Rice Genome Resequencing Reveals a Major Quantitative Trait Locus for Resistance to Bakanae Disease Caused by <i>Fusarium fujikuroi</i>

Rice Genome Resequencing Reveals a Major Quantitative Trait Locus for Resistance to Bakanae Disease Caused by <i>Fusarium fujikuroi</i>

Bakanae disease (BD), caused by the fungal pathogen <i>Fusarium fujikuroi</i>, has become a serious threat in rice-cultivating regions worldwide. In the present study, quantitative trait locus (QTL) mapping was performed using F2 and F3 plants derived after crossing a BD-resistant and a...

Full description

Bibliographic Details
Main Authors: Do-Yu Kang, Kyeong-Seong Cheon, Jun Oh, Hyoja Oh, Song Lim Kim, Nyunhee Kim, Eungyeong Lee, Inchan Choi, Jeongho Baek, Kyung-Hwan Kim, Nam-Jin Chung, Hyeonso Ji
Format: Article
Language:English
Published: MDPI AG 2019-05-01
Series:International Journal of Molecular Sciences
Subjects:
bakanae disease
resequencing
genetic map
quantitative trait locus
Online Access:https://www.mdpi.com/1422-0067/20/10/2598
id doaj-db14d2cf560c429081463d7c43fe520a
record_format Article
spelling doaj-db14d2cf560c429081463d7c43fe520a2020-11-25T02:28:28ZengMDPI AGInternational Journal of Molecular Sciences1422-00672019-05-012010259810.3390/ijms20102598ijms20102598Rice Genome Resequencing Reveals a Major Quantitative Trait Locus for Resistance to Bakanae Disease Caused by <i>Fusarium fujikuroi</i>Do-Yu Kang0Kyeong-Seong Cheon1Jun Oh2Hyoja Oh3Song Lim Kim4Nyunhee Kim5Eungyeong Lee6Inchan Choi7Jeongho Baek8Kyung-Hwan Kim9Nam-Jin Chung10Hyeonso Ji11Department of Agricultural Biotechnology, National Institute of Agricultural Sciences (NIAS), Jeonju 54874, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences (NIAS), Jeonju 54874, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences (NIAS), Jeonju 54874, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences (NIAS), Jeonju 54874, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences (NIAS), Jeonju 54874, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences (NIAS), Jeonju 54874, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences (NIAS), Jeonju 54874, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences (NIAS), Jeonju 54874, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences (NIAS), Jeonju 54874, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences (NIAS), Jeonju 54874, KoreaDepartment of Crop Science and Biotechnology, Chonbuk National University, Jeonju 54896, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences (NIAS), Jeonju 54874, KoreaBakanae disease (BD), caused by the fungal pathogen <i>Fusarium fujikuroi</i>, has become a serious threat in rice-cultivating regions worldwide. In the present study, quantitative trait locus (QTL) mapping was performed using F2 and F3 plants derived after crossing a BD-resistant and a BD-susceptible Korean japonica rice variety, &#8216;Samgwang&#8217; and &#8216;Junam&#8217;, respectively. Resequencing of &#8216;Junam&#8217; and &#8216;Samgwang&#8217; genomes revealed 151,916 DNA polymorphisms between the two varieties. After genotyping 188 F2 plants, we constructed a genetic map comprising 184 markers, including 175 kompetitive allele-specific PCR markers, eight cleaved amplified polymorphic sequence (CAPS) markers, and a derived CAPS (dCAPS) marker. The degree of BD susceptibility of each F2 plant was evaluated on the basis of the mortality rate measured with corresponding F3 progeny seedlings by in vitro screening. Consequently, <i>qFfR9</i>, a major QTL, was discovered at 30.1 centimorgan (cM) on chromosome 9 with a logarithm of the odds score of 60.3. For the QTL interval, 95% probability lay within a 7.24&#8722;7.56 Mbp interval. In this interval, we found that eight genes exhibited non-synonymous single nucleotide polymorphisms (SNPs) by comparing the &#8216;Junam&#8217; and &#8216;Samgwang&#8217; genome sequence data, and are possibly candidate genes for <i>qFfR9</i>; therefore, <i>qFfR9</i> could be utilized as a valuable resource for breeding BD-resistant rice varieties.https://www.mdpi.com/1422-0067/20/10/2598bakanae diseaseresequencinggenetic mapquantitative trait locus
collection DOAJ
language English
format Article
sources DOAJ
author Do-Yu Kang
Kyeong-Seong Cheon
Jun Oh
Hyoja Oh
Song Lim Kim
Nyunhee Kim
Eungyeong Lee
Inchan Choi
Jeongho Baek
Kyung-Hwan Kim
Nam-Jin Chung
Hyeonso Ji
spellingShingle Do-Yu Kang
Kyeong-Seong Cheon
Jun Oh
Hyoja Oh
Song Lim Kim
Nyunhee Kim
Eungyeong Lee
Inchan Choi
Jeongho Baek
Kyung-Hwan Kim
Nam-Jin Chung
Hyeonso Ji
