Phylogenetic Relationships, Breeding Implications, and Cultivation History of Hawaiian Taro (Colocasia Esculenta) Through Genome-Wide SNP Genotyping

Chloroplast capture and range extension after hybridization in taro (Colocasia esculenta)

Complete chloroplast genomes of 17 samples from six species of Colocasia (Araceae) were sequenced, assembled, and aligned together with two previously reported complete genome sequences from taro (Colocasia esculenta). Analysis provides a well-supported phylogenetic tree for taro and closely-related wild Colocasia species in Southeast Asia. Two chloroplast lineages (CI and CII) form a well-defined haplotype group and are found in cultivated taros known as var. esculenta (dasheen, CI), var. antiquorum (eddoe, CII), and in a widespread, commensal wild form known as var. aquatilis (CI). A third lineage (CIII) is also found in wild taros known as var. aquatilis and in the wild species C. lihengiae, C. formosana, and C. spongifolia. We suggest three different scenarios to explain the grouping of CIII wild taros (C. esculenta) with other wild Colocasia species. Chloroplast lineages CI and CIII in C. esculenta and an unknown parent species may be involved in an as yet undated history of hybridization, chloroplast capture, and range extension. Substantial taxonomic revision may be needed for C. esculenta after further studies of morphological and genetic diversity within the crop, in wild populations, and in closely related wild species. The results also point to the Bengal delta as a region of key interest for future research on the origins of tropical wetland taros.

Taro Roots: An Underexploited Root Crop

Taro (Colocasia esculenta) is a root crop that remains largely underutilized and undervalued despite its abundance and affordability. In comparison to other root vegetables, such as potatoes, yams, carrots, and cassava, taro stands out as a plentiful and low-cost option. As global hunger increases, particularly in Africa, it becomes essential to address food insecurity by maximizing the potential of existing food resources, including taro, and developing improved food products derived from it. Taro possesses a wealth of carbohydrates, dietary fiber, vitamins, and minerals, thereby making it a valuable nutritional source. Additionally, while not a significant protein source, taro exhibits higher protein content than many other root crops. Consequently, utilizing taro to create food products, such as plant-based milk alternatives, frozen desserts, and yogurt substitutes, could play a crucial role in raising awareness and increasing taro production. Unfortunately, taro has been stigmatized in various cultures, which has led to its neglect as a food crop. Therefore, this review aims to highlight the substantial potential of taro as an economical source of dietary energy by exploring the rich fiber, potassium, vitamin C, protein, and other micronutrient content of taro, and providing a foundation for the formulation of novel food products. Furthermore, this paper assesses the nutritional benefits of taro, its current utilization, and its antinutritional properties. It emphasizes the need for further research to explore the various applications of taro and improve on-farm processing conditions for industrial purposes.

Assessment of ethnobotanical uses, household, and regional genetic diversity of aroid species grown in northeastern India

Aroids are an important group of indigenous tuber crops, grown widely for their leaves, petioles, stolons, corms, and cormels. A total of 53 genotypes were evaluated for their genetic diversity in northeastern region of India. At household level, a total of 16 landraces of Aroids were recorded having different ethnobotanical uses. Based on the population study under Jhum/Shifting farming, landrace Rengama was dominant in area with 47% of the total population followed by Tamachongkham and Tasakrek. However, Pugarkusu and Chigi occupied 33.0 and 24.0% of the population, respectively under backyard farming, and were considered as major landraces. Tamachongkham, high in acridity and total oxalate content (0.82%), was used for cooking with meat, while Tasakrek was used as a baby food due to high total sugar (>3.0%), low in acridity, and total oxalate content (<0.12%). The Simpson’s diversity index of the backyards was higher (0.80) as compared to Jhum field (0.63). The genotypes showed wider variability in growth and yield attributes like; plant height (89.4–206.1 cm), number of side shoots (1.84–5.92), corm weight (38.0–683.3 g), cormel weight (14.0–348.3 g), yield (0.24–1.83 kg plant−1). Similarly, wide variations were also observed for quality traits like total sugar (1.93–4.94%); starch (15.32–32.49%), total oxalate (0.10–0.82%), and dry matter (16.75–27.08%) content. Except for total oxalate, all the growth and yield attributes have shown high heritability and moderate to high genetic advance. Molecular analysis (33 polymorphic SSR markers) detected a total of 136 alleles, ranged 3 to 8 alleles per marker. The observed heterozygosity (0.24) was less than expected heterozygosity (0.69). The group-wise maximum genetic divergence was observed between Colocasia fallax (cv. Chigi) to C. esculenta var. aquatilis (cv. Tharsing); C. fallax (cv. Chigi) to C. gigantea (cv. Ganima) and C. gigantea (cv. Ganima) to Xanthosoma spp., while it was least between eddo and dasheen. The findings indicated, a wider diversity and distinct ethnobotanical uses of Aroid landraces at the house hold levels, which should be conserved and popularized to ensure nutritional security.

