Using variation in arbuscular mycorrhizal fungi to drive the productivity of the food security crop cassava

Abstract

Tel: +41 79 536 7546 12 13 14 2 The unprecedented challenge to feed the rapidly growing human population can only be 15 achieved with major changes in how we combine technology with agronomy 1 . Despite their 16 potential few beneficial microbes have truly been demonstrated to significantly increase 17 productivity of globally important crops in real farming conditions 2,3 . The way microbes are 18 employed has largely ignored the successes of crop breeding where naturally occurring 19 intraspecific variation of plants has been used to increase yields. Doing this with microbes 20 requires establishing a link between variation in the microbes and quantitative traits of crop 21 growth along with a clear demonstration that intraspecific microbial variation can potentially 22 lead to large differences in crop productivity in real farming conditions. Arbuscular mycorrhizal 23 fungi (AMF), form symbioses with globally important crops and show great potential to improve 24 crop yields 2 . Here we demonstrate the first link between patterns of genome-wide intraspecific 25 AMF variation and productivity of the globally important food crop cassava. Cassava, one of the 26 most important food security crops, feeds approximately 800 million people daily 4 . In 27 subsequent field trials, inoculation with genetically different isolates of the AMF Rhizophagus 28 irregularis altered cassava root productivity by up to 1.46-fold in conventional cultivation in 29 Colombia. In independent field trials in Colombia, Kenya and Tanzania, clonal sibling progeny 30 of homokaryon and dikaryon parental AMF enormously altered cassava root productivity by up 31 to 3 kg per plant and up to a 3.69-fold productivity difference. Siblings were clonal and, thus, 32 qualitatively genetically identical. Heterokaryon siblings can vary quantitatively but monokaryon 33 siblings are identical. Very large among-AMF sibling effects were observed at each location 34 although which sibling AMF was most effective depended strongly on location and cassava 35 variety. We demonstrate the enormous potential of genetic, and possibly epigenetic variation, in 36 AMF to greatly alter productivity of a globally important crop that should not be ignored. A 37 microbial improvement program to accelerate crop yield increases over that possible by plant 38 breeding or GMO technology alone is feasible. However, such a paradigm shift can only be 39 realised if researchers address how plant genetics and local environments affect mycorrhizal 40 responsiveness of crops to predict which fungal variant will be effective in a given location.41 For millennia farmers have improved crops using naturally occurring intraspecific plant genetic variation 42 to improve productivity. However, rates of yield increase attributed to plant breeding and GMO-crop 43 technology are not considered sufficient to feed the projected global human population 1 . Beneficial soil 65 there was a significant phylogenetic signal on spore density and clustering (Supplementary figure 1; 66Supplementary infor...

Genetic variation and evolutionary history of a mycorrhizal fungus regulate the currency of exchange in symbiosis with the food security crop cassava

“…S1). This lack in trait differences is probably due to stage at which the plants were harvested, as cassava growth was shown to vary in response to different AMF but only at late stages of growth [16,46]. The pattern of fungal gene transcription was clearly discernible among the fungal groups ( Figs.…”

Genetically Different Isolates of the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis Induce Differential Responses to Stress in Cassava

“…Parental isolates (C2 and C3) originated from the Hausweid field station, at Tänikon, Switzerland (Koch et al, 2004), where they have been maintained in identical conditions at the University of Lausanne in vitro since 2000. Single-spore cultures, also known as single spore lines (SSLs), were raised in-vitro at the University of Lausanne, and originated from parental isolates (C2 and C3) (Ceballos et al, 2019; Supplementary Table S1) in exactly the same conditions as parental isolates. All cultures were transferred to Symbiom s.r.o.…”

“…Rhizophagus irregularis is a model AMF species commonly found in soils worldwide (Savary et al, 2018) and has a great potential to improve the productivity of cassava (Ceballos et al, 2013(Ceballos et al, , 2019Rodriguez and Sanders, 2015;Aliyu et al, 2019). Furthermore, this AMF species can be cultivated in-vitro and can be efficiently produced on a large-scale, making it a promising candidate for inoculation of cassava.…”

“…Additionally, genetic variation in this fungus has been extensively studied (Wyss et al, 2016;Chen et al, 2018;Savary et al, 2018;Masclaux et al, 2019), and shown to significantly alter plant growth (Munkvold et al, 2004;Koch et al, 2006Koch et al, , 2017. However, clonally produced R. irregularis siblings of a given R. irregularis isolate also display very large differences in fungal quantitative growth traits and plant growth, for example, in rice and cassava (Angelard et al, 2010;Ehinger et al, 2012;Ceballos et al, 2019). R. irregularis isolates exist as dikaryons, which means that they contain a population of nuclei with two distinct genotypes, or as homokaryons where all nuclei are of one identical genotype.…”

“…R. irregularis isolates exist as dikaryons, which means that they contain a population of nuclei with two distinct genotypes, or as homokaryons where all nuclei are of one identical genotype. Clonally grown offspring of both dikaryon and homokaryon isolates induce very large differences in cassava growth in conventional farming conditions in Colombia, Kenya and Tanzania (Ceballos et al, 2019). The role of variation in AMF in influencing drought stress responses of cassava remains poorly investigated.…”