Effect of advanced intercrossing on genome structure and on the power to detect linked quantitative trait loci in a multi-parent population: A simulation study in rice

Eiji Yamamoto, Hiroyoshi Iwata, Takanari Tanabata, Ritsuko Mizobuchi, Jun ichi Yonemaru, Toshio Yamamoto, Masahiro Yano

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Background: In genetic analysis of agronomic traits, quantitative trait loci (QTLs) that control the same phenotype are often closely linked. Furthermore, many QTLs are localized in specific genomic regions (QTL clusters) that include naturally occurring allelic variations in different genes. Therefore, linkage among QTLs may complicate the detection of each individual QTL. This problem can be resolved by using populations that include many potential recombination sites. Recently, multi-parent populations have been developed and used for QTL analysis. However, their efficiency for detection of linked QTLs has not received attention. By using information on rice, we simulated the construction of a multi-parent population followed by cycles of recurrent crossing and inbreeding, and we investigated the resulting genome structure and its usefulness for detecting linked QTLs as a function of the number of cycles of recurrent crossing.Results: The number of non-recombinant genome segments increased linearly with an increasing number of cycles. The mean and median lengths of the non-recombinant genome segments decreased dramatically during the first five to six cycles, then decreased more slowly during subsequent cycles. Without recurrent crossing, we found that there is a risk of missing QTLs that are linked in a repulsion phase, and a risk of identifying linked QTLs in a coupling phase as a single QTL, even when the population was derived from eight parental lines. In our simulation results, using fewer than two cycles of recurrent crossing produced results that differed little from the results with zero cycles, whereas using more than six cycles dramatically improved the power under most of the conditions that we simulated.Conclusion: Our results indicated that even with a population derived from eight parental lines, fewer than two cycles of crossing does not improve the power to detect linked QTLs. However, using six cycles dramatically improved the power, suggesting that advanced intercrossing can help to resolve the problems that result from linkage among QTLs.

Original languageEnglish
Article number50
JournalBMC Genetics
Volume15
DOIs
Publication statusPublished - Apr 27 2014
Externally publishedYes

Fingerprint

Quantitative Trait Loci
Genome
Population
Power (Psychology)
Oryza
Internal-External Control
Inbreeding
Genetic Recombination

Keywords

  • Advanced intercrossing
  • QTL
  • Rice
  • Simulation

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Effect of advanced intercrossing on genome structure and on the power to detect linked quantitative trait loci in a multi-parent population : A simulation study in rice. / Yamamoto, Eiji; Iwata, Hiroyoshi; Tanabata, Takanari; Mizobuchi, Ritsuko; Yonemaru, Jun ichi; Yamamoto, Toshio; Yano, Masahiro.

In: BMC Genetics, Vol. 15, 50, 27.04.2014.

Research output: Contribution to journalArticle

Yamamoto, Eiji ; Iwata, Hiroyoshi ; Tanabata, Takanari ; Mizobuchi, Ritsuko ; Yonemaru, Jun ichi ; Yamamoto, Toshio ; Yano, Masahiro. / Effect of advanced intercrossing on genome structure and on the power to detect linked quantitative trait loci in a multi-parent population : A simulation study in rice. In: BMC Genetics. 2014 ; Vol. 15.
@article{555fc91b52e84e8db6aeb917c21eabc2,
title = "Effect of advanced intercrossing on genome structure and on the power to detect linked quantitative trait loci in a multi-parent population: A simulation study in rice",
abstract = "Background: In genetic analysis of agronomic traits, quantitative trait loci (QTLs) that control the same phenotype are often closely linked. Furthermore, many QTLs are localized in specific genomic regions (QTL clusters) that include naturally occurring allelic variations in different genes. Therefore, linkage among QTLs may complicate the detection of each individual QTL. This problem can be resolved by using populations that include many potential recombination sites. Recently, multi-parent populations have been developed and used for QTL analysis. However, their efficiency for detection of linked QTLs has not received attention. By using information on rice, we simulated the construction of a multi-parent population followed by cycles of recurrent crossing and inbreeding, and we investigated the resulting genome structure and its usefulness for detecting linked QTLs as a function of the number of cycles of recurrent crossing.Results: The number of non-recombinant genome segments increased linearly with an increasing number of cycles. The mean and median lengths of the non-recombinant genome segments decreased dramatically during the first five to six cycles, then decreased more slowly during subsequent cycles. Without recurrent crossing, we found that there is a risk of missing QTLs that are linked in a repulsion phase, and a risk of identifying linked QTLs in a coupling phase as a single QTL, even when the population was derived from eight parental lines. In our simulation results, using fewer than two cycles of recurrent crossing produced results that differed little from the results with zero cycles, whereas using more than six cycles dramatically improved the power under most of the conditions that we simulated.Conclusion: Our results indicated that even with a population derived from eight parental lines, fewer than two cycles of crossing does not improve the power to detect linked QTLs. However, using six cycles dramatically improved the power, suggesting that advanced intercrossing can help to resolve the problems that result from linkage among QTLs.",
keywords = "Advanced intercrossing, QTL, Rice, Simulation",
author = "Eiji Yamamoto and Hiroyoshi Iwata and Takanari Tanabata and Ritsuko Mizobuchi and Yonemaru, {Jun ichi} and Toshio Yamamoto and Masahiro Yano",
year = "2014",
month = "4",
day = "27",
doi = "10.1186/1471-2156-15-50",
language = "English",
volume = "15",
journal = "BMC Genetics",
issn = "1471-2156",
publisher = "BioMed Central",

