Background

While a multitude of genotyping platforms have been developed for rice, the majority of them have not been optimized for breeding where cost, turnaround time, throughput and ease of use, relative to density and informativeness are critical parameters of their utility. With that in mind we report the development of the 1K-Rice Custom Amplicon, or 1k-RiCA, a robust custom sequencing-based amplicon panel of ~ 1000-SNPs that are uniformly distributed across the rice genome, designed to be highly informative within indica rice breeding pools, and tailored for genomic prediction in elite indica rice breeding programs.

Results

Empirical validation tests performed on the 1k-RiCA showed average marker call rates of 95% with marker repeatability and concordance rates of 99%. These technical properties were not affected when two common DNA extraction protocols were used. The average distance between SNPs in the 1k-RiCA was 1.5 cM, similar to the theoretical distance which would be expected between 1,000 uniformly distributed markers across the rice genome. The average minor allele frequencies on a panel of indica lines was 0.36 and polymorphic SNPs estimated on pairwise comparisons between indica by indica accessions and indica by japonica accessions were on average 430 and 450 respectively. The specific design parameters of the 1k-RiCA allow for a detailed view of genetic relationships and unambiguous molecular IDs within indica accessions and good cost vs. marker-density balance for genomic prediction applications in elite indica germplasm. Predictive abilities of Genomic Selection models for flowering time, grain yield, and plant height were on average 0.71, 0.36, and 0.65 respectively based on cross-validation analysis. Furthermore the inclusion of important trait markers associated with 11 different genes and QTL adds value to parental selection in crossing schemes and marker-assisted selection in forward breeding applications.

Conclusions

This study validated the marker quality and robustness of the 1k-RiCA genotypic platform for genotyping populations derived from indica rice subpopulation for genetic and breeding purposes including MAS and genomic selection. The 1k-RiCA has proven to be an alternative cost-effective genotyping system for breeding applications.

中文翻译：

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1k-RiCA（1K-Rice Custom Amplicon）是一种基于扩增子的新型基因分型 SNP 检测，适用于水稻遗传和育种应用。

背景

虽然已经开发了多种水稻基因分型平台，但其中大多数尚未针对育种进行优化，其中成本、周转时间、通量和易用性（相对于密度和信息量）是其效用的关键参数。考虑到这一点，我们报告了1K-Rice Custom Amplicon （或 1k-RiCA）的开发，这是一个强大的基于定制测序的扩增子面板，由大约 1000 个 SNP 组成，均匀分布在水稻基因组中，旨在为籼稻提供丰富的信息水稻育种池，并为优良籼稻育种计划中的基因组预测量身定制。

结果

对 1k-RiCA 进行的经验验证测试显示，平均标记检出率为 95%，标记重复性和一致性率为 99%。当使用两种常见的 DNA 提取方案时，这些技术特性不受影响。1k-RiCA 中 SNP 之间的平均距离为 1.5 cM，与水稻基因组中 1,000 个均匀分布的标记之间预期的理论距离相似。一组籼稻品系的平均次要等位基因频率为 0.36，通过籼稻与籼稻种质和籼稻与粳稻种质之间的成对比较估计的多态性 SNP平均分别为 430 和 450。1k-RiCA 的具体设计参数允许详细查看籼稻种质内的遗传关系和明确的分子 ID，并在优良籼稻种质的基因组预测应用中实现良好的成本与标记密度平衡。根据交叉验证分析，基因组选择模型对开花时间、籽粒产量和株高的预测能力平均分别为 0.71、0.36 和 0.65。此外，包含与 11 个不同基因和 QTL 相关的重要性状标记为杂交方案中的亲本选择和远期育种应用中的标记辅助选择增加了价值。

结论

本研究验证了 1k-RiCA 基因型平台的标记质量和稳健性，用于对源自籼稻亚群的群体进行基因分型，用于遗传和育种目的，包括 MAS 和基因组选择。1k-RiCA 已被证明是一种适合育种应用的经济高效的基因分型系统。