**5. Conclusions**

In the present study, a GWAS for mesocotyl length in 208 rice accessions was conducted. Mesocotyl length varied in di fferent culture conditions and sowing depths. GWAS have identified 16 loci significantly associated with mesocotyl elongation, which explained phenotypic variations ranged from 7.1% to 10.0%. Furthermore, five high-confidence candidate genes were identified on chromosomes 1, 3, 5, 9 and 12. The accessions with longer mesocotyl and the markers significantly associated with mesocotyl length can be used to promote the process of rice breeding. This study will facilitate our uanderstanding on the genetic architecture of rice mesocotyl length.

**Supplementary Materials:** The following are available online at http://www.mdpi.com/2073-4425/11/1/49/s1, Table S1: Detailed information of 208 rice accessions, Table S2: SNPs significantly associated with mesocotyl length under different environments, Table S3: Candidate genes for mesocotyl length in 208 rice landraces or varieties, Table S4: Accessions used in qRT-PCR analysis, Table S5: Primers used in this study. The raw Illumina sequencing data will be available upon the request.

**Author Contributions:** Conceived and designed the experiments: H.L., Y.W., G.Y. Performed the experiments: H.L., J.Z., X.L. Analyzed the data: H.L., J.L. (Jiaolong Li), G.Y. Wrote and revised the paper: H.L., J.Z., J.L. (Jindong Liu), Y.W., G.Y. All authors have read and agreed to the published version of the manuscript.

**Funding:** This work was supported by Agricultural Science and Technology Innovation Program Cooperation and Innovation Mission (Grant No. CAAS-XTCX2016001) and Shenzhen Science and Technology Projects (No. JSGG20160608160725473).

**Acknowledgments:** We thank Guosheng Xiong for providing some of the germplasms used in this study. We are grateful to the field research assistant Bingmei Lin in phenotyping and other field work.

**Conflicts of Interest:** The authors declare no conflict of interest.
