A unified DNA sequence and non-DNA sequence mapping model of complex traits

Yanru Zeng, Xuli Zhu, Chixiang Chen, Kalins Banerjee, Lidan Sun, Weiwu Yu, Bingsong Zheng, Rongling Wu

Research output: Contribution to journalArticle

Abstract

Increasing evidence shows that quantitative inheritance is based on both DNA sequence and non-DNA sequence variants. However, how to simultaneously detect these variants from a mapping study has been unexplored, hampering our effort to illustrate the detailed genetic architecture of complex traits. We address this issue by developing a unified model of quantitative trait locus (QTL) mapping based on an open-pollinated design composed of randomly sampling maternal plants from a natural population and their half-sib seeds. This design forms a two-level hierarchical platform for a joint linkage-linkage disequilibrium analysis of population structure. The EM algorithm was implemented to estimate and test DNA sequence-based effects and non-DNA sequence-based effects of QTLs. We applied this model to analyze genetic mapping data from the OP design of a gymnosperm coniferous species, Torreya grandis, identifying 25 significant DNA sequence and non-DNA sequence QTLs for seedling height and diameter growth in different years. Results from computer simulation show that the unified model has good statistical properties and is powerful for QTL detection. Our model enables the tests of how a complex trait is affected differently by DNA-based effects and non-DNA sequence-based transgenerational effects, thus allowing a more comprehensive picture of genetic architecture to be charted and quantified.

Original languageEnglish (US)
Pages (from-to)784-795
Number of pages12
JournalPlant Journal
Volume99
Issue number4
DOIs
StatePublished - Jan 1 2019

Fingerprint

quantitative trait loci
Quantitative Trait Loci
nucleotide sequences
Taxaceae
Gymnosperms
Torreya
Linkage Disequilibrium
Seedlings
Computer Simulation
Population
Seeds
linkage disequilibrium
Joints
Mothers
computer simulation
chromosome mapping
linkage (genetics)
inheritance (genetics)
population structure
DNA

All Science Journal Classification (ASJC) codes

  • Genetics
  • Plant Science
  • Cell Biology

Cite this

Zeng, Yanru ; Zhu, Xuli ; Chen, Chixiang ; Banerjee, Kalins ; Sun, Lidan ; Yu, Weiwu ; Zheng, Bingsong ; Wu, Rongling. / A unified DNA sequence and non-DNA sequence mapping model of complex traits. In: Plant Journal. 2019 ; Vol. 99, No. 4. pp. 784-795.
@article{2b651fe9ec814d10b049d7709509f603,
title = "A unified DNA sequence and non-DNA sequence mapping model of complex traits",
abstract = "Increasing evidence shows that quantitative inheritance is based on both DNA sequence and non-DNA sequence variants. However, how to simultaneously detect these variants from a mapping study has been unexplored, hampering our effort to illustrate the detailed genetic architecture of complex traits. We address this issue by developing a unified model of quantitative trait locus (QTL) mapping based on an open-pollinated design composed of randomly sampling maternal plants from a natural population and their half-sib seeds. This design forms a two-level hierarchical platform for a joint linkage-linkage disequilibrium analysis of population structure. The EM algorithm was implemented to estimate and test DNA sequence-based effects and non-DNA sequence-based effects of QTLs. We applied this model to analyze genetic mapping data from the OP design of a gymnosperm coniferous species, Torreya grandis, identifying 25 significant DNA sequence and non-DNA sequence QTLs for seedling height and diameter growth in different years. Results from computer simulation show that the unified model has good statistical properties and is powerful for QTL detection. Our model enables the tests of how a complex trait is affected differently by DNA-based effects and non-DNA sequence-based transgenerational effects, thus allowing a more comprehensive picture of genetic architecture to be charted and quantified.",
author = "Yanru Zeng and Xuli Zhu and Chixiang Chen and Kalins Banerjee and Lidan Sun and Weiwu Yu and Bingsong Zheng and Rongling Wu",
year = "2019",
month = "1",
day = "1",
doi = "10.1111/tpj.14354",
language = "English (US)",
volume = "99",
pages = "784--795",
journal = "Plant Journal",
issn = "0960-7412",
publisher = "Wiley-Blackwell",
number = "4",

