High-density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe

Siyao Liu, Lindsay V. Clark, Kankshita Swaminathan, Justin M. Gifford, John A. Juvik, Erik J. Sacks

Research output: Contribution to journalArticle

Abstract

Miscanthus is a perennial C4 grass that has recently become an important bioenergy crop. The efficiency of breeding improved Miscanthus biomass cultivars could be greatly increased by marker-assisted selection. Thus, a high-density genetic map is critical to Miscanthus improvement. In this study, a mapping population of 261 F1 progeny was developed from a cross between two diploid M. sinensis cultivars, 'Strictus' and 'Kaskade'. High-density genetic maps for the two parents were produced with 3044 newly developed single nucleotide polymorphisms (SNPs) obtained from restriction site-associated DNA sequencing, and 138 previously mapped GoldenGate SNPs. The female parent ('Strictus') map spanned 1599 cM, with 1989 SNPs on 19 linkage groups, and an average intermarker spacing of 0.8 cM. The length of the male parent ('Kaskade') map was 1612 cM, with 1821 SNPs, and an average intermarker spacing of 0.9 cM. The utility of the map was confirmed by locating quantitative trait loci (QTL) for the zebra-striped trait, which was segregating in this population. Three QTL for zebra-striped presence/absence (zb1, zb2 on LG 7, and zb3 on LG 10) and three for zebra-striped intensity (zbi1, zbi2, zbi3 on LGs 7, 10, 3) were identified. Each allele that caused striping was recessive. Incomplete penetrance was observed for each zb QTL, but penetrance was greatest when two or more zb QTL were homozygous for the causative alleles. Similarly, the intensity of striping was greatest when two or more zbi QTL were homozygous for alleles that conferred the trait. Comparative mapping indicated putative correspondence between zb3 and/or zbi2 on LG 10 to previously sequenced genes conferring zebra stripe in maize and rice. These results demonstrate that the new map is useful for identifying marker-trait associations. The mapped markers will become a valuable community resource, facilitating comparisons among studies and the breeding of Miscanthus.

Original languageEnglish (US)
Pages (from-to)616-630
Number of pages15
JournalGCB Bioenergy
Volume8
Issue number3
DOIs
StatePublished - May 1 2016

Fingerprint

Miscanthus sinensis
zebras
Miscanthus
quantitative trait loci
inheritance (genetics)
single nucleotide polymorphism
Nucleotides
Polymorphism
polymorphism
penetrance
allele
alleles
spatial distribution
cultivar
spacing
breeding
energy crops
cultivars
linkage groups
marker-assisted selection

Keywords

  • Bioenergy
  • Chlorophyll
  • Chloroplast
  • Gene
  • Linkage QTL
  • Mapping
  • Poaceae
  • Restriction site-associated DNA sequencing
  • Single nucleotide polymorphisms
  • Synteny

ASJC Scopus subject areas

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

Cite this

High-density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe. / Liu, Siyao; Clark, Lindsay V.; Swaminathan, Kankshita; Gifford, Justin M.; Juvik, John A.; Sacks, Erik J.

In: GCB Bioenergy, Vol. 8, No. 3, 01.05.2016, p. 616-630.

Research output: Contribution to journalArticle

Liu, Siyao ; Clark, Lindsay V. ; Swaminathan, Kankshita ; Gifford, Justin M. ; Juvik, John A. ; Sacks, Erik J. / High-density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe. In: GCB Bioenergy. 2016 ; Vol. 8, No. 3. pp. 616-630.
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