Utilization of Phytochemical and Molecular Diversity to Develop a Target-Oriented Core Collection in Tea Germplasm

Tea has received attention due to its phytochemicals. For the direct use of tea germplasm in breeding programs, a core collection that retains the genetic diversity and various phytochemicals in tea is needed. In this study, we evaluated the content of eight phytochemicals over two years and the genetic diversity through 33 SSR (simple sequence repeats) markers for 462 tea accessions (entire collection, ENC) and developed a target-oriented core collection (TOCC). Significant phytochemical variation was observed in the ENC between genotypes and years. The genetic diversity of ENC showed high levels of molecular variability. These results were incorporated into developing TOCCs. The TOCC showed a representation of the ENC, where the mean difference percentage, the variance difference percentage, the variable rate of coefficient of variance percentage, and the coincidence rate of range percentage were 7.88, 39.33, 120.79, and 97.43, respectively. The Shannon’s diversity index (I) and Nei’s gene diversity (H) of TOCC were higher than those of ENC. Furthermore, the accessions in TOCC were shown to be selected proportionally, thus accurately reflecting the distribution of the overall accessions for each phytochemical. This is the first report describing the development of a TOCC retaining the diversity of phytochemicals in tea germplasm. This TOCC will facilitate the identification of the genetic determinants of trait variability and the effective utilization of phytochemical diversity in crop improvement programs.

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Re-defining the yam (Dioscorea spp.) core collection using morphological traits

Plant Genetic Resources ◽

10.1017/s1479262117000144 ◽

2017 ◽

Vol 16 (3) ◽

pp. 193-200 ◽

Cited By ~ 6

Author(s):

Gezahegn Girma ◽

Ranjana Bhattacharjee ◽

Antonio Lopez-Montes ◽

Badara Gueye ◽

Sam Ofodile ◽

...

Keyword(s):

Core Collection ◽

Morphological Traits ◽

Diversity Index ◽

Crop Improvement ◽

Principal Component ◽

Dioscorea Rotundata ◽

Entire Collection ◽

Improvement Programs ◽

Dioscorea Cayenensis ◽

Dioscorea Bulbifera

AbstractDevelopment of core collection representing the diversity in the entire germplasm creates a better access and enhanced utilization of the main collection thus allowing rapid evaluation in crop improvement programs. Core collections are dynamic in nature and needs revisiting when additional germplasm and information becomes available. In the current study, an attempt was made to re-define the previously developed yam (Dioscorea spp) core collection using 56 morphological traits. Information on additional acquired germplasm and presence of duplicates or mislabelled accessions in the entire collection was also used. The re-defined core collection consisted of 843 accessions and represented about 20% of the entire collection. It included six Dioscorea species, of which accessions of Dioscorea rotundata are in the majority (73.54%) followed by Dioscorea alata (21.35%), Dioscorea bulbifera (1.66%), Dioscorea cayenensis (1.42%), Dioscorea dumetorum (1.42%) and Dioscorea esculenta (0.59%). The Shannon weaver diversity index and principal component analysis revealed the maximum diversity captured in the core from the base collection. This re-defined core collection is more valuable than the original core since it represents true-to-type accessions ensuring reliability for enhanced utilization of germplasm in yam improvement programs.

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Population structure and core collection construction of apricot (Prunus armeniaca L.) in North Africa based on microsatellite markers

Plant Genetic Resources ◽

10.1017/s1479262115000313 ◽

2015 ◽

Vol 15 (1) ◽

pp. 21-28 ◽

Cited By ~ 1

Author(s):

