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

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 wasmore » 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.« less

Authors:
 [1];  [1];  [1];  [1];  [1];  [1]
  1. Univ. of Illinois, Urbana-Champaign, IL (United States)
Publication Date:
Research Org.:
Univ. of Illinois, Urbana-Champaign, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1246699
Alternate Identifier(s):
OSTI ID: 1345702; OSTI ID: 1436490
Grant/Contract Number:  
SC0006634
Resource Type:
Journal Article: Published Article
Journal Name:
Global Change Biology. Bioenergy
Additional Journal Information:
Journal Volume: 8; Journal Issue: 3; Journal ID: ISSN 1757-1693
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; bioenergy; chlorophyll; chloroplast; gene; linkage QTL; mapping; Poaceae; restriction site-associated DNA sequencing; single nucleotide polymorphisms; synteny

Citation Formats

Liu, Siyao, Clark, Lindsay V., Swaminathan, Kankshita, Gifford, Justin M., Juvik, John A., and Sacks, Erik J. High-density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe. United States: N. p., 2015. Web. doi:10.1111/gcbb.12275.
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. United States. doi:10.1111/gcbb.12275.
Liu, Siyao, Clark, Lindsay V., Swaminathan, Kankshita, Gifford, Justin M., Juvik, John A., and Sacks, Erik J. Wed . "High-density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe". United States. doi:10.1111/gcbb.12275.
@article{osti_1246699,
title = {High-density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe},
author = {Liu, Siyao and Clark, Lindsay V. and Swaminathan, Kankshita and Gifford, Justin M. and Juvik, John A. and Sacks, Erik J.},
abstractNote = {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.},
doi = {10.1111/gcbb.12275},
journal = {Global Change Biology. Bioenergy},
issn = {1757-1693},
number = 3,
volume = 8,
place = {United States},
year = {2015},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1111/gcbb.12275

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Cited by: 4 works
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Works referenced in this record:

Feedstocks for Lignocellulosic Biofuels
journal, August 2010

  • Somerville, Cris; Youngs, Heather; Taylor, Caroline
  • Science, Vol. 329, Issue 5993, p. 790-792
  • DOI: 10.1126/science.1189268