Yuxing Xu

Strigolactones are ecologically, developmentally, and physiologically important hormones, yet much remains unknown about their evolution and functions in non-model species. Sorghum, a globally important C4 cereal, exhibits natural variation in root-exuded strigolactones. Differences in sorghum strigolactone stereochemistry are associated with resistance to parasitic plants but with evidence for potential trade-offs. We studied sorghum mutants of the strigolactone biosynthetic genes, CAROTENOID CLEAVAGE DIOXYGENASE 8 (SbCCD8b) and LOW GERMINATION STIMULANT 1 (LGS1), both previously shown to be Striga resistant by stimulating little germination of the parasite. CRISPR-Cas9 deletions of SbCCD8b changed the accumulation of low abundance metabolites, reduced net carbon assimilation rate, altered root architecture and anatomy, and diminished the establishment and benefit of mycorrhizal symbionts. For LGS1 CRISPR-Cas9 deletions, differentially expressed genes were enriched with promoter motifs that regulate stress response and growth pathways, net carbon assimilation rate was reduced, and the colonization of mycorrhizal symbionts was delayed. We additionally restored functional LGS1 into the RTx430 genetic background, which normally has the lgs1-2 natural deletion allele. While root exudates from LGS1 insertion mutants rescued Striga susceptibility, we did not see consistent rescue of other traits altered in LGS1 deletion mutants. We hypothesize that epistasis with a neighboring strigolactone synthesis gene, which is rarely lost without concomitant loss of LGS1, may alter the phenotypic effects of LGS1 variation. These findings provide context for potential trade-offs associated with host resistance to parasitic plants and further define the roles of strigolactones in shaping sorghum physiology growth, and development.

Although the green revolution adapted a handful of crops to homogeneous and high-input industrialized agriculture, much of the global population still relies on the local production of variable crop cultivars by low-input smallholder farms. This diversity of unhomogenized crops¹, like that of the grain and bioenergy crop sorghum^2,3,4,5, offers raw materials for genetic gain and cultivar improvement. However, breeding efforts can be constrained by highly specialized traits and breeding targets⁶. Here, to bridge this diversity, we constructed a 33-member pangenome reference and a diversity panel across 1,984 cultivars and landraces. We leveraged these resources to explore the complex interplay among historical contingency, ongoing adaptation and previously uncharacterized structural diversity. Specifically, our analyses conclusively demonstrated multiple nested and deeply diverged structural variants in the domestication gene SHATTERING1, which distinguish the previously established multicentric origin of sorghum. We then applied landscape genomics to reveal how gene flow and secondary contact created the complex genetic mosaic in contemporary breeding networks. As proof of concept for pangenome-accelerated trait discovery, we connected biosynthetic gene cluster structural variation to phenotypic leaf concentration of the cyanogenic glucoside dhurrin. Combined, these approaches will accelerate breeding and trait discovery and provide a framework for similar applications in other crops.

Strigolactones are ecologically, developmentally, and physiologically important hormones, but much remains unknown about their evolution and role in non-model species. Sorghum is a globally important C ₄ cereal and exhibits natural variation in root-exuded strigolactones. Differences in sorghum strigolactone stereochemistry are associated with resistance to parasitic plants, but with evidence for potential trade-offs. We studied sorghum mutants of loci in the strigolactone biosynthetic pathway, C AROTENOID CLEAVAGE DIOXYGENASE 8 (Sb CCD8b ) and LOW GERMINATION STIMULANT 1 ( LGS1 ), previously shown to be Striga resistant by stimulating little germination of the parasite. Sb CCD8b CRISPR-Cas9 deletions changed the accumulation of low abundance metabolites, reduced net carbon assimilation rate, altered root architecture and anatomy, and diminished the establishment and benefit of mycorrhizal symbionts. For Striga- resistant LGS1 CRISPR-Cas9 deletions, differentially expressed genes were enriched with promoter motifs for stress response and growth pathways, net carbon assimilation rate was reduced, and the colonization of mycorrhizal symbionts was delayed. We additionally restored functional LGS1 into the RTx430 genetic background, which normally has the lgs1 -2 natural deletion allele. While root exudates from LGS1 insertion mutants rescued Striga susceptibility, we did not see consistent rescue of other traits impacted in LGS1 loss-of-function mutants. We hypothesize that epistasis with a neighboring strigolactone synthesis gene, which is rarely lost without concomitant loss of LGS1, may alter the phenotypic effects of LGS1 variation. Our study gives context to potential trade-offs associated with host resistance to parasitic plants and, more broadly, builds on the contribution of strigolactones in shaping sorghum physiological processes, growth, and development.

The genus Armillaria (Basidiomycota, Agaricales, Physalacriaceae) comprises pathogenic fungi that cause root-rot disease in plants, as well as species with low pathogenicity, some of which are hosts of the fully mycoheterotrophic orchid plant Gastrodia elata (Orchidaceae). To investigate the mechanisms underlying such special interactions between Armillaria fungi and G. elata, it is crucial to establish genetic transformation platforms for the Armillaria fungi and G. elata. In this study, an Armillaria strain Arm37 was isolated from G. elata, which can form symbiosis with G. elata in axenic culture under laboratory conditions. A vector pYT-EV containing a cassette for hygromycin-resistance selection and a cassette for expressing or silencing target genes was constructed. An Agrobacterium tumefaciens-mediated transformation (ATMT) system for Arm37 was successfully developed and optimized to achieve a transformation efficiency of 32%. The ATMT system was successfully used to express the reporter genes eGFP encoding enhanced green fluorescent protein and GUS encoding β-glucuronidase and to effectively silence the endogenous gene URA3 encoding orotidine-5′-phosphate decarboxylase in Arm37. This ATMT system established for Arm37 provides an efficient genetic tool for exploring the Arm37 genes that are involved in the unique interaction between the Armillaria fungi and fully mycoheterotrophic plant G. elata.