Hedia Bourguiba ◽

Mohamed-Amine Batnini ◽

Lamia Krichen ◽

Neila Trifi-Farah ◽

Jean-Marc Audergon

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Markers ◽

North Africa ◽

Core Collection ◽

Diversity Index ◽

Gene Diversity ◽

Association Studies ◽

Conservation Strategies ◽

Phenotypic Data

North Africa enclosed original apricot genetic resources with the cohabitation of grafting and seed-propagated accessions. In this study, we assessed the genetic diversity and population structure of 183 apricot accessions using 24 microsatellite markers distributed evenly in the Prunus genome. A total of 192 alleles and a high level of gene diversity (0.593) were detected among the whole panel. Genetic structure analysis revealed the presence of four genetic clusters. We also found that both geographical origin and mode of propagation are important factors structuring genetic diversity in apricot species. Results confirmed the presence of gene exchange between the northern and southern countries of the Mediterranean Basin. Subsequently, a core collection of 98 accessions based on M (maximization) strategy showing 99.47% of allele retention ratio was constructed. No significant differences for Shannon's information index and Nei's diversity index were observed between the core and entire collections. Our results provide an effective aid for future germplasm preservation and conservation strategies as well as genetic association studies development in relation to phenotypic data.

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Molecular diversity analysis in hexaploid wheat (Triticum aestivum L.) and two Aegilops species (Aegilops crassa and Aegilops cylindrica) using CBDP and SCoT markers

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-021-00157-8 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Ghazal Ghobadi ◽

Alireza Etminan ◽

Ali Mehras Mehrabi ◽

Lia Shooshtari

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Crop Improvement ◽

Wild Relatives ◽

Resolving Power ◽

Start Codon ◽

Aegilops Cylindrica ◽

Aegilops Crassa

Abstract Background Evaluation of genetic diversity and relationships among crop wild relatives is an important task in crop improvement. The main objective of the current study was to estimate molecular variability within the set of 91 samples from Triticum aestivum, Aegilops cylindrica, and Aegilops crassa species using 30 CAAT box–derived polymorphism (CBDP) and start codon targeted (SCoT) markers. Results Fifteen SCoT and Fifteen CBDP primers produced 262 and 298 fragments which all of them were polymorphic, respectively. The number of polymorphic bands (NPB), polymorphic information content (PIC), resolving power (Rp), and marker index (MI) for SCoT primers ranged from 14 to 23, 0.31 to 0.39, 2.55 to 7.49, and 7.56 to 14.46 with an average of 17.47, 0.34, 10.44, and 5.69, respectively, whereas these values for CBDP primers were 15 to 26, 0.28 to 0.36, 3.82 to 6.94, and 4.74 to 7.96 with a mean of 19.87, 0.31, 5.35, and 6.24, respectively. Based on both marker systems, analysis of molecular variance (AMOVA) indicated that the portion of genetic diversity within species was more than among them. In both analyses, the highest values of the number of observed (Na) and effective alleles (Ne), Nei’s gene diversity (He), and Shannon’s information index (I) were estimated for Ae. cylindrica species. Conclusion The results of cluster analysis and population structure showed that SCoT and CBDP markers grouped all samples based on their genomic constitutions. In conclusion, the used markers are very effective techniques for the evaluation of the genetic diversity in wild relatives of wheat.

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Assessment of Genetic Diversity of Promising Castor Been (Ricinus communis L.) Genotypes in Nigeria

Notulae Scientia Biologicae ◽

10.15835/nsb11310346 ◽

2019 ◽

Vol 11 (3) ◽

pp. 467-474

Author(s):

Bolaji Zuluqurineen SALIHU ◽

Olamide Ahmed FALUSI ◽

Adeyinka Olufemi ADEPOJU ◽

Ibrahim Wasiu AROLU ◽

Oladipupo Yusuf DAUDU ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Index ◽

