Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal

Anthony J. Travis, Gareth J. Norton, Sutapa Datta, Ramendra Sarma, Tapash Dasgupta, Filipe L. Savio, Malcolm Macaulay, Peter E. Hedley, Kenneth L. McNally, Mahmud H. Sumon, M. Rafiqul Islam, Adam H. Price*

*Corresponding author for this work

Research output: Contribution to journalArticle

19 Citations (Scopus)
4 Downloads (Pure)

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.

Original languageEnglish
Article number35
Number of pages9
JournalRice
Volume8
Issue number1
Early online date1 Dec 2015
DOIs
Publication statusPublished - 2015

Fingerprint

Bangladesh
cultivar
rice
India
genetic variation
cultivars
subpopulation
landraces
genetic diversity
principal component analysis
growing season
genome
assay
winter
assays

Keywords

  • Aus
  • Boro
  • Ecotype
  • Genotype
  • Rice
  • SNP

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Plant Science
  • Soil Science

Cite this

Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal. / Travis, Anthony J.; Norton, Gareth J.; Datta, Sutapa; Sarma, Ramendra; Dasgupta, Tapash; Savio, Filipe L.; Macaulay, Malcolm; Hedley, Peter E.; McNally, Kenneth L.; Sumon, Mahmud H.; Islam, M. Rafiqul; Price, Adam H.

In: Rice, Vol. 8, No. 1, 35, 2015.

Research output: Contribution to journalArticle

Travis, AJ, Norton, GJ, Datta, S, Sarma, R, Dasgupta, T, Savio, FL, Macaulay, M, Hedley, PE, McNally, KL, Sumon, MH, Islam, MR & Price, AH 2015, 'Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal', Rice, vol. 8, no. 1, 35. https://doi.org/10.1186/s12284-015-0068-z
Travis, Anthony J. ; Norton, Gareth J. ; Datta, Sutapa ; Sarma, Ramendra ; Dasgupta, Tapash ; Savio, Filipe L. ; Macaulay, Malcolm ; Hedley, Peter E. ; McNally, Kenneth L. ; Sumon, Mahmud H. ; Islam, M. Rafiqul ; Price, Adam H. / Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal. In: Rice. 2015 ; Vol. 8, No. 1.
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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.",
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note = "Acknowledgements This work was funded by BBSRC research project BB/J00336/1. FS and a part of the proportion of the cost of the Illumina genotyping was funded by a Beachell-Borlag International Fellowship. The authors would like to acknowledge the help of Dr MK Sarmah in collecting seed samples of the landraces and improved cultivars from Assam used in this study and Dr. Ma. Elizabeth B. Naredo and Ms. Sheila Mae Q. Mercado for handling of IRGC accessions and preparation of DNAs for genotyping. All rice seeds used here were obtained with MTA agreements and seed and dry leaves imported into the UK under import licence IMP⁄SOIL⁄18⁄2009 issued by Science and Advice for Scottish Agriculture.",
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AU - Travis, Anthony J.

AU - Norton, Gareth J.

AU - Datta, Sutapa

AU - Sarma, Ramendra

AU - Dasgupta, Tapash

AU - Savio, Filipe L.

AU - Macaulay, Malcolm

AU - Hedley, Peter E.

AU - McNally, Kenneth L.

AU - Sumon, Mahmud H.

AU - Islam, M. Rafiqul

AU - Price, Adam H.

N1 - Acknowledgements This work was funded by BBSRC research project BB/J00336/1. FS and a part of the proportion of the cost of the Illumina genotyping was funded by a Beachell-Borlag International Fellowship. The authors would like to acknowledge the help of Dr MK Sarmah in collecting seed samples of the landraces and improved cultivars from Assam used in this study and Dr. Ma. Elizabeth B. Naredo and Ms. Sheila Mae Q. Mercado for handling of IRGC accessions and preparation of DNAs for genotyping. All rice seeds used here were obtained with MTA agreements and seed and dry leaves imported into the UK under import licence IMP⁄SOIL⁄18⁄2009 issued by Science and Advice for Scottish Agriculture.

PY - 2015

Y1 - 2015

N2 - 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.

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