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

Abstract

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.

Plant Responses and Tolerance to Salt Stress: Physiological and Molecular Interventions

“…Next generation gene sequencing opens the avenue to revealing salt tolerance mechanisms more precisely. Min et al [20] reported that haplotype analysis of BADH1 by next-generation sequencing reveals an association with salt tolerance in rice during domestication. Despite the unclear association between BADH1 and salt stress, these findings can be useful for future research development related to its gene expression [20].…”

Harnessing γ-TMT Genetic Variations and Haplotypes for Vitamin E Diversity in the Korean Rice Collection

“…Previous research has highlighted a narrower genetic diversity in japonica compared to indica rice, likely due to a domestication bottleneck [22,53]. Furthermore, breeding efforts over the past century have further narrowed the genetic diversity among cultivars, particularly those selected for cultivation in diverse agro-ecological environments [53,54]. In terms of Tajima's D measurement, indica was the only group with a positive value, suggesting that rare alleles are more likely to be lost during bottleneck events [55].…”

Multi-omics analysis reveals the genetic basis of rice fragrance mediated by betaine aldehyde dehydrogenase 2

“…A transcript level analysis revealed the constitutive expression of BADH2 under normal and stress conditions and the upregulation in BADH1 expression by salt and drought stresses [12] , [50] , [51] . Various studies have revealed the involvement of BADH1 in salt stress tolerance [52] , [53] , [54] , [55] . Furthermore, BADH1 has a much lower affinity for GABAld and higher affinities for other aldehyde substrates than those of BADH2 [12] , [53] , [56] , [57] .…”