STRUCTURE is a software package that uses molecular data from multiple loci to analyze population structure. To analyze Single Nucleotide Polymorphism (SNP) data using STRUCTURE, a specific input file format is required. However, because SNP studies often involve thousands of loci, these input files are typically too large to edit manually. To address this challenge, several software tools and functions have been developed. However, in the case of plant data, some of these tools either fail to process the data correctly or generate inaccurate input files. To overcome these issues, a new software tool - SNP2STR - has been developed. SNP2STR converts SNP data into the input format required by Structure. It generates a file with an optional first row containing marker names, followed by two rows of data per individual, formatted according to the corresponding markers. The software is open-source and available on GitHub. It also offers potential for future upgrades based on user feedback.

This study aimed to examine the genetic variability of tartary buckwheat populations (Fagopyrum tataricum (L.) Gaertn.) from Bosnia and Herzegovina. Sampling was performed on a total of 25 samples with 5 samples from each population. Collected samples were lyophilized and afterward, DNA extraction was conducted using a peqGOLD plant DNA kit. A total of ten primers were used for DNA amplification, where seven primers pairs resulted in successful amplification. The results showed that polymorphisms were detected on all of the analyzed loci. Also, significant genetic differences between populations of tartary buckwheat from different production regions of this agricultural species have been proven.

This study aimed to analyze the genetic diversity of common bean (Phaseolus vulagris L.) landraces from the existing collection maintained at the Gene-bank of the Faculty of Agriculture and Food Sciences, University of Sarajevo using microsatellite markers (SSR). A total of 21 accessions of common bean were genotyped using ten SSR markers. The obtained molecular data was analyzed using genetic structure and factorial correspondence analyses. The examined accessions of common bean were not completely structured in accordance to the gene center of origin, which indicates that during the long cultivation period of common bean in Bosnia and Herzegovina (B&H), spontaneous crosses occurred between Mesoamerican and Andean common bean genotypes. The results of analyses confirmed that this was a heterogeneous and very interesting genetic material.

A genome-wide association study on resistance to the phytopathogenic fungus V. inaequalis was conducted on traditional Bosnian-Herzegovinian apple cultivars. Since the software for conducting GWAS, PLINK ver. 1.9, is adapted to work with diploids, it was necessary to identify and remove triploid varieties beforehand. Triploid identification was performed using axiomFP.py ver. 1.2 software, revealing that 20% of the examined collection were triploids. Based on the ploidy analysis, leaf samples from 35 diploid varieties were collected from the ex situ collection in Goražde (Bosnia and Herzegovina) for further research. The disease intensity was then determined by classifying the leaves into six categories (1-6) using the SAD. By calculating McKinney's disease index, a variation was observed, ranging from 27.2% ('Senabija') to 61.1% ('Crvenka'), indicating differences in variety resistance. After isolating and reisolating the pathogen and examining its morphological characteristics, V. inaequalis was identified, and its presence in the mentioned orchard was confirmed. GWAS revealed strong signals on chromosomes 04, 05, and 16 for resistance to this pathogen, using high- resolution SNP markers. This study offers insights into the genetic basis of resistance in traditional apple germplasm from Bosnia and Herzegovina to the phytopathogenic fungus V. inaequalis, the causal agent of apple scab, highlighting the need for further research to develop varieties that are more resistant to this pathogen.

axiomFP.py is an open-source software developed to diagnose ploidy level and call quality for samples genotyped on Affymetrix Axiom SNP arrays by making frequency plots of normalized SNP call positions among SNPs meeting specific clustering parameters. This research outlines the methods employed in the development of the software, and presents the results obtained through its application on a dataset of mixed ploidy apple (Malus spp.) cultivars and germplasm accessions. The tools required to prepare the input files and operate the software are also described. The frequency plots generated by the software require a visual inspection to assess ploidy and call quality. The results have been validated using the available ploidy data, as well as flow cytometry, and have shown complete accuracy. The software is available on GitHub at https://github.com/allmiraria/axiomFP.

