scholarly journals Genetic Diversity and Primary Core Collection Construction of Turnip (Brassica rapa L. ssp. rapifera Matzg) Landraces in Tibet Revealed via Morphological and SSR Markers

Agronomy ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1901
Author(s):  
Rongrong Li ◽  
Fangyuan Zhou ◽  
Yingying Gao ◽  
Chenlu Liu ◽  
Shubo Yu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Brassica Rapa ◽  
Core Collection ◽  
Morphological Characteristics ◽  
Germplasm Conservation ◽  
Tibet Plateau ◽  
Initial Population ◽  
Sampling Ratio ◽  
Primary Core

Turnip, one of the oldest groups of cultivated Brassica rapa species, is a traditional crop as well as a form of animal fodder, a vegetable, and a herbal medicine that is widely cultivated in farming and farming-pastoral regions in Tibet. Different regions of the Qinghai–Tibet Plateau (QTP) are home to a rich diversity of turnip owing to their high altitudes and variable climate types. However, information on the morphology and genetic diversity of Tibetan turnip remains limited. Therefore, the genetic diversity of 171 turnip varieties from China and elsewhere (Japan, Korea, and Europe) was analyzed using 58 morphological characteristics and 31 simple sequence repeat (SSR) markers in this study. The varieties showed that the genetic distance ranged from 0.12 to 1.00, and the genetic similarity coefficient ranged between 0.73 and 0.95. Cluster tree showed two distinct clusters. Both morphotype and geography contributed to the group classification. A combination of morphological traits and molecular markers could refine the precision of accurate identification compared to the separate morphological and molecular data analyses. The sampling ratio of 15% to utmost precisely represent the initial population was compared to ratios of 10% and 20%, and the sampling ratio of 15% is recommended for future works when a primary core collection of turnip resources is constructed. These results could furnish a foundation for germplasm conservation and effective turnip breeding in future studies.

scholarly journals Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8038
Author(s):  
Yanli Xiong ◽  
Wenhui Liu ◽  
Yi Xiong ◽  
Qingqing Yu ◽  
Xiao Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Western China ◽  
Tibet Plateau ◽  
Group Method ◽  
Breeding Strategies ◽  
Population Genetic Differentiation ◽  
Principal Coordinates ◽  
Geographical Regions ◽  
Genetic Diversity And Structure

Hosting unique and important plant germplasms, the Qinghai-Tibet Plateau (QTP), as the third pole of the world, and Xinjiang, located in the centre of the Eurasian continent, are major distribution areas of perennial Triticeae grasses, especially the widespread Elymus species. Elymus excelsus Turcz. ex Griseb, a perennial forage grass with strong tolerance to environmental stresses, such as drought, cold and soil impoverishment, can be appropriately used for grassland establishment due to its high seed production. To provide basic information for collection, breeding strategies and utilization of E. excelsus germplasm, microsatellite markers (SSR) were employed in the present study to determine the genetic variation and population structure of 25 wild accessions of E. excelsus from Xinjiang (XJC) and the QTP, including Sichuan (SCC) and Gansu (GSC) of western China. Based on the 159 polymorphic bands amplified by 35 primer pairs developed from three related species, the average values of the polymorphic information content (PIC), marker index (MI), resolving power (Rp), Nei’s genetic diversity (H) and Shannon’s diversity index (I) of each pair of primers were 0.289, 1.348, 1.897, 0.301 and 0.459, respectively, validating that these SSR markers can also be used for the evaluation of genetic diversity of E. excelsus germplasms, and demonstrating the superior versatility of EST-SSR vs. G-SSR. We found a relatively moderate differentiation (Fst = 0.151) among the XJC, SCC and GSC geo-groups, and it is worth noting that, the intra-group genetic diversity of the SCC group (He = 0.197) was greater than that of the GSC (He = 0.176) and XJC (He = 0.148) groups. Both the Unweighted Pair Group Method with Arithmetic (UPGMA) clustering and principal coordinates analysis (PCoA) divided the 25 accessions into three groups, whereas the Bayesian STRUCTURE analysis suggested that E. excelsus accessions fell into four main clusters. Besides, this study suggested that geographical distance and environmental variables (annual mean precipitation and average precipitation in growing seasons), especially for QTP accessions, should be combined to explain the population genetic differentiation among the divergent geographical regions. These data provided comprehensive information about these valuable E. excelsus germplasm resources for the protection and collection of germplasms and for breeding strategies in areas of Xinjiang and QTP in western China.

scholarly journals Assessment of genetic diversity and population structure of oil palm (Elaeis guineensis Jacq.) field genebank: A step towards molecular-assisted germplasm conservation

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0255418
Author(s):  
Siou Ting Gan ◽  
Chin Jit Teo ◽  
Shobana Manirasa ◽  
Wei Chee Wong ◽  
Choo Kien Wong
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Oil Palm ◽  
Core Collection ◽  
Elaeis Guineensis ◽  
Germplasm Conservation ◽  
Ex Situ ◽  
Fixation Index ◽  
Core Set ◽  
Genetic Diversity And Structure

