Abstract
Myanmar is well known as a primary center of plant genetic resources for rice. A considerable number of genetic diversity studies have been conducted in Myanmar using various DNA markers. However, this is the first report using DArTseq technology for exploring the genetic diversity of Myanmar rice. In our study, two ultra-high-throughput diversity array technology markers were employed to investigate the genetic diversity and population structure of local rice varieties in the Ayeyarwady delta, the major region of rice cultivation. The study was performed using 117 rice genotypes with 7643 SNP and 4064 silicoDArT markers derived from the DArT platform. Genetic variance among the genotypes ranged from 0 to 0.753 in SNPs, and from 0.001 to 0.954 in silicoDArT. Two distinct population groups were identified from SNP data analysis. Cluster analysis with both markers clearly separated traditional Pawsan varieties and modern high-yielding varieties. A significant divergence was found between populations according to the Fst values (0.737) obtained from the analysis of molecular variance, which revealed 74% genetic variation at the population level. These findings support rice researchers in identifying useful DNA polymorphisms in genes and pinpointing specific genes conferring desirable phenotypic traits for further genome-wide association studies and parental selection for recombination breeding to enhance rice varietal development and release.
Highlights
Rice (Oryza sativa L.) is one of the most widely cultivated cereal crops distributed across the world and serves as a major food source for more than half of the global human population [1]
A total of 16,160 silicoDArT markers were generated and they had an average of 99% reproducibility and 93% call rate and 87% of all the identified markers had a >0.1 average one ratio (Table S2 and Figure S1)
Considering all of the quality parameters, 4064 silicoDArT markers were used for subsequent analysis
Summary
Rice (Oryza sativa L.) is one of the most widely cultivated cereal crops distributed across the world and serves as a major food source for more than half of the global human population [1]. Rice is the main staple food crop in Myanmar, but is cultivated as the most important cash crop for the majority of farmers, with large export potential. It is grown extensively across the whole country, covering an area of 7.26 million ha, and its annual production reaches 28.1 million tons with an average yield of 3.92 t/ha [4]. Myanmar has diverse landscapes and geographic variation ranging from the delta area of the Ayeyarwady River in the southern region to the mountainous areas in the north This landscape heterogeneity resulted in the diversification of rice production systems, such as deep-water fields in the delta areas, irrigated and rainfed paddy fields in plain areas, and slash-and-burn fields in the mountainous areas. Geographic and crop diversity coupled with diverse traditional agricultural systems contribute to the high diversity of crop genetic resources in Myanmar [5,6]
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