Genetic mapping of biomass yield in three interconnected Miscanthus populations

Hongxu Dong, Siyao Liu, Lindsay V. Clark, Shailendra Sharma, Justin M. Gifford, John A Juvik, Alexander Edward Lipka, Erik J Sacks

Research output: Contribution to journalArticle

Abstract

Improving biomass yield is a major goal of Miscanthus breeding. We conducted a study on one interspecific Miscanthus sinensis × 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 resolution of QTLs compared to the other three methods across all meta-QTLs. Strong, frequently advantageous transgressive segregation in the three populations indicated a promising future for breeding new higher-yielding cultivars of Miscanthus.

Original languageEnglish (US)
Pages (from-to)165-185
Number of pages21
JournalGCB Bioenergy
Volume10
Issue number3
DOIs
StatePublished - Mar 2018

Fingerprint

Miscanthus
chromosome mapping
quantitative trait loci
Biomass
biomass
breeding
Composite materials
Nucleotides
analysis
Polymorphism
high-yielding varieties
sorghum
transgressive segregation
DNA
methodology
Sorghum bicolor
Genes
cultivar
single nucleotide polymorphism
polymorphism

Keywords

  • QTL mapping
  • bioenergy
  • biomass
  • interconnected-population
  • restriction site-associated DNA sequencing
  • single-nucleotide polymorphism

ASJC Scopus subject areas

  • Forestry
  • Renewable Energy, Sustainability and the Environment
  • Agronomy and Crop Science
  • Waste Management and Disposal

Cite this

Genetic mapping of biomass yield in three interconnected Miscanthus populations. / Dong, Hongxu; Liu, Siyao; Clark, Lindsay V.; Sharma, Shailendra; Gifford, Justin M.; Juvik, John A; Lipka, Alexander Edward; Sacks, Erik J.

In: GCB Bioenergy, Vol. 10, No. 3, 03.2018, p. 165-185.

Research output: Contribution to journalArticle

Dong, Hongxu ; Liu, Siyao ; Clark, Lindsay V. ; Sharma, Shailendra ; Gifford, Justin M. ; Juvik, John A ; Lipka, Alexander Edward ; Sacks, Erik J. / Genetic mapping of biomass yield in three interconnected Miscanthus populations. In: GCB Bioenergy. 2018 ; Vol. 10, No. 3. pp. 165-185.
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