Summary: A dodder (Cuscuta) often simultaneously parasitizes two or more adjacent hosts. Phosphate (Pi) deficiency is a common stress for plants, and plants often interact with soil microbes, including arbuscular mycorrhizal fungi (AMF), to cope with Pi stress. Little is known about whether dodder transmits Pi deficiency‐induced systemic signals between different hosts. In this study, dodder‐connected plant clusters, each composed of two tobacco (Nicotiana tabacum) plants connected by a dodder, were established, and in each cluster, one of the two tobacco plants was treated with Pi starvation. AMF colonization efficiency, rhizosphere bacterial community, and transcriptome were analyzed in the other dodder‐connected Pi‐replete tobacco plant to study the functions of interplant Pi signals. We found that dodder transfers Pi starvation‐induced systemic signals between host plants, resulting in enhanced AMF colonization, changes of rhizosphere bacterial communities, and alteration of transcriptomes in the roots of Pi‐replete plants. Importantly, genetic analyses indicated that microRNA399s (miR399s) and strigolactones suppress the systemic Pi signals and negatively affect AMF colonization in the Pi‐replete plants. These findings provide new insight into the ecological role of dodder in mediating host–host and host–microbe interactions and highlight the importance of strigolactone and miR399 pathways in systemic Pi signaling.

Parasitic plants have evolved to be subtly or severely dependent on host plants to complete their life cycle. To provide new insights into the biology of parasitic plants in general, we assembled genomes for members of the sandalwood order Santalales, including a stem hemiparasite (Scurrula) and two highly modified root holoparasites (Balanophora) that possess chimaeric host–parasite tubers. Comprehensive genome comparisons reveal that hemiparasitic Scurrula has experienced a relatively minor degree of gene loss compared with autotrophic plants, consistent with its moderate degree of parasitism. Nonetheless, patterns of gene loss appear to be substantially divergent across distantly related lineages of hemiparasites. In contrast, Balanophora has experienced substantial gene loss for the same sets of genes as an independently evolved holoparasite lineage, the endoparasitic Sapria (Malpighiales), and the two holoparasite lineages experienced convergent contraction of large gene families through loss of paralogues. This unprecedented convergence supports the idea that despite their extreme and strikingly divergent life histories and morphology, the evolution of these and other holoparasitic lineages can be shaped by highly predictable modes of genome reduction. We observe substantial evidence of relaxed selection in retained genes for both hemi- and holoparasitic species. Transcriptome data also document unusual and novel interactions between Balanophora and host plants at the host–parasite tuber interface tissues, with evidence of mRNA exchange, substantial and active hormone exchange and immune responses in parasite and host.

Parasitic plants use a special organ, the haustorium, to attach to and penetrate host tissues, forming phloem and/or xylem fusion with the host vascular systems. Across this haustorium–host interface, not only water and nutrients are extracted from the host by the parasitic plant, but also secondary metabolites, messenger RNAs, noncoding RNAs, proteins, and systemic signals are transported between the parasite and host and even among different hosts connected by a parasite. Furthermore, mycorrhizal fungi can form common mycelial networks (CMNs) that simultaneously interconnect multiple plants. Increasing lines of evidence suggest that CMNs can function as conduits, transferring stress-related systemic signals between plants. Between-plant signaling mediated by haustoria and CMNs likely has a profound impact on plant interactions with other organisms and adaptation to environmental factors. Here, we summarize the findings regarding between-plant transfer of biomolecules and systemic signals and the current understanding of the physiological and ecological implications of between-plant signaling.

Both herbivory and jasmonic acid (JA) activate the biosynthesis of defensive metabolites in maize, but the mechanism underlying this remains unclear. We generated maize mutants in which ZmMYC2a and ZmMYC2b, two transcription factor genes important in JA signaling, were individually or both knocked out. Genetic and biochemical analyses were used to elucidate the functions of ZmMYC2 proteins in the maize response to simulated herbivory and JA. Compared with the wild‐type (WT) maize, the double mutant myc2ab was highly susceptible to insects, and the levels of benzoxazinoids and volatile terpenes, and the levels of their biosynthesis gene transcripts, were much lower in the mutants than in the WT maize after simulated insect feeding or JA treatment. Moreover, ZmMYC2a and ZmMYC2b played a redundant role in maize resistance to insects and JA signaling. Transcriptome and Cleavage Under Targets and Tagmentation‐Sequencing (CUT&Tag‐Seq) analysis indicated that ZmMYC2s physically targeted 60% of the JA‐responsive genes, even though only 33% of these genes were transcriptionally ZmMYC2‐dependent. Importantly, CUT&Tag‐Seq and dual luciferase assays revealed that ZmMYC2s transactivate the benzoxazinoid and volatile terpene biosynthesis genes IGPS1/3, BX10/11/12/14, and TPS10/2/3/4/5/8 by directly binding to their promoters. Furthermore, several transcription factors physically targeted by ZmMYC2s were identified, and these are likely to function in the regulation of benzoxazinoid biosynthesis. This work reveals the transcriptional regulatory landscapes of both JA signaling and ZmMYC2s in maize and provides comprehensive mechanistic insight into how JA signaling modulates defenses in maize responses to herbivory through ZmMYC2s.