Development of a minimal KASP marker panel for distinguishing genotypes in apple collections

Abstract

Accurate identification of named accessions in germplasm collections is extremely important, especially for vegetatively propagated crops which are expensive to maintain. Thus, an inexpensive, reliable, and rapid genotyping method is essential because it avoids the need for laborious and time-consuming morphological comparisons. Single Nucleotide Polymorphism (SNP) marker panels containing large numbers of SNPs have been developed for many crop species, but such panels are much too large for basic cultivar identification. Here, we have identified a minimum set of SNP markers sufficient to distinguish apple cultivars held in the English and Welsh national collections providing a cheaper and automatable alternative to the markers currently used by the community. We show that SNP genotyping with a small set of well selected markers is equally efficient as microsatellites for the identification of apple cultivars and has the added advantage of automation and reduced cost when screening large numbers of samples.

Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species

“…Previous studies 23 , 63 , 64 recommended two or three SNPs per chromosome and a minimum of 20–25 KASP markers to serve as diagnostic markers to distinguish genotypes in germplasm collections; we have worked to follow these guidelines. However, only one SNP per chromosome was retained for each of the group-specific G1, G4, G5 and G6.…”

“…The cost of KASP genotyping services is reasonable for CGIAR Centers and national agricultural research systems (NARS) in developing countries, which have agreements with KASP genotyping service providers. The cost per sample is reduced with higher numbers of data points generated, and service includes both DNA extraction and SNP genotyping 5 , 63 . The use of this service will help the AfricaRice genebank team and other genebanks to correct/update traditional passport data of their germplasm collections focusing on the four species ( O. barthii , O. glaberrima , O. longistaminata , and O. sativa spp.…”

Development of a Next Generation SNP Genotyping Array for Wheat

“…Additionally, SNPs were checked by BLAST (blastn v2.6.0+) against the IWGSC v1.0 Chinese Spring genome assembly and those matching multiple locations were excluded. Each chromosome was then divided into 1.5 Mb intervals and up to six SNPs representing the highest combined discriminatory power were selected for each interval (Winfield et al ., 2020). The haplotype optimisation pipeline is available at https://github.com/pr0kary0te/GenomeWideSNP-development.…”

Harnessing Landrace Diversity Empowers Wheat Breeding for Climate Resilience

“…Up to six of the highest ranked SNPs were assigned to each bin. This approach has been described previously for the selection of a minimal set of SNP markers capable of discriminating apple varieties 82 , where the SNP with the highest varietal discrimination is chosen initially, and further SNPs are selected to add the 51 maximum additional discrimination until either all varieties are discriminated, the addition of more SNPs does not improve discrimination, or all available SNPs have been evaluated. SNPs designed with this approach were supplemented with 1974 DaRTseq markers (supplied by Susanne Dreisigacker, CIMMYT) and 6388 markers from the existing Wheat Breeder's Axiom array 58 for cross-compatibility of results and to infill some spaces that became available on the array late in the design process.…”