DArTSeq SNP-based genetic diversity and population structure studies among taro [(Colocasia esculenta (L.) Schott] accessions sourced from Nigeria and Vanuatu

Taro is a valuable staple food crop among resource-poor rural people in countries such as Nigeria and Ghana, among others. Characterization of genetic diversity is a prerequisite for proper management of breeding programs and conservation of genetic resources. Two hundred seventy one taro accessions obtained from Nigeria and Vanuatu were genotyped using DArTseq-based SNP markers with the objectives of investigating the genetic diversity and population structure. In the analysis, 10,391 SNP markers were filtered from the sequence and used. The analysis revealed higher transition than transversion types of SNPs in the ratio of 1.43:1. The polymorphism ranged from 0.26 to 0.29 for the markers, indicating moderate genetic diversity. A model-based Bayesian clustering analysis of taro accessions yielded five subgroups and revealed the admixture situation in 19.19% of all accessions in the study. Vanuatu taro accessions exhibited more genetic diversity than Nigerian taro accessions. The population diversity estimate (PhiPt) was relatively higher (0.52) for accessions originating from Vanuatu than for Nigerian accessions. Analysis of molecular variance (AMOVA) revealed that most variation existed among individuals within a population at 52%. Nei's genetic distance showed that relatedness is based on geographical proximity. Collection of taro genetic resources should give more emphasis to within regions to utilize diversity in taro breeding program. This study also demonstrated the efficiency of DArTseq-based SNP genotyping for large-scale genome analysis in taro. The genotypic markers provided in this study are useful for association mapping studies.

Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers

Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro.

Evolutionary origins of taro (Colocasia esculenta) in Southeast Asia

As an ancient clonal root and leaf crop, taro (Colocasia esculenta, Araceae) is highly polymorphic with uncertain genetic and geographic origins. We explored chloroplast DNA diversity in cultivated and wild taros, and closely related wild taxa, and found cultivated taro to be polyphyletic, with tropical and temperate clades that appear to originate in Southeast Asia sensu lato. A third clade was found exclusively in wild populations from Southeast Asia to Australia and Papua New Guinea. Our findings do not support the hypothesis of taro domestication in Papua New Guinea, despite archaeological evidence for early use or cultivation there, and the presence of apparently natural wild populations in the region (Australia and Papua New Guinea).

Taro Genome Assembly and Linkage Map Reveal QTLs for Resistance to Taro Leaf Blight

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 vs. ∼70 (∼182 and ∼46 complete). The mapping population data revealed 16 major linkage groups with 520 markers, and 10 quantitative trait loci (QTL) 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.

The origin of Oxalis corniculata L

Background

Oxalis corniculata L. is a weed with a world-wide distribution and unknown origin. Though it belongs to a section of the genus from South America, the evidence that this species came from there is weak.

Methods

We reviewed the evidence for the origin of O. corniculata using herbarium specimens, historic literature and archaeobotanical research. We also summarized ethnobotanical literature to understand where this species is most used by humans as a medicine.

Results

Despite numerous claims that it is native to Europe there is no strong evidence that O. corniculata occurred in Europe before the 15th century. Nor is there reliable evidence that it occurred in North or South America before the 19th century. However, there is direct archaeobotanical evidence of it occurring in south–east Asia at least 5,000 years ago. There is also evidence from historic literature and archaeobotany that it reached Polynesia before European expeditions explored these islands. Examination of the traditional use of O. corniculata demonstrates that is most widely used as a medicine in south–east Asia, which, while circumstantial, also points to a long association with human culture in this area.

Discussion

The most likely origin for O. corniculata is south–east Asia. This is consistent with a largely circum-Pacific distribution of section Corniculatae of Oxalis. Nevertheless, it is likely that O. corniculata spread to Europe and perhaps Polynesia before the advent of the modern era through trade routes at that time.

High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing

BACKGROUND

Flavonoids are important components that confer upon tea plants a unique flavour and health functions. However, the traditional breeding method for selecting a cultivar with a high or unique flavonoid content is time consuming and labour intensive. High-density genetic map construction associated with quantitative trait locus (QTL) mapping provides an effective way to facilitate trait improvement in plant breeding. In this study, an F1 population (LJ43×BHZ) was genotyped using 2b-restriction site-associated DNA (2b-RAD) sequencing to obtain massive single nucleotide polymorphism (SNP) markers to construct a high-density genetic map for a tea plant. Furthermore, QTLs related to flavonoids were identified using our new genetic map.

RESULTS

A total of 13,446 polymorphic SNP markers were developed using 2b-RAD sequencing, and 4,463 of these markers were available for constructing the genetic linkage map. A 1,678.52-cM high-density map at an average interval of 0.40 cM with 4,217 markers, including 427 frameset simple sequence repeats (SSRs) and 3,800 novel SNPs, mapped into 15 linkage groups was successfully constructed. After QTL analysis, a total of 27 QTLs related to flavonoids or caffeine content (CAF) were mapped to 8 different linkage groups, LG01, LG03, LG06, LG08, LG10, LG11, LG12, and LG13, with an LOD from 3.14 to 39.54, constituting 7.5% to 42.8% of the phenotypic variation.

CONCLUSIONS

To our knowledge, the highest density genetic map ever reported was constructed since the largest mapping population of tea plants was adopted in present study. Moreover, novel QTLs related to flavonoids and CAF were identified based on the new high-density genetic map. In addition, two markers were located in candidate genes that may be involved in flavonoid metabolism. The present study provides valuable information for gene discovery, marker-assisted selection breeding and map-based cloning for functional genes that are related to flavonoid content in tea plants.