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

Abstract

BackgroundGenetic 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.ResultsThe 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.ConclusionsExamining 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-015-0068-z) contains supplementary material, which is available to authorized users.

Between China and South Asia: A Middle Asian corridor of crop dispersal and agricultural innovation in the Bronze Age

“…What is more, these regions of Bangladesh and Assam are the centres of cultivation of aus-type rices, which have recently been recognized as distinct from either indica or japonica , not sharing all the same domestication-related alleles and therefore to represent a third lineage of domesticated rice (Civáň et al, 2015; Schwatz et al, 2014; Travis et al, 2015). There are also very few genotypic japonica varieties found in Assam or West Bengal (Travis et al, 2015). In contrast, less than 3% of rice landraces in Yunnan are attributed to aus/boro varieties whereas >75% of landraces are japonica (Zeng et al, 2007).…”

Biomass and elemental concentrations of 22 rice cultivars grown under alternate wetting and drying conditions at three field sites in Bangladesh

“…At each site, 22 cultivars were tested (Table 1). The cultivars used in this study are a subset of the cultivars previously genotyped, using a 384 SNP array (Travis et al 2015). The cultivars were either from the aus subpopulation originating from Bangladesh or India, or were improved Bangladeshi cultivars (BR 6, BRRI Dhan 28, and BRRI Dhan 47).…”

Morphophysiological and molecular effects of drought stress in rice

“…This is an important preliminary step before identification of candidate genes related to particular phenotypes. Such diversity panels have also been established for rice using SNP markers (Travis et al, 2015). Use of insertion and deletions (INDELs) as well as SNPs to study the diversity between drought susceptible and tolerant rice indicates that QTLs related to photosynthesis are particularly important in drought stress tolerance in rice (Zhang et al, 2016).…”