Genetic Diversity and Variability in Endangered Pantesco and Two Other Sicilian Donkey Breeds Assessed by Microsatellite Markers

The genetic variability of Pantesco and other two Sicilian autochthonous donkey breeds (Ragusano and Grigio Siciliano) was assessed using a set of 14 microsatellites. The main goals were to describe the current differentiation among the breeds and to provide genetic information useful to safeguard the Pantesco breed as well as to manage Ragusano and Grigio Siciliano. In the whole sample, that included 108 donkeys representative of the three populations, a total of 85 alleles were detected. The mean number of alleles was lower in Pantesco (3.7), than in Grigio Siciliano and Ragusano (4.4 and 5.9, resp.). The three breeds showed a quite low level of gene diversity (He) ranging from 0.471 in Pantesco to 0.589 in Grigio. The overall genetic differentiation index (Fst) was quite high; more than 10% of the diversity was found among breeds. Reynolds’ () genetic distances, correspondence, and population structure analysis reproduced the same picture, revealing that, (a) Pantesco breed is the most differentiated in the context of the Sicilian indigenous breeds, (b) within Ragusano breed, two well-defined subgroups were observed. This information is worth of further investigation in order to provide suitable data for conservation strategies.

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Genetic variability and relationship among different accessions of Froriepia subpinata Bail (Gijavash) an endangered medicinal plant from Iran revealed by ISSR and IRAP markers

Advances in Horticultural Science ◽

10.36253/ahsc-8107 ◽

2021 ◽

Vol 35 (1) ◽

Author(s):

Abbas Jorkesh ◽

Yousef Hamidoghli ◽

Jamalali Olfati ◽

Habibollah Samizadeh ◽

Davood Bakhshi

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Variability ◽

Medicinal Plant ◽

Genetic Information ◽

Conservation Strategies ◽

Polymorphic Band ◽

Mean Values ◽

Endangered Medicinal Plant ◽

Irap Markers

The genetic variability of Froriepia subpinata Ledeb. Bail., an endangered Iranian endemic species, has been estimated with a total of 52 accessions using 20 markers including ISSR and IRAP. The results showed the polymorphic band produced by primers was 82.3%. The best mean values of genetic diversity parameters observed in ISSRs markers, being UBC873, UBC811, and UBC873 the best primers tested. The similarity range among accessions was 34.45% to 93.3%. The cluster analysis classified the accessions into five main groups that in totally, accessions with similarity in region generally were clustered in the same group. Overall, present study could provide elementary information for formulation of conservation strategies and invaluable elementary genetic information for next breeding or designing conservation programs.

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Genetic Diversity and Population Structure of Traditional Greek and Cypriot Melon Cultigens (Cucumis melo L.) Based on Simple Sequence Repeat Variability

HortScience ◽

10.21273/hortsci.44.7.1820 ◽

2009 ◽

Vol 44 (7) ◽

pp. 1820-1824 ◽

Cited By ~ 13

Author(s):

Emmanouil N. Tzitzikas ◽

Antonio J. Monforte ◽

Abdelhak Fatihi ◽

Zacharias Kypriotakis ◽

Tefkros A. Iacovides ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variability ◽

Ssr Markers ◽

Structure Analysis ◽

Simple Sequence Repeat ◽

Cucumis Melo ◽

Sequence Repeat ◽

Population Structure Analysis ◽

Simple Sequence

Seventeen simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure among traditional Greek and Cypriot melon cultigens (Cucumis melo L.). All SSR markers were polymorphic with a total number of 81 alleles, whereas all cultigens could be distinguished with at least one SSR, except cultigens 43 and 41. Reference accessions showed larger genetic variability with an average of four alleles per locus and 0.65 gene of diversity compared with an average of 2.47 alleles per locus and 0.30 of gene diversity for the Greek/Cypriot cultigens. Observed heterozygosity was very low, indicating a lack of outcrossing, at least in recent times. Unrooted neighbor-joining tree analysis and population structure analysis clustered the cultigens and the reference genotypes into five groups. All cultigens could be distinguished; the Cypriot cultigens were more closely related to the inodorus ‘Piel de Sapo’, whereas the Greek cultigens were located in an intermediate position between the inodorus ‘Piel de Sapo’ and the cantalupensis ‘Védrantais’. The cultigen ‘Kokkini’ was the most divergent among the Greek and Cypriot cultigens. This association between geographic origin and genetic similarity among Greek and Cypriot cultigens indicates geographic isolation. Most of the cultivars from the same cultivar group (i.e., inodorus, cantalupensis) clustered together, but some exceptions were found, suggesting that former inodorus landraces would have been transformed to cantalupensis as a result of intercrossing and further selection by farmers. Results of population structure analysis support mixing between cantalupensis and inodorus. ‘Agiou Basileiou’, an inodorus cultigen, was assigned to the subpopulation IV/II of which II is a pure cantalupensis subpopulation. Greek and Cypriot melon cultigens were developed from a broader germplasm base than western Mediterranean cultivars and exhibited useful for melon breeding programs genetic variability.

