University of Illinois Urbana-Champaign

Data from: 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.

Content Files
11Map1 GoldenGate SNP_LocusXDNA edited.xlsx
140411Map1GoldenGateSNPanalysis.R
140919 zstripe pheno R input file.csv
141004Combined_3056RAD&241GGSNPs_261obs.jmd.zip
141004Combined_3056RAD&241GGSNPs_261obs.jmp
141004Female_2054RAD&241GGSNPs_261obs.jmd.zip
141004Female_2054RAD&241GGSNPs_261obs.jmp
141004Male_1862RAD&241GGSNPs_261obs.jmd.zip
141004Male_1862RAD&241GGSNPs_261obs.jmp
141004Map1RAD-seqSNPanalysis_final.R
141015 zb qtrait.txt
141017 zb qtrait.txt
141215 male map file R input (LG15 added).csv
141215 male map geno (138obs).txt
141215 male map geno R input (LG15 added & 138 inds).csv
141215 male map geno R input (LG15 added & 261 inds).csv
141215 male map geno.txt
141215 male map.txt
141215zebrastripeRqtl.R
141215zebrastripeSMA.R
141217 map1 Mis Sor synteny map file.csv
141217Map1SorghumAlignment.R
GoldenGateSNPs_94obs_241markers.txt
HapMap.fas.txt
HapMap.hmc.txt
HapMap.hmp.txt
README.txt
tagPair.tps

Permalink

https://hdl.handle.net/2142/79522

Description

Title
Data from: High-density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe
Author(s)
  • Liu, Siyao
  • Clark, Lindsay V.
  • Swaminathan, Kankshita
  • Gifford, Justin M.
  • Juvik, John A.
  • Sacks, Erik J.
Issue Date
2015-07-28
Keyword(s)
  • bioenergy
  • chlorophyll
  • chloroplast
  • gene
  • linkage QTL
  • mapping
  • Poaceae
  • restriction site-associated DNA sequencing
  • single nucleotide polymorphisms
  • synteny
Date of Ingest
2015-09-20T00:04:10Z
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.
Publisher
Wiley
Type of Resource
  • text
  • dataset / spreadsheet
Genre of Resource
Data
Language
eng
Permalink
http://hdl.handle.net/2142/79522
DOI
https://doi.org/10.1111/gcbb.12275
Sponsor(s)/Grant Number(s)
  • Energy Biosciences Institute
  • HATCH project ILLU-802-311
  • DOE Office of Science, Office of Biological and Environmental Research (BER), Grant No. DE-SC0006634

Owning Collections

Miscanthus genetics PRIMARY