Rice Genome Resequencing Reveals a Major Quantitative Trait Locus for Resistance to Bakanae Disease Caused by <i>Fusarium fujikuroi</i>
International Journal of Molecular Sciences
bakanae disease
resequencing
genetic map
quantitative trait locus
author_facet Do-Yu Kang
Kyeong-Seong Cheon
Jun Oh
Hyoja Oh
Song Lim Kim
Nyunhee Kim
Eungyeong Lee
Inchan Choi
Jeongho Baek
Kyung-Hwan Kim
Nam-Jin Chung
Hyeonso Ji
author_sort Do-Yu Kang
title Rice Genome Resequencing Reveals a Major Quantitative Trait Locus for Resistance to Bakanae Disease Caused by <i>Fusarium fujikuroi</i>
title_short Rice Genome Resequencing Reveals a Major Quantitative Trait Locus for Resistance to Bakanae Disease Caused by <i>Fusarium fujikuroi</i>
title_full Rice Genome Resequencing Reveals a Major Quantitative Trait Locus for Resistance to Bakanae Disease Caused by <i>Fusarium fujikuroi</i>
title_fullStr Rice Genome Resequencing Reveals a Major Quantitative Trait Locus for Resistance to Bakanae Disease Caused by <i>Fusarium fujikuroi</i>
title_full_unstemmed Rice Genome Resequencing Reveals a Major Quantitative Trait Locus for Resistance to Bakanae Disease Caused by <i>Fusarium fujikuroi</i>
title_sort rice genome resequencing reveals a major quantitative trait locus for resistance to bakanae disease caused by <i>fusarium fujikuroi</i>
publisher MDPI AG
series International Journal of Molecular Sciences
issn 1422-0067
publishDate 2019-05-01
description Bakanae disease (BD), caused by the fungal pathogen <i>Fusarium fujikuroi</i>, has become a serious threat in rice-cultivating regions worldwide. In the present study, quantitative trait locus (QTL) mapping was performed using F2 and F3 plants derived after crossing a BD-resistant and a BD-susceptible Korean japonica rice variety, &#8216;Samgwang&#8217; and &#8216;Junam&#8217;, respectively. Resequencing of &#8216;Junam&#8217; and &#8216;Samgwang&#8217; genomes revealed 151,916 DNA polymorphisms between the two varieties. After genotyping 188 F2 plants, we constructed a genetic map comprising 184 markers, including 175 kompetitive allele-specific PCR markers, eight cleaved amplified polymorphic sequence (CAPS) markers, and a derived CAPS (dCAPS) marker. The degree of BD susceptibility of each F2 plant was evaluated on the basis of the mortality rate measured with corresponding F3 progeny seedlings by in vitro screening. Consequently, <i>qFfR9</i>, a major QTL, was discovered at 30.1 centimorgan (cM) on chromosome 9 with a logarithm of the odds score of 60.3. For the QTL interval, 95% probability lay within a 7.24&#8722;7.56 Mbp interval. In this interval, we found that eight genes exhibited non-synonymous single nucleotide polymorphisms (SNPs) by comparing the &#8216;Junam&#8217; and &#8216;Samgwang&#8217; genome sequence data, and are possibly candidate genes for <i>qFfR9</i>; therefore, <i>qFfR9</i> could be utilized as a valuable resource for breeding BD-resistant rice varieties.
topic bakanae disease
resequencing
genetic map
quantitative trait locus
url https://www.mdpi.com/1422-0067/20/10/2598
work_keys_str_mv AT doyukang ricegenomeresequencingrevealsamajorquantitativetraitlocusforresistancetobakanaediseasecausedbyifusariumfujikuroii
AT kyeongseongcheon ricegenomeresequencingrevealsamajorquantitativetraitlocusforresistancetobakanaediseasecausedbyifusariumfujikuroii
AT junoh ricegenomeresequencingrevealsamajorquantitativetraitlocusforresistancetobakanaediseasecausedbyifusariumfujikuroii
AT hyojaoh ricegenomeresequencingrevealsamajorquantitativetraitlocusforresistancetobakanaediseasecausedbyifusariumfujikuroii
AT songlimkim ricegenomeresequencingrevealsamajorquantitativetraitlocusforresistancetobakanaediseasecausedbyifusariumfujikuroii
AT nyunheekim ricegenomeresequencingrevealsamajorquantitativetraitlocusforresistancetobakanaediseasecausedbyifusariumfujikuroii
AT eungyeonglee ricegenomeresequencingrevealsamajorquantitativetraitlocusforresistancetobakanaediseasecausedbyifusariumfujikuroii
AT inchanchoi ricegenomeresequencingrevealsamajorquantitativetraitlocusforresistancetobakanaediseasecausedbyifusariumfujikuroii
AT jeonghobaek ricegenomeresequencingrevealsamajorquantitativetraitlocusforresistancetobakanaediseasecausedbyifusariumfujikuroii
AT kyunghwankim ricegenomeresequencingrevealsamajorquantitativetraitlocusforresistancetobakanaediseasecausedbyifusariumfujikuroii
AT namjinchung ricegenomeresequencingrevealsamajorquantitativetraitlocusforresistancetobakanaediseasecausedbyifusariumfujikuroii
AT hyeonsoji ricegenomeresequencingrevealsamajorquantitativetraitlocusforresistancetobakanaediseasecausedbyifusariumfujikuroii
_version_ 1724837751508959232

Similar Items