Gene Diversity ◽

Ricinus Communis ◽

Polymorphic Information Content ◽

Block Design ◽

Genetic Material ◽

Morphological Data ◽

Research Attention ◽

Ricinus Communis L

Castor oil plant (Ricinus communis L.) is an important oil crop with little research attention in Nigeria. In the present research, extent of genetic diversity among 20 Nigerian castor genotypes was determined using morphological descriptors and molecular markers. The genotypes were laid out on a randomized complete block design with three replicated plots. Molecular genotyping of the genotypes was carried out using genomic Simple Sequence Repeats (SSR). The genotypes revealed high divergence in seed colour, seed shape, seed mottle, seed caruncle and seed sizes. Seedling establishment varied from 70.18% (in Acc. 006) to 93.25% (Acc. 001) with average mean of 81.53%. Raceme length ranged from 15.90 cm to 29.54 cm with population mean of 20.80 cm. The highest seed yield (1222.98 kg/ha) was recorded in Acc. 001 and the least (611.46 kg/ha) was observed in Acc. 006. Seed oil content varied between 32.15% in Acc. 042 and 54.03% in Acc. 006. Agglomerative cluster dendrogram constructed from morphological data showed random distribution of the genotypes into three cluster groups irrespective of the sources/collection points. The genetic diversity based on SSR Marker Analysis revealed high average expected heterozygosity (0.74), Polymorphic information content (0.68), Nei’s gene diversity index (0.72) and Shannon's Information index (1.43). The dendrogram constructed from molecular data grouped the twenty genotypes into three groups at coefficient of 0.34. From these findings, it showed that the twenty genotypes evaluated are divergent in nature and they could serve as good genetic material for castor breeding in Nigeria.

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Population structure and genetic diversity analysis in Sali (Oryza sativa) rice germplasm of Assam using microsatellite markers

ORYZA- An International Journal on Rice ◽

10.35709/ory.2021.58.2.4 ◽

2021 ◽

Vol 58 (2) ◽

pp. 279-286

Author(s):

Sandhani Saikia ◽

Pratap Jyoti Handique ◽

Mahendra K Modi

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Genetic Improvement ◽

Crop Improvement ◽

Mean Value ◽

Diversity Analysis ◽

Rice Cultivars ◽

Improvement Program ◽

Information Index ◽

Improvement Programs

Genetic diversity is the source of novel allelic combinations that can be efficiently utilized in any crop improvement program. To facilitate future crop improvement programs in rice, a study was designed to identify the underlying genetic variations in the Sali rice germplasms of Assam using SSR markers. The 129 SSR markers that were used in the study amplified a total of 765 fragments with an average of 5.93 alleles per locus. The Shannon's Information Index was found to be in the range from 0.533 to 1.786. The Polymorphism Information Content (PIC) fell into the range from 0.304 to 0.691 with a mean value of 0.55. The overall FST value was found to be 0.519 that indicated the presence of genetic differentiation amongst the genotypes used in the study. The Sali population was divided into two clusters. The information obtained from the present study will facilitate the genetic improvement of Sali rice cultivars.

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Enrichment of chickpea genetic resources collection monitored by microsatellites

Czech Journal of Genetics and Plant Breeding ◽

10.17221/49/2008-cjgpb ◽

2009 ◽

Vol 45 (No. 1) ◽

pp. 11-17 ◽

Cited By ~ 4

Author(s):

K. Jomová ◽

M. Benková ◽

J. Kraic

Keyword(s):

Genetic Diversity ◽

Genetic Resources ◽

Slovak Republic ◽

Diversity Index ◽

Polymorphic Information Content ◽

Microsatellite Analysis ◽

Entire Collection ◽

Single Fragment ◽

New Germplasm ◽

New Alleles

A set of 49 chickpea accessions maintained in the collection of the Genebank of the Slovak Republic was analyzed using microsatellite markers. The level of genetic diversity and the effectivity of new germplasm acquisition for the collection enrichment were evaluated. Five primer pairs used generated 50 different amplified alleles. Four of them, TA2, TA5, TR1, and TR7, containing a long TAA-tandem repeat, were polymorphic with 11–13 alleles per locus. A single fragment was obtained from all the accessions with the primer pair CATPER flanking a small microsatellite repetition in the mRNA sequence of chickpea cationic peroxidase. The genetic diversity was expressed as a diversity index (DI) and polymorphic information content (PIC) with values in the range from 0.885 to 0.904 and from 0.972 to 0.991, respectively. Recently acquired new germplasm contributed 13 new alleles to the entire collection, i.e. almost 70% of microsatellite diversity originated from the recently acquired accessions. Remarkable is also, that one accession carries a unique allel, not present in the remaining collection. Microsatellite analysis revealed the importance of collecting missions for the enrichment of collections of genetic resources.

