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Title: Genetic mapping of biomass yield in three interconnected Miscanthus populations

Journal Article · · Global Change Biology. Bioenergy
DOI:https://doi.org/10.1111/gcbb.12472· OSTI ID:1375469

Improving biomass yield is a major goal of Miscanthus breeding. We conducted a study on one interspecific Miscanthus sinensis x Miscanthus sacchariflorus F1 population and two intraspecific M. sinensis F1 populations, each of which shared a common parent. A field trial was established at Urbana, IL during spring 2011, and phenotypic data were collected in 2012 and 2013 for fourteen yield traits. Six high-density parental genetic maps, as well as a consensus genetic map integrating M. sinensis and M. sacchariflorus, were developed via the pseudotestcross strategy for noninbred parents with ≥1214 single-nucleotide polymorphism markers generated from restriction site-associated DNA sequencing. We confirmed for the first time a whole-genome duplication in M. sacchariflorus relative to Sorghum bicolor, similar to that observed previously for M. sinensis. Four quantitative trait locus (QTL) analysis methods for detecting marker-trait associations were compared: (1) individual parental map composite interval mapping analysis, (2) individual parental map stepwise analysis, (3) consensus map single-population stepwise analysis and (4) consensus map joint-population stepwise analysis. These four methods detected 288, 264, 133 and 109 total QTLs, which resolved into 157, 136, 106 and 86 meta-QTLs based on QTL congruency, respectively, including a set of 59 meta-QTLs common to all four analysis methods. Composite interval mapping and stepwise analysis co-identified 118 meta-QTLs across six parental maps, suggesting high reliability of stepwise regression in QTL detection. Joint-population stepwise analysis yielded the highest resolu-tion of QTLs compared to the other three methods across all meta-QTLs. Strong, frequently advantageous trans-gressive segregation in the three populations indicated a promising future for breeding new higher-yielding cultivars of Miscanthus.

Research Organization:
Univ. of Illinois at Urbana-Champaign, Champaign, IL (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
SC0006634
OSTI ID:
1375469
Alternate ID(s):
OSTI ID: 1375470; OSTI ID: 1511045
Journal Information:
Global Change Biology. Bioenergy, Journal Name: Global Change Biology. Bioenergy; ISSN 1757-1693
Publisher:
WileyCopyright Statement
Country of Publication:
United Kingdom
Language:
English
Citation Metrics:
Cited by: 26 works
Citation information provided by
Web of Science

References (75)

