Molecular characterization of avocado germplasm with a new set of SSR and EST-SSR markers: genetic diversity, population structure, and identification of race-specific markers in a group of cultivated genotypes

2012 ◽  
Vol 9 (2) ◽  
pp. 539-555 ◽  
Author(s):  
Eduardo Gross-German ◽  
Maria Angeles Viruel
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Molecular Characterization ◽  
Ssr Markers

scholarly journals Discovery of miRNAs and Development of Heat-Responsive miRNA-SSR Markers for Characterization of Wheat Germplasm for Terminal Heat Tolerance Breeding

2021 ◽  
Vol 12 ◽  
Author(s):  
Pooja Sihag ◽  
Vijeta Sagwal ◽  
Anuj Kumar ◽  
Priyanka Balyan ◽  
Reyazul Rouf Mir ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Heat Stress ◽  
Ssr Markers ◽  
Heat Tolerance ◽  
Wheat Varieties ◽  
Wheat Genotypes ◽  
Wheat Germplasm ◽  
Heat Tolerant

A large proportion of the Asian population fulfills their energy requirements from wheat (Triticum aestivum L.). Wheat quality and yield are critically affected by the terminal heat stress across the globe. It affects approximately 40% of the wheat-cultivating regions of the world. Therefore, there is a critical need to develop improved terminal heat-tolerant wheat varieties. Marker-assisted breeding with genic simple sequence repeats (SSR) markers have been used for developing terminal heat-tolerant wheat varieties; however, only few studies involved the use of microRNA (miRNA)-based SSR markers (miRNA-SSRs) in wheat, which were found as key players in various abiotic stresses. In the present study, we identified 104 heat-stress-responsive miRNAs reported in various crops. Out of these, 70 miRNA-SSR markers have been validated on a set of 20 terminal heat-tolerant and heat-susceptible wheat genotypes. Among these, only 19 miRNA-SSR markers were found to be polymorphic, which were further used to study the genetic diversity and population structure. The polymorphic miRNA-SSRs amplified 61 SSR loci with an average of 2.9 alleles per locus. The polymorphic information content (PIC) value of polymorphic miRNA-SSRs ranged from 0.10 to 0.87 with a mean value of 0.48. The dendrogram constructed using unweighted neighbor-joining method and population structure analysis clustered these 20 wheat genotypes into 3 clusters. The target genes of these miRNAs are involved either directly or indirectly in providing tolerance to heat stress. Furthermore, two polymorphic markers miR159c and miR165b were declared as very promising diagnostic markers, since these markers showed specific alleles and discriminated terminal heat-tolerant genotypes from the susceptible genotypes. Thus, these identified miRNA-SSR markers will prove useful in the characterization of wheat germplasm through the study of genetic diversity and population structural analysis and in wheat molecular breeding programs aimed at terminal heat tolerance of wheat varieties.

scholarly journals Development and use of miRNA-derived SSR markers for the study of genetic diversity, population structure, and characterization of genotypes for breeding heat tolerant wheat varieties

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0231063
Author(s):  
Sandhya Tyagi ◽  
Anuj Kumar ◽  
Tinku Gautam ◽  
Renu Pandey ◽  
Sachin Rustgi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Heat Stress ◽  
Ssr Markers ◽  
Allelic Diversity ◽  
Abiotic Factor ◽  
Wheat Genotypes ◽  
Mirna Genes ◽  
Heat Tolerant

Heat stress is an important abiotic factor that limits wheat production globally, including south-east Asia. The importance of micro (mi) RNAs in gene expression under various biotic and abiotic stresses is well documented. Molecular markers, specifically simple sequence repeats (SSRs), play an important role in the wheat improvement breeding programs. Given the role of miRNAs in heat stress-induced transcriptional regulation and acclimatization, the development of miRNA-derived SSRs would prove useful in studying the allelic diversity at the heat-responsive miRNA-genes in wheat. In the present study, efforts have been made to identify SSRs from 96 wheat heat-responsive miRNA-genes and their characterization using a panel of wheat genotypes with contrasting reactions (tolerance/susceptible) to heat stress. A set of 13 miRNA-derived SSR markers were successfully developed as an outcome. These miRNA-SSRs are located on 11 different common wheat chromosomes (2A, 3A, 3B, 3D, 4D, 5A, 5B, 5D, 6A, 6D, and 7A). Among 13 miRNA-SSRs, seven were polymorphic on a set of 37 selected wheat genotypes. Within these polymorphic SSRs, three makers, namely HT-169j, HT-160a, and HT-160b, were found promising as they could discriminate heat-tolerant and heat-susceptible genotypes. This is the first report of miRNA-SSR development in wheat and their deployment in genetic diversity and population structure studies and characterization of trait-specific germplasm. The study suggests that this new class of molecular makers has great potential in the marker-assisted breeding (MAB) programs targeted at improving heat tolerance and other adaptability or developmental traits in wheat and other crops.

