Identification of a Novel QTL for Chlorate Resistance in Rice (<i>Oryza</i> <i>sativa</i> L.)
Chlorate resistance analysis is an effective approach commonly used to distinguish the genetic variation between <i>Oryza sativa</i> L. ssp. <i>indica</i> and <i>japonica,</i> and predict the nitrogen use efficiency (NUE). This study aimed at investigating the res...
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MDPI AG
2020-08-01
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| Series: | Agriculture |
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| Online Access: | https://www.mdpi.com/2077-0472/10/8/360 |
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| author | Nkulu Rolly Kabange So-Yeon Park Dongjin Shin So-Myeong Lee Su-Min Jo Youngho Kwon Jin-Kyung Cha You-Chun Song Jong-Min Ko Jong-Hee Lee |
| author_facet | Nkulu Rolly Kabange So-Yeon Park Dongjin Shin So-Myeong Lee Su-Min Jo Youngho Kwon Jin-Kyung Cha You-Chun Song Jong-Min Ko Jong-Hee Lee |
| author_sort | Nkulu Rolly Kabange |
| collection | DOAJ |
| description | Chlorate resistance analysis is an effective approach commonly used to distinguish the genetic variation between <i>Oryza sativa</i> L. ssp. <i>indica</i> and <i>japonica,</i> and predict the nitrogen use efficiency (NUE). This study aimed at investigating the response of a doubled haploid (DH) population derived from anther culture of 93-11 × Milyang352 exposed to 0.1% potassium chlorate (KClO<sub>3</sub>) at the seedling stage. The results revealed that the parental rice lines 93-11 (<i>indica</i>) and Milyang352 (<i>japonica</i>) showed distinctive phenotypic responses. The parental line 93-11 scored highly sensitive (0% survival) and Milyang352 scored resistant (66.7% survival) 7 days after treatment. The DH lines reflected the differential phenotypic response observed in parental lines. Interestingly, we identified a novel quantitative trait locus (QTL) for chlorate resistance on chromosome 3 <i>(qCHR-3</i>, 136 cM, logarithm of the odds—LOD: 4.1) using Kompetitive Allele-Specific PCR (KASP) markers. The additive effect (−11.97) and phenotypic variation explained (PVE; 14.9%) indicated that the allele from Milyang352 explained the observed phenotypic variation. In addition, shoot growth showed a significant difference between parental lines, but not root growth. Moreover, in silico analysis identified candidate genes with diverse and interesting molecular and physiological functions. Therefore, this study suggested that the QTL <i>qCHR-3</i> harbors promising candidate genes that could play a role in the regulation of nitrogen metabolism in rice. |
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| language | English |
| last_indexed | 2024-03-10T17:23:58Z |
| publishDate | 2020-08-01 |
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| series | Agriculture |
| spelling | doaj.art-fb818ea35c5345c787cbe8a8f0a9038a2023-11-20T10:16:43ZengMDPI AGAgriculture2077-04722020-08-0110836010.3390/agriculture10080360Identification of a Novel QTL for Chlorate Resistance in Rice (<i>Oryza</i> <i>sativa</i> L.)Nkulu Rolly Kabange0So-Yeon Park1Dongjin Shin2So-Myeong Lee3Su-Min Jo4Youngho Kwon5Jin-Kyung Cha6You-Chun Song7Jong-Min Ko8Jong-Hee Lee9Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, KoreaChlorate resistance analysis is an effective approach commonly used to distinguish the genetic variation between <i>Oryza sativa</i> L. ssp. <i>indica</i> and <i>japonica,</i> and predict the nitrogen use efficiency (NUE). This study aimed at investigating the response of a doubled haploid (DH) population derived from anther culture of 93-11 × Milyang352 exposed to 0.1% potassium chlorate (KClO<sub>3</sub>) at the seedling stage. The results revealed that the parental rice lines 93-11 (<i>indica</i>) and Milyang352 (<i>japonica</i>) showed distinctive phenotypic responses. The parental line 93-11 scored highly sensitive (0% survival) and Milyang352 scored resistant (66.7% survival) 7 days after treatment. The DH lines reflected the differential phenotypic response observed in parental lines. Interestingly, we identified a novel quantitative trait locus (QTL) for chlorate resistance on chromosome 3 <i>(qCHR-3</i>, 136 cM, logarithm of the odds—LOD: 4.1) using Kompetitive Allele-Specific PCR (KASP) markers. The additive effect (−11.97) and phenotypic variation explained (PVE; 14.9%) indicated that the allele from Milyang352 explained the observed phenotypic variation. In addition, shoot growth showed a significant difference between parental lines, but not root growth. Moreover, in silico analysis identified candidate genes with diverse and interesting molecular and physiological functions. Therefore, this study suggested that the QTL <i>qCHR-3</i> harbors promising candidate genes that could play a role in the regulation of nitrogen metabolism in rice.https://www.mdpi.com/2077-0472/10/8/360quantitative trait locuschlorate resistancenitrogen use efficiencydoubled haploidrice |
| spellingShingle | Nkulu Rolly Kabange So-Yeon Park Dongjin Shin So-Myeong Lee Su-Min Jo Youngho Kwon Jin-Kyung Cha You-Chun Song Jong-Min Ko Jong-Hee Lee Identification of a Novel QTL for Chlorate Resistance in Rice (<i>Oryza</i> <i>sativa</i> L.) Agriculture quantitative trait locus chlorate resistance nitrogen use efficiency doubled haploid rice |
| title | Identification of a Novel QTL for Chlorate Resistance in Rice (<i>Oryza</i> <i>sativa</i> L.) |
| title_full | Identification of a Novel QTL for Chlorate Resistance in Rice (<i>Oryza</i> <i>sativa</i> L.) |
| title_fullStr | Identification of a Novel QTL for Chlorate Resistance in Rice (<i>Oryza</i> <i>sativa</i> L.) |
| title_full_unstemmed | Identification of a Novel QTL for Chlorate Resistance in Rice (<i>Oryza</i> <i>sativa</i> L.) |
| title_short | Identification of a Novel QTL for Chlorate Resistance in Rice (<i>Oryza</i> <i>sativa</i> L.) |
| title_sort | identification of a novel qtl for chlorate resistance in rice i oryza i i sativa i l |
| topic | quantitative trait locus chlorate resistance nitrogen use efficiency doubled haploid rice |
| url | https://www.mdpi.com/2077-0472/10/8/360 |
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