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. 2024 Aug 9;15(8):1047.
doi: 10.3390/genes15081047.

A Public Mid-Density Genotyping Platform for Hexaploid Sweetpotato (Ipomoea batatas [L.] Lam)

Dongyan Zhao  1 , Alexander M Sandercock  1 , Maria Katherine Mejia-Guerra  1 , Marcelo Mollinari  2 , Kasia Heller-Uszynska  3 , Phillip A Wadl  4 , Seymour A Webster  5 , Craig T Beil  1 , Moira J Sheehan  1
Affiliations

A Public Mid-Density Genotyping Platform for Hexaploid Sweetpotato (Ipomoea batatas [L.] Lam)

Dongyan Zhao et al. Genes (Basel). .

Abstract

Small public breeding programs focused on specialty crops have many barriers to adopting technology, particularly creating and using genetic marker panels for genomic-based decisions in selection. Here, we report the creation of a DArTag panel of 3120 loci distributed across the sweetpotato (Ipomoea batatas [L.] Lam) genome for molecular-marker-assisted breeding and genomic prediction. The creation of this marker panel has the potential to bring cost-effective and rapid genotyping capabilities to sweetpotato breeding programs worldwide. The open access provided by this platform will allow the genetic datasets generated on the marker panel to be compared and joined across projects, institutions, and countries. This genotyping resource has the power to make routine genotyping a reality for any breeder of sweetpotato.

Keywords: DArTag genotyping; amplicon-sequencing; microhaplotype; plant breeding; sweetpotato.

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Conflict of interest statement

The authors declare no conflicts of interest. There are no financial or non-financial conflicts of interest due to or resulting from collaboration with DArT, K.H.U., or DArT employes. Breeding Insight purchased services from DArT, and although the DArTag platform is proprietary to DArT, DArT will work with anyone interested in their services.

Figures

Figure 1
Figure 1
Selection of the 3120 SNPs that comprise the 3K DArTag panel. (A) The SNP filters and criteria applied to select the 3K DArTag panel from the WGS of a sweetpotato diversity panel. Abbreviations: M is millions, K is thousands. (B) The distribution of the 3120 DArTag panel SNPs across the sweetpotato physical genome.
Figure 2
Figure 2
DArTag sequencing reads from locus Chr01_000084128. Each sequence is a microhaplotype detected in breeding material tested on the panel. The DArTag assay was designed to detect the target locus (box) and distinguish the Reference allele from the Alternative allele. Additional variant nucleotide positions (yellow fill) distinguish the individual microhaplotypes. An indel is indicated by “-” at the genomic position (orange fill). The top row refers to the physical nucleotide position within the genome on chromosome 1.
Figure 3
Figure 3
Assessment of a mid-density DArTag genotyping panel for sweetpotato using a diverse population and three bi-parental populations. (A) Plot of the first two principal components. (B) Plot of principal components 1 and 3. Each point represents an individual, colorized by germplasm passport information. The three bi-parental populations mostly cluster together, demonstrating the relatedness of individuals within these groups. However, there are some exceptions where individuals from these populations spread into the area primarily occupied by the diverse population. These patterns support the expected clustering of related individuals and scattering of unrelated ones.
Figure 4
Figure 4
Genetic map of bi-parental reciprocal cross populations between ‘Beauregard’ and ‘Regal’. (A) Regeneration of the 15 linkage groups of the sweetpotato genome. The scale bar shown is in centiMorgans (cM). (B) Relationship plots of genetic distance (cM) to I. t. reference genome physical distance (Mbp) for each of the 15 linkage groups.
See this image and copyright information in PMC

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