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

Assessment of nutritional quality of taro (Colocasia esculenta L. Schott.) genotypes of the Eastern Himalaya, India

Introduction

The eastern Himalayan region of India with diverse agro-climatic conditions is one of the important hotspots of the world's biodiversity. A wide range of genetic variability of plant species like Colocasia is available in the region which is consumed by the local tribes.

Materials and methods

A field study was conducted during 2022-23 to evaluate the yield, biochemical, mineral, and an-tioxidant parameters of 30 Colocasia esculenta L. Schott. genotypes under a split-plot design with three replications.

Results and discussion

Significant (p < 0.05) variations were observed among genotypes for all traits. Tamachongkham exhibited the highest corm weight and yield, while Tamitin recorded the maximum cormel weight and total yield. Megha Taro-2 and Megha Taro-1 had the highest cormel numbers and cormel yield, respectively. In mineral composition, Tamitin had the highest N, K, Zn, Cu, and Mn, Tagitung White recorded the highest P, and BCC-2 had the highest Fe and Ca + Mg. Biochemically, Tamachongkham had the highest dry matter content; Khweng-2 had the highest starch, total sugar, and reducing sugar; Rengama had the highest crude protein, and crude fiber; and Mairang Local had the highest ash content. A significant positive correlation was observed between total yield and corm, cormel yield, cormel weight, and corm weight, while correlations with starch and other parameters were non-significant. Total phenolic content and anthocyanin were significantly correlated with Ferric Reducing Antioxidant Power (FRAP). Genotype-by-trait biplot analysis using the first two principal components (PC1: 19.4%, PC2: 14%) high-lighted total sugar, reducing sugar, cormel numbers, crude fiber, anthocyanin, and FRAP as major contributors to phenotypic diversity. The observed variations indicate the potential of these genotypes for future breeding programs aimed at improving taro production in the Eastern Himalayas.

Integrated Transcriptome and Proteome Analysis Provides New Insights into Starch and Sucrose Metabolism and Regulation of Corm Expansion Process in Colocasia esculenta

The global significance of Colocasia esculenta, a tuber crop rich in nutritional value and starch, prompts further investigation into its corm development.

BACKGROUND

Previous studies have focused on starch accumulation within the tubers, yet the genetic and proteomic basis of corm expansion remains largely unexplored. This study aims to elucidate the key genes and proteins involved in this process.

METHODS

We selected 'Lipu Taro No.1' and conducted a longitudinal starch content analysis, full-length transcriptome sequencing, and a proteomic analysis during three distinct stages of corm development.

RESULTS

Our findings reveal a significant increase in both amylose and amylopectin contents as the corm develops, indicating the temporal regulation of starch biosynthesis. The integration of transcriptome and proteomic data identified differentially expressed genes and proteins associated with starch and sucrose metabolism, as well as plant hormone signal transduction.

CONCLUSIONS

This study delineates a temporal gene expression pattern that is crucial for starch synthesis and provides insights into the regulatory mechanisms controlling corm expansion and starch deposition, offering valuable references for future molecular breeding strategies to enhance taro yield and quality.

Complete mitochondrial genome assembly and comparative analysis of Colocasia esculenta

Colocasia esculenta ranks as the fifth most important tuber crop and is known for its high nutritional and medicinal value. However, there is no research on its mitochondrial genome, hindering in-depth exploration of its genomic resources and genetic relationships. Using second- and third-generation sequencing technologies, we assembled and annotated the mitogenome of C. esculenta. Its mitogenome mainly consists of five circular DNA molecules, with a total length of 594,811 bp and a GC content of 46.25%. A total of 55 genes, 157 simple sequence repeats, 29 tandem repeat sequences, 202 dispersed repeat sequences, and 625 RNA editing sites were detected. Most protein-coding genes use ATG as the start codon, and the third position of the codon tends to be A or T (U). GAA, AUU, and UUU are the most common codons in C. esculenta mitochondria. Finally, based on 28 representative plant species, a phylogenetic tree was constructed, revealing a close relationship between C. esculenta and Araceae. This study provides comprehensive information on C. esculenta, laying a foundation for crop genetics and molecular breeding.

