Development of Functional Molecular Markers for Viviparous Germination Resistance in Rice
Rice (<i>Oryza sativa</i>) plays a pivotal role in global food security. Understanding the genetics of rice cultivation is crucial, particularly for traits such as viviparous germination, which significantly influences germination and yield. Our research aimed to elucidate the genetic an...
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MDPI AG
2024-12-01
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| author | So-Myeong Lee Youngho Kwon Sung-Ryul Kim Ju-Won Kang Hyeonjin Park Jin-Kyung Cha Dong-Soo Park Jun-Hyun Cho Woojae Kim Gyu-Hyeon Eom Jong-Hee Lee |
| author_facet | So-Myeong Lee Youngho Kwon Sung-Ryul Kim Ju-Won Kang Hyeonjin Park Jin-Kyung Cha Dong-Soo Park Jun-Hyun Cho Woojae Kim Gyu-Hyeon Eom Jong-Hee Lee |
| author_sort | So-Myeong Lee |
| collection | DOAJ |
| description | Rice (<i>Oryza sativa</i>) plays a pivotal role in global food security. Understanding the genetics of rice cultivation is crucial, particularly for traits such as viviparous germination, which significantly influences germination and yield. Our research aimed to elucidate the genetic and molecular mechanisms by which the <i>Sdr4</i> gene influences viviparous germination and to develop novel molecular markers for this gene to enhance breeding strategies against viviparous germination. In all, 683 rice cultivars and 100 F<sub>2</sub> plants were used for viviparous germination and genetic analysis using KASP (Kompetitive Allele-Specific PCR) and agarose gel-based markers related to viviparous germination tolerance. We developed and used a polymorphic agarose gel-based marker and a KASP marker targeting the <i>Sdr4</i> gene. A genetic analysis of field-grown rice cultivars and the F<sub>2</sub> population revealed that the two markers on <i>Sdr4</i> were functional for the genomic selection of SNPs and InDels related to dormancy. The Pearson correlation coefficient (r = 0.74, <i>p</i>-value = 3.31 × 10<sup>−8</sup>) between the Sdr4-IND KASP marker genotype and viviparous germination rate demonstrated a significant positive correlation, supporting the marker’s utility for selecting rice varieties with diminished viviparous germination. This insight serves as a critical theoretical foundation for breeding strategies for developing early-maturing rice varieties with enhanced resistance to viviparous germination, addressing pivotal challenges in rice cultivation, and ensuring food security. |
| format | Article |
| id | doaj-art-8668a85508e941cfa04a0fe508085a21 |
| institution | DOAJ |
| issn | 2073-4395 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
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| series | Agronomy |
| spelling | doaj-art-8668a85508e941cfa04a0fe508085a212025-08-20T02:50:56ZengMDPI AGAgronomy2073-43952024-12-011412289610.3390/agronomy14122896Development of Functional Molecular Markers for Viviparous Germination Resistance in RiceSo-Myeong Lee0Youngho Kwon1Sung-Ryul Kim2Ju-Won Kang3Hyeonjin Park4Jin-Kyung Cha5Dong-Soo Park6Jun-Hyun Cho7Woojae Kim8Gyu-Hyeon Eom9Jong-Hee Lee10Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of KoreaRice Breeding Innovation Department, International Rice Research Institute, Los Baños 4031, PhilippinesDepartment of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of KoreaRice (<i>Oryza sativa</i>) plays a pivotal role in global food security. Understanding the genetics of rice cultivation is crucial, particularly for traits such as viviparous germination, which significantly influences germination and yield. Our research aimed to elucidate the genetic and molecular mechanisms by which the <i>Sdr4</i> gene influences viviparous germination and to develop novel molecular markers for this gene to enhance breeding strategies against viviparous germination. In all, 683 rice cultivars and 100 F<sub>2</sub> plants were used for viviparous germination and genetic analysis using KASP (Kompetitive Allele-Specific PCR) and agarose gel-based markers related to viviparous germination tolerance. We developed and used a polymorphic agarose gel-based marker and a KASP marker targeting the <i>Sdr4</i> gene. A genetic analysis of field-grown rice cultivars and the F<sub>2</sub> population revealed that the two markers on <i>Sdr4</i> were functional for the genomic selection of SNPs and InDels related to dormancy. The Pearson correlation coefficient (r = 0.74, <i>p</i>-value = 3.31 × 10<sup>−8</sup>) between the Sdr4-IND KASP marker genotype and viviparous germination rate demonstrated a significant positive correlation, supporting the marker’s utility for selecting rice varieties with diminished viviparous germination. This insight serves as a critical theoretical foundation for breeding strategies for developing early-maturing rice varieties with enhanced resistance to viviparous germination, addressing pivotal challenges in rice cultivation, and ensuring food security.https://www.mdpi.com/2073-4395/14/12/2896ricefunctional markerviviparous germinationbreedinggenetic analysis |
| spellingShingle | So-Myeong Lee Youngho Kwon Sung-Ryul Kim Ju-Won Kang Hyeonjin Park Jin-Kyung Cha Dong-Soo Park Jun-Hyun Cho Woojae Kim Gyu-Hyeon Eom Jong-Hee Lee Development of Functional Molecular Markers for Viviparous Germination Resistance in Rice Agronomy rice functional marker viviparous germination breeding genetic analysis |
| title | Development of Functional Molecular Markers for Viviparous Germination Resistance in Rice |
| title_full | Development of Functional Molecular Markers for Viviparous Germination Resistance in Rice |
| title_fullStr | Development of Functional Molecular Markers for Viviparous Germination Resistance in Rice |
| title_full_unstemmed | Development of Functional Molecular Markers for Viviparous Germination Resistance in Rice |
| title_short | Development of Functional Molecular Markers for Viviparous Germination Resistance in Rice |
| title_sort | development of functional molecular markers for viviparous germination resistance in rice |
| topic | rice functional marker viviparous germination breeding genetic analysis |
| url | https://www.mdpi.com/2073-4395/14/12/2896 |
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