Microsatellite Genotyping of the Wheat Yellow Rust Pathogen Puccinia striiformis

High Genetic Diversity in the Himalayan Common Bean (Phaseolus vulgaris) Germplasm with Divergence from Its Center of Origin in the Mesoamerica and Andes

The common bean is found in the Himalayan region of Pakistan with substantial morphological variability. Genetic diversity within any crop species is a precursor for genetic improvement; however, little is known about common bean genetic diversity in this region. We explored the genetic diversity in the common bean from the Himalayan region (Khyber Pakhtunkhwa, Gilgit-Baltistan, Kashmir) of Pakistan. Microsatellite genotyping was carried out for 147 samples with 40 simple sequence repeat (SSR) markers. The results revealed a clear divergence of the Pakistani population from the primary gene pool (with FST values of 0.2 with Andes and 0.27 with Mesoamerica). However, within the Himalayan germplasm, no clear evidence of spatial structure was observed (with the maximum FST values of only 0.025), probably due to the dispersal of seeds by human activity within the region. This was further elucidated by the discriminant analyses of principal components. Considering the diversity parameters, high genotypic diversity was observed for the indigenous lines (0.990), comparable to the primary gene pool (0.976 for Mesoamerica and 0.976 for Andes populations). A high genotypic diversity was observed within the Himalayan population (ranging from 0.500 for Upper Dir to 0.952 for Mansehra). Gene diversity across loci varied between 0.28 for Chitral to 0.38 for Kurram. Our results suggested a divergent and independent evolution of the Himalayan population, which might have led to the diversification of the common bean germplasm in the region postintroduction into the region. The diversity observed could also be exploited in future breeding programs for the development and introduction of climate-resilient varieties.

Field response and molecular screening of European wheat germplasm against powdery mildew at the Himalayan region of Pakistan

Wheat powdery mildew possesses a significant threat to wheat crops not only on a global scale but also in the northern region of Pakistan. Recognizing the need for effective measures, the exploration and utilization of exotic germplasm take on critical importance. To address this, a series of trials were made to investigate the response of 30 European (EU) lines, in addition to the local checks (Siran, Atta-Habib (AH) and Ghanimat-e-IBGE) against wheat powdery mildew at the Himalayan region of Pakistan. The study involved field testing from 2018 to 2022 across multiple locations, resulting in 38 different environments (location × year). In addition to field evaluations, molecular genotyping was also performed. The disease was absent on the tested lines during 2018, 2019, and 2020 whereas it ranged from 0 to 100% at Chitral location during 2021, where 100% was observed only for one EU wheat line "Matrix." The disease prevailed only at Gilgit location (0-60% for EU wheat line "F236") and at Nagar location (0-10% for EU wheat lines Substance and Nelson) during the disease season of 2022. Most of the EU wheat lines showed very low ACI values, due to an overall low disease pressure. Matrix showed the maximum ACI (1.54) followed by Ritter (1.25) and Bli_autrichion (0.87), whereas the minimum (0.1) was for Substance, JB_Asano, and KWS_Loft followed by Canon (0.19), all exhibiting partial resistance. The molecular marker-based screening revealed that Pm38 was the most prevalent and detected in 100% of wheat lines followed by Pm39 (60%) and Pm8 (30%). Six wheat lines (20%) possessed all three Pm genes (Pm8, Pm38, and Pm39) concurrently. The variability observed in this study can be utilized in future breeding efforts aimed at developing resistant wheat varieties.

Himalayan mountains imposing a barrier on gene flow of wheat yellow rust pathogen in the bordering regions of Pakistan and China

The wheat yellow rust pathogen has been shown to be diverse and potentially originated in the Himalayan region. Although Himalayan populations of Pakistan, Nepal and Bhutan have been previously compared, little is known about the relative divergence and diversity in Puccinia striiformis populations in the bordering regions of Pakistan and China. To assess the relative diversity and divergence in these regions of Pakistan (Gilgit-Baltistan, Hazara and Azad Jammu Kashmir) and China (Xinjiang, Qinghai, Tibet, Sichuan, Guizhou and Yunnan), a total of 1245 samples were genotyped using 17 microsatellite SSR markers. A clear divergence was observed between the bordering regions of Pakistan and China (F_ST = 0.28) without any resampling of genetic groups and multilocus genotypes across two sides of the Himalayan mountains. The closest subpopulations across the two countries were Xinjiang and Gilgit-Baltistan (Nei's distance = 0.147), which were close geographically. A very high diversity and recombinant population structure was observed in both populations, though slightly higher in China (Genotypic diversity = 0.970; r¯d = 0.000) than in Pakistan (Genotypic diversity = 0.902; r¯d = 0.065). The distribution of genetic groups and resampling of MLGs revealed more gene flow across Yunnan, Guizhou and Sichuan regions in China, while between Hazara and Azad-Jammu Kashmir in Pakistan. The lack of gene flow between Pakistan and China populations is due to geographical barriers and a large patch of land without wheat. The information on the relative diversity and divergence in different geographical zones of the pathogen center of diversity and neighboring region should be considered in resistant wheat deployment while considering the invasion potential of the pathogen at regional and global contexts.

