Resequencing Reveals Different Domestication Rate for BADH1 and BADH2 in Rice (Oryza sativa)

PLoS One. 2015 Aug 10;10(8):e0134801. doi: 10.1371/journal.pone.0134801. eCollection 2015.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Betaine-Aldehyde Dehydrogenase / genetics*
  • Breeding
  • Evolution, Molecular*
  • Exons
  • Genes, Plant
  • Genotype
  • Haplotypes
  • Homozygote
  • Linkage Disequilibrium
  • Mutation
  • Oryza / enzymology
  • Oryza / genetics*
  • Phenotype
  • Plant Proteins / genetics*
  • Polymorphism, Genetic
  • Salt Tolerance
  • Sequence Analysis, DNA

Substances

  • Plant Proteins
  • Betaine-Aldehyde Dehydrogenase

Grants and funding

This work was supported by a grant from the Next-Generation BioGreen 21 Program (No.PJ01116101), Rural Development Administration, Republic of Korea. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Seedpia Inc provided support in the form of salaries for authors [YHC], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.