Flowering induction in the bioenergy grass Miscanthus sacchariflorus is a quantitative short-day response, whilst delayed flowering under long days increases biomass accumulation journal November 2012
Consequences of Recombination Rate Variation on Quantitative Trait Locus Mapping Studies: Simulations Based on the Drosophila melanogaster Genome journal October 2001
The Sorghum bicolor genome and the diversification of grasses journal January 2009
Identification of QTLs influencing combustion quality in Miscanthus sinensis Anderss. II. Chlorine and potassium content journal March 2003
Comparative Analysis of Miscanthus and Saccharum Reveals a Shared Whole-Genome Duplication but Different Evolutionary Fates journal June 2014
Feedstocks for Lignocellulosic Biofuels journal August 2010
BioMercator V3: an upgrade of genetic map compilation and quantitative trait loci meta-analysis algorithms journal June 2012
Genome-wide association study of leaf architecture in the maize nested association mapping population journal January 2011
Genetic architecture of complex traits in plants journal April 2007
A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy journal January 2012
Comparative analysis of QTLs affecting plant height and flowering among closely-related diploid and polyploid genomes journal October 2002
LPmerge: an R package for merging genetic maps by linear programming journal February 2014
Genetic Analysis of Visually Scored Orange Kernel Color in Maize journal January 2013
Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. journal August 1994
Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol journal January 2013
ASYMMETRIC LEAVES2-LIKE1gene, a member of the AS2/LOB family, controls proximal?distal patterning in Arabidopsis petals journal March 2005
A footprint of past climate change on the diversity and population structure of Miscanthus sinensis journal June 2014
Screening Miscanthus genotypes in field trials to optimise biomass yield and quality in Southern Germany journal March 2002
Biomass yield and changes in chemical composition of sweet sorghum cultivars grown for biofuel journal March 2009
Global changes in mineral transporters in tetraploid switchgrasses (Panicum virgatum L.) journal January 2014
Variability and adaptability of Miscanthus species evaluated for energy crop domestication: MISCANTHUS SPECIES FOR DOMESTICATION journal May 2011
Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize journal April 2011
R/qtl: QTL mapping in experimental crosses journal May 2003
The weediness of wild plants: molecular analysis of genes influencing dispersal and persistence of johnsongrass, Sorghum halepense (L.) Pers. journal June 1995
Joint QTL Linkage Mapping for Multiple-Cross Mating Design Sharing One Common Parent journal March 2011
Location of major effect genes in sorghum (Sorghum bicolor (L.) Moench) journal June 2010
Preliminary interspecific genetic maps of the Populus genome constructed from RAPD markers journal August 2001
High-density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe journal July 2015
Genome-wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grass Miscanthus sinensis journal December 2013
The Genetic Architecture of Maize Flowering Time journal August 2009
Phenotypic and Biomass Yield Variations in Natural Populations of Prairie Cordgrass (Spartina pectinata Link) in the USA journal March 2015
Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species journal August 2011
Genetic Design and Statistical Power of Nested Association Mapping in Maize journal January 2008
Influencing combustion quality in Miscanthus sinensis Anderss.: identification of QTLs for calcium, phosphorus and sulphur content journal April 2003
Precision mapping of quantitative trait loci. journal April 1994
Non-structural carbohydrate profiles and ratios between soluble sugars and starch serve as indicators of productivity for a bioenergy grass journal January 2015
QTL analysis of transgressive segregation in an interspecific tomato cross. journal June 1993
The linkage maps of Dendrobium species based on RAPD and SRAP markers journal March 2010
Distinct Genetic Architectures for Male and Female Inflorescence Traits of Maize journal November 2011
Effect of Change in Time of Flowering, Induced by Altering Photoperiod or Temperature, on Attributes Related to Yield in Maize1 journal January 1979
Characterizing a Germplasm Collection for Yield, Yield Components, and Genotype × Environment Interactions journal January 2015
Nomenclature of Miscanthus xgiganteus (Poaceae) journal January 2001
Characterization of flowering time diversity in Miscanthus species: FLOWERING TIME DIVERSITY IN MISCANTHUS journal March 2011
TASSEL: software for association mapping of complex traits in diverse samples journal June 2007
Quantitative genetics of bud phenology, frost damage, and winter survival in an F2 family of hybrid poplars journal September 2000
Nitrogen Recycling and Flowering Time in Perennial Bioenergy Crops journal January 2013
Genetic variation in Miscanthus × giganteus and the importance of estimating genetic distance thresholds for differentiating clones journal June 2014
Mapping the genome of Miscanthus sinensis for QTL associated with biomass productivity journal June 2014
Key traits for biomass production identified in different Miscanthus species at two harvest dates journal January 2011
Fast gapped-read alignment with Bowtie 2 journal March 2012
Joint linkage QTL analyses for partial resistance to Phytophthora sojae in soybean using six nested inbred populations with heterogeneous conditions journal November 2013
BLAST+: architecture and applications journal January 2009
The Estimation of map Distances from Recombination Values journal January 1943
Convergent Domestication of Cereal Crops by Independent Mutations at Corresponding Genetic Loci journal September 1995
Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression journal January 2015
The Gene Pool of Miscanthus Species and Its Improvement book July 2012
SSR-based genetic maps of Miscanthus sinensis and M. sacchariflorus, and their comparison to sorghum journal January 2012
Accelerating the domestication of a bioenergy crop: identifying and modelling morphological targets for sustainable yield increase in Miscanthus journal September 2013
Heterosis journal July 2010
TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data journal July 2016
High Resolution Genetic Mapping by Genome Sequencing Reveals Genome Duplication and Tetraploid Genetic Structure of the Diploid Miscanthus sinensis journal March 2012
Mapping QTL Controlling Southern Leaf Blight Resistance by Joint Analysis of Three Related Recombinant Inbred Line Populations journal January 2011
Do Large Effect QTL Fractionate? A Case Study at the Maize Domestication QTL teosinte branched1 journal April 2011
Contrasting allelic distribution of CO / Hd1 homologues in Miscanthus sinensis from the East Asian mainland and the Japanese archipelago journal June 2015
Preliminary genetic linkage map of Miscanthus sinensis with RAPD markers journal November 2002
Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data journal July 2016
Putative sugarcane FT/TFL1 genes delay flowering time and alter reproductive architecture in Arabidopsis journal May 2014
Cinnamoyl CoA reductase, the first committed enzyme of the lignin branch biosynthetic pathway: cloning, expression and phylogenetic relationships journal March 1997
Ensemble Learning of QTL Models Improves Prediction of Complex Traits journal August 2015
Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia journal July 2016
Cold-Tolerance of Seedlings and Effects of Spring and Autumn Frosts on Mature Clonally Replicated Cultivars journal January 2015
Identification of QTLs influencing agronomic traits in Miscanthus sinensis Anderss. I. Total height, flag-leaf height and stem diameter journal June 2003
Joint-multiple family linkage analysis predicts within-family variation better than single-family analysis of the maize nested association mapping population journal January 2015
Convergent evolution of perenniality in rice and sorghum journal March 2003
Phylogenetics of Miscanthus , Saccharum and related genera (Saccharinae, Andropogoneae, Poaceae) based on DNA sequences from ITS nuclear ribosomal DNA and plastid trnL intron and trnL-F intergenic spacers journal October 2002