1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice

Abstract

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. Electronic supplementary material The online version of this article (10.1186/s12284-019-0311-0) contains supplementary material, which is available to authorized users.

An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies

“…Although cost comparisons can be difficult to make between genotyping platforms due to differences in SNP call rates, informativeness, and varying prices depending on sample commitments, the C7AIR gives the global research community a uniform tool to easily compare across research programs while being of high enough density to meet the requirements for a variety of research applications. It has also served as a resource to identify informative SNPs that can be deployed in low-cost, low-density genotyping assays such as KASP assays widely used for marker-assisted selection in forward breeding, or the 1K-Rice Custom Amplicon (1k-RiCA) SNP assay (https://gsl.irri.org/services/genotyping/rica) used for genomic selection [35].…”

More and more of less and less: Is genomics‐based breeding of dry direct‐seeded rice (DDSR) varieties the need of hour?

“…They further suggested that GS, informed by GWAS interpretations of genetic architecture and population structure, can be an effective tool to increase the efficiency of rice breeding as genotyping is becoming cost effective. Recently, a robust genotypic platform, 1K‐Rice Custom Amplicon (1k‐RiCA), is reported as an alternative cost‐effective genotypic platform for indica rice breeding programmes, which can enhance the efficiency of MAS and GS in indica rice germplasm pools (Arbelaez et al ., 2019).…”

Relative genomic impacts of translocation history, hatchery practices, and farm selection in Pacific oysterCrassostrea gigasthroughout the Northern Hemisphere

“…Identifying, preserving, and using these genetic resources effectively is essential for sustainable development of aquaculture species (Guo, 2009). Genetic markers that differentiate populations can be useful to assign unknown origin individuals to populations of origin (Beacham et al, 2017), to detect domestic population influence (e.g., introgression of domesticated alleles) (Wringe et al, 2018), and to manage broodstock (Arbelaez et al, 2019). Once markers are identified, they can be used to generate robust, multi-purpose high throughput amplicon sequencing panels (Meek & Larson, 2019) or be added to SNP chips (Gutierrez et al, 2017).…”