Genetic diversity and population structure of Vernonia [Vernonia galamensis (Cass.) Less] populations from Ethiopia revealed by SSR markers

Abstract BackgroundVernonia (Vernonia galamensis) is a potential novel industrial crop due to high demand for its natural epoxidised oil, which can be used for the manufacturing of oleochemicals such as paints, plastic formulations (polyvinyl chloride), and pharmaceutical products. This study is initiated for the systematic and intensive genetic diversity assessment of V. galamensis accessions by SSR molecular markers to minimize the existing research gaps, provide a clue for germplasm conservation and further research. ResultsTwenty SSR markers were used for genetic diversity analyses of 150 individual V. galamensis accessions representing 10 populations, from which a total of 79 bands were identified across the entire loci. All the loci used showed high polymorphism that ranged from 0.50 to 0.96, while the mean observed heterozygosity (Ho) was 0.15 across all the 20 markers evaluated. The molecular variance analysis (AMOVA) showed significant variations despite low differentiation among populations which accounted for only 11% of the total variations. Populations clustering showed that the dendrogram and principal coordinate’s analysis roughly classified the 150 accessions into four groups. However, the Bayesian model-based clustering (STRUCTURE) grouped into 6 (K = 6) major gene pools. These analyses showed accessions collected from the same region of origin did not often grouped entirely together within a given major groups. ConclusionsThe result suggested that the markers applied to ten populations, in which East Showa and East Harerghe revealed higher genetic diversity, signaled that these areas are the hotspots for in-situ conservation of V. galamensis. In addition, the values of SSR markers such as heterozygosity, Shannon‘s index, polymorphic information content, and population clusters are important baseline information for future V. galamensis cultivation, breeding and genetic resource conservation endeavors in Ethiopia.

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Genetic diversity and population structure of Vernonia [Vernonia galamensis (Cass.) Less] populations from Ethiopia revealed by SSR markers

10.21203/rs.2.18928/v2 ◽

2020 ◽

Author(s):

Alemneh Mideksa Egu ◽

Kassahun Tesfaye ◽

Kifle Dagne New ◽

Xuebo Hu New

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Ssr Markers ◽

Polymorphic Information Content ◽

In Situ Conservation ◽

Germplasm Conservation ◽

Pharmaceutical Products ◽

Gene Pools ◽

Vernonia Galamensis ◽

Diversity Assessment

Abstract Background: Vernonia (Vernonia galamensis) is a potential novel industrial crop due to high demand for its natural epoxidized oil, which can be used for the manufacturing of oleochemicals such as paints, plastic formulations (polyvinyl chloride), and pharmaceutical products. This study was initiated for the systematic and intensive genetic diversity assessment of V. galamensis accessions by SSR molecular markers to minimize the existing research gaps, provide a clue for germplasm conservation and further research. Results: Twenty SSR markers were used for genetic diversity analyses of 150 individual V. galamensis accessions representing 10 populations, from which a total of 79 bands were identified for the 20 loci. All the loci used showed high polymorphism that ranged from 0.50 to 0.96, while the mean observed heterozygosity (Ho) was 0.15 across all the 20 markers evaluated. The molecular variance analysis (AMOVA) showed significant variations among populations which accounted for 11% of the variations. Populations clustering showed that the dendrogram and principal coordinate’s analysis roughly classified the accessions into four groups. However, the Bayesian model-based clustering (STRUCTURE) grouped into 6 (K = 6) major gene pools. Since, the cluster and the STRUCTURE analyses did not group the populations into sharply distinct clusters, due to presence of gene flow and mode of reproduction of the plant. Conclusions: The SSR molecular markers used in this study are highly polymorphic. Among the ten populations, East Showa and East Hararghe revealed higher genetic diversity, signaled that these areas are the hotspots for in-situ conservation of V. galamensis. In addition, the values of SSR markers such as heterozygosity, Shannon‘s index, polymorphic information content, and population clusters are important baseline information for future V. galamensis cultivation, breeding and genetic resource conservation endeavors in Ethiopia.

