Genetic analysis of global faba bean diversity, agronomic traits and selection signatures

Faba bean (Vicia faba L.) is a high-protein grain legume crop with great potential for sustainable protein production. However, little is known about the genetics underlying trait diversity. In this study, we used 21,345 high-quality SNP markers to genetically characterize 2678 faba bean genotypes. We performed genome-wide association studies of key agronomic traits using a seven-parent-MAGIC population and detected 238 significant marker-trait associations linked to 12 traits of agronomic importance. Sixty-five of these were stable across multiple environments. Using a non-redundant diversity panel of 685 accessions from 52 countries, we identified three subpopulations differentiated by geographical origin and 33 genomic regions subjected to strong diversifying selection between subpopulations. We found that SNP markers associated with the differentiation of northern and southern accessions explained a significant proportion of agronomic trait variance in the seven-parent-MAGIC population, suggesting that some of these traits were targets of selection during breeding. Our findings point to genomic regions associated with important agronomic traits and selection, facilitating faba bean genomics-based breeding

The giant diploid faba genome unlocks variation in a global protein crop

Publisher Copyright: © 2023, The Author(s).Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.Peer reviewe

Gatunki z rodzaju Fusarium oraz toksyny fuzaryjne w ziarnie pszenicy ozimej i jarej w Polsce

The aim of the study was to determine the presence of Fusarium species and mycotoxins in wheat grain from harvest in 2009 and 2010 in Poland. Samples from different locations were analyzed for the content of DNA of Fusarium species and mycotoxins. In 2009, DNA of F. graminearum and F. poae was present in all samples, F. culmorum in 82% of samples, and F. avenaceum in 55% of samples. In 2010, the highest content of DNA was found for F. graminearum followed by F. avenaceum, F. poae and F. langsethiae. The amount of F. culmorum DNA was very low. The most frequently occurring species were F. poae and F. graminearum, however, the amount of F. poae DNA was lower. In 2009, deoxynivalenol was detected in all samples. In 2010, the average content of deoxynivalenol was lower than in 2009. Nivalenol was detected at very low concentration in both years. Significant correlations between content of F. graminearum DNA and deoxynivalenol concentration in the grain and between content of F. poae DNA and nivalenol concentration in the grain in 2009 were found.Celem badania było określenie obecności gatunków Fusarium i mykotoksyn występujących w ziarnie pszenicy w Polsce w latach 2009 i 2010. Próby ziarna pochodzące z różnych regionów Polski zostały przeanalizowane pod kątem zawartości DNA grzybów z rodzaju Fusarium oraz mykotoksyn. W 2009 roku DNA F. graminearum i F. poae było obecne we wszystkich próbach, F. culmorum w 82% prób, F. avenaceum w 55% próbek. W 2010 r. najwyższą zawartość DNA stwierdzono dla F. graminearum, a następnie F. avenaceum, F. poae i F. langsethiae. Ilość DNA F. culmorum była bardzo niska. Najczęściej występującymi gatunkami były F. poae i F. graminearum. Jednakże ilość DNA F. poae była niższa. W 2009 r. we wszystkich próbach wykryto deoksyniwalenol. W 2010 r. średnia zawartość deoksyniwalenolu była niższa niż w 2009 r. Niwalenol wykryto w bardzo niskim stężeniu w obu latach. Stwierdzono istotność korelacji między zawartością DNA F. graminearum a stężeniem deoksyniwalenolu w ziarnie oraz między zawartością DNA F. poae a stężeniem niwalenolu w ziarnie w 2009 r

Gatunki Fusarium oraz toksyny fuzaryjne w ziarnie jęczmienia w Polsce w 2009 i 2010r. Komunikat

Grain samples of spring barley from the 2009 and 2010 harvest were analysed for the content of DNA of Fusarium species and Fusarium toxins (type B trichothecenes). Samples originated from different fields in Radzików, Central Poland. Qualitative and quantitative determination of Fusarium species in the grain was performed using a real-time PCR. Fusarium toxins in the grain were analysed by gas chromatography. Seven Fusarium species were detected in barley grain. The dominating species were F. avenaceum, F. graminearum and F. poae. The presence of F. culmorum, F. langsethiae, F. sporotrichioides and F. tricinctum was also detected. The concentration of trichothecene toxins in grain (deoxynivalenol, nivalenol) was low. The highest correlation coefficient of deoxynivalenol vs. Fusarium DNA was found for F. graminearum. Regarding nivalenol, the highest correlation coefficient was with F. poae DNA.  Próby ziarna jęczmienia jarego ze zbiorów w 2009 i 2010r. zostały przeanalizowane pod kątem zawartości DNA gatunków Fusarium i toksyn fuzaryjnych (trichotecenów B). Próbki pochodziły z różnych pól z Radzikowa, w środkowej Polsce. Jakościowe i ilościowe oznaczanie gatunków Fusarium w ziarnie przeprowadzono techniką real-time PCR. Toksyny fuzaryjne w ziarnie analizowano metodą chromatografii gazowej. W ziarnie jęczmienia wykryto siedem gatunków Fusarium. Dominujące gatunki to F. avenaceum, F. graminearum i F. poae. Wykryto również występowanie F. culmorum, F. langsethiae, F. sporotrichioides i F. tricinctum. Stężenie trichotecenów B (deoksyniwalenolu, niwalenolu) w ziarnie było niskie. Najwyższy współczynnik korelacji deoksyniwalenol vs. DNA Fusarium stwierdzono dla F. graminearum. Jeśli chodzi o niwalenol, najwyższy był współczynnik korelacji z DNA F. poae.

Relationship between Fusarium Head Blight, Kernel Damage, Concentration of Fusarium Biomass, and Fusarium Toxins in Grain of Winter Wheat Inoculated with Fusarium culmorum

Winter wheat lines were evaluated for their reaction to Fusarium head blight (FHB) after inoculation with Fusarium culmorum in two field experiments. A mixture of two F. culmorum chemotypes was applied (3ADON—deoxynivalenol producing, NIV—nivalenol producing). Different types of resistance were evaluated, including head infection, kernel damage, Fusarium biomass content and trichothecenes B (deoxynivalenol (DON), and nivalenol (NIV)) accumulation in grain. The aim of the study was to find relationships between different types of resistance. Head infection (FHB index) and Fusarium damaged kernels (FDK) were visually scored. Fusarium biomass was analysed using real-time PCR. Trichothecenes B accumulation was analysed using gas chromatography. Wheat lines differ in their reaction to inoculation for all parameters describing FHB resistance. We found a wide variability of FHB indexes, FDK, and Fusarium biomass content. Both toxins were present. DON content was about 60% higher than NIV and variability of this proportion between lines was observed. Significant correlation was found between head infection symptoms and FDK. Head infection was correlated with F. culmorum biomass and NIV concentration in grain. No correlation was found between the FHB index and DON concentration. Similarly, FDK was not correlated with DON content, but it was with NIV content; however, the coefficients were higher than for the FHB index. Fusarium biomass amount was positively correlated with both toxins as well as with the FHB index and FDK. Environmental conditions significantly influenced the DON/NIV ratio in grain. In locations where less F. culmorum biomass was detected, the DON amount was higher than NIV, while in locations where more F. culmorum biomass was observed, NIV prevailed over DON

The giant diploid faba genome unlocks variation in a global protein crop

International audienceIncreasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones