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

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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Characterization of Hemerocallis citrina Transcriptome and Development of EST-SSR Markers for Evaluation of Genetic Diversity and Population Structure of Hemerocallis Collection

Frontiers in Plant Science ◽

10.3389/fpls.2020.00686 ◽

2020 ◽

Vol 11 ◽

Author(s):

Sen Li ◽

Fangfang Ji ◽

Feifan Hou ◽

Huliang Cui ◽

Qingqing Shi ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Hemerocallis Citrina

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Assessing genetic variation for heat stress tolerance in Indian bread wheat genotypes using morpho-physiological traits and molecular markers

Plant Genetic Resources ◽

10.1017/s1479262116000241 ◽

2016 ◽

Vol 15 (6) ◽

pp. 539-547 ◽

Cited By ~ 5

Author(s):

P. Sharma ◽

S. Sareen ◽

M. Saini ◽

Shefali

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Heat Stress ◽

Molecular Markers ◽

Heat Tolerance ◽

Polymorphic Information Content ◽

Physiological Traits ◽

Phenotypic Traits ◽

Phenotypic Data ◽

Wheat Genotypes

AbstractHeat stress greatly limits the productivity of wheat in many regions. Knowledge on the degree of genetic diversity of wheat varieties along with their selective traits will facilitate the development of high yielding, stress-tolerant wheat cultivar. The objective of this study were to determine genetic variation in morpho-physiological traits associated with heat tolerance in 30 diverse wheat genotypes and to examine genetic diversity and relationship among the genotypes varying heat tolerance using molecular markers. Phenotypic data of 15 traits were evaluated for heat tolerance under non-stress and stress conditions for two consecutive years. A positive and significant correlation among cell membrane stability, canopy temperature depression, biomass, susceptibility index and grain yield was shown. Genetic diversity assessed by 41 polymorphic simple sequence repeat (SSR) markers was compared with diversity evaluated for 15 phenotypic traits averaged over stress and non-stress field conditions. The mean polymorphic information content for SSR value was 0.38 with range of 0.12–0.75. Based on morpho-physiological traits and genotypic data, three groups were obtained based on their tolerance (HHT, MHT and LHT) levels. Analysis of molecular variance explained 91.7% of the total variation could be due to variance within the heat tolerance genotypes. Genetic diversity among HHT was higher than LHT genotypes and HHT genotypes were distributed among all cluster implied that genetic basis of heat tolerance in these genotypes was different thereby enabling the wheat breeders to combine these diverse sources of genetic variation to improve heat tolerance in wheat breeding programme.

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Genetic diversity and population structure using linked SSR markers for heat stress tolerance in rice

ORYZA- An International Journal on Rice ◽

10.5958/2249-5266.2017.00021.2 ◽

2017 ◽

Vol 54 (2) ◽

pp. 158

Author(s):

Sudipti Mohapatra ◽

E Pandit ◽

SR Barik ◽

BC Patra ◽

J Meher ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Heat Stress ◽

Stress Tolerance ◽

Ssr Markers ◽

Heat Stress Tolerance

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Evaluation of seedling proline content of wheat genotypes in relation to heat tolerance

Bangladesh Journal of Botany ◽

10.3329/bjb.v40i1.7991 ◽

1970 ◽

Vol 40 (1) ◽

pp. 17-22 ◽

Cited By ~ 15

Author(s):

JU Ahmed ◽

MA Hassan

Keyword(s):

Heat Stress ◽

High Temperature ◽

Heat Tolerance ◽

Negative Correlation ◽

Significant Negative Correlation ◽

Proline Content ◽

Membrane Injury ◽

Wheat Genotypes ◽

Membrane Thermostability ◽

Heat Tolerant

Seedling of 20 wheat genotypes were grown in Phytotron at about 25 and 35°C for measuring membrane injury in per cent and seedling proline content to investigate seedling proline as screening criterion against heat stress. The wheat genotypes (Bijoy, Sufi, Kanchan, Fang 60, BAW 1059, BL 1883, BL 1022, IVT 7, IVT 8, IVT 9, IVT 10 and BAW 917) showing < 50% membrane injury were grouped as heat tolerant (HT) and the genotypes (Shatabdi, Prodip, BAW 1064, Gourab, Pavon 76, Sonora, Kalyansona and IVT 6) showing ≥ 50% membrane injury were classified as heat sensitive (HS). At high temperature (35°C) the HT genotypes produced more than double (> 200%) proline than that of 25°C but the HS genotypes produced less quantity of proline at 35°C compared to that in HT genotypes. The seedling proline content at 35°C and membrane injury (%) maintained a significant negative correlation (r = – 0.619**) across the 20 wheat genotypes tested. Key words: Membrane thermostability; Seedling proline; Heat tolerance; Wheat DOI: http://dx.doi.org/10.3329/bjb.v40i1.7991 Bangladesh J. Bot. 40(1): 17-22, 2011 (June)

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