Genetic Diversity and Population Structure of <i>Didymella</i> <i>rabiei</i> Affecting Chickpea in Ethiopia

Ascochyta blight, also known as chickpea blight, which is caused by the fungal pathogen, <i>Didymella</i> <i>rabiei</i>, is an important disease affecting chickpea (<i>Cicer arietinum</i> L.) in many countries. We studied the genetic diversity and population structure of 96 <i>D.</i> <i>rabiei</i> isolates collected from three geographic populations in Ethiopia using simple sequence repeat (SSR) markers. We confirmed the genetic identity of 89 of the <i>D. rabiei</i> isolates by sequencing their rRNA internal transcribed spacer region genes. The chickpea blight pathogen isolates were genetically diverse, with a total of 51 alleles identified across 6 polymorphic SSR loci, which varied from 3 to 18 (average 8.5) alleles per SSR marker. The observed heterozygosity and expected heterozygosity ranged from 0.01 to 0.92 and 0.19 to 0.86, respectively. The mean polymorphic information content value of the <i>D. rabiei</i> populations was 0.58, with a mean gene diversity of 0.61 among loci. Gene flow (Nm = number of migrants) for the three populations of <i>D. rabiei</i> isolates ranged from 1.51 to 24.10 (average 6.2) migrants/cluster. However, the genetic variation between the <i>D. rabiei</i> populations was small (8%), with most of the variation occurring within populations (92%). Principal component analysis to visualize genetic variation showed that the <i>D. rabiei</i> isolates obtained from most of the chickpea samples formed roughly three groups on a two-dimensional coordinate plane. Similarly, the clustering of individuals into populations based on multi-locus genotypes (using Clumpak) grouped isolates into three clusters but with individual isolate admixtures. Hence, no clear geographic origin-based structuring of populations could be identified. To our knowledge, this is the first report of <i>D. rabiei</i> diversity in Ethiopia. Virulence studies should be conducted to develop chickpea varieties that are resistant to more aggressive pathogen populations.