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Genetic Variation in Invasive Populations of Yellow Toadflax (Linaria vulgaris) in the Western United States

Weed Science ◽

10.1614/ws-07-157.1 ◽

2008 ◽

Vol 56 (3) ◽

pp. 394-399 ◽

Cited By ~ 24

Author(s):

Sarah M. Ward ◽

Scott D. Reid ◽

Judy Harrington ◽

Jason Sutton ◽

K George Beck

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Recombination ◽

Diversity Index ◽

Gene Diversity ◽

Group Method ◽

Restricted Gene Flow ◽

Genetic Structuring ◽

Invasive Weed ◽

Yellow Toadflax

Intraspecific genetic variation may contribute significantly to invasiveness and control problems, but has been characterized to date in relatively few invasive weed species. We examined 56 intersimple sequence repeat (ISSR) loci in 220 individuals from 11 invading populations of yellow toadflax sampled across five western states. All populations showed high levels of genetic diversity. Estimated values for Shannon's diversity measure ranged from 0.217 to 0.388, and for expected heterozygosity from 0.178 to 0.260. Nei's total gene diversity index (HT), on the basis of all individuals across all populations, was 0.267. Partitioning of genetic variance using analysis of molecular variance revealed 1.7% of genetic variation among regional population groups, 29.1% among populations within groups, and 69.2% within populations, consistent with expectations for an outcrossing species but suggesting little geographic differentiation. Pairs of adjacent individuals identical at all ISSR loci that appeared to be ramets of a single clone were detected in only one population. This indicates that patch expansion in yellow toadflax is driven more by sexual reproduction via seed than by rhizomatous clonal spread, at least at the spatial scale of sampling for this study. Eight populations had significant values for Mantel's R at P = 0.05, suggesting some fine-scale positive genetic structuring, possibly from restricted gene flow. Population clustering on the basis of Nei's genetic distance between populations and unweighted pair group method with arithmetic mean did not reflect geographic location. It is likely that multiple introductions of this species have occurred across the Intermountain West, followed by extensive genetic recombination. High levels of genetic diversity within yellow toadflax populations pose management challenges, as already seen in reports of variable response to herbicide application and limited impacts of biocontrol agent releases.

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GENETIC DIVERSITY OF UPLAND RICE LANDRACES FROM JAVA ISLAND AS REVEALED BY SSR MARKERS

Indonesian Journal of Agricultural Science ◽

10.21082/ijas.v16n1.2015.1-10 ◽

2015 ◽

Vol 16 (1) ◽

pp. 1

Author(s):

Sutoro Sutoro ◽

Puji Lestari ◽

Hakim Kurniawan

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Ssr Markers ◽

Upland Rice ◽

Diversity Index ◽

Crop Improvement ◽

Conservation Strategy ◽

Genetic Diversity Index ◽

Rice Landraces ◽

Glutinous Rice

Java Island is one of origins of a large number of indigenous upland rice accessions, which may serve as valuable plant genetic resources for future crop improvement in Indonesia. However, these landraces especially non-glutinous and glutinous rice are rapidly being lost because of land-use, agricultural practices and other factors. A better understanding of genetic diversity of local upland rice is important for crop improvement program, crop management and conservation strategy. This study aimed to evaluate the genetic diversity of upland rice landraces originating from Java Island. A total of 82 upland rice accessions comprising of 55 non-glutinous rice and 27 glutinous type were genotyped using the 16 simple sequence repeat (SSR) markers. The result showed that a total of 74 alleles were found with major allele frequency found on RM431 (0.96). Most of the SSR markers (56.3%) showed high discriminating power as represented by polymorphic informa-tion content (PIC) value higher than 0.5. A moderate genetic diversity index was detected in all landraces, which was 0.55. Genetic diversity index of non-glutinous and glutinous rice were 0.54 and 0.53, respectively. Their genetic distance was about 0.057. The phylogenetic tree generated two main clusters that demonstrated discrimination among landraces according to the individual genetic properties rather than their geographical origins and grain types (non-glutinous and glutinous type). The levels of genetic diversity were varied across rice types and geographical origins. According to the regions, the closest genetic distance was found between upland rice landraces from Central Java and West Java (0.040). The information derived from this study is important, in combination with phenotypic data, to identify desired useful traits came from different origins of the gene pool to be used for breeding purposes.