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Testing the breeding strategy of Hungarian Bronze turkey strains for maintaining genetic diversity with microsatellites

Archives Animal Breeding ◽

10.5194/aab-54-419-2011 ◽

2011 ◽

Vol 54 (4) ◽

pp. 419-429

Author(s):

S. Kusza ◽

S. Mihók ◽

L. Czeglédi ◽

A. Jávor ◽

M. Árnyasi

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Mating System ◽

Breeding Strategy ◽

Shannon Index ◽

Inbreeding Coefficient ◽

Control Population ◽

Conservation Strategies ◽

The Mean ◽

Two Populations

Abstract. The aim of the study was to provide information on the genetic variability of the Hungarian Bronze turkey gene reserve population and its difference from the Broad-breasted turkey, and offer guidance and proposals for its future conservation strategies. Altogether, 239 Hungarian Bronze turkeys from 10 strains and 13 Broad-breasted turkeys as a control population were genotyped for 15 microsatellites. All loci were polymorphic with the average number of alleles per locus 3.20±1.146 in the Hungarian Bronze turkey. The mean expected (Hexp) and observed heterozygosity (Hobs) were not different (0.392 and 0.376, respectively) in the overall population, and similar values were obtained for hens and bucks and among hen strains. Inbreeding coefficient (FIS) and Shannon index (I) indicated that there was low inbreeding within hens and bucks. Our results confirm that the genetic diversity in the Hungarian Bronze turkey population has been preserved by the rotational mating system. Differences between the Hungarian Bronze turkey and the Broad-breasted turkey populations were determined. Nei’s unbiased values clearly indicated that the two populations are highly genetically differentiated.

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Genetic Diversity and Differentiation of Alpinia Oxyphylla Miquel as Revealed by AFLP Markers

10.21203/rs.3.rs-781962/v1 ◽

2021 ◽

Author(s):

Kun Pan ◽

Jie Hou ◽

Wenqin Su ◽

Bo Yi ◽

Bingmiao Gao

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Diversity ◽

Germplasm Conservation ◽

Aflp Markers ◽

Group Method ◽

High Genetic Diversity ◽

Geographic Population ◽

Arithmetic Average ◽

Population Structure Analysis

Abstract In this study, we analyzed the genetic diversity and population structure of 90 A. oxyphylla accessions from Hainan island using amplified fragment length polymorphism (AFLP) markers. These 90 accessions were composed of 15 populations from different geographic locations and divided into 4 clusters (A, B, C, and D) using the Unweighted pair group method based on arithmetic average (UPGMA). The genetic similarity between individuals ranged from 0.47 to 1.00 (average of 0.74), and most accessions from the same geographic population were grouped together. Principal coordinate analysis (PCA) showed a clear distinction among three clusters (A, B and C). Based on the loci information, the population structure analysis results by STRUCTURE and TESS were consistent with the clustering of PCA. Nine AFLP primer combinations generated 1537 polymorphic bands displaying rich polymorphism, thus indicating high genetic diversity among these 15 populations with an average Nei’s gene diversity of 0.1328 ± 0.160. In conclusion, AFLP markers efficiently analyzed the genetic diversity in A. oxyphylla, demonstrating highly significant genetic variation within and among populations. However, intrapopulation genetic variance was much higher than interpopulation variability, suggesting that efforts should be made for in situ germplasm conservation and resistant varieties cultivation.

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Genetic diversity of the Colombian Creole donkey in the Department of Sucre

Veterinarska stanica ◽

10.46419/vs.51.6.2 ◽

2020 ◽

Vol 51 (6) ◽

pp. 611-619

Author(s):

