Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam
Background. Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. Results The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. Conclusions Some of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development.
Main Authors: | , , , , , , , , , , |
---|---|
Format: | article biblioteca |
Language: | eng |
Subjects: | F30 - Génétique et amélioration des plantes, F62 - Physiologie végétale - Croissance et développement, Oryza sativa, génome, génotype, carte génétique, développement biologique, système racinaire, racine, variété, locus des caractères quantitatifs, marqueur génétique, http://aims.fao.org/aos/agrovoc/c_5438, http://aims.fao.org/aos/agrovoc/c_3224, http://aims.fao.org/aos/agrovoc/c_3225, http://aims.fao.org/aos/agrovoc/c_24002, http://aims.fao.org/aos/agrovoc/c_921, http://aims.fao.org/aos/agrovoc/c_16034, http://aims.fao.org/aos/agrovoc/c_6651, http://aims.fao.org/aos/agrovoc/c_8157, http://aims.fao.org/aos/agrovoc/c_37974, http://aims.fao.org/aos/agrovoc/c_24030, http://aims.fao.org/aos/agrovoc/c_8227, |
Online Access: | http://agritrop.cirad.fr/580236/ http://agritrop.cirad.fr/580236/1/580236.pdf |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
id |
dig-cirad-fr-580236 |
---|---|
record_format |
koha |
institution |
CIRAD FR |
collection |
DSpace |
country |
Francia |
countrycode |
FR |
component |
Bibliográfico |
access |
En linea |
databasecode |
dig-cirad-fr |
tag |
biblioteca |
region |
Europa del Oeste |
libraryname |
Biblioteca del CIRAD Francia |
language |
eng |
topic |
F30 - Génétique et amélioration des plantes F62 - Physiologie végétale - Croissance et développement Oryza sativa génome génotype carte génétique développement biologique système racinaire racine variété locus des caractères quantitatifs marqueur génétique http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_921 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_6651 http://aims.fao.org/aos/agrovoc/c_8157 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_8227 F30 - Génétique et amélioration des plantes F62 - Physiologie végétale - Croissance et développement Oryza sativa génome génotype carte génétique développement biologique système racinaire racine variété locus des caractères quantitatifs marqueur génétique http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_921 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_6651 http://aims.fao.org/aos/agrovoc/c_8157 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_8227 |
spellingShingle |
F30 - Génétique et amélioration des plantes F62 - Physiologie végétale - Croissance et développement Oryza sativa génome génotype carte génétique développement biologique système racinaire racine variété locus des caractères quantitatifs marqueur génétique http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_921 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_6651 http://aims.fao.org/aos/agrovoc/c_8157 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_8227 F30 - Génétique et amélioration des plantes F62 - Physiologie végétale - Croissance et développement Oryza sativa génome génotype carte génétique développement biologique système racinaire racine variété locus des caractères quantitatifs marqueur génétique http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_921 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_6651 http://aims.fao.org/aos/agrovoc/c_8157 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_8227 Phung, Nhung Thi Phuong Mai, Chung Duc Hoang, Giang Thi Truong, Hue Thi Minh Lavarenne, Jeremy Gonin, Mathieu Nguyen, Khanh L. Ha, Thuy Thi Do, Vinh Nang Gantet, Pascal Courtois, Brigitte Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam |
description |
Background. Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. Results The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. Conclusions Some of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development. |
format |
article |
topic_facet |