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Comparing the efficiency of sampling strategies to establish a representative in the phenotypic-based genetic diversity core collection of orchardgrass (Dactylis glomerata L.)

Czech Journal of Genetics and Plant Breeding ◽

10.17221/9/2012-cjgpb ◽

2013 ◽

Vol 49 (No. 1) ◽

pp. 36-47 ◽

Cited By ~ 4

Author(s):

M. Studnicki ◽

W. Mądry ◽

J. Schmidt

Keyword(s):

Genetic Diversity ◽

Core Collection ◽

Dactylis Glomerata ◽

Sampling Strategy ◽

Sampling Strategies ◽

Core Collections ◽

The Core ◽

Entire Collection ◽

The Mean ◽

Dactylis Glomerata L

Establishing a core collection that represents the genetic diversity of the entire collection with a minimum loss of its original diversity and minimal redundancies is an important problem for gene bank curators and crop breeders. In this paper, we assess the representativeness of the original genetic diversity in core collections consisting of one-tenth of the entire collection obtained according to 23 sampling strategies. The study was performed using the Polish orchardgrass Dactylis glomerata L. germplasm collection as a model. The representativeness of the core collections was validated by the difference of means (MD%) and difference of mean squared Euclidean distance (d‒D%) for the studied traits in the core subsets and the entire collection. In this way, we compared the efficiency of a simple random and 22 (20 cluster-based and 2 direct cluster-based) stratified sampling strategies. Each cluster-based stratified sampling strategy is a combination of 2 clusterings, 5 allocations and 2 methods of sampling in a group. We used the accession genotypic predicted values for 8 quantitative traits tested in field trials. A sampling strategy is considered more effective for establishing core collections if the means of the traits in a core are maintained at the same level as the means in the entire collection (i.e., the mean of MD% in the simulated samples is close to zero) and, simultaneously, when the overall variation in a core collection is greater than in the entire collection (i.e., the mean of d‒D% in the simulated samples is greater than that obtained for the simple random sampling strategy). Both cluster analyses (unweighted pair group method with arithmetic mean UPGMA and Ward) were similarly useful in constructing those sampling strategies capable of establishing representative core collections. Among the allocation methods that are relatively most useful for constructing efficient samplings were proportional and D2 (including variation). Within the Ward clusters, the random sampling was better than the cluster-based sampling, but not within the UPGMA clusters.

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Genetic diversity of selected accessions for seed protein among pigeonpea minicore collection

Legume Research - An International Journal ◽

10.18805/lr.v0iof.9486 ◽

2016 ◽

Author(s):

L. G. Jaggal ◽

B. R. Patil ◽

P. M. Naik ◽

K. Priya

Keyword(s):

Genetic Diversity ◽

Molecular Characterization ◽

Core Collection ◽

Seed Protein ◽

Polymorphic Information Content ◽

Efficient System ◽

Major Allele Frequency ◽

Entire Collection ◽

Major Allele ◽

Simple Sequence

Protein is an important part of our diet and legumes viz., pigeonpea, chickpea, groundnut, cowpea, blackgram, greengram, etc are very rich source of protein. Among them, pigeonpea consists of about 20 to 22% of seed protein. Minicore collection set is consisted of approximately 10 % of core collection and 1% of entire collection with lot of diversity present in it. Nitrogen content of pigeonpea minicore collection set was estimated using Micro-Kjeldhal method and was ranged from 9.82 to 21.45 %. Based on per cent seed protein, twelve accessions of high and twelve accessions of low seed protein were selected for molecular characterization using 23 simple sequence repeat (SSR) markers. The PowerMarker result depicted that, among twenty three amplified markers, twenty markers generated polymorphism with mean polymorphic information content (PIC), major allele frequency (MAF) and genetic diversity of 0.479, 0.589 and 0.525 respectively. Based on molecular characterization, the dendrogram was constructed using DARwin 5.0 software distinguished the selected accessions of both high and low seed protein separately into different clusters showing diversity The results illustrate the potential of marker systems to distinguish the content of seed protein in pulses crop at genus level. Use of these markers also offers an efficient system for the assessment of genetic diversity within minicore set of pigeonpea.

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