scholarly journals Molecular Characterization of Kiwifruit (Actinidia) Cultivars and Selections Using SSR Markers

2004 ◽  
Vol 129 (3) ◽  
pp. 374-382 ◽  
Author(s):  
Yiqi Zhen ◽  
Zuozhou Li ◽  
Hongwen Huang ◽  
Ying Wang
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
Ssr Markers ◽  
Rapd Markers ◽  
Reliable Method ◽  
Cultivar Identification ◽  
Direct Count ◽  
Polymorphic Loci ◽  
Single Genotype

Forty-eight kiwifruit cultivars and selections, representing more than 90% of total world kiwifruit production, were investigated using nine SSR markers to establish genetic identities, and evaluate genetic diversity and relatedness. These nine SSRs were polymorphic and a total of 213 alleles were detected, resulting in a mean number of 23.7 alleles per locus, ranging from nine to 38 alleles. One hundred and thirty-three alleles were found to be common to both A. chinensis and A. deliciosa, while 33 and 36 were specific to A. chinensis and A. deliciosa, respectively. In addition, 34 alleles were specific to one single genotype and provided a set of valuable alleles for cultivar identification. A single SSR locus UDK 96-414 could differentiate all 48 genotypes except two presumable clones. Mean number of alleles per locus (A), percentage of polymorphic loci (P), and direct count heterozygosity (Ho) assessed for each genotype over all loci revealed considerable differences among these 48 genotypes. On average, A = 2.6, P = 89.4% and Ho = 0.546 were found in A. chinensis cultivars, while A = 3.5, P = 97.0% and Ho = 0.671 in A. deliciosa cultivars. Consensus fingerprint profiling using SSR markers is a useful and reliable method for establishing genetic identities of kiwifruit cultivars and selections. It also improves evaluation effectiveness of genetic diversity and relatedness compared to RAPD markers.

scholarly journals Molecular Characterization of Apple Cultivars in Japan by S-RNase Analysis and SSR Markers

2005 ◽  
Vol 130 (6) ◽  
pp. 885-892 ◽  
Author(s):  
Kentaro Kitahara ◽  
Shogo Matsumoto ◽  
Toshiya Yamamoto ◽  
Junichi Soejima ◽  
Tetsuya Kimura ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
Ssr Markers ◽  
Maternal Parent ◽  
Golden Delicious ◽  
Apple Cultivars ◽  
Paternal Parent

We examined the genetic diversity and relatedness among apple (Malus ×domestica Borkh.) cultivars in Japan. The 42 apple cultivars, including major cultivars in Japan, were divided into five groups based on SSR genotypes. Most economically important cultivars belong in three groups: Fuji-Delicious, Golden Delicious, and Jonathan groups, and their genetic backgrounds seemed to be narrow. We also investigated the parent-offspring relationships of nine apple cultivars. `Jonathan', `Fuji', and `Rero 11' were identified as the respective paternal parents of three cultivars described as having unknown paternal parents (i.e., `Akagi', `Ambitious', and `Hokuto'). `Starking Delicious', `Senshu', and `Golden Delicious', rather than `Ralls Janet', `Hatsuaki', and `Indo', seemed to be the paternal parents of `Kinsei', `Kiou', and `Mellow', respectively. `Carolina Red June' was excluded as a paternal parent of `Ranzan'. Both attributed parents of `Scarlet' (`Akane' and `Starking Delicious') were excluded, and it was suggested that `Fuji' was used as either a maternal or a paternal parent of `Scarlet'. `Jonathan' rather than `McIntosh' seems to be a maternal parent of `Yukari'.