Countrywide inter-epidemic region migration pattern suggests the role of southwestern population in wheat stripe rust epidemics in China

Understanding countrywide pathogen population structure and inter-epidemic region spread is crucial for deciphering crop potential losses. Wheat stripe rust caused by Puccinia striiformis f. sp. tritici is a destructive disease that affects worldwide wheat production, widespread in China, representing largest epidemic region globally. This study aimed to understand the population structure and migration route of P. striiformis f. sp. tritici across China based on sampling from 15 provinces representing six epidemic zones, viz., over-summering, over-wintering, eastern, Yun-Gui, Xinjiang and Tibet epidemic regions. High genotypic diversity was recorded in over-summering, Tibet and over-wintering epidemic regions. Epidemic regions partly explain population subdivision with variable divergence (F_ST  = 0.005-0.344). Xinjiang and Tibet epidemic regions were independent epidemic zones with least sharing of genotypes. Among other epidemic zones, i.e. over-summering, over-wintering, eastern and Yun-Gui epidemic zones, re-sampling MLGs, clustering-based structure, DAPC analyses, relative migration and low divergence (F_ST from 0.006 to 0.073) revealed frequent geneflow. Yun-Gui epidemic regions, with a potential for both over-summering and over-wintering, could play an important role in causing epidemics in main wheat-cultivating areas of China. High diversity, recombination signatures and inter-epidemic region migration patterns need to be considered in host-resistant cultivar development in China and neighbouring countries, considering risk of long-distance migration capacity of pathogen.

Diversity in Puccinia striiformis populations causing the 2013 yellow rust epidemics on major wheat cultivars of Pakistan

Wheat yellow/stripe rust pathogen Puccinia striiformis is highly diverse and recombinant in the north of Pakistan in the Himalayan region. However, little is known about the role of this diversity in disease epidemics in areas where wheat yellow rust is an important disease in both irrigated and rain-fed wheat (i.e., in the plains of Pakistan). We explored the population diversity in P. striiformis during the rust epidemics of 2013 in the major wheat-growing regions of Pakistan (the Himalayan region, central Khyber Pakhtunkhwa [KP], southern KP, central and northern Punjab). Disease severities among commonly grown cultivars ranged from 5% to 100%. Microsatellite genotyping with 16 simple sequence repeat (SSR) markers revealed a high diversity among 266 isolates collected during the season, with the Simpson diversity index (Simpson 1949) ranging from 0.870 (Himalayan) to 0.955 (southern KP). The recombination signature was stronger in the Himalayan population and central KP compared with wheat-growing regions of Punjab and southern KP. The overall diversity was higher in Pakistan relative to the clonal populations present in Europe, Australia, and the Americas. Analyses of population subdivision revealed no clear evidence of spatial structure for samples from Pakistan, with a maximum fixation index (F_ST) value of only 0.10. The lack of clear population subdivision could be attributed to migration of pathogen. In turn, the high diversity of P. striiformis in Pakistan represents a potential threat to wheat production in the region and worldwide, as a possible source to found clonal populations in diverse wheat-growing areas.

Genetic diversity in exotic oat germplasm & resistance against barley yellow dwarf virus

Oat (Avena sativa L.) is an important fodder crop of Pakistan, though with low productivity. The present study was conducted to evaluate the performance and genetic diversity of exotic oat germplasm, with emphasis on cereal yellow dwarf virus resistance. A total of 16 exotic line (introduced from Aarhus University Denmark) and 1 local line (provided by The University of Agriculture Peshawar), were grown during the season 2017–18 in Completely Randomized Block Design with three replications across two locations of Khyber Pakhtunkhwa i.e., Peshawar and Kohat. Field testing enabled to collect the data on BYDV incidence, BYDV severity, aphid infestation, plant height, leaf area, panicle length, panicle weight, spikelets per panicle, 1000 grain weight (g), grain yield (g), biological yield (g) and harvest index (%). Prevalence of BYDV was variable across location and over time. Six weeks data showed high disease pressure at Peshawar (85%), with SA-O-01 genotype having AUDPC value of 95%. Almost all the varieties showed less tolerance towards the Aphids attack. Line SA-O-15 showed the maximum 1000 grain weight (42.6 g) at Kohat, while SA-O-4 showed the maximum 1000 grain weight (60.7 g) at Peshawar. Line SA-O-05 (3634 g per (0.9 m²) plot) gave the maximum biological yield at Kohat station, while Line SA-O-01 gave the maximum biological yield (2517 g) at Peshawar. Mean grain yield for Kohat was recorded 0.155 g per (0.9 m²) plot while for Peshawar it was 0.231 g per (0.9 m²) plot. At Kohat line SA-O-10 produced the maximum grain yield (0.229 g), while line SA-O-12 produced the maximum grain yield at Peshawar (0.288 g). Molecular genotyping with a set of 4 RAPD primers revealed substantial diversity among17 oat lines. A total of 23 loci were amplified showing a high level of variations and polymorphism among the proposed lines. The maximum number of loci was recorded for GLA-04 (8), while the minimum number of loci was recorded for GLD-18 (4). Among the tested RAPD primers the maximum gene diversity (0.529) was recorded for loci GLA-03B230, GLA-04B130, GLA-04B300, GLB-05B150 and GLA-18B100 while the minimum (0.118) genetic diversity was recorded for loci GLA-03B600, GLB-05B330 and GLA-18B500. A clear divergence was found between most of the exotic oat lines. The observed genetic diversity in exotic oat germplasm and its resistance towards Barley Yellow Dwarf virus could be useful for oat genetic improvement and broadening the genetic background of cultivated oat germplasm.