Taro (Colocasia esculenta) is a food staple widely cultivated in the humid tropics of Asia, Africa, Pacific and the Caribbean. One of the greatest threats to taro production is Taro Leaf Blight caused by the oomycete pathogen Phytophthora colocasiae. Here we describe a de novo taro genome assembly and use it to analyze sequence data from a Taro Leaf Blight resistant mapping population. The genome was assembled from linked-read sequences (10x Genomics; ∼60x coverage) and gap-filled and scaffolded with contigs assembled from Oxford Nanopore Technology long-reads and linkage map results. The haploid assembly was 2.45 Gb total, with a maximum contig length of 38 Mb and scaffold N50 of 317,420 bp. A comparison of family-level (Araceae) genome features reveals the repeat content of taro to be 82%, >3.5x greater than in great duckweed (Spirodela polyrhiza), 23%. Both genomes recovered a similar percent of Benchmarking Universal Single-copy Orthologs, 80% and 84%, based on a 3,236 gene database for monocot plants. A greater number of nucleotide-binding leucine-rich repeat disease resistance genes were present in genomes of taro than the duckweed, ∼391 versus ∼70 (∼182 and ∼46 complete). The mapping population data revealed 16 major linkage groups with 520 markers, and 10 quantitative trait loci (QTLs) significantly associated with Taro Leaf Blight disease resistance. The genome sequence of taro enhances our understanding of resistance to TLB, and provides markers that may accelerate breeding programs. This genome project may provide a template for developing genomic resources in other understudied plant species.

Taro, Colocasia esculenta, is one of the world’s oldest root crops and is of particular economic and cultural significance in Hawai’i, where historically more than 150 different landraces were grown. We developed a genome-wide set of more than 2400 high-quality single nucleotide polymorphism (SNP) markers from 70 taro accessions of Hawaiian, South Pacific, Palauan, and mainland Asian origins, with several objectives: 1) uncover the phylogenetic relationships between Hawaiian and other Pacific landraces, 2) shed light on the history of taro cultivation in Hawai’i, and 3) develop a tool to discriminate among Hawaiian and other taros. We found that almost all existing Hawaiian landraces fall into 5 monophyletic groups that are largely consistent with the traditional Hawaiian classification based on morphological characters, for example, leaf shape and petiole color. Genetic diversity was low within these clades but considerably higher between them. Population structure analyses further indicated that the diversification of taro in Hawai’i most likely occurred by a combination of frequent somatic mutation and occasional hybridization. Unexpectedly, the South Pacific accessions were found nested within the clades mainly composed of Hawaiian accessions, rather than paraphyletic to them. This suggests that the origin of clades identified here preceded the colonization of Hawai’i and that early Polynesian settlers brought taro landraces from different clades with them. In the absence of a sequenced genome, this marker set provides a valuable resource towards obtaining a genetic linkage map and to study the genetic basis of phenotypic traits of interest to taro breeding such as disease resistance.

Sorghum/sorghum–sudangrass hybrids (SSgH) have been used as a cover crop to improve soil health by adding soil organic matter, enhancing microbial activities, and suppressing soil-borne pathogens in various cropping systems. A series of SSgH were screened for (1) allelopathic suppression and (2) improvement of soil edaphic factors and soil microbial profile against plant-parasitic nematode (PPNs). The allelopathic potential of SSgH against PPNs is hypothesized to vary by variety and age. In two greenhouse bioassays, ‘NX-D-61′ sorghum and the ‘Latte’ SSgH amendment provided the most suppressive allelopathic effect against the female formation of Meloidogyne incognita on mustard green seedlings when using 1-, 2-, or 3-month-old SSgH tissue, though most varieties showed a decrease in allelopathic effect as SSgH mature. A field trial was conducted where seven SSgH varieties were grown for 2.5 months and terminated using a flail mower, and eggplant was planted in a no-till system. Multivariate analysis of measured parameters revealed that increase in soil moisture, microbial biomass, respiration rate, nematode enrichment index, and sorghum biomass were negatively related to the initial abundance of PPNs and the root-gall index at 5 months after planting eggplant in a no-till system. These results suggested that improvement of soil health by SSgH could lead to suppression of PPN infection.

Soil tillage is generally recognized as having a negative effect on soil health and weed seed predators. Recent advancements in conservation tillage practices allow for further comparison of how different levels of soil disturbances could influence soil food web communities. Field trials were conducted in 2017 and 2018 at two different sites to measure the effects of four cover crop termination treatments: conventional till (CT), no-till (NT), strip-till following roller-crimping (ST-RC), and strip-till with a living mulch between crop rows (ST-LM) on soil health using nematode community indices as soil health bioindicators. Following cover crop termination, the soil was monitored in the subsequent bell pepper (Capsicum annuum) crop over three sampling dates (June, August, and October). In the ST-RC treatment plots, soil nutrients were enriched (increased Enrichment Index, EI) and the soil food web structure was improved (higher Structure Index, SI) by the mid-season of the 2017 trial. In the 2018 trial, the ST-RC treatment enhanced fungal decomposition pathways (fungivore/fungivore + bacterivore ratio) throughout the bell pepper crop cycle and enhanced bacterial decomposition (abundance of bacterivorous nematodes) by the end of the cropping cycle compared to the no-till treatment, suggesting that the ST-RC treatment can further improve soil health conditions achieved by the NT treatment. Scatter plots of sampling points revealed that the treatments CT and NT had very distinct nematode-weed community assemblages in both trials, with the ST-RC and ST-LM treatments distributed closely with the NT treatment. Multivariate analysis among soil health bioindicators, weed pressure and weed seed predation explained 76.4 and 55.7% of the variance in the 2017 and 2018 trials, respectively. Weed pressure was consistently negatively related to (1) the SI, indicating soil disturbance would lead to more weed pressure; (2) the EI, indicating soil with higher weed pressure was linked to poor soil nutrient cycling, (3) cover crop residues left in the field from conservation tillage, or (4) how well the living mulch of red clover covered the ground. This study did not show that weed seed predation would lead to lower weed pressure but weed seed predation increased as weed biomass increased.