Adrian Medina-Montes ◽

Darwin Hernández-Herrera ◽

Javier Beltrán-Herrera ◽

Donicer Montes-Vergara

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Markers ◽

Structure Analysis ◽

Genetic Distances ◽

Entire Population ◽

Polymorphic Loci ◽

Population Structure Analysis

The objective of this study was to evaluate the genetic diversity of the Colombian Creole donkey in the Department of Sucre using Random Amplified Microsatellites (RAM) molecular markers. In 100 individuals from the five subregions of the department, DNA was extracted and five RAM primers were amplified by PCR. In all, 291 bands were found, on average 11.96±1.45 per primer, the highest value in CCA (18±2.23) and the lowest in TG and GT (8.8±0.44). CA was the most polymorphic primer (88.09±10.91%) with the highest heterozygosity value (He) (0.376±0.021), while the lowest was GT (0.341±0.076 and 0.101±0.040, respectively). Intrapopulation analysis showed an average of 66.50±1.72 bands, of which 89.86±24.04% were polymorphic. The highest number of bands (63±3.84) was found in the Gulf of Morrosquillo (GO) subpopulation, and the lowest in Mojana (MO) (48±2.88); however, the highest value of polymorphic loci (81.16%) and He (0.335±0.022) were found in the Montes de María (MM) subpopulation, making it the most diverse. The average genetic diversity for the entire population was 0.351±0.021 bands. The population structure analysis showed a 10% variation between subpopulations, with an FST value of 0.17±0.01 (P<0.05). Genetic distances between subpopulations showed that MO and GO were the most distant. The RAM markers are effective in assessing the genetic diversity of the Creole donkey, which has high values of genetic diversity, particularly the MM subpopulation. The genetic revealed structure could be the result of natural geographical barriers between the subregions.

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Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d221036 ◽

2021 ◽

Vol 22 (10) ◽

Author(s):

Zulfahmi Zulfahmi ◽

Parjanto Parjanto ◽

Edi Purwanto ◽

Ahmad Yunus

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Genetic Differentiation ◽

Gene Diversity ◽

In Situ Conservation ◽

Genetic Material ◽

Ex Situ ◽

Breeding Programs ◽

The Mean

Abstract. Zulfahmi, Parjanto, Purwanto E, Yunus A. 2021. Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia. Biodiversitas 22: 4431-4439. Information on genetic variation within and among populations of Eurycoma apiculata plants is important to develop strategies for their conservation, sustainable use, and genetic improvement. To date, no information on genetic variation within and among populations of the E. apiculata has been reported. This study aims to assess genetic diversity within and among populations of E. apiculata based on RAPD markers, and to determine populations to collect E. apiculata genetic material for conservation and breeding programs. Young leaves of E. apiculata were collected from six natural populations. Fifteen RAPD primers were used to assess the genetic diversity of each population. The data obtained were analyzed with POPGEN and Arlequin software. The amplification results of 15 selected primers produced 3-16 loci with all primers 100% polymorphic. At the species level, the mean allele per locus (Na), number of effective alleles (Ne), percentage of polymorphic loci (PPL), Nei’s gene diversity index (He) and Shannon information index (I) were 2.000, 1.244, 100%, 0.167, and 0.286, respectively. At the population level, the mean values for Na, Ne, PPL, He and I were 1.393, 1.312, 39.27%, 0.119, and 0.186, respectively. The highest value of gene diversity within population (He) was found in the Lingga-1 population and the lowest value was found in the Rumbio population. The value of genetic differentiation among populations (GST) of E. apiculata is 0.284, consistent with the results of the AMOVA analysis which found that genetic variation among populations was 23.14%, indicates that the genetic variation of E. apiculata was more stored within populations than among populations. The gene flow (Nm) value of E. apiculata was 1.259 migrants per generation among populations. The Nm value of this species was high category, and could inhibit genetic differentiation among populations. The clustering of E. apiculata population based on the UPGMA dendrogram and PCA was inconsistent with its geographic distribution, reflecting the possibility that genes migration occurred between islands in the past. The main finding of this study was the genetic variation of the E. apiculata mostly stored within the population. Therefore, the population with the highest genetic diversity is a priority for in-situ conservation, and collection of E. apiculata genetic material for ex-situ conservation and breeding programs should be carried out minimum from Lingga-1 and Pokomo populations.

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Understanding genetic diversity, population structure and development of a core collection of Indian accessions of watermelon (Citrullus lanatus (Thunb.) Matsum. and Nakai)

Plant Genetic Resources ◽

10.1017/s1479262120000386 ◽

2020 ◽

pp. 1-10

Author(s):

Saheb Pal ◽

Muttanna Revadi ◽

RN Thontadarya ◽

DC Lakshmana Reddy ◽

B. Varalakshmi ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Core Collection ◽

Gene Diversity ◽

Citrullus Lanatus ◽

Population Analysis ◽

Maximum Magnitude ◽

Phenotypic Data ◽

Genetic Base ◽

Population Structure Analysis

Abstract Most of the modern-day improved watermelon varieties succumb to various biotic and abiotic stresses mainly because of their narrow genetic base. Insights into the genetic diversity and population structure are crucial for broadening the genetic base and improving the adaptive value. The present experiment was conducted to study the genetic diversity and population structure of a germplasm panel comprising 336 Citrullus sp. accessions. Another objective was to formulate a core collection of Indian Citrullus sp. accessions. Data from 23 highly polymorphic microsatellite markers were used for genetic diversity and population structure analysis while both molecular and phenotypic data from 17 traits were used to formulate the core set. The markers yielded a total of 69 alleles with an average of three alleles per locus. Initially, the accessions clustered into two populations and an admixture group. Intra-population analysis revealed three and two statistically distinct subpopulations in Pop I and Pop II, respectively. The exotic collections were predominant in Pop I-A, Pop II-A and Pop II-B while the Indian accessions were preponderant in Pop I-B and Pop I-C. Pop I-B recorded the maximum magnitude of gene diversity and the highest number of alleles. The well-adapted Indian landraces could be deployed in future watermelon improvement programmes. The formulated core collection (n = 46; 23.71% of the entire collection studied) would ease in maintenance of the diversity present among indigenous Citrullus sp. accessions; would ease trait search while exploring Indian diversity and can be pooled with other collection(s) to form a global core of watermelon.

