On-farm Evolution of Genetic Diversity of Four Old Varieties of Phaseolus vulgaris L.

On-farm evolution of crop genetic diversity has a key role in adaptation of agricultural systems to changes. The aim of this work was to understand how four different old common bean varieties, which being made of different genotypes can be referred to as populations, evolved on-farm during three years of multiplication (from 2012 to 2014) in two different experimental sites (Brittany and Luxembourg) under organic farming conditions. The four populations (Flageolet Chevrier Vert, Rognon de Coq, Roi des Belges, Saint Esprit à Œil Rouge) were chosen among those grown by two small-scale organic seed farmers while the commercial variety (Calima) was included as control. In 2015 the initial and the evolved populations were grown in a common field and characterized with morpho-phenological traits. In the same year, young leaf tissues were collected from 94 samples per population (total of 470 samples) for DNA extraction and molecular characterization. Genotyping was carried out using 22 SSR loci and fluorescent PCR amplicons analysed on an ABI3130xl sequencer. Molecular data were then used for multivariate analysis, analysis of molecular variance and pair-wise Fst statistics calculation.
Genotyping resulted in the production of about 20K data points. A total of 83 different alleles were identified in 16 polymorphic loci ranging from two (BMb293, BM156, BMd-44) to 18 (BMd-43). The first two axis of the Principal Coordinates analysis (PCoA) explained 76,13% of total diversity and clearly distinguished the five groups of populations. Analysis of Molecular Variance (AMOVA) showed that 76, 20 and 4% of total diversity is among populations, individuals and within individuals, respectively. Only for multiplications carried out in Luxemburg significant differentiation between the original populations and final populations were found in two old varieties (Flageolet Chevrier Vert and Rognon de Coq, Fst = 0.117 and 0.143, respectively, P≤0.001). The results showed that in Luxemburg farmer practices and pedo-climatic conditions significantly shaped the diversity of the two populations. This is confirmed by phenotypic observations, as these multiplications also significantly differed (p<0.05) for flowering date for all varieties except 'Roi des Belges'.