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Genetic diversity and population structure of Vernonia [Vernonia galamensis (Cass.) Less] populations from Ethiopia revealed by SSR markers

10.21203/rs.2.12914/v1 ◽

2019 ◽

Author(s):

Alemneh Mideksa Egu ◽

Kifle Dagne ◽

Kassahun Tesfaye ◽

Xuebo Hu

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Polymorphic Information Content ◽

In Situ Conservation ◽

Germplasm Conservation ◽

Pharmaceutical Products ◽

Gene Pools ◽

Vernonia Galamensis ◽

Principal Coordinates ◽

The Mean

Abstract Background Vernonia (Vernonia galamensis) is a potential novel industrial crop due to high demand to its natural epoxidised oil, which can be used for the manufacturing of polyvinyl chloride, adhesives, and petrochemicals, cosmetic and pharmaceutical products. This study is initiated for the systematic and intensive assessment of V. galamensis accessions genetic diversity through SSR molecular markers to minimize the existing research gaps, and provide a clue for germplasm conservation and further research. Results A total of 150 V. galamensis accessions were analyzed using 20 SSR markers. The markers detected a total of 79 with an average of 3.9 alleles per locus. The mean number of effective alleles was 3.06 and, the mean observed heterozygosity (Ho) was 0.15 across all the 20 markers evaluated. The marker also showed the highest percent of polymorphism that ranged from 0.50 to 0.96 with an average of 0.76. The analysis of molecular variance showed only 11% variation was among populations, 22% among individuals within populations and 67% within individuals. The largest number of migrants per generation was occurred between Derashie and Wollo (Nm=7.37) whereas the lowest values was between East Harerghe and West Harerghe (Nm =1.42). A factor analysis including dendrogram clusters and principal coordinates classified the 150 accessions into 4 groups. However, the Bayesian model based clustering (STRUCTURE) grouped into 3 (K = 3) major gene pools. These analyses showed accessions collected from the same region of origin did not often grouped entirely together within a given major groups. Conclusions Molecular genetic diversity analysis, using SSR markers was the first report in V. galamensis. All the markers used were polymorphic in the population studied. The markers detected the larger number of alleles, higher expected heterozygosity than observed heterozygosity. The markers applied to ten populations, in which East Showa and West Harerghe revealed higher genetic diversity, and can be considered as the hotspots for in-situ conservation of V. galamensis. In addition, the values of SSR markers such as heterozygosity, Shannon‘s index, polymorphic information content and population clusters are an important baseline information for future V. galamensis cultivation, breeding and genetic resource conservation endeavors in Ethiopia.

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Genetic diversity and population structure of Vernonia [Vernonia galamensis (Cass.) Less] populations from Ethiopia revealed by SSR markers

10.21203/rs.2.18928/v3 ◽

2021 ◽

Author(s):

