Analysis of genetic diversity in Phytophthora colocasiae causing leaf blight of taro (Colocasia esculenta) using AFLP and RAPD markers

Antagonistic and plant growth promotion of rhizobacteria against Phytophthora colocasiae in taro

Taro leaf blight caused by Phytophthora colocasiae adversely affects the growth and yield of taro. The management of this disease depends heavily on synthetic fungicides. These compounds, however, pose potential hazards to human health and the environment. The present study aimed to investigate an alternative approach for plant growth promotion and disease control by evaluating seven different bacterial strains (viz., Serratia plymuthica, S412; S. plymuthica, S414; S. plymuthica, AS13; S. proteamaculans, S4; S. rubidaea, EV23; S. rubidaea, AV10; Pseudomonas fluorescens, SLU-99) and their different combinations as consortia against P. colocasiae. Antagonistic tests were performed in in vitro plate assays and the effective strains were selected for detached leaf assays and greenhouse trials. Plant growth-promoting and disease prevention traits of selected bacterial strains were also investigated in vitro. Our results indicated that some of these strains used singly (AV10, AS13, S4, and S414) and in combinations (S4+S414, AS13+AV10) reduced the growth of P. colocasiae (30-50%) in vitro and showed disease reduction ability when used singly or in combinations as consortia in greenhouse trials (88.75-99.37%). The disease-suppressing ability of these strains may be related to the production of enzymes such as chitinase, protease, cellulase, and amylase. Furthermore, all strains tested possessed plant growth-promoting traits such as indole-3-acetic acid production, siderophore formation, and phosphate solubilization. Overall, the present study revealed that bacterial strains significantly suppressed P. colocasiae disease development using in vitro, detached leaf, and greenhouse assays. Therefore, these bacterial strains can be used as an alternative strategy to minimize the use of synthetic fungicides and fertilizers to control taro blight and improve sustainable taro production.

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.

A high-quality genome of taro (Colocasia esculenta (L.) Schott), one of the world's oldest crops

Taro (Colocasia esculenta (L.), Schott), from the Araceae family, is one of the oldest crops with important edible, medicinal, nutritional and economic value. Taro is a highly polymorphic species including diverse genotypes adapted to a broad range of environments, but the taro genome has rarely been investigated. Here, a high-quality chromosome-level genome of C. esculenta was assembled using data sequenced by Illumina, PacBio and Nanopore platforms. The assembled genome size was 2,405 Mb with a contig N50 of 400.0 kb and a scaffold N50 of 159.4 Mb. In total, 2,311 Mb (96.09%) of the contig sequences was anchored onto 14 chromosomes to form pseudomolecules, and 2,126 Mb (88.43%) was annotated as repetitive sequences. Of the 28,695 predicted protein-coding genes, 26,215 genes (91.4%) could be functionally annotated. On the basis of phylogenetic analysis using 769 genes, C. esculenta and Spirodela polyrhiza were placed on one branch of the tree that diverged approximately 73.23 million years ago. The synteny analyses showed that there have been two whole-genome duplication events in C. esculenta separated by a relatively short gap. According to comparative genome analysis, a larger number (1,189) of distinct gene families and long terminal repeats were enriched in C. esculenta. Our high-quality taro genome will provide valuable resources for further genetic, ecological and evolutionary analyses of taro or other species in the Araceae.