Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs

Abstract

Quality assurance and control (QA/QC) is an essential element of a breeding program's optimization efforts towards increased genetic gains. Due to auto-hexaploid genome complexity, a low-cost marker platform for routine QA/QC in sweetpotato breeding programs is still unavailable. We used 662 parents of the International Potato Center (CIP)'s global breeding program spanning Peru, Uganda, Mozambique and Ghana, to develop a low-density highly informative single nucleotide polymorphism (SNP) marker set to be deployed for routine QA/QC. Segregation of the selected 30 SNPs (two SNPs per base chromosome) in a recombined breeding population was evaluated using 282 progeny from some of the parents above. The progeny were replicated from in-vitro, screenhouse and field, and the selected SNP-set was confirmed to identify relatively similar mislabeling error rates as a high density SNP-set of 10,159 markers. Six additional trait-specific markers were added to the selected SNP set from previous quantitative trait loci mapping studies. The 36-SNP set will be deployed for QA/QC in breeding pipelines and in fingerprinting of advanced clones or released varieties to monitor genetic gains in famers' fields. The study also enabled evaluation of CIP's global breeding population structure and the effect of some of the most devastating stresses like sweetpotato virus disease on genetic variation management. These results will inform future deployment of genomic selection in sweetpotato.

Novel sources of drought tolerance from landraces and wild sorghum relatives

“…The SNP marker set developed here for QC will enhance germplasm characterization, parentage verification, and confirmation of purity of genotypes. However, these markers will need to be developed into quick assays as has been done in other crops (Chen et al, 2016;Ertiro et al, 2015;Gemenet et al, 2020;Ndjiondjop et al, 2018) for more efficient application.…”

Genetic Characterization of Global Cultivated Potato Clones, Including Korean Potatoes, Using Genome-Wide Single Nucleotide Polymorphism Markers

“…Regarding the approaches employed in this study to reveal the genetic diversity and population structure of cultivated potatoes, dosage genotype calls could lead to more reasonable and accurate results than diploid genotype calls (Table 1). If no packages that support polyploid data are available, biallelic markers could be called in a diploidized version which means that the three heterozygous classes expected in potato were converted into one heterozygous class [17,22]. The use of appropriate methods for integrating different sources of SNP data could result in biologically meaningful outcomes, because previously, we recognized "strange" outcomes when we simply merged the publicly available genotype datasets (data not shown).…”

“…Characterizing germplasm identity and purity is an essential component of breeding and germplasm management [16]. Recently, SNP quality assurance and control genotyping methods based on low-density SNPs have been investigated in maize [16] and sweetpotato [17]. In sweetpotato, a 30 SNP-set with uniform distribution across chromosomes was selected to identify relatively similar mislabeling error rates as a high density SNP-set of 10,159 markers, while a minimum of 80 selected SNP markers was employed to distinguish each of the CIMMYT maize inbred lines (CMLs) entries from one another.…”

Kompetitive Allele Specific PCR (KASP) Markers for Potato: An Effective Tool for Increased Genetic Gains

“…Markers with a minor allele frequency (MAF) < 0.2 were separately removed from both populations, and only the 1523 markers in both populations were considered for further steps. Low sequencing depth in next-generation sequencing methods can lead to an overestimation of homozygous calls and, therefore, to an underestimation of heterozygosity, in addition to genotyping errors and frequently missed data that, in turn, can lead to biases in subsequent population genetic analyses [3,[45][46][47]. Therefore, for further analyses, the markers were reduced to their diploid form (AAAA = AA, BBBB = BB, heterozygous (AAAB, AABB, and ABBB) = AB) to reduce heterozygous dosage bias.…”

“…Therefore, quality control (QC) analysis is essential to ensure the traceability and identification of clones at key stages during the breeding process (e.g., identity control and hybrid purity), during conservation in the germplasm bank, and when sharing breeding materials. QC analysis refers to the process of identifying the mistakes or errors in the quality of breeding lines, germplasm accession, variety, or any other products throughout the breeding pipeline [3].…”