Haplotype Analysis of <i>BADH1</i> by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication
Betaine aldehyde dehydrogenase 1 (<i>BADH1)</i>, a paralog of the fragrance gene <i>BADH2</i>, is known to be associated with salt stress through the accumulation of synthesized glycine betaine (GB), which is involved in the response to abiotic stresses. Despite the unclear a...
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MDPI AG
2021-07-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/14/7578 |
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| author | Myeong-Hyeon Min Thant Zin Maung Yuan Cao Rungnapa Phitaktansakul Gang-Seob Lee Sang-Ho Chu Kyu-Won Kim Yong-Jin Park |
| author_facet | Myeong-Hyeon Min Thant Zin Maung Yuan Cao Rungnapa Phitaktansakul Gang-Seob Lee Sang-Ho Chu Kyu-Won Kim Yong-Jin Park |
| author_sort | Myeong-Hyeon Min |
| collection | DOAJ |
| description | Betaine aldehyde dehydrogenase 1 (<i>BADH1)</i>, a paralog of the fragrance gene <i>BADH2</i>, is known to be associated with salt stress through the accumulation of synthesized glycine betaine (GB), which is involved in the response to abiotic stresses. Despite the unclear association between <i>BADH1</i> and salt stress, we observed the responses of eight phenotypic characteristics (germination percentage (GP), germination energy (GE), germination index (GI), mean germination time (MGT), germination rate (GR), shoot length (SL), root length (RL), and total dry weight (TDW)) to salt stress during the germination stage of 475 rice accessions to investigate their association with <i>BADH1</i> haplotypes. We found a total of 116 SNPs and 77 InDels in the whole <i>BADH1</i> gene region, representing 39 haplotypes. Twenty-nine haplotypes representing 27 mutated alleles (two InDels and 25 SNPs) were highly (<i>p</i> < 0.05) associated with salt stress, including the five SNPs that have been previously reported to be associated with salt tolerance. We observed three predominant haplotypes associated with salt tolerance, Hap_2, Hap_18, and Hap_23, which were Indica specific, indicating a comparatively high number of rice accessions among the associated haplotypes. Eight plant parameters (phenotypes) also showed clear responses to salt stress, and except for MGT (mean germination time), all were positively correlated with each other. Different signatures of domestication for <i>BADH1</i> were detected in cultivated rice by identifying the highest and lowest Tajima’s D values of two major cultivated ecotypes (Temperate Japonica and Indica). Our findings on these significant associations and <i>BADH1</i> evolution to plant traits can be useful for future research development related to its gene expression. |
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| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T09:37:07Z |
| publishDate | 2021-07-01 |
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| record_format | Article |
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| spelling | doaj.art-40449d6b848845a0815e444e2d1ef19a2023-11-22T04:00:47ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-07-012214757810.3390/ijms22147578Haplotype Analysis of <i>BADH1</i> by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during DomesticationMyeong-Hyeon Min0Thant Zin Maung1Yuan Cao2Rungnapa Phitaktansakul3Gang-Seob Lee4Sang-Ho Chu5Kyu-Won Kim6Yong-Jin Park7Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, KoreaDepartment of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, KoreaDepartment of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, KoreaDepartment of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, KoreaAgricultural Biotechnology Department, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, KoreaCenter of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, KoreaAgricultural Biotechnology Department, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, KoreaDepartment of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, KoreaBetaine aldehyde dehydrogenase 1 (<i>BADH1)</i>, a paralog of the fragrance gene <i>BADH2</i>, is known to be associated with salt stress through the accumulation of synthesized glycine betaine (GB), which is involved in the response to abiotic stresses. Despite the unclear association between <i>BADH1</i> and salt stress, we observed the responses of eight phenotypic characteristics (germination percentage (GP), germination energy (GE), germination index (GI), mean germination time (MGT), germination rate (GR), shoot length (SL), root length (RL), and total dry weight (TDW)) to salt stress during the germination stage of 475 rice accessions to investigate their association with <i>BADH1</i> haplotypes. We found a total of 116 SNPs and 77 InDels in the whole <i>BADH1</i> gene region, representing 39 haplotypes. Twenty-nine haplotypes representing 27 mutated alleles (two InDels and 25 SNPs) were highly (<i>p</i> < 0.05) associated with salt stress, including the five SNPs that have been previously reported to be associated with salt tolerance. We observed three predominant haplotypes associated with salt tolerance, Hap_2, Hap_18, and Hap_23, which were Indica specific, indicating a comparatively high number of rice accessions among the associated haplotypes. Eight plant parameters (phenotypes) also showed clear responses to salt stress, and except for MGT (mean germination time), all were positively correlated with each other. Different signatures of domestication for <i>BADH1</i> were detected in cultivated rice by identifying the highest and lowest Tajima’s D values of two major cultivated ecotypes (Temperate Japonica and Indica). Our findings on these significant associations and <i>BADH1</i> evolution to plant traits can be useful for future research development related to its gene expression.https://www.mdpi.com/1422-0067/22/14/7578betaine aldehyde dehydrogenase 1 (BADH1)salt stressdomesticationcultivated ricewild rice |
| spellingShingle | Myeong-Hyeon Min Thant Zin Maung Yuan Cao Rungnapa Phitaktansakul Gang-Seob Lee Sang-Ho Chu Kyu-Won Kim Yong-Jin Park Haplotype Analysis of <i>BADH1</i> by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication International Journal of Molecular Sciences betaine aldehyde dehydrogenase 1 (BADH1) salt stress domestication cultivated rice wild rice |
| title | Haplotype Analysis of <i>BADH1</i> by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication |
| title_full | Haplotype Analysis of <i>BADH1</i> by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication |
| title_fullStr | Haplotype Analysis of <i>BADH1</i> by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication |
| title_full_unstemmed | Haplotype Analysis of <i>BADH1</i> by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication |
| title_short | Haplotype Analysis of <i>BADH1</i> by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication |
| title_sort | haplotype analysis of i badh1 i by next generation sequencing reveals association with salt tolerance in rice during domestication |
| topic | betaine aldehyde dehydrogenase 1 (BADH1) salt stress domestication cultivated rice wild rice |
| url | https://www.mdpi.com/1422-0067/22/14/7578 |
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