Oil palm (Elaeis guineensis) germplasm is exclusively maintained as ex situ living collections in the field for genetic conservation and evaluation. However, this is not for long term and the maintenance of field genebanks is expensive and challenging. Large area of land is required and the germplasms are exposed to extreme weather conditions and casualty from pests and diseases. By using 107 SSR markers, this study aimed to examine the genetic diversity and relatedness of 186 palms from a Nigerian-based oil palm germplasm and to identify core collection for conservation. On average, 8.67 alleles per SSR locus were scored with average effective number of alleles per population ranging from 1.96 to 3.34 and private alleles were detected in all populations. Mean expected heterozygosity was 0.576 ranging from 0.437 to 0.661 and the Wright’s fixation index calculated was -0.110. Overall moderate genetic differentiation among populations was detected (mean pairwise population FST = 0.120, gene flow Nm = 1.117 and Nei’s genetic distance = 0.466) and this was further confirmed by AMOVA analysis. UPGMA dendogram and Bayesian structure analysis concomitantly clustered the 12 populations into eight genetic groups. The best core collection assembled by Core Hunter ver. 3.2.1 consisted of 58 palms accounting for 31.2% of the original population, which was a smaller core set than using PowerCore 1.0. This core set attained perfect allelic coverage with good representation, high genetic distance between entries, and maintained genetic diversity and structure of the germplasm. This study reported the first molecular characterization and validation of core collections for oil palm field genebank. The established core collection via molecular approach, which captures maximum genetic diversity with minimum redundancy, would allow effective use of genetic resources for introgression and for sustainable oil palm germplasm conservation. The way forward to efficiently conserve the field genebanks into next generation without losing their diversity was further discussed.

scholarly journals Assessment of Genetic Diversity and Population Genetic Structure of Santalum album L. in India by Genic and Genomic SSR markers

2021 ◽  
Author(s):  
Tanzeem Fatima ◽  
Ashutosh Srivastava ◽  
Vageeshbabu S Hanur ◽  
M. Srinivasa Rao
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ssr Markers ◽  
Germplasm Conservation ◽  
Principal Component ◽  
Santalum Album ◽  
High Genetic Diversity ◽  
Information Index ◽  
Genomic Ssr ◽  
Santalum Album L

Sandalwood (Santalum album L.) is highly valued aromatic tropical tree. It is known for its high quality heartwood and oil. In this study 39 genic and genomic SSR markers were used to analyze the genetic diversity and population structure of 177 S. album accessions from 14 populations of three states in India. High genetic diversity was observed in terms of number of alleles 127 expected heterozygosity (He) ranged from 0.63-0.87 and the average PIC was 0.85. The selected population had relatively high genetic diversity with Shannons information index (I) >1.0. 0.02 mean coefficient of genetic differentiation (FST) and 10.55 gene flow were observed. AMOVA revealed that 92% of the variation observed within individuals. Based on cluster and Structure result individuals were not clustered as per their geographical origin. Furthermore the clusters were clearly distinguished by principal component analysis analysis and the result revealed that PC1 reflected the moderate contribution in genetic variation (6%) followed by PC2 (5.5%). From this study, high genetic diversity and genetic differentiation was found in S. album populations. The genetic diversity information of S. album populations can be used for selection of superior genotypes and germplasm conservation to promote the tree improvement of S. album populations.

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

2019 ◽  
Author(s):  
Alemneh Mideksa Egu ◽  
Kifle Dagne ◽  
Kassahun Tesfaye ◽  
Xuebo Hu
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Major Gene ◽  
In Situ Conservation ◽  
Germplasm Conservation ◽  
Pharmaceutical Products ◽  
Gene Pools ◽  
Vernonia Galamensis ◽  
Diversity Assessment

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.

Genetic Diversity and Core Collection for Potato (Solanum tuberosum L.) Cultivars from Cameroon as Revealed by SSR Markers

2017 ◽  
Vol 94 (4) ◽  
pp. 449-463 ◽  
Author(s):  
Mariette Anoumaa ◽  
Nasser Kouadio Yao ◽  
Eric Bertrand Kouam ◽  
Gabriel Kanmegne ◽  
Eunice Machuka ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Solanum Tuberosum ◽  
Ssr Markers ◽  
Core Collection ◽  
Solanum Tuberosum L

scholarly journals Genetic Diversity Analysis and Potential Distribution Prediction of Sophora moorcroftiana Endemic to Qinghai–Tibet Plateau, China

