Biology subjects

Lopes, M. S.

Publications and source records attributed to Lopes, M. S..

4 recordsLinked to original sources

bioRxiv2025

Tracking the evolutionary trajectory of a young hybrid plant pathogen

A common mechanism by which emerging plant pathogens gain the ability to infect new hosts is hybridization. Despite its widespread occurrence, the outcomes of hybridization remain largely unpredictable within current evolutionary frameworks, making empirical studies key for identifying patterns and establishing principles underlying hybrid evolution. Here, we track the evolutionary trajectory of Blumeria graminis forma specialis triticale (B.g. triticale), or triticale powdery mildew, a pathogen that emerged recently through hybridization of two powdery mildew forms specialized on wheat (B.g. tritici) and rye (B.g. secalis). Using a genomic dataset of 652 isolates from the three formae speciales, we show that they persist as three isolated lineages. Results from our infection assays and sampling suggest that B.g. triticale is not well adapted to infect wheat under field conditions, indicating that isolation between B.g. tritici and B.g. triticale may be maintained by partial niche separation. We investigated the genomic changes following hybridization and found that at least a third of the hybrid genome is fixed for B.g. tritici ancestry in contemporary populations, and around 1% is fixed for the B.g. secalis ancestry. We identified several loci to be under recent positive selection in B.g. triticale, most of which coincide with known genes and regions of fixed or nearly fixed local ancestry. Overall, we highlight the role of ecological isolation in preventing gene flow between B.g. triticale and its parental lineages. We reveal the rapid stabilization of its genome after hybridization and show that some of these changes were likely shaped by selection. Significance statementEmerging plant diseases pose serious risks to biodiversity and food production. A common mechanism by which fungal plant pathogens emerge on previously uncolonized hosts is hybridization. Hybridization brings together novel genetic combinations from different lineages that can facilitate adaptation to new environments. However, the evolutionary fate of hybrid pathogens is difficult to predict, and empirical studies of natural populations can help shed light on the dynamics of pathogen evolution following hybridization. Here, we use genomic data and infection assays to follow the evolutionary trajectory of a recently emerged hybrid plant pathogen. We show that the hybrid persists as an independent lineage distinct from both parents and analyze the genomic changes that have occurred in the few decades since initial hybridization.

evolutionary biology↗

bioRxiv2024

Population genomics and molecular epidemiology of wheat powdery mildew in Europe

Agricultural diseases are a major threat to sustainable food production. Yet, for many pathogens we know exceptionally little about their epidemiological and population dynamics, and this knowledge gap is slowing the development of efficient control strategies. Here we study the population genomics and molecular epidemiology of wheat powdery mildew, a disease caused by the biotrophic fungus Blumeria graminis forma specialis tritici (Bgt). We sampled Bgt for two consecutive years, 2022 and 2023, from 22 countries in Europe and surrounding regions, and compiled a genomic dataset of 415 Bgt isolates. We found one single epidemic unit in the north of Europe, consisting of a highly homogeneous population. Conversely, the south of Europe hosts smaller local populations which are less interconnected. In addition, we show that the population structure can be largely predicted by the prevalent wind patterns. We identified several loci that were under selection in the recent past, including fungicide targets and avirulence genes. Some of these loci are common between populations, while others are not, suggesting different local selective pressures. We reconstructed the evolutionary history of one of these loci, AvrPm17, coding for an effector recognized by the wheat receptor Pm17. We found evidence for a soft sweep on standing genetic variation. Multiple AvrPm17 haplotypes, which can partially escape recognition by Pm17, spread rapidly throughout the continent upon its introduction in the early 2000s. We also identified a new virulent variant, which emerged more recently and can evade Pm17 resistance altogether. Overall, we highlight the potential of genomic surveillance in resolving the evolutionary and epidemiological dynamics of agricultural pathogens, as well as in guiding control strategies.

