title: Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal.
abstract: BACKGROUND
  Genetic diversity among rice cultivars from Bangladesh and North East India was assessed using a custom 384-SNP microarray assay. A total of 511 cultivars were obtained from several sources, choosing landraces likely to be from the aus subpopulation and modern improved cultivars from Bangladesh. Cultivars from the OryzaSNP set and Rice Diversity Panel 1 (RDP1) were also included for reference.
  
  
  RESULTS
  The population analysis program STRUCTURE was used to infer putative population groups in the panel, revealing four groups: indica (76 cultivars), japonica (55) and two distinct groups within the aus subpopulation (aus-1 = 99, aus-2 = 151). Principal Component Analysis was used to confirm the four population groups identified by STRUCTURE. The analysis revealed cultivars that belonged to neither aus-1 nor aus-2 but which are clearly aus based on the combined probabilities of their membership of the two aus groups which have been termed aus-admix (96). Information obtained from the panel of 511 cultivars was used to assign rice groups to 74 additional landraces obtained from Assam and West Bengal. While both the aus-1 and aus-2 groups were represented approximately equally in India, aus-2 (which includes cultivar N 22) was more common in Bangladesh, but was not found at all in West Bengal.
  
  
  CONCLUSIONS
  Examining the distribution of landrace names within theaus-1 and aus-2 groups suggests that aus-1 is associated with the term "boro", a word used to describe a winter growing season in Bangladesh and Assam. The information described here has been used to select a population of 300 cultivars for Genome Wide Association studies of the aus rice subpopulation.
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK.
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Travis
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK.
authors.forename: Gareth J
authors.initials: GJ
authors.lastname: Norton
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK.|Department of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India.
authors.forename: Sutapa
authors.initials: S
authors.lastname: Datta
authors.affiliation: Department of Plant Breeding and Genetics, Assam Agricultural University, Jorhat, 785013, Assam, India.
authors.forename: Ramendra
authors.initials: R
authors.lastname: Sarma
authors.affiliation: Department of Genetics and Plant Breeding, Calcutta University, 35 B.C. Road, Kolkata, 700 019, West Bengal, India.
authors.forename: Tapash
authors.initials: T
authors.lastname: Dasgupta
authors.affiliation: Luiz de Queiroz College of Agriculture, University of São Paulo, Avenida Pádua Dias, 11, Bairro Agronomia, Piracicaba, São Paulo, Brazil.
authors.forename: Filipe L
authors.initials: FL
authors.lastname: Savio
authors.affiliation: Cell & Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
authors.forename: Malcolm
authors.initials: M
authors.lastname: Macaulay
authors.affiliation: Cell & Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
authors.forename: Peter E
authors.initials: PE
authors.lastname: Hedley
authors.affiliation: International Rice Research Institute (IRRI), DAPO 7777, Metro Manila, 1031, The Philippines.
authors.forename: Kenneth L
authors.initials: KL
authors.lastname: McNally
authors.affiliation: Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh.
authors.forename: Mahmud H
authors.initials: MH
authors.lastname: Sumon
authors.affiliation: Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh.
authors.forename: M Rafiqul
authors.initials: MR
authors.lastname: Islam
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK. a.price@abdn.ac.uk.
authors.forename: Adam H
authors.initials: AH
authors.lastname: Price
keywords: Aus; Boro; Ecotype; Genotype; Rice; SNP