Parallel Domestication of the Heading Date 1 Gene in Cereals

Mol Biol Evol. 2015 Oct;32(10):2726-37. doi: 10.1093/molbev/msv148. Epub 2015 Jun 27.


Flowering time is one of the key determinants of crop adaptation to local environments during domestication. However, the genetic basis underlying flowering time is yet to be elucidated in most cereals. Although staple cereals, such as rice, maize, wheat, barley, and sorghum, have spread and adapted to a wide range of ecological environments during domestication, it is yet to be determined whether they have a common genetic basis for flowering time. In this study, we show, through map-based cloning, that flowering time in sorghum is controlled by a major quantitative trait locus (QTL) Heading Date 1 (HD1), located on chromosome 10. The causal gene encodes the CONSTANS gene family which contains a CCT domain. A 5-bp deletion of a minor allele present in the coding sequence leads to a gene frameshift that delays flowering in sorghum. In contrast, in foxtail millet, association mapping of HD1 showed a common causal site with a splicing variant from "GT" to "AT" that was highly correlated with flowering time. In addition, the rice HD1 gene is known to harbor several causal variants controlling flowering time. These data indicate that the major flowering time QTL HD1 was under parallel domestication in sorghum, foxtail millet, and rice. The pattern of common mixed minor, or even rare, causal alleles in HD1 across different species may be representative of the genetic basis of the domestication syndrome. Furthermore, large DNA sequence analysis of HD1 revealed multiple origins for domesticated sorghum and a single origin for domesticated foxtail millet.

Keywords: comparative mapping; flowering time; parallel domestication.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Agriculture*
  • Amino Acid Sequence
  • Base Pairing / genetics
  • Chromosome Mapping
  • Cloning, Molecular
  • DNA, Plant / genetics
  • Edible Grain / genetics*
  • Genes, Plant*
  • Genetic Loci
  • Genetic Variation
  • Molecular Sequence Data
  • Oryza / genetics
  • Plant Proteins / chemistry
  • Plant Proteins / genetics
  • Protein Structure, Tertiary
  • Selection, Genetic
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Sequence Deletion
  • Setaria Plant / genetics
  • Sorghum / genetics


  • DNA, Plant
  • Plant Proteins