evolutionary biology↗

bioRxiv2023

Large scale sequence-based screen for recessive variants allows for identification and monitoring of rare deleterious variants in pigs

Most deleterious variants are recessive and segregate at relatively low frequency. Therefore, high sample sizes are required to identify these variants. In this study we report a large-scale sequence based genome-wide association study (GWAS) in pigs, with a total of 120,000 Large White and 80,000 Synthetic breed animals imputed to sequence using a reference population of approximately 1,100 whole genome sequenced pigs. We imputed over 20 million variants with high accuracies (R2>0.9) even for low frequency variants (1-5% minor allele frequency). This sequence-based analysis revealed a total of 13 additive and 8 non-additive significant quantitative trait loci (QTLs) for growth rate and backfat thickness. With the non-additive (recessive) model, we identified a deleterious missense SNP in the CDHR2 gene reducing growth rate and backfat in homozygous Large White animals. For the Synthetic breed, we revealed a QTL on chromosome 15 with a frameshift variant in the OBSL1 gene. This QTL has a major impact on both growth rate and backfat, resembling human 3M-syndrome 2 which is related to the same gene. With the additive model, we confirmed known QTLs on chromosomes 1 and 5 for both breeds, including variants in the MC4R and CCND2 genes. On chromosome 1, we disentangled a complex QTL region with multiple variants affecting both traits, harboring 4 independent QTLs in the span of 5 Mb. Together we present a large scale sequence-based association study that provides a key resource to scan for novel variants at high resolution for breeding and to further reduce the frequency of deleterious alleles at an early stage in the breeding program. Author SummaryIn this study we investigated the effect of over 20 million genetic variants on the growth rate and backfat thickness of approximately 140,000 pigs across two commercial breeds, with specific focus on recessive harmful variation. We identified 14 regions with a significant additive effect and 8 regions with a significant recessive effect on these traits. By looking at recessive effects we identified several rare deleterious variants with high impacts on animal fitness. These include a deletion on chromosome 15 in the OBSL1 gene, which leads to a growth reduction of 100 grams a day on average. Interestingly, loss-of-function mutations in OBSL1 are associated with short stature in humans. Looking at additive effects with this high-resolution dataset allowed us to gain more insight into the locus around the MC4R gene on chromosome 1. Here we found a small complex region containing several independent variants affecting both growth rate and backfat. With this study we have shown that by using several gene models and a large dataset, we can identify novel genetic variants at high resolution (<0.01 frequency) with significant impact on animal fitness and production. These results can help us in further eradicating deleterious genetic variants from pig populations.

genomics↗

bioRxiv2021

Identification of QTL hotspots affecting agronomic traits and high-throughput vegetation indices in rainfed wheat

Understanding the genetic basis of agronomic traits is essential for wheat breeding programmes to develop new cultivars with enhanced grain yield under climate change conditions. The use of high-throughput phenotyping (HTP) technologies for the assessment of agronomic performance through drought-adaptive traits opens new possibilities in plant breeding. HTP together with a genome-wide association study (GWAS) mapping approach can become a useful method to dissect the genetic control of complex traits in wheat to enhance grain yield under drought stress. This study aimed to identify molecular markers associated with agronomic and remotely sensed vegetation index (VI)-related traits under rainfed conditions in bread wheat and to use an in silico candidate gene (CG) approach to search for upregulated CGs under abiotic stress. The plant material consisted of 170 landraces and 184 modern cultivars from the Mediterranean basin that were phenotyped for agronomic and VI traits derived from multispectral images over three and two years, respectively. GWAS identified 2579 marker-trait associations (MTAs). The QTL overview index statistic detected 11 QTL hotspots involving more than one trait in at least two years. A candidate gene analysis detected 12 CGs upregulated under abiotic stress in 6 QTL hotspots. The current study highlights the utility of VI to identify chromosome regions that contribute to yield and drought tolerance under rainfed Mediterranean conditions.

plant biology↗