F30 - Génétique et amélioration des plantes F62 - Physiologie végétale - Croissance et développement Oryza sativa génome génotype carte génétique développement biologique système racinaire racine variété locus des caractères quantitatifs marqueur génétique http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_921 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_6651 http://aims.fao.org/aos/agrovoc/c_8157 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_8227 |
author |
Phung, Nhung Thi Phuong Mai, Chung Duc Hoang, Giang Thi Truong, Hue Thi Minh Lavarenne, Jeremy Gonin, Mathieu Nguyen, Khanh L. Ha, Thuy Thi Do, Vinh Nang Gantet, Pascal Courtois, Brigitte |
author_facet |
Phung, Nhung Thi Phuong Mai, Chung Duc Hoang, Giang Thi Truong, Hue Thi Minh Lavarenne, Jeremy Gonin, Mathieu Nguyen, Khanh L. Ha, Thuy Thi Do, Vinh Nang Gantet, Pascal Courtois, Brigitte |
author_sort |
Phung, Nhung Thi Phuong |
title |
Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam |
title_short |
Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam |
title_full |
Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam |
title_fullStr |
Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam |
title_full_unstemmed |
Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam |
title_sort |
genome-wide association mapping for root traits in a panel of rice accessions from vietnam |
url |
http://agritrop.cirad.fr/580236/ http://agritrop.cirad.fr/580236/1/580236.pdf |
work_keys_str_mv |
AT phungnhungthiphuong genomewideassociationmappingforroottraitsinapanelofriceaccessionsfromvietnam AT maichungduc genomewideassociationmappingforroottraitsinapanelofriceaccessionsfromvietnam AT hoanggiangthi genomewideassociationmappingforroottraitsinapanelofriceaccessionsfromvietnam AT truonghuethiminh genomewideassociationmappingforroottraitsinapanelofriceaccessionsfromvietnam AT lavarennejeremy genomewideassociationmappingforroottraitsinapanelofriceaccessionsfromvietnam AT goninmathieu genomewideassociationmappingforroottraitsinapanelofriceaccessionsfromvietnam AT nguyenkhanhl genomewideassociationmappingforroottraitsinapanelofriceaccessionsfromvietnam AT hathuythi genomewideassociationmappingforroottraitsinapanelofriceaccessionsfromvietnam AT dovinhnang genomewideassociationmappingforroottraitsinapanelofriceaccessionsfromvietnam AT gantetpascal genomewideassociationmappingforroottraitsinapanelofriceaccessionsfromvietnam AT courtoisbrigitte genomewideassociationmappingforroottraitsinapanelofriceaccessionsfromvietnam |
_version_ |
1798165039973138432 |
spelling |
dig-cirad-fr-5802362024-04-30T12:34:07Z http://agritrop.cirad.fr/580236/ http://agritrop.cirad.fr/580236/ Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam. Phung Nhung Thi Phuong, Mai Chung Duc, Hoang Giang Thi, Truong Hue Thi Minh, Lavarenne Jeremy, Gonin Mathieu, Nguyen Khanh L., Ha Thuy Thi, Do Vinh Nang, Gantet Pascal, Courtois Brigitte. 2016. BMC Plant Biology, 16 (1), 19 p.https://doi.org/10.1186/s12870-016-0747-y <https://doi.org/10.1186/s12870-016-0747-y> Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam Phung, Nhung Thi Phuong Mai, Chung Duc Hoang, Giang Thi Truong, Hue Thi Minh Lavarenne, Jeremy Gonin, Mathieu Nguyen, Khanh L. Ha, Thuy Thi Do, Vinh Nang Gantet, Pascal Courtois, Brigitte eng 2016 BMC Plant Biology F30 - Génétique et amélioration des plantes F62 - Physiologie végétale - Croissance et développement Oryza sativa génome génotype carte génétique développement biologique système racinaire racine variété locus des caractères quantitatifs marqueur génétique http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_921 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_6651 http://aims.fao.org/aos/agrovoc/c_8157 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_24030 Viet Nam http://aims.fao.org/aos/agrovoc/c_8227 Background. Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. Results The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. Conclusions Some of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/580236/1/580236.pdf text Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1186/s12870-016-0747-y 10.1186/s12870-016-0747-y info:eu-repo/semantics/altIdentifier/doi/10.1186/s12870-016-0747-y info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1186/s12870-016-0747-y info:eu-repo/semantics/reference/purl/http://tropgenedb.cirad.fr/tropgene/JSP/interface.jsp?module=RICE |