Analyses of genetic diversity and population structure of anchote (Coccinia abyssinica (Lam.) Cogn.) using newly developed EST-SSR markers

Tolera, Bekele Serbessa; Woldegebriel, Kifle Dagne; Gari, Abel Teshome; Geleta, Mulatu; Geletu, Kassahun Tesfaye

doi:10.1007/s10722-021-01132-5

Cited by 8 publications

(3 citation statements)

References 22 publications

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“…Since a reference genome sequence is not available for noug yet, the genomic positions of the SSRs identified in the present study is currently unknown. With the annotation of the unigenes used, it will be possible to select genome-wide single-copy SSRs for genotyping a diverse panel of noug genotypes and then develop gene-associated polymorphic SSRs for their numerous applications in noug and other Guizotia species, as the rate of cross-species transferability of transcriptome-derived SSR markers is proved high ( Lu et al, 2013 ; Teshome et al, 2015 ; Zhou et al, 2016 ; Gadissa et al, 2018 ; Serbessa Tolera et al, 2021 ). The applications include genetic diversity analyses for conservation and breeding, as well as genetic linkage mapping and genome-wide association studies.…”

Section: Discussionmentioning

confidence: 99%

RNA-Seq Provides Novel Genomic Resources for Noug (Guizotia abyssinica) and Reveals Microsatellite Frequency and Distribution in Its Transcriptome

et al. 2022

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Genomic resources and tools are essential for improving crops and conserving their genetic resources. Guizotia abyssinica (noug), an outcrossing edible oilseed crop, has highly limited genomic resources. Hence, RNA-Seq based transcriptome sequencing of 30 noug genotypes was performed to generate novel genomic resources and assess their usefulness. The genotypes include self-compatible and self-incompatible types, which differ in maturity time, photoperiod sensitivity, or oil content and quality. RNA-Seq was performed on Illumina HiSeq 2500 platform, and the transcript was reconstructed de novo, resulting in 409,309 unigenes. The unigenes were characterized for simple sequence repeats (SSRs), and served as a reference for single nucleotide polymorphism (SNP) calling. In total, 40,776 SSRs were identified in 35,639 of the 409,309 unigenes. Of these, mono, di, tri, tetra, penta and hexanucleotide repeats accounted for 55.4, 20.8, 21.1, 2.3, 0.2, and 0.2%, respectively. The average G+C content of the unigenes and their SSRs were 40 and 22.1%, respectively. The vast majority of mononucleotide repeat SSRs (97%) were of the A/T type. AG/CT and CCA/TGG were the most frequent di and trinucleotide repeat SSRs. A different number of single nucleotide polymorphism (SNP) loci were discovered in each genotype, of which 1,687 were common to all 30 genotypes and 5,531 to 28 of them. The mean observed heterozygosity of the 5,531 SNPs was 0.22; 19.4% of them had polymorphism information content above 0.30 while 17.2% deviated significantly from Hardy-Weinberg equilibrium (P < 0.05). In both cluster and principal coordinate analyses, the genotypes were grouped into four major clusters. In terms of population structure, the genotypes are best represented by three genetic populations, with significant admixture within each. Genetic similarity between self-compatible genotypes was higher, due to the narrow genetic basis, than that between self-incompatible genotypes. The genotypes that shared desirable characteristics, such as early maturity, and high oil content were found to be genetically diverse, and hence superior cultivars with multiple desirable traits can be developed through crossbreeding. The genomic resources developed in this study are vital for advancing research in noug, such as genetic linkage mapping and genome-wide association studies, which could lead to genomic-led breeding.

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Section: Discussionmentioning

confidence: 99%

RNA-Seq Provides Novel Genomic Resources for Noug (Guizotia abyssinica) and Reveals Microsatellite Frequency and Distribution in Its Transcriptome

et al. 2022

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“…Among the SSR markers, the expressed sequence tag-derived simple sequence repeats (EST-SSRs) have become popular due to their various advantages such as high transferability among closely related taxa, relative ease, and cost-effectiveness to develop (Teshome et al, 2015;Chombe et al, 2017;Gadissa et al, 2018;Serbessa et al, 2021). Due to the fact that they represent expressed parts of a genome, they have a higher average rate of transferability across species than genomic SSRs (Gupta et al, 2003), and they are highly associated with differentially expressed genes (Saha et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Novel Expressed Sequence Tag-Derived and Other Genomic Simple Sequence Repeat Markers Revealed Genetic Diversity in Ethiopian Finger Millet Landrace Populations and Cultivars

