Genotyping by Sequencing (GBS) in Apricots and Genetic Diversity Assessment with GBS-Derived Single-Nucleotide Polymorphisms (SNPs)

Abstract

Genotyping by sequencing (GBS), which is a highly promising technique for molecular breeding, has been implemented in apricots, including Turkish, European, and Plum Pox Virus-resistant accessions. DNA samples were digested with the ApeKI restriction enzyme to construct a genome-complexity-reduced 90-plex GBS library. After filtering the raw sequences, approximately 28 G of clean data were generated, and 17,842 high-quality single-nucleotide polymorphism (SNP) loci were discovered. A total of 561 SNP loci with 0 or 1 missing reads for the 90 accessions produced 1162 markers that were used for the cluster and population structure analysis of the same collection. The results of the SNP analysis indicated that the relation of the European accessions with the western Turkish apricots was accurately positioned. The resistant accessions from different sources were clustered together, confirming the previous finding that SEO/Harlayne-type resistance probably originated from the same source. The Malatya accessions produce most of the world's dried apricots and are likely to be a genetically distinct group. Simple sequence repeat (SSR) and self-incompatibly (SI) locus characterization of the accessions was also included. SI genotyping supported the SNP findings, demonstrating both the reliability of SNP genotyping and the usefulness of SI genotyping for understanding the history of apricot breeding. The SSR genotyping revealed a characterization similar to that of SNP genotyping with a slightly lower resolution in the dendrogram. In conclusion, the GBS approach was validated in apricots, with the discovery of a large number of SNPs, and was demonstrated to be reliable by fingerprinting the accessions in a more informative manner.

Genotyping by Sequencing in Almond: SNP Discovery, Linkage Mapping, and Marker Design

“…The mean number of sequence reads per sample that was obtained here (2.1 million) is similar to what has been reported for other Prunus species: 1.8 million for sweet cherry ( Guajardo et al 2015 ), 2.4 million for peach ( Bielenberg et al 2015 ), 2.3 million for Japanese plum ( Salazar et al 2017 ), and 3.5 million for apricot ( Gürcan et al 2016 ). Of the sequences generated, 68% were anchored to unique positions in the peach genome sequence assembly.…”

“…To select a restriction enzyme that might be suitable for digestion of the almond genome, in silico restriction of the peach whole genome sequence assembly v1.0 ( www.rosaceae.org ) was conducted using Biopython ( Cock et al 2009 ) for each of three methylation-sensitive restriction enzymes: Ape KI, Pst I, and Hpa II. The enzyme Ape KI, which has been used in GBS for other plants ( Elshire et al 2011 ; Lu et al 2013 ; Bielenberg et al 2015 ; Guajardo et al 2015 ; Kujur et al 2015 ; Gürcan et al 2016 ; Salazar et al 2017 ), was selected. Of the three enzymes, it was predicted to yield the highest number of fragments within the size range that is considered suitable for GBS (between 150 and 500 bp) (Table S3 in File S1 ).…”

“…This method has been applied in many plant species, including peach ( Bielenberg et al 2015 ), sweet cherry ( P. avium L.) ( Guajardo et al 2015 ), Japanese plum ( P. salicina Lindl.) ( Salazar et al 2017 ), and apricot ( P. armeniaca L.) ( Gürcan et al 2016 ).…”

Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function

“…In Prunus species, single-digest GBS has been used for identification of a high number of SNPs for linkage maps construction [32][33][34][35] and analysis of population genetic structure [36][37][38] . The use of double-digest GBS in Prunus has not been reported as far as the authors know.…”

Genome-wide identification of single nucleotide polymorphisms (SNPs) and molecular characterization ofPrunusrootstock germplasm using a genotyping-by-sequencing (GBS) approach

“…Using the GBS methodology on genomic DNA from the 53 Prunus rootstocks and five scion cultivars, we developed the first whole-genome analysis considering members from three different subgenera (Amygdalus, Prunus and Cerasus) of the Prunus genus. SNPs identified from GBS have been previously used study the phylogenetic and population structure in apricot (Gürcan et al, 2016), using 90 accessions of different origins and DNA digestion using ApeKI restriction enzyme. In our case, a double-digest restriction enzyme protocol (PstI/MspI) was used to obtain a representation of the genome of each Prunus sample.…”