A QTL on the Ca7 chromosome of chickpea affects resistance to the root-lesion nematode Pratylenchus thornei.

The root-lesion nematode Pratylenchus thornei Sher & Allen, 1953 is a damaging parasite of many crop plants, including the grain legume chickpea (Cicer arietinum L.). Within cultivated chickpea, there are no known sources of strong resistance to P. thornei, but some cultivars have partial resistance. In the research reported here, the genetic basis for differences in P. thornei resistance was analysed using a population derived by accelerated single seed descent from a cross between a partially resistant cultivar, PBA HatTrick, and a very susceptible cultivar, Kyabra. A genetic linkage map was constructed from genotyping-by-sequencing data. Two quantitative trait loci were mapped, one on the Ca4 chromosome and one on the Ca7 chromosome. The Ca7 locus had a greater and more consistent effect than the Ca4 locus. Marker assays designed for single nucleotide polymorphisms on Ca7 were applied to a panel of chickpea accessions. Some of these markers should be useful for marker-assisted selection in chickpea breeding. Haplotype analysis confirmed the Iranian landrace ICC14903 to be the source of the resistance allele in PBA HatTrick and indicated that other Australian cultivars inherited the same allele from other Iranian landraces. A candidate region was defined on the Ca7 pseudomolecule. Within that region, 69 genes have been predicted with high confidence. Among these, two have annotations related to biotic stress response. Three others have previously been reported to be expressed in roots of PBA HatTrick and Kyabra, including one that is more highly expressed in PBA HatTrick than in Kyabra. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-021-01271-8.

Vertical Distribution of Pratylenchus spp. in Silt Loam Soil and Pacific Northwest Dryland Crops.

Dryland field crops in the Pacific Northwest United States are commonly produced in silt loams infested by the root-lesion nematodes Pratylenchus neglectus and P. thornei. Soils at 30 sites in Oregon were sampled from 0 to 120 cm depth to examine the vertical distribution of these Pratylenchus spp. Both species were distributed through entire soil profiles of all cropping systems. Populations were generally greatest in the surface 30 cm, but sometimes high populations were detected at depths greater than 45 cm. Sampling to 30 cm depth allowed detection of more than 50% of the population in most sites, while sampling to 45 cm depth yielded more than 75% of the population in over 75% of the sites evaluated. Therefore, soil samples should be collected to 30 to 45 cm depth to accurately estimate populations of Pratylenchus spp. in dryland crops produced on silt loams in the Pacific Northwest. Populations of Pratylenchus spp. were found to be related to the most recently planted crop, with populations after barley, after wheat, and during summer fallow being detected in ascending order.

Detection and Discrimination of Pratylenchus neglectus and P. thornei in DNA Extracts from Soil.

A species-specific polymerase chain reaction (PCR) method was developed to detect and identify the root-lesion nematodes Pratylenchus neglectus and P. thornei from soil. A primer set was designed from Pratylenchus 28S rRNA gene sequences of the D3 expansion domain. Primer specificity was confirmed with 23 isolates of 15 nematode species and other plant-parasitic and non-plant-parasitic nematodes typically present in the soil communities, and with six fungal species commonly associated with wheat root rot. DNA obtained using a commercially available kit and a method developed in our laboratory gave comparable amplification. PCR conditions were optimized and the two species were differentiated by PCR products of 144 bp for P. neglectus and 288 bp for P. thornei. With this assay, we detected a single juvenile in 1 g of sterile, inoculated soil. Examination of 30 field soil samples revealed that this method was applicable to a range of soils naturally infested with these two pathogens in Oregon. This PCR-based method is rapid, efficient, and reliable, does not require expertise in nematode taxonomy and morphology, and could be used as a rapid diagnostic tool for commercial and research applications for disease forecasting and management.