ORIGINAL ARTICLE Genotyping by sequencing of 270 Indica rice varieties revealed genetic markers probably related to heavy metal accumulation Yuhu Liang 1 | Xiao Dong 2 | Xuemei Ni 2,3 | Qi Wang 1 | Sunil Kumar Sahu 3 | Junliang Hou 2,3 | Manzhong Liang 4 | Liangbi Chen 4 | Gengyun Zhang 2,3 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 Correspondence Gengyun Zhang, State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China. Email: zhanggengyun@genomics.cn and Liangbi Chen, College of Life Sciences, Hunan Normal University, Changsha, China. Email: chenliangbi@126.com Funding information National Key Technology R&D Program, Grant/Award Number: 2015BAD02B01-7; Nation High Technology Research and Development Program of China, Grant/ Award Number: 2014AA10A602-4; Technology Innovation Program of Shenzhen Municipal Government, Grant/Award Number: CXZZ20150330171810060, JSGG20130918102805062 Communicated by: Rajeev Varshney 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 identifica- tion 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 vari- ances 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. KEYWORDS cadmium accumulation, genotyping by sequencing, heavy metals, Indica rice, single nucleotide polymorphisms 1 | INTRODUCTION Genomic variations in rice have been comprehensively studied in the past decades with developing of the second‐generation sequencing technologies. Whole‐genome resequencing has been conducted to representative strains of rice for identification of genomewide varia- tions including single nucleotide polymorphisms (SNPs), insertions and deletions (INDELs) and structure variations (SVs) (3,000 Rice Genomes Project, 2014; Xu et al., 2012). In addition, with phenotype information of the sequenced strains, previous studies have been carried out to figure out genotype–phenotype association, identifying genes related to important traits (Fan et al., 2006; Huang et al., 2010, 2012). Despite these proceedings, further studies on genomic variations of rice were still needed to identify more variations in dif- ferent rice strains and also to find out a more cost‐effective way of genotyping, other than whole‐genome resequencing, which can be applied in breeding practice. Genotyping by sequencing (GBS) has been developed, and combin- ing with the multiplex second‐generation sequencing technologies, it has been used in large‐scale population sequencing for marker Received: 11 April 2018 | Revised: 10 May 2018 | Accepted: 2 June 2018 DOI: 10.1111/pbr.12625 Plant Breeding. 2018;1–7. wileyonlinelibrary.com/journal/pbr © 2018 Blackwell Verlag GmbH | 1