}

Zeng, Y, Zhu, X, Chen, C, Banerjee, K, Sun, L, Yu, W, Zheng, B & Wu, R 2019, 'A unified DNA sequence and non-DNA sequence mapping model of complex traits', Plant Journal, vol. 99, no. 4, pp. 784-795. https://doi.org/10.1111/tpj.14354

A unified DNA sequence and non-DNA sequence mapping model of complex traits. / Zeng, Yanru; Zhu, Xuli; Chen, Chixiang; Banerjee, Kalins; Sun, Lidan; Yu, Weiwu; Zheng, Bingsong; Wu, Rongling.

In: Plant Journal, Vol. 99, No. 4, 01.01.2019, p. 784-795.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A unified DNA sequence and non-DNA sequence mapping model of complex traits

AU - Zeng, Yanru

AU - Zhu, Xuli

AU - Chen, Chixiang

AU - Banerjee, Kalins

AU - Sun, Lidan

AU - Yu, Weiwu

AU - Zheng, Bingsong

AU - Wu, Rongling

PY - 2019/1/1

Y1 - 2019/1/1

N2 - Increasing evidence shows that quantitative inheritance is based on both DNA sequence and non-DNA sequence variants. However, how to simultaneously detect these variants from a mapping study has been unexplored, hampering our effort to illustrate the detailed genetic architecture of complex traits. We address this issue by developing a unified model of quantitative trait locus (QTL) mapping based on an open-pollinated design composed of randomly sampling maternal plants from a natural population and their half-sib seeds. This design forms a two-level hierarchical platform for a joint linkage-linkage disequilibrium analysis of population structure. The EM algorithm was implemented to estimate and test DNA sequence-based effects and non-DNA sequence-based effects of QTLs. We applied this model to analyze genetic mapping data from the OP design of a gymnosperm coniferous species, Torreya grandis, identifying 25 significant DNA sequence and non-DNA sequence QTLs for seedling height and diameter growth in different years. Results from computer simulation show that the unified model has good statistical properties and is powerful for QTL detection. Our model enables the tests of how a complex trait is affected differently by DNA-based effects and non-DNA sequence-based transgenerational effects, thus allowing a more comprehensive picture of genetic architecture to be charted and quantified.

AB - Increasing evidence shows that quantitative inheritance is based on both DNA sequence and non-DNA sequence variants. However, how to simultaneously detect these variants from a mapping study has been unexplored, hampering our effort to illustrate the detailed genetic architecture of complex traits. We address this issue by developing a unified model of quantitative trait locus (QTL) mapping based on an open-pollinated design composed of randomly sampling maternal plants from a natural population and their half-sib seeds. This design forms a two-level hierarchical platform for a joint linkage-linkage disequilibrium analysis of population structure. The EM algorithm was implemented to estimate and test DNA sequence-based effects and non-DNA sequence-based effects of QTLs. We applied this model to analyze genetic mapping data from the OP design of a gymnosperm coniferous species, Torreya grandis, identifying 25 significant DNA sequence and non-DNA sequence QTLs for seedling height and diameter growth in different years. Results from computer simulation show that the unified model has good statistical properties and is powerful for QTL detection. Our model enables the tests of how a complex trait is affected differently by DNA-based effects and non-DNA sequence-based transgenerational effects, thus allowing a more comprehensive picture of genetic architecture to be charted and quantified.

UR - http://www.scopus.com/inward/record.url?scp=85067606053&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85067606053&partnerID=8YFLogxK

U2 - 10.1111/tpj.14354

DO - 10.1111/tpj.14354

M3 - Article

C2 - 31009159

AN - SCOPUS:85067606053

VL - 99

SP - 784

EP - 795

JO - Plant Journal

JF - Plant Journal

SN - 0960-7412

IS - 4

ER -

Zeng Y, Zhu X, Chen C, Banerjee K, Sun L, Yu W et al. A unified DNA sequence and non-DNA sequence mapping model of complex traits. Plant Journal. 2019 Jan 1;99(4):784-795. https://doi.org/10.1111/tpj.14354