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

Abstract

Improving biomass yield is a major goal of Miscanthus breeding. We conducted a study on one interspecific Miscanthus sinensis x Miscanthus sacchariflorus F 1 population and two intraspecific M. sinensis F 1 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 allmore » 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.« less

Authors:
ORCiD logo [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1]
  1. Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W Gregory Dr Urbana IL USA
Publication Date:
Research Org.:
Univ. of Illinois at Urbana-Champaign, Champaign, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1375469
Alternate Identifier(s):
OSTI ID: 1375470; OSTI ID: 1511045
Grant/Contract Number:  
SC0006634
Resource Type:
Published Article
Journal Name:
Global Change Biology. Bioenergy
Additional Journal Information:
Journal Name: Global Change Biology. Bioenergy; Journal ID: ISSN 1757-1693
Publisher:
Wiley
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; bioenergy; biomass; interconnected-population; QTL mapping; restriction site-associated DNA sequencing; single-nucleotide polymorphism

Citation Formats

Dong, Hongxu, Liu, Siyao, Clark, Lindsay V., Sharma, Shailendra, Gifford, Justin M., Juvik, John A., Lipka, Alexander E., and Sacks, Erik J. Genetic mapping of biomass yield in three interconnected Miscanthus populations. United Kingdom: N. p., 2017. Web. doi:10.1111/gcbb.12472.
Dong, Hongxu, Liu, Siyao, Clark, Lindsay V., Sharma, Shailendra, Gifford, Justin M., Juvik, John A., Lipka, Alexander E., & Sacks, Erik J. Genetic mapping of biomass yield in three interconnected Miscanthus populations. United Kingdom. doi:10.1111/gcbb.12472.
Dong, Hongxu, Liu, Siyao, Clark, Lindsay V., Sharma, Shailendra, Gifford, Justin M., Juvik, John A., Lipka, Alexander E., and Sacks, Erik J. Sat . "Genetic mapping of biomass yield in three interconnected Miscanthus populations". United Kingdom. doi:10.1111/gcbb.12472.
@article{osti_1375469,
title = {Genetic mapping of biomass yield in three interconnected Miscanthus populations},
author = {Dong, Hongxu and Liu, Siyao and Clark, Lindsay V. and Sharma, Shailendra and Gifford, Justin M. and Juvik, John A. and Lipka, Alexander E. and Sacks, Erik J.},
abstractNote = {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.},
doi = {10.1111/gcbb.12472},
journal = {Global Change Biology. Bioenergy},
number = ,
volume = ,
place = {United Kingdom},
year = {2017},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
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DOI: 10.1111/gcbb.12472

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