Genotyping by sequencing of 270 Indica rice varieties revealed genetic markers probably related to heavy metal accumulation |
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| Authors: | Yuhu Liang Xiao Dong Xuemei Ni Qi Wang Sunil Kumar Sahu Junliang Hou Manzhong Liang Liangbi Chen Gengyun Zhang |
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| Affiliation: | 1. BGI Education Center, University of Chinese Academy of Sciences, Beijing, China;2. BGI‐Shenzhen, Shenzhen, China;3. State Key Laboratory of Agricultural Genomics, BGI‐Shenzhen, Shenzhen, China;4. College of Life Sciences, Hunan Normal University, Changsha, China |
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| Abstract: | Genotyping by sequencing (GBS) has been applied to identify genetic markers in crops for trait association and breeding purposes. Here, we applied GBS technology to study a natural population of 270 Indica rice strains, which resulted in identification of 79,545 genomewide single nucleotide polymorphisms. Using these SNPs, we found the close relationship between the 270 Indica rice strains. Furthermore, we tested the feasibility of using these 270 Indica strains in studying important rice traits by analysing the cadmium and other metal accumulation of these strains and correlating the traits with genetic markers. We identified 32 SNPs to be associated with cadmium (Cd) accumulation, explaining 61.25% of the Cd concentration variances in grains. The genetic markers provided here are valuable resources for future rice studies, and further characterization of the candidate loci identified in this study can also aid the development of low Cd‐accumulating rice varieties. |
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| Keywords: | cadmium accumulation genotyping by sequencing heavy metals Indica rice single nucleotide polymorphisms |
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