engleski

Genome-Wide Association Studies of Mineral Content in Common Bean Landraces

Common bean (Phaseolus vulgaris L.) is a species of great interest worldwide. It is grown in Europe, Asia and Africa, where it presents similarities to Andean and Mesoamerican domestication centers or forms hybrids between both genepools [1]. In Croatia the production is based on landraces which display high levels of diversity and are important reservoirs of natural genetic variations [2]. On the basis of results of our research, 135 out of 174 accessions were assigned to 14 morpho-genetic groups originating from distinct domestication events: (1) Mesoamerican ('Trešnjevac', 'Tetovac', 'Kukuruzar', 'Biser'), (2) Andean - indeterminate type ('Sivi', 'Puter', 'Maslina', 'Dan i noć', 'Visoki Trešnjevac'), and (3) Andean - determinate type ('Niski Trešnjevac', 'Dan i noć', 'Puter', Bijeli', 'Zelenčec'). The rest of the accessions could represent putative hybrids among morpho-genetic groups including the hybrids among the gene pools. Common bean is one of the most beneficial crop species while in diet it provides macro- and micronutrients. However, there is a substantial variability present in seed mineral content among genotypes. As reported by Palčić et al. (2018) [3] among investigated Croatian common bean landraces the highest nitrogen (N) content in seed dry weight was in 'Visoki Trešnjevac' (3.92%) while the lowest was in 'Zelenčec' (3.13%). Moreover, average N content of indeterminate types was significantly higher compared to determinate types. Phosphorus (P) values varied from 0.49% ('Puter') to 0.57% ('Biser') where determined P content in landraces of Andean gene pool was significantly lower compared to landraces of Mesoamerican gene pool. Significantly lower seed potassium content was determined in 'Niski Trešnjevac' (1.42%) and 'Zelenčec' (1.38%). Calcium content in all studied landraces varied from 0.34 ('Kukuruzar') to 0.42% ('Biser'), with no significant differences among the researched landraces. Also, there were no significant differences in magnesium content among landraces. Magnesium content varied from 0.17 to 0.2% ('Puter'), with the average of 0.18% ('Biser'). Concerning the investigated micronutrients content, we can conclude that the highest iron content was found in landrace 'Niski Trešnjevac' while the lowest was in 'Kukuruzar'. 'Kukuruzar' also had the lowest value of manganese (Mn) content (15.19 mg kg-1) and zinc (Zn) content (24.98 mg kg-1) while the highest Mn content was in 'Biser' (19.94 mg kg-1) whereas the highest Zn content was determined in 'Visoki Trešnjevac' landrace (27.84 mg kg-1). Genotyping was carried out using microsatellite and DArTseq-based SNP markers to be used in genome-wide association study (GWAS). Linkage disequilibrium (LD) based GWAS has gained popularity particularly for screening a great number of accessions and to associate markers with desired traits in crops [4]. The unified mixed-model approach [5] allows the correction for population structure and family relatedness in order to remove false positives. Mixed model Q matrix was based on population structure obtained by model-based clustering method [6], while K matrix was constructed by calculating Loiselle's kinship coefficients [7] in SPAGeDi [8]. Genome-wide scan for association between markers and nutrient content was performed using single marker approach as implemented in TASSEL [9] as well as multi-locus approach implemented in R package “mlmm” [10].

GWAS, landraces, minerals, Phaseolus vulgaris L., SNPs

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