Alemneh Mideksa Egu ◽

Kassahun Tesfaye ◽

Kifle Dagne ◽

Xuebo Hu

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Genetic Resource ◽

In Situ Conservation ◽

Resource Conservation ◽

Pharmaceutical Products ◽

Gene Pools ◽

Vernonia Galamensis ◽

Genetic Resource Conservation

Abstract Background: Vernonia (Vernonia galamensis) is a potential novel industrial crop due to high demand for its natural epoxidized oil, which can be used for the manufacturing of oleochemicals such as paints, plastic formulations (polyvinyl chloride), and pharmaceutical products. Assessment of the extent of genetic diversity in V. galamensis was the first and the most step in cultivation, breeding and genetic resource conservation. Hence, this study was aimed to assess the genetic diversity and population structure of this plant from different agro-ecologies in Ethiopia using SSR markers. Results: Twenty SSR markers were used for genetic diversity analyses of 150 individual V. galamensis accessions representing 10 populations, from which a total of 79 bands were identified for the 20 loci. All the loci used showed high polymorphism that ranged from 0.50 to 0.96, while the mean observed heterozygosity (Ho) was 0.15 across all the 20 markers evaluated. The molecular variance analysis (AMOVA) showed significant variations among populations which accounted for 11% of the variations. Populations clustering showed that the dendrogram and principal coordinate’s analysis roughly classified the accessions into four groups. However, the Bayesian model-based clustering (STRUCTURE) grouped into 6 (K = 6) major gene pools. Since, the cluster and the STRUCTURE analyses did not group the populations into sharply distinct clusters, due to presence of gene flow and mode of reproduction of the plant. Conclusions: The SSR molecular markers used in this study are highly polymorphic. Among the ten populations, East Showa and East Hararghe revealed higher genetic diversity, signaled that these areas are the hotspots for in-situ conservation of V. galamensis. In addition, the values of SSR markers such as heterozygosity, Shannon‘s index, polymorphic information content, and population clusters are important baseline information for future V. galamensis cultivation, breeding and genetic resource conservation endeavors in Ethiopia.

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Assessment of genetic diversity and wilt disease resistance in hot pepper (Capsicum annuum) germplasm from Ethiopia

Biodiversity Research and Conservation ◽

10.2478/biorc-2021-0006 ◽

2021 ◽

Vol 63 (1) ◽

pp. 31-40

Author(s):

Dawit Bedane Woubit ◽

Shiferaw Eleni ◽

Sileshi Fitsum ◽

Assefa Mekonnen ◽

Aklilu Shimeles

Keyword(s):

Genetic Diversity ◽

Disease Resistance ◽

Capsicum Annuum ◽

Ssr Markers ◽

Gene Diversity ◽

Disease Incidence ◽

In Situ Conservation ◽

Wilt Disease ◽

Hot Pepper ◽

Diversity Assessment

Abstract Hot pepper (Capsicum annuum L.) is an economically important crop in Ethiopia. Wide variability in hot pepper germplasm in Ethiopia is expected due to the presence of diverse environmental conditions and variation in farming systems. The present study was carried out to evaluate the resistance of 75 hot pepper accessions to wilt disease and assess their genetic diversity using SSR markers. Out of 75 accessions tested, the present study identified 23 accessions that showed resistance (R) with the value of 1-10% disease incidence. The genetic diversity assessment using 13 polymorphic SSR markers allowed the detection of 111 clear and scorable bands. The number of alleles per locus ranged from 5 to 13, with an average of 8.54. The PIC value ranged from 0.27 to 0.87 with an average of 0.59. The gene diversity indices were highly variable across SSR loci and ranged from 0.29 to 0.88 with mean genetic diversity of 0.62. Observed heterozygosity was also highly variable between loci (0.01-0.45) indicating that the accessions were not fixed to homozygosity. Furthermore, genetic diversity parameters were estimated among populations by grouping accessions based on their origin. Within populations, the PIC value ranged from 0.31 to 0.77. The genetic distances among the eight populations ranged from 0.15 to 0.48. The observed highest genetic diversity (0.80) in the Amhara region (Gojam) may indicate this area as the primary site for designing in situ conservation for this crop in Ethiopia. The research findings provide baseline information on disease resistance germplasm sources to be used for the breeding program, as well as the status of genetic diversity of the accessions for efficient conservation and proper utilization of the existing genetic resources in the country.

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Genetic Diversity Assessment in Pea (Pisum sativum L.) using Microsatellite Markers

International Journal of Bio-resource and Stress Management ◽

10.23910/1.2021.2374a ◽

2021 ◽

Vol 12 (5) ◽

pp. 402-408

Author(s):