In the Croatian apple germplasm, there are, presumably, unique genotypes that have not yet been documented in reference molecular databases. Due to similarities between accessions, incorrect names are often used, which creates a problem in the identification of accessions. Overall, 169 apple accessions and 11 reference cultivars from the largest ex situ apple collection in the Republic of Croatia were investigated within this study. The examined accessions have been genotyped using SSR markers. In order to assess the advantage of a high-resolution marker system, such as SNPs, compared to low-resolution markers, such as SSRs, a subset of 23 unique apple accessions and eight reference cultivars were genotyped using the 480K Affymetrix Axiom SNP array. Results obtained through the use of two marker systems revealed 26 synonyms, 40 duplicates, 13 mislabeling accessions, 45 accessions with confirmed identity (known cultivars), and 45 unique accessions, as well as the true identity of a large number of accessions, currently maintained at the Croatian National Apple Germplasm Bank. In order to investigate the pomological variability of unique apples, a three-year study was carried out on eleven pomological traits. The researched germplasm shows an exceptional diversity of pomological properties. Many of the accessions can be considered unique, and the results of the pomological characterization indicated that this germplasm contains valuable traits of interest for future breeding programs.

The cultivated apple (Malus domestica Borkh.) is an economically important fruit crop in countries worldwide, including Bosnia and Herzegovina (BIH).The gene bank activities in BIH were initiated in the 1930s and continued until the war in the 1990s, when much of the documentation was lost. Since then, uncoordinated efforts were made to establish apple collections in different regions, but a comprehensive analysis of genetic resources was lacking. This prompted the current study where we present the first thorough overview of the national genetic resources of BIH apples. Thus, we analyzed 165 accessions in the apple gene bank at the Institute for Genetic Resources (IGR) established at Banja Luka using the 20 K apple Infinium® single nucleotide polymorphism (SNP) array. We combined the results with previously published data on the germplasm collections at Srebrenik and Goražde, genotyped using the Axiom® Apple 480 K SNP array. In total, 234 accessions were included in the study of which 220 were presumed to be local cultivars and 14 were known international reference cultivars. We identified numerous genotypic duplicates within and between collections and suggested preferred names to be used in the future. We found the BIH germplasm to have relatively few parent-offspring relationships, particularly among local cultivars, which might reflect the country’s history and patterns of apple cultivar introduction. A number of cultivars unique to BIH and a weakly defined genetic group were identified via STRUCTURE analysis, representing interesting targets for future research and preservation efforts.

The main morphological and genetic characterization of seven introduced almond cultivars in Bosnia & Herzegovina was conducted. The almond cultivars included three from Italy (Tuono, Genco, Supernova), two from France (Ferragnes and Ferraduel), and two from the USA (Texas and Nonpareil). Genetic characterization was utilized by using 10 microsatellite markers, with nine markers from Prunus persicae and one from Prunus armeniaca. The results of genetic characterization revealed an average of 5.40 alleles per primer per locus. The average number of effective alleles for the 10 SSR loci of introduced cultivars was 3.92. The Shannon Information Index averaged 1.41. The observed heterozygosity (Ho) and expected heterozygosity (He) averaged 0.53 and 0.69, respectively. Morphological analyses of the fruit of introduced almond cultivars in Bosnia & Herzegovina indicated favorable agroecological conditions for their cultivation and spread. The results suggest that these introduced almond cultivars could be utilized in breeding programs to enhance the genetic diversity of the local almond population in Bosnia & Herzegovina.

In order to ensure the long-term sustainability of the conservation process of Norwegian plum germplasm, as well as to enhance the possibility of its utilization, a central plum heritage cultivar collection was established in 2020. In this study, 40 plum accessions maintained at the Ullensvang plum heritage cultivar collection were genetically characterized using a set of nine microsatellite markers recently approved by the ECPGR Prunus working group. The obtained molecular data were used to investigate the genetic identity, diversity, and structure among the analyzed accessions. No redundancies were detected among the plum accessions, which is in stark contrast to the previous molecular study on plum samples collected through an on-farm inventory of Southern Norway. Furthermore, the obtained data indicate that the Ullensvang collection contains a significant genetic diversity of Norwegian plum germplasm, previously held in decentralized sites. With that in mind, this collection can certainly be considered for the role of the National Clonal Plum Germplasm Repository. The nine microsatellite markers, recommended by ECPGR, revealed a genetic structure not entirely tied to previously proposed pomological groups, possibly indicating a history of hybridization among members of the various groups.