Genetic diversity and population structure studies of West African sweetpotato [Ipomoea batatas (L.) Lam] collection using DArTseq

BACKGROUND

Sweetpotato is a vegetatively propagated crop cultivated worldwide, predominantly in developing countries, valued for its adaptability, short growth cycle, and high productivity per unit land area. In most sub-Saharan African (SSA) countries, it is widely grown by smallholder farmers. Niger, Nigeria, and Benin have a huge diversity of sweetpotato accessions whose potential has not fully been explored to date. Diversity Arrays Technology (DArTseq), a Genotyping by Sequencing (GBS) method, has been developed and enables genotyping with high-density single nucleotide polymorphisms (SNPs) in different crop species. The aim of this study was to assess the genetic diversity and population structure of the West African sweetpotato collection using Diversity Arrays Technology through Genotyping by Sequencing (GBS).

RESULTS

29,523 Diversity Arrays Technology (DArTseq) single nucleotide polymorphism markers were used to genotype 271 sweetpotato accessions. Genetic diversity analysis revealed an average polymorphic information content (PIC) value of 0.39, a minor allele frequency of 0.26, and an observed heterozygosity of 10%. The highest value of polymorphic information content (PIC) (0.41) was observed in chromosomes 4, while the highest proportion of heterozygous (He) (0.18) was observed in chromosomes 11. Molecular diversity revealed high values of polymorphic sites (Ps), theta (θ), and nucleotide diversity (π) with 0.973, 0.158, and 0.086, respectively, which indicated high genetic variation. The pairs of genetic distances revealed a range from 0.08 to 0.47 with an overall average of 0.34. Population structure analysis divided the 271 accessions into four populations (population 1 was characterised by a mixture of accessions from all countries; population 2, mostly comprised of Nigerian breeding lines; population 3 contained exclusively landraces from Benin; and population 4 was composed by only landraces from West African countries) at K = 4, and analysis of molecular variance (AMOVA) based on PhiPT values showed that most of the variation was explained when accessions were categorized based on population structure at K = 4 (25.25%) and based on cluster analysis (19.43%). Genetic distance showed that group 4 (which constituted by landraces of Niger and Benin) was genetically distant (0.428) from groups 2 (formed by 75% of breeding lines of Nigeria), while group 1 was the closest (0.182) to group 2.

CONCLUSIONS

This study employed 7,591 DArTseq-based SNP markers, revealing extensive polymorphism and variation within and between populations. Variability among countries of origin (11.42%) exceeded that based on biological status (9.13%) and storage root flesh colour (7.90%), emphasizing the impact of migration on genetic diversity. Population structure analysis using principal component analysis (PCA), Neighbor-Joining (NJ) tree, and STRUCTURE at K = 4 grouped 271 accessions into distinct clusters, irrespective of their geographic origins, indicating widespread genetic exchange. Group 4, dominated by landraces (95%), showed significant genetic differentiation (Nei's Gst = 0.428) from Group 2, mainly comprising breeding lines, suggesting their potential as heterotic groups for breeding initiatives like HEBS or ABS.

A comparative study of population structure and genetic diversity of commercial and indigenous chickens from different agro-ecological zones in Ghana using SilicoDArT and SNP markers