Hanuman Ram ◽

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Ssr Markers ◽

Molecular Diversity ◽

Polymorphic Information Content ◽

Association Studies ◽

Pisum Sativum L ◽

Diversity Assessment ◽

Potential Use ◽

Simple Sequence

The present study was conducted on genetic diversity analyses among 24 pea genotypes during 2017–2018 to assess the molecular diversity of pea genotypes using SSR markers. Out of 62, eleven markers were found to be polymorphic and the polymorphic information content (PIC) of the simple sequence repeat (SSR) markers ranged from 0.19 to as high as 0.64. Molecular profiling of these genotypes using 11 SSRs distributed throughout the genome generated 32 alleles with a mean of 2.91 alleles per locus. The genetic dissimilarity based on simple matching coefficient for 24 genotypes ranged from 0.00 to 0.91 with an average of 0.52. Cluster analyses grouped 24 genotypes into two major clusters with one outlier and supported by principal coordinate analysis (PCoA) in which genotypes were distributed across four quadrangles. Analysis of molecular variance (AMOVA) showed significant estimated value at degree of 1000 permutations. Percentage of variability was higher among individual (67%) than among populations (11%). Percentage of variability within individual was also higher (22%) than among populations (11%). Pop1 (I=0.707, He=0.446, and uHe=0.466) shows higher diversity than pop2 (I=0.630, He=0.381 and uHe=0.398). The percentage of polymorphic loci per population (PPL) ranged from 81.82% (pop2) to 90.91% (pop1) with an average of 86.36%. The present study demonstrates the utility of microsatellite markers for estimating molecular diversity as well as genotype identification in pea. This study also suggests a potential use of these markers in further association studies.

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Genetic variability and population structure of Ethiopian chickpea (Cicer arietinum L.) germplasm

PLoS ONE ◽

10.1371/journal.pone.0260651 ◽

2021 ◽

Vol 16 (11) ◽

pp. e0260651

Author(s):

Sintayehu Admas ◽

Kassahun Tesfaye ◽

Teklehaimanot Haileselassie ◽

Eleni Shiferaw ◽

K. Colton Flynn

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Germplasm Conservation ◽

Genetic Distances ◽

Geographic Region ◽

Ex Situ ◽

Conservation Strategies ◽

Breeding Programs

Evaluation of the genetic diversity and an understanding of the genetic structure and relationships of chickpea genotypes are valuable to design efficient germplasm conservation strategies and crop breeding programs. Information is limited, in these regards, for Ethiopian chickpea germplasms. Therefore, the present study was carried out to estimate the genetic diversity, population structure, and relationships of 152 chickpea genotypes using simple sequence repeats (SSR) markers. Twenty three SSR markers exhibited polymorphism producing a total of 133 alleles, with a mean of 5.8 alleles per locus. Analyses utilizing various genetic-based statistics included pairwise population Nei’s genetic distance, heterozygosity, Shannon’s information index, polymorphic information content, and percent polymorphism. These analyses exemplified the existence of high genetic variation within and among chickpea genotypes. The 152 genotypes were divided into two major clusters based on Nei’s genetic distances. The exotic genotypes were grouped in one cluster exclusively showing that these genotypes are distinct to Ethiopian genotypes, while the patterns of clustering of Ethiopian chickpea genotypes based on their geographic region were not consistent because of the seed exchange across regions. Model-based population structure clustering identified two discrete populations. These finding provides useful insight for chickpea collections and ex-situ conservation and national breeding programs for widening the genetic base of chickpea.

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SSR-based and carotenoid diversity assessment of tropical yellow endosperm maize inbred lines

Plant Genetic Resources ◽

10.1017/s1479262113000294 ◽

2013 ◽

Vol 12 (1) ◽

pp. 67-73 ◽

Cited By ~ 2

Author(s):

