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. 2018 Mar 16;9:332. doi: 10.3389/fpls.2018.00332

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Copyright © 2018 Zhao, Zhao, Jiang, Wang, Xiong, Todorovska, Yin, Chen, Wang, Xie, Pan, Rashid, Zhang, Li and Li.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Summary of non-synonymous SNPs detected in the full population and their distribution associated with mesocotyl length in the indica genome. (A) Termination codon SNP (T-C SNP) along the genome. (B) Non-synonymous SNPs (N-S SNP) along the genome. Histograms of minor allele frequencies (MAFs) of non-synonymous SNPs in the (C) full population, (D) indica, and (E) japonica. Distributions of (F) SDSs and (G) ESDSs along the indica genome. SDS and ESDS show SNPs with significant and extremely significant differences (p < 0.05; p < 0.01) in allele frequency between polar pools. For each 500 kb sliding window, the numbers of SDSs and ESDSs were plotted on the entire genome. The sliding step is 50 kb. Adjacent chromosomes are delineated using different colors. Horizontal black lines show the thresholds for the 99th percentile of 10,000 permutations of the SDS and ESDS numbers.