Development and Characterization of SSR Markers to Study Genetic Diversity and Population Structure of Horsegram Germplasm (Macrotyloma uniflorum)

2017 ◽  
Vol 35 (5) ◽  
pp. 550-561 ◽  
Author(s):  
R. K. Chahota ◽  
Divya Shikha ◽  
Maneet Rana ◽  
Vikas Sharma ◽  
Akshay Nag ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Macrotyloma Uniflorum

scholarly journals Molecular Characterization of 170 New gDNA-SSR Markers for Genetic Diversity in Button Mushroom (Agaricus bisporus)

Mycobiology ◽  
2019 ◽  
Vol 47 (4) ◽  
pp. 527-532
Author(s):  
Hyejin An ◽  
Ick-Hyun Jo ◽  
Youn-Lee Oh ◽  
Kab-Yeul Jang ◽  
Won-Sik Kong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
Ssr Markers ◽  
Agaricus Bisporus ◽  
Button Mushroom

scholarly journals In-Depth Genetic Diversity and Population Structure of Endangered Peruvian Amazon Rosewood Germplasm Using Genotyping by Sequencing (GBS) Technology

Forests ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 197
Author(s):  
Muhammad Azhar Nadeem ◽  
Stalin Juan Vasquez Guizado ◽  
Muhammad Qasim Shahid ◽  
Muhammad Amjad Nawaz ◽  
Ephrem Habyarimana ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Molecular Characterization ◽  
Clustering Algorithms ◽  
Genotyping By Sequencing ◽  
Diversity Indices ◽  
Peruvian Amazon ◽  
Mean Values ◽  
Management Plans

Research studies on conservative genetics of endangered plants are very important to establish the management plans for the conservation of biodiversity. Rosewood is an evergreen tree of the Amazon region and its essential oil has great acceptance in the medical and cosmetic industry. The present study aimed to explore the genetic diversity and population structure of 90 rosewood accessions collected from eight localities of Peruvian Amazon territory through DArTseq markers. A total of 7485 informative markers resulted from genotyping by sequencing (GBS) analysis were used for the molecular characterization of rosewood germplasm. Mean values of various calculated diversity parameters like observed number of alleles (1.962), the effective number of alleles (1.669), unbiased expected heterozygosity (0.411), and percent polymorphism (93.51%) over the entire germplasm showed the existence of a good level of genetic variations. Our results showed that the Mairiricay population was more diverse compared to the rest of the populations. Tamshiyacu-2 and Mairiricay-15 accessions were found genetically distinct accessions. The analysis of molecular variance (AMOVA) reflected maximum variations (75%) are due to differences within populations. The implemented clustering algorithms, i.e., STRUCTURE, neighbor-joining analysis and principal coordinate analysis (PCoA) separated the studied germplasm on the basis of their geographical locations. Diversity indices for STRUCTURE-based populations showed that subpopulation A is more diverse population than the rest of the populations, for such reason, individuals belonging to this subpopulation should be used for reintroduction or reinforcement plans of rosewood conservation. We envisage that molecular characterization of Peruvian rosewood germplasm with DArTseq markers will provide a platform for the conservation, management and restoration of endangered rosewood in upcoming years.

scholarly journals Development and Use of miRNA-derived SSR Markers to Study Genetic Diversity, Population Structure and Characterization of Genotypes for Heat Tolerance Breeding in Bread Wheat (Triticum aestivum L.)

2020 ◽  
Author(s):  
Sandhya Tyagi ◽  
Anuj Kumar ◽  
Tinku Gautam ◽  
Renu Pandey ◽  
Reyazul Rouf Mir
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Heat Tolerance ◽  
Triticum Aestivum L ◽  
Breeding Programs ◽  
Mirna Genes ◽  
Novel Mirna ◽  
The World

AbstractWheat is one of the most important cereal crop in the world. Heat stress is an important abiotic stress limiting wheat production and productivity in the world including south-east Asia. The importance of miRNAs in gene expression under various biotic and abiotic stresses is well documented. Molecular markers, especially SSR markers, plays an important role for the success in molecular plant breeding programs. The discovery of SSRs from non-coding regions has been a challenging task. Therefore, development of novel miRNA-based SSRs from the conserved portions of the genome will prove useful for the study of genetic diversity of heat-responsive miRNA-genes in wheat. In the present study, efforts are made to mine SSR markers from 96 members of heat-responsive miRNA-genes of wheat followed by their validation using 37 contrasting (heat tolerance/susceptible) wheat genotypes. Among a set of 13 miRNA-SSRs used,7 SSRs were found polymorphic. Among these polymorphic SSR markers, three found to be very informative SSRs (HT-169j, HT-160a and HT-160b) and could largely discriminate heat tolerant genotypes from the heat susceptible ones. Further analysis based on Polymorphism Information Content (PIC) revealed that miRNA genes were more diverse in susceptible genotypes compared to tolerant genotypes. Ours is the first report that the genic/miRNA markers could be successfully used to study wheat diversity, population structure and characterization of trait specific germplasm. The important and useful miRNA-based SSRs, therefore, would serve as best markers in the marker-assisted breeding programs aimed at enhancing heat tolerance of Indian wheat.

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