Whole Genome Diversity, Population Structure, and Linkage Disequilibrium Analysis of Chickpea (Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers.

Characterization of genetic diversity, population structure, and linkage disequilibrium is a prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes, including advanced "Kabuli" breeding lines and Iranian landrace "Desi" chickpea genotypes, were genotyped using DArTseq-Based single nucleotide polymorphism (SNP) markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that was covered by SNPs varied from 16,236.36 kbp (LG8) to 67,923.99 kbp (LG5), while LG4 showed a higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6, and LG8 showed higher mean PIC value than average. Unweighted neighbor joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and discriminant analysis of principal component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r2 ≥ 0.8, while 2961 pairs of markers showed complete LD (r2 = 1), and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggest the presence of a high genetic diversity among the studied chickpea genotypes. This study also demonstrates the efficiency of DArTseq-based SNP genotyping for large-scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits, such as seed yield, abiotic, and biotic stresses, and therefore can be efficiently used in breeding programs to improve chickpea.

Pathogenic Diversity of Ascochyta rabiei Isolates and Identification of Resistance Sources in Core Collection of Chickpea Germplasm.

Ascochyta blight caused by Ascochyta rabiei (Pass.) Lab. (Telomorph: Didymella rabiei) (Kov.) is one of the most important fungal diseases in chickpea worldwide. Knowledge about pathogen aggressiveness and identification resistance sources to different pathotypes is very useful for proper decisions in breeding programs. In this study, virulence of 32 A. rabiei isolates from different part of Iran were analyzed on seven chickpea differentials and grouped into six races based on 0-9 rating scale and susceptibility/resistant pattern of chickpea differentials. The least and most frequent races were race V and race I, respectively. Race V and VI showed highly virulence on most of differential, while race I showed least aggressiveness. Resistance pattern of 165 chickpea genotypes also were tested against six different A. rabiei races. ANOVA analysis showed high significant difference for isolate, chickpea genotypes and their interactions. Overall chickpea × isolate (race) interactions, 259 resistance responses (disease severity ≤ 4) were identified. Resistance spectra of chickpea genotypes showed more resistance rate to race I (49.70%) and race III (35.15%), while there were no resistance genotypes to race VI. Cluster analysis based on disease severity rate, grouped chickpea genotypes into four distinct clusters. Interactions between isolates or races used in this study, showed the lack of a genotype with complete resistance. Our finding for virulence pattern of A. rabiei and newly identified resistance sources could be considerably important for integration of ascochyta blight resistance genes into chickpea breeding programs and proper decision in future for germplasm conservation and diseases management.

Natural Occurrence of Tomato leaf curl New Delhi virus in Iranian Cucurbit Crops.

The main areas for field-grown vegetable production in Iran were surveyed during the years of 2012-2014 to determine the occurrence of begomoviruses infecting these crops. A total of 787 leaf samples were collected from vegetables and some other host plants showing virus-like symptoms and tested by an enzyme-linked immunosorbent assay (ELISA) using polyclonal antibodies produced against Tomato yellow leaf curl virus (TYLCV). According to the ELISA results, 81 samples (10.3%) positively reacted with the virus antibodies. Begomovirus infections were confirmed by polymerase chain reaction (PCR) using previously described TYLCV-specific primer pair TYLCV-Sar/TYLCV-Isr or universal primer pair Begomo-F/Begomo-R. The PCR tests using the primer pair TYLCV-Sar/TYLCV-Isr resulted in the amplification of the expected fragments of ca. 0.67-kb in size for ELISA-positive samples tested from alfalfa, pepper, spinach and tomato plants, confirming the presence of TYLCV. For one melon sample, having a week reaction in ELISA and no reaction in PCR using TYLCV-specific primers, the PCR reaction using the primer pair Begomo-F/Begomo-R resulted in the amplification fragments of the expected size of ca. 2.8 kb. The nucleotide sequences of the DNA amplicons derived from the isolate, Kz-Me198, were determined and compared with other sequences available in GenBank. BLASTN analysis confirmed the begomovirus infection of the sample and showed 99% identities with Tomato leaf curl New Delhi virus (ToLCNDV); phylogenetic analysis supported the results of the database searches. This study reports the natural occurrence of TYLCV in different hosts in Iran. Our results also reveal the emergence of ToLCNDV in Iranian cucurbit crops.

Evidence for presence of types A and B of beet necrotic yellow vein virus (BNYVV) in Iran.

Rhizomania a viral disease, caused by beet necrotic yellow vein benyvirus (BNYVV), is now widely spread, throughout the sugar beet growing areas of Iran. Genomes of BNYVV are composed of five RNA molecules with specific functions. In this study sequence analyses were conducted on the major coat protein gene (CP21), and parts of RNA3 and RNA4 of an Iranian strain of BNYVV from the Fars province. Sequence alignments of Iran Fars CP21 with other isolates showed closed similarities at nucleotide and amino acid levels with BNYVV pathotype A isolates; S from Japan, and YU2 from Yugoslavia. These results suggest that Iran-Fars isolate probably originated from Asia or neighboring European countries rather than from Germany or France.