Study of Genetic Diversity Among Some Rainfed Bread and Durum Wheat Genotypes, Using SSR Markers

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.

Download Full-text

Association analysis and evaluation of genetic diversity in wheat genotypes using SSR markers

Biologia Futura ◽

10.1007/s42977-021-00088-y ◽

2021 ◽

Author(s):

S. Farhangian-kashani ◽

A. Azadi ◽

Sh. Khaghani ◽

M. Changizi ◽

M. Gomarian

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Association Analysis ◽

Wheat Genotypes ◽

Analysis And Evaluation

Download Full-text

Investigation of Genetic Diversity in Afghan Bread Wheat Genotypes Using SSR and AFLP Markers

Turkish Journal of Agriculture - Food Science and Technology ◽

10.24925/turjaf.v7i9.1263-1267.2165 ◽

2019 ◽

Vol 7 (9) ◽

pp. 1263

Author(s):

Mohammad Bahman Sadeqi ◽

Said Dadshani ◽

Mohammad Yousefi ◽

Gul Mohammad Ajir

Keyword(s):

Genetic Diversity ◽

Bread Wheat ◽

Ssr Markers ◽

Average Distance ◽

Wheat Breeding ◽

Aflp Markers ◽

Ammonium Bromide ◽

Aflp Data ◽

Wheat Genotypes ◽

Diversity Assessment

Genetic diversity assessment is the principle component for conservation and characterization of germplasm. Genetic diversity study of Afghan bread wheat genotypes is a first step to identify and to select high performance genotypes and distribute to wheat breeding programs. The main objective of this study is to investigate of genetic diversity in 35 Afghan bread wheat genotypes by using Simple Sequence Repeat (SSR) and Amplified Fragment Length Polymorphism (AFLP) markers. DNA extraction according to Cetyl Trimethyl Ammonium Bromide (CTAB) method was conducted and the total genomic DNA was isolated from each variety. Sixty-four SSR primer markers were used and eighteen EcoRI+(N)/MseI+(N) primer combinations with their primer sequences were used for selective polymerase chain reaction (PCR) amplification. Every SSR and AFLP fragment was scored as present (1) or absent (0) within all genotypes under study. Marker/ Value ratio of pairwise genetic distance between genotypes according to the SSRs data was from 0.508 to 0.691 with an average distance of 0.599. Relatively different grouping pattern in comparison to AFLP data observed through cluster analysis. Both types of molecular markers (AFLP and SSR) used in this research proved to be suitable for investigating genetic diversity in the genotypes of Afghan bread wheat, however, AFLP markers gave better view of genetically relationships among genotypes than the SSR markers. The grouping generated by AFLP data showed a special agreement with the origin regions of genotypes (Ariana-07 and Mazar-99 originating from the north of Afghanistan, Lalmi-03 and Kabul-02. Large number of DNA bands identified with AFLP markers might provide a better estimation of genetic similarity than those of SSR markers.

Download Full-text

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.

Download Full-text

GENETIC DIVERSITY IN WHEAT GENOTYPES USING SIMPLE SEQUENCE REPEAT (SSR) MARKERS

Research Journal of Applied Biotechnology ◽

10.21608/rjab.2016.59913 ◽

2016 ◽

Vol 2 (1) ◽

pp. 127-138

Author(s):

M. El-Rawy ◽

A. Taghian ◽

H. El-Aref ◽

B. Abd El-fatah ◽

S. El-Sanousy

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Sequence Repeat ◽

Wheat Genotypes ◽

Simple Sequence

Download Full-text

Genetic Diversity in Domestic and Introduced Wheats

Agriculture (Pol nohospodárstvo) ◽

10.2478/agri-2013-0009 ◽

2013 ◽

Vol 59 (3) ◽

pp. 101-110

Author(s):