Forests ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1106
Author(s):  
Lan Yang ◽  
Huie Li ◽  
Qian Li ◽  
Qiqiang Guo ◽  
Jiangrong Li
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Potential Distribution ◽  
Germplasm Conservation ◽  
Woody Species ◽  
Cold Weather ◽  
Tibet Plateau ◽  
Conservation Strategies ◽  
Qinghai Tibet Plateau ◽  
Sophora Moorcroftiana

Sophora moorcroftiana (Benth.) Baker is an endemic woody species distributed in the Qinghai–Tibet Plateau (QTP), a part of the world characterized by high altitude and cold weather. In this study, the genetic diversity of S. moorcroftiana was evaluated based on 300 representative samples of 15 populations using 20 polymorphic SSR markers, and its potential distribution was predicted according to 19 bioclimatic factors using MaxEnt modeling. Results showed the population genetic diversity of S. moorcroftiana was generally not high (around 0.5), and the range of variation was small (0.437–0.539). Altitude, rather than other environmental factors, was the key factor affecting the present genetic diversity. Moreover, due to climate change in the QTP, the suitable area is increasing and will continue to increase by 48.35%, 84.44%, 101.98%, and 107.30% in the four future periods of 2030s, 2050s, 2070s, and 2090s, respectively, compared to the present, which is beneficial for S. moorcroftiana. These results will provide a theoretical basis for the development of germplasm conservation strategies for S. moorcroftiana and enrich information on the impacts of climate change on plants in the QTP.

scholarly journals Population Structure and Genetic Diversity in a Rice Core Collection (Oryza sativa L.) Investigated with SSR Markers

PLoS ONE ◽  
2011 ◽  
Vol 6 (12) ◽  
pp. e27565 ◽  
Author(s):  
Peng Zhang ◽  
Jinquan Li ◽  
Xiaoling Li ◽  
Xiangdong Liu ◽  
Xingjuan Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Oryza Sativa ◽  
Ssr Markers ◽  
Core Collection ◽  
Oryza Sativa L

Evaluation of Genetic Diversity of Local-Colored Rice Landraces Using SSR Markers

2018 ◽  
Vol 67 ◽  
pp. 24-34 ◽  
Author(s):  
Hoang Thi Hue ◽  
La Tuan Nghia ◽  
Hoang Tuyet Minh ◽  
La Hoang Anh ◽  
Le Thi Thu Trang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Relationships ◽  
Germplasm Conservation ◽  
Similarity Coefficients ◽  
Breeding Programs ◽  
Rice Landraces ◽  
Local Germplasm ◽  
Rice Improvement ◽  
Colored Rice

Analysis of genetic diversity of 90 Vietnamese local-colored rice accessions was evaluated by using 40 SSR markers. The numbers of polymorphic alleles ranged from 3 to 12 alleles per locus and average of 7.1 alleles per locus. The similarity coefficients of the rice landraces fluctuated from 0.76 to 0.93; at a genetic correlation level of 0.78. Ninety accessions of rice landraces were divided into five groups based on analysis of genetic relationships. The results have indicated that 11 markers included: M250, RM302, RM10926, RM208, RM227, RM17231, RM23251, RM5647, RM1376, RM339 and RM228 which gave the unique allele. These markers can be used effectively for genetic diversity of colored rice and provided a specific database and useful materials for landraces identification, local germplasm conservation for further colored rice improvement on rice quality via rice breeding programs in Vietnam.

scholarly journals Genetic Diversity Within and Among Populations of Roseroot (Rhodiola rosea L.) Based on Molecular Markers

2012 ◽  
Vol 40 (2) ◽  
pp. 266 ◽  
Author(s):  
Zsuzsanna GYORGY ◽  
Maria SZABO ◽  
Dmitry BACHAROV ◽  
Andrzej PEDRYC
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Geographic Origin ◽  
Morphological Characteristics ◽  
Population Level ◽  
Shannon Index ◽  
Rhodiola Rosea ◽  
Pharmacologically Active ◽  
Cool Climate

Rhodiola rosea L. is a perennial adaptogenic medicinal plant found in cool climate of the northern hemisphere. The species is very diverse both in terms of morphological characteristics and in the content of the pharmacologically active substances. The genetic diversity of four geographically distant roseroot populations was studied with ISSR and SSR markers. Using 7 ISSR primers 64 DNA fragments were generated and 85,94% of those were found to be polymorphic, indicating high genetic variability at the species level (gene diversity = 0.33, Shannon index = 0.48). Lower level of diversity was detected at the population level (Shannon-index ranged from 0.2173 to 0.2696). Only four out of the eight SSR markers used were informative during this study. The primer pairs for these four SSR markers produced 25 fragments with an average of 6.25 putative alleles per locus. Observed heterozygosity ranged from 0.4 to 1.0, whereas expected heterozygosity ranged from 0.47 to 0.84. Cluster analysis based on both markers revealed the same groups, individuals clustered according to their geographic origin. The Southern-Uralian population was the most genetically isolated. ITS analysis was used for the determination whether these Southern-Uralian individuals belong to the same species.

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