Abstract
BADH1 and BADH2 are two homologous genes, encoding betaine aldehyde dehydrogenase in rice. In the present study, we scanned BADHs sequences of 295 rice cultivars, and 10 wild rice accessions to determine the polymorphisms, gene functions and domestication of these two genes. A total of 16 alleles for BADH1 and 10 alleles for BADH2 were detected in transcribed region of cultivars and wild species. Association study showed that BADH1 has significant correlation with salt tolerance in rice during germination stage, the SNP (T/A) in exon 4 is highly correlated with salt tolerance index (STI) (P<10−4). While, BADH2 was only responsible for rice fragrance, of which two BADH2 alleles (8 bp deletion in exon 7 and C/T SNP in exon 13) explain 97% of aroma variation in our germplasm. Theses indicate that there are no overlapping functions between the two homologous genes. In addition, a large LD block was detected in BADH2 region, however, there was no large LD blocks in a 4-Mb region of BADH1. We found that BADH2 region only showed significant bias in Tajima’s D value from the balance. Extended haplotype homozygosity study revealed fragrant accessions had a large LD block that extended around the mutation site (8 bp deletion in exon 7) of BADH2, while both of the BADH1 alleles (T/A in exon 4) did not show large extended LD block. All these results suggested that BADH2 was domesticated during rice evolution, while BADH1 was not selected by human beings.
Highlights
Betaine aldehyde dehydrogenase (BADH) is an enzyme found in a large number of plant species, and its catalyst glycine betaine (GB) is a powerful osmoprotectant associated with salt and drought stress tolerance [1]
Fitzgerald et al (2010) suggested that BADH2 is responsible for salt stress tolerance
Various studies have reported conflicting results [1,2,5]. These inconsistencies could be attributable to the differences either in rice germplasm materials or growth stages that they investigated for their studies
Summary
Betaine aldehyde dehydrogenase (BADH) is an enzyme found in a large number of plant species, and its catalyst glycine betaine (GB) is a powerful osmoprotectant associated with salt and drought stress tolerance [1]. In many plant species, such as mangrove, spinach (Spinacia oleracea L.), amaranth (Aramanthus spp.), barley (Hordeum vulgare L.) and sorghum (Sorghum bicolor L.), BADH plays a role in abiotic stress tolerance through the accumulation of GB from betaine aldehyde (BA). Plant species such as tobacco (Nicotiana tabacum L.), PLOS ONE | DOI:10.1371/journal.pone.0134801. BADH1 and BADH2 Have Different Domestication Rate in Rice roles of these authors are articulated in the ‘author contributions’ section
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