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

Abstract

<jats:title>Abstract</jats:title><jats:p>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 <jats:italic>in-vitro</jats:italic>, 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. 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 biotic stresses like sweetpotato virus disease on genetic variation management. These results will inform future deployment of genomic selection in sweetpotato.</jats:p><jats:sec><jats:title>Key Message</jats:title><jats:p>A 36-SNP diagnostic marker set has been developed for quality assurance and control to support global sweetpotato breeding optimization efforts. Breeding population structure is shaped by sweetpotato virus disease prevalence.</jats:p></jats:sec>

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.…”

Identification of diagnostic KASP‐SNP markers for routine breeding activities in yam (Dioscorea spp.)

“…Routine breeding activities (assessment of genetic diversity or identification of mislabeled genotypes, pedigree verification, variety tracking, so on), also known as quality control (QC) in crop breeding leveraging molecular breeding tools, have been employed as a routine practice in many breeding and seed programs to harness genetic gain and delivery of quality products to the end users. These practices have been developed and deployed in several crops, including maize (Zea mays L.) (Chen et al, 2016;Gowda et al, 2017;Semagn et al, 2012), rice (Oryza sativa) (Ndjiondjop et al, 2018), sweetpotato (Ipomoea batatas (L.) Lam) (Gemenet et al, 2020), cowpea (Vigna unguiculata (L.) Walp. ; Ongom et al, 2021), and soybean (Glycine max; Chander et al, 2021).…”