkins, Sarah

AU - Thomas-Jones, Sian

AU - Ma, Xue-Feng

AU - Huang, Lin

AU - Swaller, Timothy

AU - Flavell, Richard

AU - Clifton-Brown, John

AU - Donnison, Iain

N1 - RONO: Grant Reference: BBSRC BBSEG00003134 (PR, GA, ID); BB/E014933/1 (EJ); BB/E024319/2 (KF); NF0426 (JCB)

PY - 2013/9

Y1 - 2013/9

N2 - Species and hybrids of Miscanthus are a promising energy crop, but their outcrossing mating systems and perennial life cycles are serious challenges for breeding programs. One approach to accelerating the domestication of Miscanthus is to harness the tremendous genetic variation that is present within this genus using phenotypic data from extensive field trials, high-density genotyping and sequencing technologies, and rapidly developing statistical methods of relating phenotype to genotype. The success of this approach, however, hinges on detailed knowledge about the population genetic structure of the germplasm used in the breeding program. We therefore used data for 120 single-nucleotide polymorphism and 52 simple sequence repeat markers to depict patterns of putatively neutral population structure among 244 Miscanthus genotypes grown in a field trial near Aberystwyth (UK) and delineate a population of 145 M. sinensis genotypes that will be used for association mapping and genomic selection. Comparative multivariate analyses of molecular marker and phenotypic data for 17 traits related to phenology, morphology/biomass, and cell wall composition revealed significant geographic patterns in this population. A longitudinal cline accounted for a substantial proportion of molecular marker variation (R2 = 0.60, P = 3.4 × 10−15). In contrast, genetic variation for phenotypic traits tended to follow latitudinal and altitudinal gradients, with several traits appearing to have been affected by divergent selection (i.e., QST >> FST). These contrasting geographic trends are unusual relative to other plants and provide opportunities for powerful studies of phenotype–genotype associations and the evolutionary history of M. sinensis.

AB - Species and hybrids of Miscanthus are a promising energy crop, but their outcrossing mating systems and perennial life cycles are serious challenges for breeding programs. One approach to accelerating the domestication of Miscanthus is to harness the tremendous genetic variation that is present within this genus using phenotypic data from extensive field trials, high-density genotyping and sequencing technologies, and rapidly developing statistical methods of relating phenotype to genotype. The success of this approach, however, hinges on detailed knowledge about the population genetic structure of the germplasm used in the breeding program. We therefore used data for 120 single-nucleotide polymorphism and 52 simple sequence repeat markers to depict patterns of putatively neutral population structure among 244 Miscanthus genotypes grown in a field trial near Aberystwyth (UK) and delineate a population of 145 M. sinensis genotypes that will be used for association mapping and genomic selection. Comparative multivariate analyses of molecular marker and phenotypic data for 17 traits related to phenology, morphology/biomass, and cell wall composition revealed significant geographic patterns in this population. A longitudinal cline accounted for a substantial proportion of molecular marker variation (R2 = 0.60, P = 3.4 × 10−15). In contrast, genetic variation for phenotypic traits tended to follow latitudinal and altitudinal gradients, with several traits appearing to have been affected by divergent selection (i.e., QST >> FST). These contrasting geographic trends are unusual relative to other plants and provide opportunities for powerful studies of phenotype–genotype associations and the evolutionary history of M. sinensis.

KW - biomass

KW - cell wall composition

KW - divergent selection

KW - Miscanthus sinensis

KW - molecular markers

KW - morphology

KW - phenology

KW - population genetic structure

UR - http://hdl.handle.net/2160/12156

U2 - 10.1111/gcbb.12025

DO - 10.1111/gcbb.12025

M3 - Article