Wheat disease surveillance, genetic structure and temporal shifts of Puccinia striiformis population across Pakistan

Abstract

Wheat is among one of the earliest crops domesticated associated with human civilization and it is still the backbone of agriculture in Pakistan because of its cultivation on 70% of the total cultivatable land. Substantial yield production is the ultimate aim of all research in wheat production, particularly the objective of wheat genetic improvement. Among various yield constraints, wheat diseases are the most important, which needs to be monitored continually. Among wide array of diseases on wheat, the diseases caused by fungal pathogens i.e. rusts (yellow, leaf and stem rust) and powdery mildew diseases are of intense important in Pakistan. This study was designed to assess the status of these diseases across Pakistan and population structure of wheat yellow rust pathogen through surveillance effort made during 2016 and 2017 and subsequent population genetic analyses. A total of 437 fields in 63 districts during 2016 and 480 fields in 69 districts during 2017 were surveyed, covering four provinces of Pakistan and AJK. The survey involved inspection and sample collection from the naturally infected (mainly farmers‟) fields across the whole country in major wheat growing regions. Although yellow rust was observed as a major disease across Pakistan during these two years, leaf rust prevailed significantly in southern areas and powdery mildew in northern areas. The diseases prevalence and severity varied across two years, yellow rust was more severe during 2016, while leaf rust and powdery mildew prevailed during 2017. High yellow rust severity (60% or higher severity) was observed in 11% fields during 2016 and in 7% fields during 2017. In KP, high disease was recorded in 76 fields, 61 fields in Punjab and 24 fields in Sindh. In AJK one field and none of the field in Baluchistan with high yellow rust was observed. High leaf rust severity was recorded in 3% fields during 2016 and 4.3% fields during 2017. High leaf rust disease was recorded in 2 fields in KP, 14 fields in Punjab and 51 fields in Sindh. In AJK one field and none of the field in Baluchistan had high leaf rust. Powdery mildew prevailed mainly in northern KP and AJK in a total of 2.3% fields with high disease severity across two years. Maximum highly infected fields were observed in KP (18 fields), in Punjab two fields and one field in AJK. Stem rust was recorded only at CDRI Karachi which was artificially inoculated to evaluate various varieties against stem rust. No natural stem rust infection was recorded over two years. A total of 18 varieties were found to be highly susceptible to yellow rust including Galaxy-13, TD-1, Kiran-95, TJ-1, TJ-83, Sehar, Bakhtawar, Ghanimat-e-IBGE, PS-05, PS-08, Shahkar, Salim, Naya Amber, Sarsabz, Morocco, Khattakwal, Skd-1 and Inqilab-91 along with some breeding line. A total of 13 wheat cultivars were highly susceptible to leaf rust viz. Galaxy-13, Sehar, TD-1, Kiran-95, TJ-1, TJ-83, Aas-11, Yecora, Morocco, Marvi, Shafaq, Sarsabz and Inqilab-91 along with some breeding lines. In case of powdery mildew, Galaxy-2013, PS-05, PS-08, Faisalabad-2008, Shahkar and some local lines were found highly susceptible to powdery mildew. Despite ii high disease pressure, some varieties like Benazir, Insaf, Pukhtunkhwa, PS-15, Gold-16, Borlaug-16, Sindhu-16, Ujala-16, Johar-16, NARC-11 etc. exhibited better performance to yellow and leaf rust diseases. From the yellow rust infected fields, regardless of the severity level, resulted in collection of around 1500 samples, which were genotyped with successful profiles generation for 1053 samples. Population genetics analyses of the multilocus genotyping of these 1053 P. striiformis samples with 16 SSR markers revealed high genotypic diversity across all locations and recombination signature at few locations. Various diversity parameters assessed for P. striiformis populations revealed high genotypic diversity during 2016 as compared to 2017. High genotypic diversity was observed in KP and AJK, while diversity was low in Sindh. The difference in mean He and Ho were significant across all location except in AJK where difference was non-significant. A non-significant difference was also observed at Hazara, Malakand, Lahore and Sahiwal divisions during 2016 only. Diversity assessed in geographical divisions revealed high genotypic diversity in Malakand, Peshawar and Hazara divisions, while least diversity was observed in samples of Karachi. No geographical based divergence was observed through analyses of population subdivision. Neighbor-joining (NJ) phylogenetic tree and PCoA analysis suggested lack of any geographical regions/province specific structure further confirmed by low FST values among all provinces. The maximum FST value was observed between Baluchistan and Punjab population (0.06) and the minimum value was calculated between AJK & Baluchistan, and Sindh & Punjab. Lack of spatial structure was also confirmed by calculating FST for all provinces population in each year. The maximum FST value was observed between Sindh_16 and AJK_17 (0.113) and the minimum was observed between AJK_17 & KP_17 and AJK_17 & Punjab_17 (0.001). Clustering analysis based on DAPC identified five distinct genetic groups. In KP all the five genetic groups with unassigned individual were present, while in Punjab, G1 and G4 genetic groups were predominant and in Sindh G2 and G3 genetic groups were predominant. Samples from AJK were assigned in G1, G3 and G4 groups. In 2017, G4 became predominant in AJK, KP and Punjab, where it was not predominant during 2016. In Sindh, G2 prevailed during 2016, while G4 prevailed in 2017 population. Our analysis also confirmed lack of any host specific structure of the pathogen. All five genetic groups were observed on Galaxy-13, the most widely deployed wheat variety in Pakistan during 2016 and 2017. Absence of regional/host specific structure was further confirmed by presence of multiple genetic groups on Galaxy-13 at a given location and dispersal of these samples on Neighbor-joining (NJ) tree. Spatial distribution of the MLGs was assessed to see the dispersal of clones across various geographical regions. Resampling of MLGs over time reflect on the very limited pass-over of clones from one year to the second year through clonality, confirming further the role of recombination in maintaining the high genetic diversity. A total of 15 MLGs were resampled over the two years. Our overall results suggested the yellow rust to be the most widespread and important disease across Pakistan, along with a very high diversity in the recombinant P. striiformis population without any spatial population and host-specific structure. These results has multiple implications to disease management and resistance gene deployment, which must be considered to keep the disease burden below the economic level, not only in Pakistan but worldwide through preemptive measures against invasive lineages from the zone of diversity in Pakistan.