scholarly journals Simple sequence repeat‐based mini‐core collection for white Guinea yam ( Dioscorea rotundata Poir.) germplasm

Crop Science ◽  
2020 ◽  
Author(s):  
Babil Pachakkil ◽  
Shinsuke Yamanaka ◽  
Gezahegn Girma ◽  
Ryo Matsumoto ◽  
Muluneh Tamiru‐Oli ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Core Collection ◽  
Sequence Repeat ◽  
Dioscorea Rotundata ◽  
Mini Core Collection ◽  
Guinea Yam ◽  
Simple Sequence

Worldwide Core Collection of Olive Cultivars Based on Simple Sequence Repeat and Morphological Markers

Crop Science ◽  
2012 ◽  
Vol 52 (1) ◽  
pp. 211-221 ◽  
Author(s):  
Concepción M. Díez ◽  
Annalisa Imperato ◽  
Luis Rallo ◽  
Diego Barranco ◽  
Isabel Trujillo
Keyword(s):  
Simple Sequence Repeat ◽  
Core Collection ◽  
Morphological Markers ◽  
Sequence Repeat ◽  
Olive Cultivars ◽  
Simple Sequence

Genetic diversity analysis of yam cultivars (Dioscorea rotundata Poir.) in Benin using simple sequence repeat (SSR) markers

2007 ◽  
Vol 5 (02) ◽  
pp. 71-81 ◽  
Author(s):  
Serge Tostain ◽  
Clément Agbangla ◽  
Nora Scarcelli ◽  
Cédric Mariac ◽  
Ogoubi Daïnou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Management Practices ◽  
Genetic Relationships ◽  
Sequence Repeat ◽  
Dioscorea Rotundata ◽  
Tuber Crop ◽  
The Mean ◽  
Simple Sequence

Guinea yam (Dioscorea rotundataPoir.) is a dioecious vegetatively propagated tuber crop. It is widely cultivated by traditional techniques in West Africa, its area of origin. The genetic diversity of 146 accessions from Benin was analysed using 10 polymorphic simple sequence repeat (SSR) nuclear markers and agromorphological traits. An average of 8.4 alleles per locus was detected. The mean heterozygosity was 0.57 and the mean polymorphism information content (PIC) for polymorphic markers was 0.51. Some cultivars (23%) were found to have an identical genotype for the 10 markers. The structure of the genetic diversity observed in Benin is the result of farmers' crop management practices and their know-how. The cultivar diversity had a geographical component. We also noted major differentiation between early and late cultivars, with higher diversity in the early ones. Cultivars from northern Benin and early cultivars had the greatest allelic richness. SSR markers proved to be powerful tools for fingerprinting each cultivar and analysing their genetic relationships. The results of this study could be useful for defining a strategy for the conservation of genetic diversity in yams.

Assessment of molecular genetic diversity and population structure of sesame (Sesamum indicum L.) core collection accessions using simple sequence repeat markers

2013 ◽  
Vol 12 (1) ◽  
pp. 112-119 ◽  
Author(s):  
Jong-Hyun Park ◽  
Sundan Suresh ◽  
Gyu-Taek Cho ◽  
Nag-Gor Choi ◽  
Hyung-Jin Baek ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Simple Sequence Repeat ◽  
Core Collection ◽  
Sesamum Indicum ◽  
Group Method ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
The Core ◽  
Simple Sequence

Sesame (Sesamum indicum L.) is one of the oldest oil crops and is widely cultivated in Asia and Africa. The aim of this study was to assess the genetic diversity, phylogenetic relationships and population structure of 277 sesame core collection accessions collected from 15 countries in four different continents. A total of 158 alleles were detected among the sesame accessions, with the number varying from 3 to 25 alleles per locus and an average of 11.3. Polymorphism information content values ranged from 0.34 to 0.84, with an average of 0.568. These values indicated a high genetic diversity at 14 loci both among and within the populations. Of these, 44 genotype-specific alleles were identified in 12 of the 14 polymorphic simple sequence repeat markers. The core collection preserved a much higher level of genetic variation. Therefore, 10.1% was selected as the best sampling percentage from the whole collection when constructing the core collection. The 277 core collection accessions formed four robust clusters in the unweighted pair group method and the arithmetic averages (UPGMA) dendrogram, although the clustering did not indicate any clear division among the sesame accessions based on their geographical locations. Similar patterns were obtained using model-based structure analysis and country-based dendrograms, as some accessions situated geographically far apart were grouped together in the same cluster. The results of these analyses will increase our understanding of the genotype-specific alleles, genetic diversity and population structure of core collections, and the information can be used for the development of a future breeding strategy to improve sesame yield.

scholarly journals Genetic Diversity of a Natural Population of Akebia trifoliata (Thunb.) Koidz and Extraction of a Core Collection Using Simple Sequence Repeat Markers

2021 ◽  
Vol 12 ◽  
Author(s):  
Yicheng Zhong ◽  
Yue Wang ◽  
Zhimin Sun ◽  
Juan Niu ◽  
Yaliang Shi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Simple Sequence Repeat ◽  
Core Collection ◽  
Polymorphic Information Content ◽  
Germplasm Conservation ◽  
Sequence Repeat ◽  
Information Index ◽  
Molecular Identity ◽  
Simple Sequence