Chicken production, both in the local and commercial sectors, contributes significantly to human livelihood and food security. Precise use of diverse genetic resources is primary in breeding programs. The study analyzed the genetic diversity and population structure of commercial chickens and indigenous chicken ecotypes from three different agro-ecological zones (Semi-Deciduous Rainforest Zone, Guinea Savannah, and Coastal Savannah) using SilicoDArT and SNP markers, utilizing whole-genome sequencing and phenotypic data. Phenotypic data were collected from 72 indigenous chicken ecotypes across the three AEZs, and 32 commercial birds kept at the Kwame Nkrumah University of Science and Technology (KNUST). DNA samples used for sequencing were obtained from 88 chickens (62 indigenous chicken ecotypes and 26 commercial chickens). A total of 54,995 SilicoDArT and 85,396 SNPs markers were generated from DArTseq genotyping. After filtering, 44,784 SilicoDArT and 58,353 SNP were used for genetic diversity and population structure analysis. Both markers showed high reproducibility and call rate. Polymorphic information content (PIC) values ranged from 0.00 to 0.50, while ≥ 50 % showed PIC values more than the median. Furthermore, we obtained FST values, Nei's genetic distance, dendrogram analysis, and principal component analysis (PCA) of commercial and indigenous chickens. The FST and Nei's genetic distance showed that there is high genetic diversity between the commercial chickens and the indigenous chicken ecotypes. However, there was low genetic diversity among the indigenous chicken ecotypes. The PCA analysis indicated a clear separation between the commercial and indigenous chicken ecotypes, while no clear separation was observed between the indigenous chicken ecotypes. The phenotypic data and the dendrogram indicated that naked and frizzle genes do not markedly alter the genetics of indigenous and commercial birds, and their influence on economic traits may be solely determined by the prevailing environmental conditions. The results indicate that there is high genetic differentiation between commercial and indigenous chickens based on SilicoDArT and SNP markers. The indigenous chickens from the agro-ecological zones have low genetic diversity and might have a common origin. Naked neck and frizzle genes do not markedly alter the genetic performance of birds in terms of economic traits. Therefore, the superiority of birds carrying these genes in economic traits may be solely due to environmental variation.

Genome-Wide Development of InDel-SSRs and Association Analysis of Important Agronomic Traits of Taro (Colocasia esculenta) in China

Taro (Colocasia esculenta (L.) Schott) is a tropical tuber crop whose underground corms are used as an important staple food. However, due to a lack of molecular markers, the genetic diversity, germplasm identification, and molecular breeding of taro are greatly limited. In this study, high-density InDel-SSR molecular markers covering the whole genome were developed based on the resequencing data of taro core germplasm. A total of 1,805,634 InDel-SSR loci were identified, and 219 highly polymorphic markers with an average polymorphism information content PIC value of 0.428 were screened. Furthermore, a genetic diversity analysis of 121 taro germplasm resources was conducted based on 219 markers, dividing the resources into three groups. In addition, an association analysis showed that, of the multiple InDel-SSR markers, g13.52 and g12.82 were significantly associated with leaf area and average cormel weight, respectively; the candidate genes CeARF17 (EVM0014444) and CeGA20ox (EVM0001890) were related to cormel expansion; and we excavated the candidate genes CeXXT2 (EVM0016820) and CeLOG1 (EVM0017064), which regulate leaf development. The InDel-SSRs and candidate genes identified in this study are expected to provide important support for genetically improving and breeding new varieties of taro.

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.

Nutritional, physicochemical, and functional properties of Hawaiian taro (Colocasia esculenta) flours: A comparative study

Taro (Colocasia esculenta) flour is a viable carbohydrate alternative and a functional additive for food formulation; however, different taro varieties may possess distinct characteristics that may influence their suitability for food production. This study evaluated the nutritional, physicochemical, and functional properties of flours from five Hawaiian taro varieties: Bun-Long, Mana Ulu, Moi, Kaua'i Lehua, and Tahitian. Tahitian, Bun-long, and Moi had high total starch contents of 40.8, 38.9, and 34.1 g/100 g, respectively. Additionally, Moi had the highest neutral detergent fiber (25.5 g/100 g), lignin (1.39 g/100 g), and cellulose (5.31 g/100 g). In terms of physicochemical properties, Tahitian showed the highest water solubility index (33.3 g/100 g), while Tahitian and Moi exhibited the two highest water absorption indices (5.81 g/g and 5.68 g/g, respectively). Regarding functional properties, Tahitian had the highest water absorption capacity (3.48 g/g), and Tahitian and Moi had the two highest oil absorption capacities (3.15 g/g and 2.68 g/g, respectively). Therefore, the flours from these Hawaiian taro varieties possess promising characteristics that could enhance food quality when used as alternative additives in food processing.

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 (&gt;3.0%), low in acridity, and total oxalate content (&lt;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.