}

TY - JOUR

T1 - Effect of advanced intercrossing on genome structure and on the power to detect linked quantitative trait loci in a multi-parent population

T2 - A simulation study in rice

AU - Yamamoto, Eiji

AU - Iwata, Hiroyoshi

AU - Tanabata, Takanari

AU - Mizobuchi, Ritsuko

AU - Yonemaru, Jun ichi

AU - Yamamoto, Toshio

AU - Yano, Masahiro

PY - 2014/4/27

Y1 - 2014/4/27

N2 - Background: In genetic analysis of agronomic traits, quantitative trait loci (QTLs) that control the same phenotype are often closely linked. Furthermore, many QTLs are localized in specific genomic regions (QTL clusters) that include naturally occurring allelic variations in different genes. Therefore, linkage among QTLs may complicate the detection of each individual QTL. This problem can be resolved by using populations that include many potential recombination sites. Recently, multi-parent populations have been developed and used for QTL analysis. However, their efficiency for detection of linked QTLs has not received attention. By using information on rice, we simulated the construction of a multi-parent population followed by cycles of recurrent crossing and inbreeding, and we investigated the resulting genome structure and its usefulness for detecting linked QTLs as a function of the number of cycles of recurrent crossing.Results: The number of non-recombinant genome segments increased linearly with an increasing number of cycles. The mean and median lengths of the non-recombinant genome segments decreased dramatically during the first five to six cycles, then decreased more slowly during subsequent cycles. Without recurrent crossing, we found that there is a risk of missing QTLs that are linked in a repulsion phase, and a risk of identifying linked QTLs in a coupling phase as a single QTL, even when the population was derived from eight parental lines. In our simulation results, using fewer than two cycles of recurrent crossing produced results that differed little from the results with zero cycles, whereas using more than six cycles dramatically improved the power under most of the conditions that we simulated.Conclusion: Our results indicated that even with a population derived from eight parental lines, fewer than two cycles of crossing does not improve the power to detect linked QTLs. However, using six cycles dramatically improved the power, suggesting that advanced intercrossing can help to resolve the problems that result from linkage among QTLs.

AB - Background: In genetic analysis of agronomic traits, quantitative trait loci (QTLs) that control the same phenotype are often closely linked. Furthermore, many QTLs are localized in specific genomic regions (QTL clusters) that include naturally occurring allelic variations in different genes. Therefore, linkage among QTLs may complicate the detection of each individual QTL. This problem can be resolved by using populations that include many potential recombination sites. Recently, multi-parent populations have been developed and used for QTL analysis. However, their efficiency for detection of linked QTLs has not received attention. By using information on rice, we simulated the construction of a multi-parent population followed by cycles of recurrent crossing and inbreeding, and we investigated the resulting genome structure and its usefulness for detecting linked QTLs as a function of the number of cycles of recurrent crossing.Results: The number of non-recombinant genome segments increased linearly with an increasing number of cycles. The mean and median lengths of the non-recombinant genome segments decreased dramatically during the first five to six cycles, then decreased more slowly during subsequent cycles. Without recurrent crossing, we found that there is a risk of missing QTLs that are linked in a repulsion phase, and a risk of identifying linked QTLs in a coupling phase as a single QTL, even when the population was derived from eight parental lines. In our simulation results, using fewer than two cycles of recurrent crossing produced results that differed little from the results with zero cycles, whereas using more than six cycles dramatically improved the power under most of the conditions that we simulated.Conclusion: Our results indicated that even with a population derived from eight parental lines, fewer than two cycles of crossing does not improve the power to detect linked QTLs. However, using six cycles dramatically improved the power, suggesting that advanced intercrossing can help to resolve the problems that result from linkage among QTLs.

KW - Advanced intercrossing

KW - QTL

KW - Rice

KW - Simulation

UR - http://www.scopus.com/inward/record.url?scp=84900026549&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84900026549&partnerID=8YFLogxK

U2 - 10.1186/1471-2156-15-50

DO - 10.1186/1471-2156-15-50

M3 - Article

C2 - 24767139

AN - SCOPUS:84900026549

VL - 15

JO - BMC Genetics

JF - BMC Genetics

SN - 1471-2156

M1 - 50

ER -