et al. 2021

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Finger millet (Eleusine coracana (L.) Geartn.) is a self-pollinating amphidiploid crop cultivated with minimal input for food and feed, as well as a source of income for small-scale farmers. To efficiently assess its genetic diversity for conservation and use in breeding programs, polymorphic DNA markers that represent its complex tetraploid genome have to be developed and used. In this study, 13 new expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were developed based on publicly available finger millet ESTs. Using 10 polymorphic SSR markers (3 genomic and 7 novel EST-derived), the genetic diversity of 55 landrace accessions and 5 cultivars of finger millet representing its major growing areas in Ethiopia was assessed. In total, 26 alleles were detected across the 10 loci, and the average observed number of alleles per locus was 5.6. The polymorphic information content (PIC) of the loci ranged from 0.045 (Elco-48) to 0.71 (UGEP-66). The level of genetic diversity did not differ much between the accessions with the mean gene diversity estimates ranging only from 0.44 (accession 216054) to 0.68 (accession 237443). Similarly, a narrow range of variation was recorded at the level of regional states ranging from 0.54 (Oromia) to 0.59 (Amhara and Tigray). Interestingly, the average gene diversity of the landrace accessions (0.57) was similar to that of the cultivars (0.58). The analysis of molecular variance (AMOVA) revealed significant genetic variation both within and among accessions. The variation among the accessions accounted for 18.8% of the total variation (FST = 0.19; P < 0.001). Similarly, significant genetic variation was obtained among the geographic regions, accounting for 6.9% of the total variation (P < 0.001). The results of the cluster, principal coordinate, and population structure analyses suggest a poor correlation between the genetic makeups of finger millet landrace populations and their geographic regions of origin, which in turn suggests strong gene flow between populations within and across geographic regions. This study contributed novel EST-SSR markers for their various applications, and those that were monomorphic should be tested in more diverse finger millet genetic resources.

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“…Cogn.) is a perennial root crop belonging to Cucurbitaceae family (Serbessa Tolera, B. et al 2021). The crop plays an important role in the local diet of rural and peri-urban communities mainly in Western and South Western Ethiopia (Zerihun, T., et .al.…”

Section: Introductionmentioning

confidence: 99%

Preparation of skin care product using coccinia abyssinica tuber extract

Berhanu¹

2021

Preprint

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Anchote (Coccinia abyssinica) is highly nutritious crop which is mostly cultivated in Wollega Zone, Oromia Regional State of Ethiopia. Anchote tubers are rich in calcium and starch which are essential for healthy skin. Thus, a new skin cream was formulated using coccinia abyssinica tuber extract for the purpose of moistening and nourishing the skin. Coccinia abyssinica tuber extract was prepared by maceration extraction method. Then, tuber extract of coccinia abyssinica was mixed with ingredients such as thickening agents, humectant, emollient, antioxidant, preservatives and fragrance to prepare a new skin cream. A newly prepared skin care product was applied to the human skin. The skin became soft, attractive and supple after using this new skin cream. It didn’t cause any side effects on the human body. The current study revealed that coccinia abyssinica skin care product enrich the body with nutrients and useful minerals.

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Analyses of genetic diversity and population structure of anchote (Coccinia abyssinica (Lam.) Cogn.) using newly developed EST-SSR markers

Cited by 8 publications

References 22 publications

RNA-Seq Provides Novel Genomic Resources for Noug (Guizotia abyssinica) and Reveals Microsatellite Frequency and Distribution in Its Transcriptome

RNA-Seq Provides Novel Genomic Resources for Noug (Guizotia abyssinica) and Reveals Microsatellite Frequency and Distribution in Its Transcriptome

Novel Expressed Sequence Tag-Derived and Other Genomic Simple Sequence Repeat Markers Revealed Genetic Diversity in Ethiopian Finger Millet Landrace Populations and Cultivars

Preparation of skin care product using coccinia abyssinica tuber extract

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