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

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.

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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 ◽

10.1371/journal.pone.0231063 ◽

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.

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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.)

10.1101/2020.03.17.995142 ◽

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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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

Tree Genetics & Genomes ◽

10.1007/s11295-012-0577-5 ◽

2012 ◽

Vol 9 (2) ◽

pp. 539-555 ◽

Cited By ~ 22

Author(s):

Eduardo Gross-German ◽

Maria Angeles Viruel

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Characterization ◽

Ssr Markers

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Analyses of genetic diversity and population structure of anchote (Coccinia abyssinica (Lam.) Cogn.) using newly developed EST-SSR markers

Genetic Resources and Crop Evolution ◽

10.1007/s10722-021-01132-5 ◽

2021 ◽

Author(s):

Bekele Serbessa Tolera ◽

Kifle Dagne Woldegebriel ◽

Abel Teshome Gari ◽

Mulatu Geleta Dida ◽

Kassahun Tesfaye Geletu

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Citrullus Lanatus ◽

Wide Range ◽

Minor Crop ◽

Ssrs Markers ◽

Expressed Sequence

AbstractAnchote (Coccinia abyssinica (Lam.) Cogn.) is a perennial root crop belonging to Cucurbitaceae family. It is endemic to Ethiopia and distributed over wide range of agro-ecologies. For further improvement and efficient conservation of this crop, characterization of its genetic diversity and its pattern of distribution is a vitally important step. Expressed sequence tags-simple sequence repeats (EST-SSRs) markers were developed from publicly available watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] ESTs in the GenBank database. Among those novel markers, eight were polymorphic and subsequently used for genetic diversity and population structure analyses of 30 anchote accessions collected from western Ethiopia. A total of 24 alleles were obtained across the eight polymorphic loci and 30 accessions that revealed moderate level of genetic diversity in this minor crop. Among the eight loci, locus CA_06 was the most informative with six alleles and polymorphic information content (PIC) of 0.76. The accessions showed about threefold variation in terms of genetic diversity, with expected heterozygosity (He) ranging from 0.15 (accession An) to 0.44 (accession Dg). Other accessions with higher genetic diversity include Ar and Gu (He = 0.43 and 0.41, respectively). Analysis of molecular variance (AMOVA) revealed that the variation within accessions and among accessions accounted for 84.7% and 15.3% of the total variation, respectively. The study revealed low but significant population differentiation in this crop with no clear pattern of population structure. The EST-SSR markers developed in this study are the first of their kind for anchote and can be used for characterization of its wider genetic resources for conservation and breeding purposes.

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