Understand genetic diversity and genetic structure of germplasm is premise of germplasm conservation and utilization. And core collection can reduce the cost and difficulty of germplasm conservation. Akebia trifoliata (Thunb.) Koidz is an important medicinal, fruit and oil crop, particularly in China. In this study, 28 simple sequence repeat (SSR) markers were used to assess the genetic diversity and genetic structure of 955 A. trifoliata germplasms, determine their molecular identity and extract a core collection. The genetic diversity of the 955 germplasms was moderately polymorphic. The average number of alleles (Na), observed heterozygosity (HO), expected heterozygosity (HE), Shannon’s information index (I∗), and polymorphic information content (PIC) were 3.71, 0.24, 0.46, 0.81, and 0.41, respectively. Four subpopulations were identified, indicating a weak genetic structure. A 955 germplasms could be completely distinguished by the characters of s28, s25, s74, s89, s68, s30, s13, s100, s72, s77, and s3. And each germplasm’s molecular identity was made up of eleven characters. The core collection was composed of 164 germplasms (17.2% of 955 total germplasms in the population) and diversity parameters differed significantly from those of a random core collection. These results have implications for germplasm conservation. At the same time, based on the results, the 955 germplasm could be better used and managed.

scholarly journals Genetic Diversity, Structure, and Core Collection of Korean Apple Germplasm Using Simple Sequence Repeat Markers

2019 ◽  
Vol 88 (3) ◽  
pp. 329-337
Author(s):  
Jeong-Hee Kim ◽  
Youngjae Oh ◽  
Gi-An Lee ◽  
Young Soon Kwon ◽  
Seon Ae Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Core Collection ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
Simple Sequence ◽  
Diversity Structure

Developing a core collection of Pyropia haitanensis using simple sequence repeat markers

Aquaculture ◽  
2016 ◽  
Vol 452 ◽  
pp. 351-356 ◽  
Author(s):  
Yan Xu ◽  
Changsheng Chen ◽  
Dehua Ji ◽  
Kai Xu ◽  
Xiaoxue Xie ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Core Collection ◽  
Pyropia Haitanensis ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
Simple Sequence

Rationalization of taro germplasm collections in the Pacific Island region using simple sequence repeat (SSR) markers

2006 ◽  
Vol 4 (3) ◽  
pp. 210-220 ◽  
Author(s):  
E. S. Mace ◽  
P. N. Mathur ◽  
L. Izquierdo ◽  
D. Hunter ◽  
M. B. Taylor ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Papua New Guinea ◽  
Simple Sequence Repeat ◽  
Core Collection ◽  
New Caledonia ◽  
Solomon Islands ◽  
New Guinea ◽  
The Other ◽  
Sequence Repeat ◽  
Simple Sequence

AbstractA regional (Oceania) core collection for taro germplasm has been developed based on phenotypic and molecular characterization. In total, 2199 accessions of taro germplasm have been collected by TaroGen (Taro Genetic Resources: Conservation and Utilisation) from 10 countries in Oceania: Papua New Guinea, Solomon Islands, Vanuatu, New Caledonia, Fiji, Palau, Niue, Tonga, Cook Islands and Samoa. Our objective was to select 10% from each country to contribute to a regional core. The larger collections from Papua New Guinea, Vanuatu and New Caledonia were analysed based on phenotypic characters, and a diverse subset representing 20% of these collections was fingerprinted. A diverse 20% subsample was also taken from the Solomon Islands. All accessions from the other six countries were fingerprinted. In total, 515 accessions were genotyped (23.4% overall) using taro specific simple sequence repeat (SSR) markers. DNA fingerprint data showed that great allelic diversity existed in Papua New Guinea and the Solomon Islands. Interestingly, rare alleles were identified in taros from the Solomon Islands province of Choiseul which were not observed in any of the other collections. Overall, 211 accessions were recommended for inclusion in the final regional core collection based on the phenotypic and molecular characterization.

Genetic variation among Spanish pea landraces revealed by Inter Simple Sequence Repeat (ISSR) markers: its application to establish a core collection

2006 ◽  
Vol 144 (1) ◽  
pp. 53-61 ◽  
Author(s):  
A. LÁZARO ◽  
I. AGUINAGALDE
Keyword(s):  
Simple Sequence Repeat ◽  
Core Collection ◽  
Genetic Relationships ◽  
Plant Genetic Resources ◽  
Molecular Data ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Sequence Repeat ◽  
Data Types ◽  
Simple Sequence

One hundred and twenty Spanish landraces of peas (Pisum sativum L.) collected in different micro-climatic areas, together with three commercial varieties and one breeding line, were subjected to molecular characterization using Inter Simple Sequence Repeat (ISSR) amplification. Landraces originated from 7 to 1427 m asl. Most accessions were collected in temperate areas with dry Mediterranean humidity regimes. ISSR markers detected high levels of variability between accessions and were useful for identification of individuals and clarification of genetic relationships between them. The 18 groups obtained with molecular data were not significantly related to 21 agro/climatic regions. Clustering based on climatic and ISSR characters differed because the data types present different aspects of genetic diversity. These results will be applied to establish a pea core collection at the Plant Genetic Resources Centre of the Spanish National Institute of Agriculture and Food Research and Technology (CRF-INIA).

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