Martina Hudcovicová ◽

Katarína Ondreičková ◽

Pavol Hauptvogel ◽

Ján Kraic

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Bread Wheat ◽

Ssr Markers ◽

Gene Diversity ◽

Polymorphic Markers ◽

Wheat Genotypes ◽

Average Gene Diversity ◽

Average Gene

Abstract A set of 33 wheat EST-SSR markers was designed and 18 from them were polymorphic and used for assessment of genetic diversity within 36 introduced genotypes of hexaploid bread wheat. Altogether 105 alleles were detected, in average 3.18 alleles per locus. Maximum number of alleles 14 was detected at the locus TDI389708. Five the most polymorphic markers were used for the evaluation and comparison of genetic variation within 46 domestic (Slovak) wheat genotypes and 36 introduced (foreign) wheat genotypes. The number of alleles per used primer pair within domestic genotypes varied from 7 to 19, with an average of 13.2 alleles, an average gene diversity 0.846 and PIC 0.980 per locus. The number of alleles per primer within introduced genotypes varied from 7 to 14, with an average of 10.8 alleles, an average gene diversity 0.780 and PIC 0.958 per locus. The level of polymorphism in EST- SSRs was sufficient for discrimination between genotypes and variation within domestic genotypes was slightly higher than in introduced genotypes. Variation revealed by 5 selected EST-SSR markers clustered genotypes according to origin. Domestic and introduced wheats were grouped distinctly into two separate groups.

Download Full-text

Genetic Characterization of Rainfed Durum Wheat Genotypes Based On Functional Markers Associated With Grain Quality Proteins

10.21203/rs.3.rs-675853/v1 ◽

2021 ◽

Author(s):

Zahra Moradi Kheibary ◽

Reza Azizinezhad ◽

Ali Mehras Mehrabi ◽

Mahmood Khosrowshahli ◽

Alireza Etminan

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Durum Wheat ◽

Agricultural Research ◽

Conservation Strategies ◽

Functional Markers ◽

Wheat Genotypes ◽

Allele Number ◽

Population Structure Analysis ◽

Gliadin Alleles

Abstract Analysis of genetic diversity provides helpful information necessary to develop the breeding and conservation strategies of crops. In this study, the genetic diversity and population structure of 90 durum wheat genotypes maintained at Sararud Dryland Agricultural Research Institute, Kermanshah, Iran, were evaluated by using 23 gene-specific markers (functional markers, FMs) encoding high and low molecular weight glutenin and gliadin alleles. Results showed that 12 out of the 23 FMs used were polymorphic and amplified 52 polymorphic loci. Primer Ax2 ⃰ had the highest discriminatory power. The population structure analysis classified the durum wheat collection into four populations. On average, population 4, consisting of 8 genotypes, had the highest allele number as well as genetic variation. Analysis of molecular variance indicated that 82% of the total variation was distributed among populations. The diversity among populations and gene flow were 0.14 and 3.03, respectively. The Jaccard distance coefficient revealed that genetic dissimilarities ranged from 0.031 between G62 and G65 to 0.725 between G36 and G51. Neighbor-joining method clustered individuals into six main groups. Results showed a remarkable level of genetic diversity among studied durum wheat genotypes which can be of interest for future breeding programs.

Download Full-text

Microsatellites in the analysis of wheat genetic diversity

Genetika ◽

10.2298/gensr1403047k ◽

2014 ◽

Vol 46 (3) ◽

pp. 1047-1063

Author(s):

Ankica Kondic-Spika ◽

Milica Nicic ◽

Ljiljana Brbaklic ◽

Dragana Trkulja ◽

Dragana Miladinovic ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Information Content ◽

Ssr Markers ◽

Microsatellite Loci ◽

Polymorphism Information Content ◽

Null Alleles ◽

Wheat Genotypes ◽

Rare Alleles ◽

High Level

Microsatellite markers (SSR) were used to study wheat genetic diversity. A set of 87 wheat genotypes was analysed with four SSR markers. Primers used for the amplification of adequate microsatellite loci (Xgwm) are according to R?DER et al. (2002). Results were obtained using Applied Biosystems 3130 genetic analyser. Total of 28 alleles were determined, i.e. average of 7 alleles per marker. Number of alleles for individual markers ranged from six (Xgwm3) to eight (Xgwm18). The presence of two null alleles for Xgwm18 and Xgwm155 was found. There were five rare alleles (frequency <2%). Polymorphism information content (PIC) values ranged from 0.52 for Xgwm408 to 0.80 for Xgwm18. Mean PIC value was 0.69 for all markers, which signifies a high level of the detected polymorphism. According to the data collected through the analysis of four markers, most genotypes can be grouped in clusters. The results show usefulness of microsatellite markers in detecting polymorphism, identifying genotypes and assessing genetic diversity.

Download Full-text