Oyenike Adeyemo ◽

Olusesan Omidiji

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Vitamin A Deficiency ◽

Inbred Lines ◽

Reproductive Age ◽

Sub Saharan Africa ◽

Provitamin A ◽

Maize Inbred Lines ◽

Diversity Assessment

Yellow endosperm maize can be used to reduce vitamin A deficiency among many pre-school children and women of reproductive age in sub-Saharan Africa. Assessment of the genetic diversity of tropical yellow endosperm maize inbred lines will have genetic gains in breeding design to develop lines with an enhanced level of provitamin A. We screened 122 tropical yellow endosperm maize inbred lines with 62 simple sequence repeat (SSR) markers and 51 SSR loci were polymorphic. We detected 190 alleles with an average of 3.72 alleles per locus, and polymorphic information content values among the inbred lines varied from 0.12 to 0.74 with an average of 0.43. Genetic distance (GD) values among all the pairs of the 122 inbred lines varied from 0.02 to 0.61 with an average of 0.41 for the SSR markers. The inbred lines exhibited a substantial level of genetic diversity. Genetic diversity was also evaluated using carotenoid data. The Euclidean GDs varied from 1.00 to 9.97 with an average of 3.81 for the carotenoid data. Cluster and principal coordinate analyses revealed clear separation of maize inbred lines into SSR-based groupings and carotenoid-based groupings. Cluster based on SSR markers were predominantly consistent with known pedigree data of the inbred lines. The correlation using Mantel's test between carotenoid-based GD estimates and SSR marker-based GD estimates gave a low r value ( − 0.06). The grouping of lines will facilitate the selection of parental lines for making crosses to develop new lines with enhanced provitamin A content.

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Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Rice ◽

10.1186/s12284-020-00445-w ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Ai-ling Hour ◽

Wei-hsun Hsieh ◽

Su-huang Chang ◽

Yong-pei Wu ◽

Han-shiuan Chin ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Indigenous Peoples ◽

Oryza Sativa L ◽

Crop Improvement ◽

Genetic Erosion ◽

Germplasm Conservation ◽

Gene Pools ◽

Improved Varieties ◽

Breeding Goals

Abstract Background Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement. Results A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding. Conclusions The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

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Diversity Assessment of Some Sesame (Sesamum indicum L.) Genotypes Cultivated in Northern Ghana Using Morphological and Simple Sequence Repeat (SSR) Markers

Advances in Agriculture ◽

10.1155/2019/6067891 ◽

2019 ◽

Vol 2019 ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

Raphael Adu-Gyamfi ◽

Ruth Prempeh ◽

Issahaku Zakaria

Keyword(s):

Genetic Diversity ◽

Plant Height ◽

Ssr Markers ◽

Analysis Of Variance ◽

Morphological Data ◽

Northern Ghana ◽

Land Races ◽

Diversity Assessment ◽

Parental Lines ◽

Number Of Seeds

In Ghana, sesame is cultivated in some districts of northern Ghana. Genotypes cultivated are land races that are low yielding leading to decline in production. There is the need for improvement of these land races to generate high yielding cultivars. Characterization of genetic diversity of the sesame land races will be of great value in assisting in parental lines selection for sesame breeding programmes in Ghana. Twenty-five sesame land races were collected from five districts in northern Ghana noted for sesame cultivation. Seeds collected were planted in three replicates in randomized complete block design and were evaluated for a number of morphological characters. Data collected were subjected to Principal Component Analysis (PCA) and a dendrogram showing similarity between the accessions were drawn. Data on number of capsules per plant, number of seeds per capsule, and plant height at flowering were subjected to analysis of variance using GenStat Discovery Edition 4. Molecular genetic diversity was assessed by using thirty eight SSR markers widely distributed across sesame genome to characterize the materials. Twenty-one out of the 38 primers were polymorphic. Cluster analyses using the Euclidean similarity test and a complete link clustering method were used to make a dendrogram out of the morphological data. Analysis of variance showed that capsule number was significantly different; a range of 54.9 and 146.7 was produced. The number of seeds per capsule varied significantly and the variation between highest and lowest accession in seed production was 33%. Plant height was also significantly different ranging from 60.6 to 94.1 cm. Using morphological traits the accessions clustered into two major groups and two minor groups and variation among accessions were 10-61%. On the other hand, SSR marker-based dendrogram revealed five major and two minor groups. It showed that variation among the accessions was low, 10-20%. Heterozygosity was 0.52, total alleles produced were 410, and average allele per locus was 19.52. Six accessions, C3, C4, S5, W1, W3, and W5 fell in five different clusters in the SSR dendrogram and in six clusters in the morphomolecular based dendrogram. These accessions were noted for high capsule number per plant and seeds number per capsule and are recommended for consideration as potential parental lines for breeding programme for high yield.

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