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Haplotype Analysis of BADH1 by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication

Betaine aldehyde dehydrogenase 1 (BADH1), a paralog of the fragrance gene BADH2, 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 BADH1 and salt stre...

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Autores principales: Min, Myeong-Hyeon, Maung, Thant Zin, Cao, Yuan, Phitaktansakul, Rungnapa, Lee, Gang-Seob, Chu, Sang-Ho, Kim, Kyu-Won, Park, Yong-Jin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8305476/
https://www.ncbi.nlm.nih.gov/pubmed/34299195
http://dx.doi.org/10.3390/ijms22147578
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author Min, Myeong-Hyeon
Maung, Thant Zin
Cao, Yuan
Phitaktansakul, Rungnapa
Lee, Gang-Seob
Chu, Sang-Ho
Kim, Kyu-Won
Park, Yong-Jin
author_facet Min, Myeong-Hyeon
Maung, Thant Zin
Cao, Yuan
Phitaktansakul, Rungnapa
Lee, Gang-Seob
Chu, Sang-Ho
Kim, Kyu-Won
Park, Yong-Jin
author_sort Min, Myeong-Hyeon
collection PubMed
description Betaine aldehyde dehydrogenase 1 (BADH1), a paralog of the fragrance gene BADH2, 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 BADH1 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 BADH1 haplotypes. We found a total of 116 SNPs and 77 InDels in the whole BADH1 gene region, representing 39 haplotypes. Twenty-nine haplotypes representing 27 mutated alleles (two InDels and 25 SNPs) were highly (p < 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 BADH1 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 BADH1 evolution to plant traits can be useful for future research development related to its gene expression.
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spelling pubmed-83054762021-07-25 Haplotype Analysis of BADH1 by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication Min, Myeong-Hyeon Maung, Thant Zin Cao, Yuan Phitaktansakul, Rungnapa Lee, Gang-Seob Chu, Sang-Ho Kim, Kyu-Won Park, Yong-Jin Int J Mol Sci Article Betaine aldehyde dehydrogenase 1 (BADH1), a paralog of the fragrance gene BADH2, 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 BADH1 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 BADH1 haplotypes. We found a total of 116 SNPs and 77 InDels in the whole BADH1 gene region, representing 39 haplotypes. Twenty-nine haplotypes representing 27 mutated alleles (two InDels and 25 SNPs) were highly (p < 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 BADH1 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 BADH1 evolution to plant traits can be useful for future research development related to its gene expression. MDPI 2021-07-15 /pmc/articles/PMC8305476/ /pubmed/34299195 http://dx.doi.org/10.3390/ijms22147578 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Min, Myeong-Hyeon
Maung, Thant Zin
Cao, Yuan
Phitaktansakul, Rungnapa
Lee, Gang-Seob
Chu, Sang-Ho
Kim, Kyu-Won
Park, Yong-Jin
Haplotype Analysis of BADH1 by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication
title Haplotype Analysis of BADH1 by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication
title_full Haplotype Analysis of BADH1 by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication
title_fullStr Haplotype Analysis of BADH1 by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication
title_full_unstemmed Haplotype Analysis of BADH1 by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication
title_short Haplotype Analysis of BADH1 by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication
title_sort haplotype analysis of badh1 by next-generation sequencing reveals association with salt tolerance in rice during domestication
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8305476/
https://www.ncbi.nlm.nih.gov/pubmed/34299195
http://dx.doi.org/10.3390/ijms22147578
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