title: Genetic relatedness among indigenous rice varieties in the Eastern Himalayan region based on nucleotide sequences of the Waxy gene.
abstract: BACKGROUND
  Indigenous rice varieties in the Eastern Himalayan region of Northeast India are traditionally classified into sali, boro and jum ecotypes based on geographical locality and the season of cultivation. In this study, we used DNA sequence data from the Waxy (Wx) gene to infer the genetic relatedness among indigenous rice varieties in Northeast India and to assess the genetic distinctiveness of ecotypes.
  
  
  RESULTS
  The results of all three analyses (Bayesian, Maximum Parsimony and Neighbor Joining) were congruent and revealed two genetically distinct clusters of rice varieties in the region. The large group comprised several varieties of sali and boro ecotypes, and all agronomically improved varieties. The small group consisted of only traditionally cultivated indigenous rice varieties, which included one boro, few sali and all jum varieties. The fixation index analysis revealed a very low level of differentiation between sali and boro (F(ST) = 0.005), moderate differentiation between sali and jum (F(ST) = 0.108) and high differentiation between jum and boro (F(ST) = 0.230) ecotypes.
  
  
  CONCLUSIONS
  The genetic relatedness analyses revealed that sali, boro and jum ecotypes are genetically heterogeneous, and the current classification based on cultivation type is not congruent with the genetic background of rice varieties. Indigenous rice varieties chosen from genetically distinct clusters could be used in breeding programs to improve genetic gain through heterosis, while maintaining high genetic diversity.
authors.affiliation: Biology Department, Forest and Evolutionary Genomics Laboratory, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St, West, Montreal, Quebec H4B 1R6, Canada. baharulchoudhury@gmail.com.
authors.forename: Baharul I
authors.initials: BI
authors.lastname: Choudhury
authors.forename: Mohammed L
authors.initials: ML
authors.lastname: Khan
authors.forename: Selvadurai
authors.initials: S
authors.lastname: Dayanandan
mesh_terms: D001483:Base Sequence; D001499:Bayes Theorem; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics*; D014644:Genetic Variation; D005843:Geography; D006239:Haplotypes; D007194:India; D008390:Markov Chains; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D013214:Starch Synthase / Q000145:classification / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins; C060756:waxy protein, plant; D013214:Starch Synthase