Development of molecular inversion probes for soybean progeny genomic selection genotyping

Abstract

Increasing rate of genetic gain for key agronomic traits through genomic selection requires the development of new molecular methods to run genome‐wide single‐nucleotide polymorphisms (SNPs). The main limitation of current methods is the cost is too high to screen breeding populations. Molecular inversion probes (MIPs) are a targeted genotyping‐by‐sequencing (GBS) method that could be used for soybean [Glycine max (L.) Merr.] that is both cost‐effective, high‐throughput, and provides high data quality to screen breeder's germplasm for genomic selection. A 1K MIP SNP set was developed for soybean with uniformly distributed markers across the genome. The SNPs were selected to maximize the number of informative markers in germplasm being tested in soybean breeding programs located in the northern‐central and middle‐southern regions of the United States. The 1K SNP MIP set was tested on diverse germplasm and a recombinant inbred line (RIL) population. Targeted sequencing with MIPs obtained an 85% enrichment for the targeted SNPs. The MIP genotyping accuracy was 93% overall, whereas homozygous call accuracy was 98% with <10% missing data. The accuracy of MIPs combined with its low per‐sample cost makes it a powerful tool to enable genomic selection within soybean breeding programs.

A medium‐density genotyping platform for cultivated strawberry using DArTag technology

“…The ability to reevaluate the same loci with high read coverage also reduces the need for imputation and supports comparisons of samples across marker datasets. Another benefit of this technology lies in its modularity: Users may add or exchange probe designs to fit their needs, making it possible to produce future iterations of the existing DArTag panels that better represent their own core germplasm diversity, or add specific probes at predictive loci (e.g., R‐genes) to perform MAS and genomic prediction with a single platform (Wang et al., 2023). We were able to identify candidate SNPs supporting designs with high probabilities of subgenome‐specific probe targeting across most of the FaRR1 physical genome landscape, demonstrating the abundance of targets that can be assayed with the technology (Figure 5; Figure S4).…”

“…In addition to high concordance between alignment‐based genotypes and WGS genomic variant genotypes, we found that the mid‐density 3K and 5K DArTag panels produce highly similar kinship estimates to those produced using the 50K SNP array markers. Accurate kinship estimates should support correspondingly high accuracy for predicting genomic breeding values (Habier et al., 2009; Wang et al., 2023). Beyond genotype calling accuracy, the 3K and 5K DArTag panels target SNPs that reflect significant genetic diversity across a range of domesticated strawberry germplasm and should therefore be useful for genomic prediction and forensic identification in most breeding populations.…”

“…The growing molecular breeding toolbox for strawberry has nevertheless needed cost-effective high-throughput marker genotyping solutions to enable genomic selection and routine forensic identification of individuals and parents on a large scale (Gezan et al, 2017;Jiménez et al, 2023;Osorio et al, 2021;Pincot et al, 2020Pincot et al, , 2021Whitaker et al, 2020). MIP-like technologies offer the advantages of high sample throughput and the ability to sequence target amplicon regions at a high read depth, reducing the likelihood of missing genotypes or genotyping errors at heterozygous sites (Wang et al, 2023). The ability to reevaluate the same loci with high read coverage also reduces the need for imputation and supports comparisons of samples across marker datasets.…”

“…Accurate kinship estimates should support correspondingly high accuracy for predicting genomic breeding values (Habier et al, 2009;Wang et al, 2023). Beyond genotype calling accuracy, the 3K and 5K DArTag panels target SNPs that reflect significant genetic diversity across a range of domesticated strawberry germplasm and should therefore be useful for genomic prediction and forensic identification in most breeding populations.…”

“…Current high‐density marker platforms such as SNP arrays are too costly for many public breeding programs to use for genotyping populations containing hundreds to thousands of individuals, posing a barrier to the introduction of genomic selection into the annual breeding cycle. The availability of low‐cost, high‐throughput, and mid‐density genetic marker screening platforms may assist in the adoption of genomic prediction and selection in polyploid specialty crop systems including strawberry (Ariza‐Suarez et al., 2022; Cerioli et al., 2022; Oh et al., 2019; Raman et al., 2022; Semalaiyappan et al., 2023; Wang et al., 2018, 2023). We developed and tested a panel of molecular inversion probe (MIP) marker assays to deploy with the “DArTag” genotyping service offered by Diversity Arrays Technology Ltd. (DArT; Canberra, Australia) in order to provide a low‐cost, mid‐density marker genotyping solution suitable for genomic prediction in strawberry.…”