Genetic diversity and population structure in a rice drought stress panel

Abstract

A drought stress panel composed of diverse accessions selected from upland, aerobic, rainfed lowland and irrigated lowland environments, was assembled to serve as germplasm for aerobic adaptation breeding. Aerobic rice requires significant levels of tolerance to drought stress due to intermittent water deficit and high soil impedance caused by aerobic conditions. Genomic information may be utilized to investigate the nature of the panel to guide varietal improvement. Using 153 simple sequence repeat and 384 single nucleotide polymorphism markers, the aim of the study was to compare the allelic properties of the two marker types, infer population structure of the panel, and estimate kinship among the accessions. There was a general agreement between the results derived from the two marker types. Marker alleles were found to occur at low frequencies, as the panel was composed mostly of improved accessions with some landraces. The panel clustered into japonica (JA), aus (AU), upland-adapted indica (UL) and lowland-adapted indica (LL) subpopulations. The AU and JA subpopulations were more divergent from the rest of the subpopulations than were the LL and UL subpopulations. Average marker-based kinship for related accessions was less than 0.20, indicating a low degree of genetic relatedness in the panel. Within the LL and UL subpopulations, the low levels of kinship imply that there is still much genetic gain to be expected from utilizing the accessions in breeding. Thus, an understanding of the genetic variation in the panel suggests focusing on improving the mean in the short term, and tapping into the exotic alleles from the AU and JA subpopulations when genetic gain declines.

Genetic Diversity, Population Structure, and Marker-Trait Association for Drought Tolerance in US Rice Germplasm

“…Genetic relatedness among the rice genotypes from six major rice growing states of the US was assessed using SSR markers, which were proven to be effective in identifying small allelic variation [7]. The average polymorphism information content (PIC) of 0.33 observed in our study was less compared to the average PIC of 0.54 in the global rice collection [23].…”

“…Simple sequence repeat (SSR) markers have been extensively used to evaluate genetic diversity in rice [5,6]. The SSR markers are multi-allelic and can detect more genetic variation compared to single nucleotide polymorphism (SNP) [7] and amplified fragment length polymorphism (AFLP) markers [8]. Narrow genetic diversity in the US rice genotypes was observed in a previous study using SSR markers [9].…”

Genetic diversity and population structure assessment of Western Canadian barley cooperative trials

“…Five independent runs were used for each subpopulation ( k -value). For each run, simulations were run for 100,000 burn-in and 100,000 Markov Chain Monte Carlo (MCMC) iterations ( Tabanao et al., 2014 ). The Delta k statistic of ( Evanno et al., 2005 ) was estimated using STRUCTURE HARVESTER ( Earl and Vonholdt, 2011 ) to determine the best k value.…”