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IRRI RiCA V5 Panel

We offer the IRRI RiCA Version 5 Panel for full-service, PlexSeq  genotyping to be used as a tool to conduct molecular breeding and production quality control tests.

 

The IRRI RiCA V5 Panel, which consists of 1076 SNPs, was developed in collaboration with the International Rice Research Institute (IRRI).

 We also offer the IRRI RiCA V5 Panel  to the public at a discounted price and expedited turnaround through the AgriPlex Connect program.

* The following is derived from the White Paper

Introduction

Molecular breeding can accelerate the process of developing new rice varieties with improved yield, quality, and disease resistance. Breeders can use molecular markers to identify genes or regions of the genome associated with desirable traits and increase the efficiency and the precision of selecting for these traits while decreasing the time and resources otherwise required by traditional breeding methods. Many new rice varieties with increased yield potential, grain quality, disease resistance, and pest resistance were developed using molecular markers. Some notable examples of successful molecular breeding programs include the development of Sub1 rice varieties that are tolerant to flooding (Xu et al., 2006), and improved disease resistance such as to bacterial blight (Jiang et al., 2012) and blast (Xiao et al., 2019).


The International Rice Research Institute (IRRI) has made significant contributions to the genetic research and molecular breeding of rice over the past several decades. IRRI’s employment of molecular markers as a research tool has resulted in the development of new breeding technologies, high-yielding varieties, and the identification of useful traits. One of these contributions is The Rice SNP Consortium Array (RiCA): a high-throughput genotyping tool developed to improve rice molecular breeding efforts (Arbelaez et al., 2019). In 2020, IRRI in collaboration with AgriPlex Genomics constructed a multiplexed version of the RiCA panel on AgriPlex Genomics’ PlexSeq platform. The multiplexed RiCA panel has been made available to the rice breeding community as RiCA version 2 and RiCA Version 4 (RiCAv4). In 2023, we have introduced the next version of this multiplexed rice SNP panel, RiCA Version 5 (V5).

The RiCA Version 5 SNP Panel

The performance of the markers in the existing RiCA V4 was evaluated and ranked based on success rate and robustness. The lowest performing 74 SNPs were purged from the panel. 

126 New markers were added to the panel. Markers were chosen to close gaps in genome coverage and optimize the genomic distribution of the panel. These improvements are displayed in Table 1 that compares the genomic distribution of the new RiCA panel with the previous version. The average distance between adjacent markers of RiCA V5 decreased to 345 Kb and the average number of markers per chromosome increased to 90 SNPs. The 126 new markers and the 949 markers carried over from RiCA V4 panel were multiplexed and validated together to construct the new RiCA v5 panel, which consists of 1076 markers and maintains the basic structure of the panel, now made of:

 

  • Genomic screen: 745 SNPs originating from the Cornell 6KArray Infinium Rice chip
    (Thomson et al., 2017) and the 3,000 Rice Genomes Project (Alexandrov et al., 2015;
    Mansueto et al., 2017; Wang et al., 2018). The markers are evenly distributed throughout
    the genome and were selected based on call rate higher than 95% and high minor allele
    frequencies (MAF ≥ 0.4). The markers added in the 5th version of the panel, were chosen to
    fill in gaps and provide more even representation of diversity of elite germplasm.

  • Trait-related markers: 310 SNPs associated with different important trait genes/QTLs. Table
    2 lists the traits and gene targets by trait categories.

  • Purity Markers: 20 SNPs chosen for their discriminatory ability amongst elite indica
    material, used in determination of genetic purity, identity, and hybridity.

The complete markers list together with their chromosomal location can be found in Appendix A

 

RiCA V5 table 1.png

Table 1: SNP numbers comparison between the RiCA V4 and updated RiCA V5 Panel.

irri v5 table 2.PNG

Table 2. List of traits and genes represented on the AgriPlex Genomics RiCA V5 Panel. 

Applications

Genomic Selection

The panel enables genomic selection in indica breeding programs. On average, any two elite indica parents will display between 300 – 500 polymorphic markers distributed across the genome (Figure 2), a density sufficient to enable imputation back to the full genome level. The combination of rapid turnaround time and low cost enables cost-effective genotyping of a prediction population during the last generation of line fixation, saving money on the cost of field space for seed increase and allowing rapid recycling of progeny as parents.

Marker-assisted backcrossing:

The RiCA V5 panel provides an excellent low-cost option for background recovery estimates in marker-assisted backcrossing programs. The combination of highly informative background markers together with a wide selection of peak trait markers allows accurate estimation of background recovery, ensures valuable genes from the recipient line are recovered, and may provide additional confirmation that a target gene is carried by the selected progeny. Background selection can reduce the number of backcross generations required by 2 or more to achieve >95% recipient recovery.

QTL Profiling

The SNP panel at AgriPlex contains 310 trait markers targeting high-value trait targets (table 2) covering a range of traits related to disease resistance, grain quality, abiotic stress tolerance, heading date, hybrid rice production and others. These markers are designed to give accurate profiling of the targeted genes and QTLs across all Oryza sativa genomic diversity, including both indica and japonica. The same, or part of these QTLs and traits can be interrogated by specific, single plex assays, providing a mechanism for initial selection based on major loci followed by validation and full genome profiling on the RiCA array.

Seed Purity and Hybridity

The RiCA V5 panel includes 20 markers specifically chosen for their ability to distinguish elite material. Combined with the genome-wide and trait markers, this makes the panel an excellent choice for applications related to genetic purity, some examples are, purity testing (uniformity), F1 hybridity tests, and varietal identity fingerprinting.

Conclusion

The RiCA V5 panel offered by AgriPlex Genomics provides an excellent, cost-effective genotyping option for applications requiring a moderate to high sample throughput at modest SNP density. The size of the panel enables genomic selection, and the substantially expanded suite of trait markers can be useful in other Marker Assisted Selection applications. The panel fits in neatly with rapid line fixation protocols, due to its low cost-per-sample and fast turnaround time. These benefits enable major-locus selection and genomic selection to occur before field amplification of seed, saving both time and money.


The addition of purity markers expands its usefulness in a range of applications, going from safeguarding line identity along breeding programs and continuing into seed production. The flexibility of the PlexSeq platform also enables continual revision and upgrading of the marker system, ensuring the technology keeps pace with current breeding and production needs.

For the full white paper and list of References, click here.

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