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Molecular Genetic Diversity and Population Structure in Ethiopian Chickpea Germplasm Accessions

Diversity ◽

10.3390/d13060247 ◽

2021 ◽

Vol 13 (6) ◽

pp. 247

Author(s):

Tsegaye Getahun ◽

Kassahun Tesfaye ◽

Asnake Fikre ◽

Teklehaimanot Haileslassie ◽

Annapurna Chitikineni ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Molecular Genetic ◽

Conservation Strategies ◽

Molecular Genetic Diversity ◽

Population Structure Analysis ◽

Trait Improvement ◽

Population Structures ◽

Germplasm Accessions

Chickpea (Cicer arietinum L.) is a cheap source of protein and rich in minerals for people living in developing countries. In order to assess the existing molecular genetic diversity and determine population structures in selected Ethiopian chickpea germplasm accessions (118), a set of 46 simple sequence repeat (SSR) markers equally distributed on the chickpea genome were genotyped. A total of 572 alleles were detected from 46 SSR markers, and the number of alleles per locus varied from 2 (ICCM0289) to 28 (TA22). The average number of alleles per locus, polymorphism information content, and expected heterozygosity were 12, 0.684, and 0.699, respectively. Phylogenetic analysis grouped the 118 chickpea genotypes from diverse sources into three evolutionary and/or biological groups (improved desi, improved kabuli, and landraces). The population structure analysis revealed six sub-populations from 118 chickpea genotypes studied. AMOVA revealed that 57%, 29%, and 14% of the total genetic variations were observed among individuals, within populations, and among populations. The insights into the genetic diversity at molecular levels in the Ethiopian germplasm lines can be used for designing conservation strategies as well as the diverse germplasm lines identified in this study can be used for trait dissection and trait improvement.

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Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers

Frontiers in Genetics ◽

10.3389/fgene.2021.726152 ◽

2021 ◽

Vol 12 ◽

Author(s):

Debjani Roy Choudhury ◽

Ramesh Kumar ◽

Vimala Devi S ◽

Kuldeep Singh ◽

N. K. Singh ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Core Collection ◽

Tamil Nadu ◽

East Coast ◽

Snp Markers ◽

The Core ◽

Core Set ◽

Population Structure Analysis ◽

The Mean

In India, rice (Oryza sativa L.) is cultivated under a variety of climatic conditions. Due to the fragility of the coastal ecosystem, rice farming in these areas has lagged behind. Salinity coupled with floods has added to this trend. Hence, to prevent genetic erosion, conserving and characterizing the coastal rice, is the need of the hour. This work accessed the genetic variation and population structure among 2,242 rice accessions originating from India’s east coast comprising Andhra Pradesh, Orissa, and Tamil Nadu, using 36 SNP markers, and have generated a core set (247 accessions) as well as a mini-core set (30 accessions) of rice germplasm. All the 36 SNP loci were biallelic and 72 alleles found with average two alleles per locus. The genetic relatedness of the total collection was inferred using the un-rooted neighbor-joining tree, which grouped all the genotypes (2,242) into three major clusters. Two groups were obtained with a core set and three groups obtained with a mini core set. The mean PIC value of total collection was 0.24, and those of the core collection and mini core collection were 0.27 and 0.32, respectively. The mean heterozygosity and gene diversity of the overall collection were 0.07 and 0.29, respectively, and the core set and mini core set revealed 0.12 and 0.34, 0.20 and 0.40 values, respectively, representing 99% of distinctiveness in the core and mini core sets. Population structure analysis showed maximum population at K = 4 for total collection and core collection. Accessions were distributed according to their population structure confirmed by PCoA and AMOVA analysis. The identified small and diverse core set panel will be useful in allele mining for biotic and abiotic traits and managing the genetic diversity of the coastal rice collection. Validation of the 36-plex SNP assay was done by comparing the genetic diversity parameters across two different rice core collections, i.e., east coast and northeast rice collection. The same set of SNP markers was found very effective in deciphering diversity at different genetic parameters in both the collections; hence, these marker sets can be utilized for core development and diversity analysis 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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