A total of 96 emmer wheat accessions from the Indian National Genebank were evaluated for terminal heat stress tolerance across three locations Delhi, Pune, and Pantnagar using an alpha lattice design under timely and late sown conditions. Significant variation was observed among accessions across locations and sowing conditions for agronomic and physiological traits. High heritability was recorded for days to anthesis (81.1

In the present study, a diverse set of 96 lentil accessions including biofortified variety IPL 220 was used to identify sources of high concentration for Fe and Zn along with low phytic acid concentration and high protein content. Further, Marker Trait Association (MTA) analysis was performed to find molecular markers controlling these nutritional traits. The average Fe, Zn and phytic acid concentration and protein content ranged from 46.5 to 94.8 (mg/kg), 21.5 to 45.3 (mg/kg), 3.7 to 9.3 (mg/kg) and 18.1-28.7 (%), respectively over the locations. This study showed variability for these traits as coefficient of variation was 11.1% for Fe, 18% for Zn, 18.3% for phytic acid and 8.71% for protein content over two locations. The standard error (S.E.) of mean ranged from 0.05 to 21.5 for Fe, 0.15 to 9.71 for Zn, 0.05 to 2.10 for phytic acid and 0.06 to 6.16 for protein content further calculated across the locations. MTA analysis following general linear model resulted in the identification of 31 MTAs for three traits at p < 0.05 explaining 10 to 26% of total phenotypic variation. Association of PBA LC0203 marker with Fe concentration explained the highest proportion of total phenotypic variation (26%) at Kanpur location. However, same marker with different loci also showed association with Fe concentration at Bhopal location explaining 11% of total phenotypic variation. This study also identified association of some genetic markers with more than two nutritional traits that provides opportunity of improving more than two positively associated nutritional traits through marker assisted selection simultaneously. In the present study, EST-SSR markers were used as functional markers for developing high yielding bio-fortified lentils.

Hybrid development is one of the most promising strategies for boosting crop yields. Parental lines used to create hybrids must have good per se performance and disease resistance for developing superior hybrids. Indian wheat line HD3209 was developed by introducing the rust resistance genes Lr19/Sr25 into the background of popular wheat variety HD2932. The wheat line HD3209 carrying Lr19/Sr25 has been successfully and rapidly converted to the CMS line A-HD3209, with 96.01% background genome recovery, based on selection for agro-morphological traits, rust resistance, pollen sterility, and foreground and background analyses utilizing SSR markers. The converted CMS line A-HD3209 was completely sterile and nearly identical to the recurrent parent HD3209. Based on high per se performance and rust resistance, the study concludes that the derived CMS line A-HD3209 is promising and can be employed successfully in hybrid development.

Emmer wheat germplasm has received little attention with regard to exploring its genetic diversity toward enhancing utilization. Agro-morphological characterization was performed on 192 emmer wheat accessions during the winter season of 2019–2020, and subsequently 96 accessions were selected for morphological and molecular diversity analysis during the winter season of 2020–2021. Genetic diversity and population structure of 96 diverse Triticum dicoccum genotypes conserved in the National Genebank of India were estimated using 56 microsatellite (simple sequence repeat) markers. The number of alleles per locus ranged from one to six, with an average of 1.68 alleles. A total of 93 alleles were detected, with the highest polymorphic information content value (0.9912) observed for the Xcfd20 marker. Based on ‘STRUCTURE’ analysis, 96 dicoccum accessions were divided into two subpopulations. The analysis of molecular variance revealed that genetic differentiation among subpopulations was low and within subpopulations was high. A cluster analysis based on Jaccard’s dissimilarity index identified two clusters which were in congruence with the population structure. Indigenous and exotic collections were categorized into distinct subclusters within the same cluster with some overlapping suggesting limited genomic differentiation between these collections. Based on the present study, it is evident that cultivated emmer wheat showed low genetic diversity and a narrow genetic base. This might be due to limited cultivation in small pockets and emphasizes a need to broaden the genetic base of emmer wheat genetic resources for enhanced utilization.

Breeders have extensively used marker-assisted selection to improve the agronomically superior varieties for disease resistance. Here, the mega wheat variety of India, HD3086, has been improved for leaf rust resistance by transferring a leaf rust resistance gene LrTrk from Triticum turgidum var. durum cv. Trinakria (AABB, 2n = 4X = 28). Taking a tetraploid donor parent instead of a hexaploid produced partial sterility in initial generations, but fertility improved beyond BC2F1 generations and aided in the rapid and higher recovery of recurrent parent genomes. Leaf rust resistance gene LrTrk was selected in every backcross generation with the help of resistance gene linked markerXgwm234 and further confirmed by rust screening. Further, rigorous phenotypic selection of plants with rust resistance gene LrTrk for their phenotypic similarity to recurrent parent HD3086 in backcross generations helped us identify six homozygous NILs in BC2F3 generation. All six NILs carried more than 95% of the recurrent parent genome (RPG) when analyzed with polymorphic markers between the parents. The six NILs also showed no difference in the ago-morphological traits compared to RP HD3086. Out of six, one NIL, HD3086+LrTrk-2, was selected with numerically higher yielding than recurrent parent HD3086 and at par performance for all other traits. This NIL will be nominated in AICRP trials before being it to the farmer's field. The improved NIL will provide an alternative for the susceptible cultivar from the farmer's field and broaden the genetic base of wheat cultivars grown in India.

Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. ciceri is a devastating disease of chickpea ( Cicer arietinum). To identify promising resistant genotypes and genomic loci for FW resistance, a core set of 179 genotypes of chickpea was tested for FW reactions at the seedling and reproductive stages under field conditions and controlled conditions in the greenhouse. Our results revealed that at the seedling stage, most of the genotypes were resistant, whereas at the reproductive stage, most of the genotypes were susceptible. Genotyping using a 50K Axiom®CicerSNP Array and trait data of FW together led to the identification of 26 significant ( P ≤ E-05) marker-trait associations (MTAs) for FW resistance. Among the 26 MTAs, 12 were identified using trait data recorded in the field (three at the seedling and nine at the reproductive stage), and 14 were identified using trait data recorded under controlled conditions in the greenhouse (six at the seedling and eight at the reproductive stage). The phenotypic variation explained by these MTAs varied from 11.75 to 15.86%, with an average of 13.77%. Five MTAs were classified as major, explaining more than 15% of the phenotypic variation for FW, and two were declared stable, being identified in two environments. One of the promising stable and major MTAs (Affx_123280060) detected in field conditions at the reproductive stage was also detected in greenhouse conditions at the seedling and reproductive stages. The stable and major (>15% PVE) MTAs can be used in chickpea breeding programs.

Tetraploid wheat, Triticum timopheevii (Zhuk.) (AtAtGG, 2n = 4x = 28) is a well-known source of resistance against many pests and diseases. It has been practically utilized in various breeding programmes against leaf rust disease. The present study developed a set of 41 introgression lines (ILs) by crossing two T. timopheevii accessions viz., T. timopheevii-191 and T. timopheevii-235 with bread wheat genotype Chinese Spring. The F1s were backcrossed thrice to susceptible cultivars, Agra Local and Kharchia Local, followed by selfing for five generations. All the ILs were screened for leaf rust resistance using leaf rust pathotype 77-5 at seedling stage in a glass house. Out of 41 ILs, 33 showed resistant reactions to leaf rust ('0;' to '13'). Two ILs, TTm Derivative-638 and TTm Derivative-793, showing high degree of resistance, were further tested against 19 different leaf rust pathotypes, produced "0;" to ";" type of infection type (IT). To characterize the genomic constitution of these two ILs and to detect the presence of introgression segment(s) of two wild Triticum timopheevii wheats, 35K Affymetrix Wheat Breeders'Axiom & REG; array was used. SNP (Single nucleotide polymorphism) analysis confirmed T. timopheevii introgressions in two ILs and was used for graphical representation using software GTM v1.0. Genomic characterization revealed 30.59 and 20.30% of introgression from wild accessions, T. timopheevi-191 and T. timopheevi-235 into ILs TTm Derivative-638 and TTm Derivative-793, respectively. Genomewise analysis in ILs TTm Derivative-638 and TTm Derivative-793 revealed maximum introgression in B genome (32.18) and A genome (22.75%), respectively. These ILs will help in widening the genetic base for leaf rust resistance in wheat.

Bread wheat (Triticum aestivum L.; Ta) is the staple cereal crop for the majority of the world's population. Leaf rust disease caused by the obligate fungal pathogen, Puccinia triticina L., is a biotrophic pathogen causing significant economic yield damage. The alteration in the redox homeostasis of the cell caused by various kinds of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in response to pathogenic infections is controlled by redox regulators. Thioredoxin (Trx) is one of the redox regulators with low molecular weight and is thermostable. Through a genome-wide approach, forty-two (42) wheat Trx genes (TaTrx) were identified across the wheat chromosome groups A, B, and D genomes containing 12, 16, and 14 Trx genes, respectively. Based on in silico expression analysis, 15 TaTrx genes were selected and utilized for further experimentation. These 15 genes were clustered into six groups by phylogenetic analysis. MicroRNA (miRNA) target analysis revealed eight different miRNA-targeted TaTrx genes. Protein-protein interaction (PPI) analysis showed TaTrx proteins interact with thioredoxin reductase, peroxiredoxin, and uncharacterized proteins. Expression profiles resulting from quantitative real-time PCR (qRT-PCR) revealed four TaTrx genes (TaTrx11-5A, TaTrx13-5B, TaTrx14-5D, and TaTrx15-3B) were significantly induced in response to leaf rust infection. Localization of ROS and its content estimation and an assay of antioxidant enzymes and expression analysis suggested that Trx have been involved in ROS homeostasis at span 24HAI-72HAI during the leaf rust resistance.

Nitric oxide (NO) modulates plant response to biotic and abiotic stresses by S-nitrosylation-mediated protein post-translational modification. Nitrate reductase (NR) and S-nitrosoglutathione reductase (GSNOR) enzymes are essential for NO synthesis and the maintenance of Nitric oxide/S-nitroso glutathione (NO/GSNO) homeostasis, respectively. S-nitrosoglutathione, formed by the S-nitrosylation reaction of NO with glutathione, plays a significant physiological role as the mobile reservoir of NO. The genome-wide analysis identified nine NR (NIA) and three GSNOR genes in the wheat genome. Phylogenic analysis revealed that the nine NIA genes +were clustered into four groups and the 3 GSNOR s into two groups. qRT-PCR expression profiling of NIAs and GSNORs was done in Chinese spring (CS), a leaf rust susceptible wheat line showing compatible interaction, and Transfer (TR), leaf rust-resistant wheat line showing incompatible interaction, post-inoculation with leaf rust pathotype 77–5 (121-R-63). All the NIA genes showed upregulation during incompatible interaction in comparison with the compatible reaction. The GSNOR genes showed a variable pattern of expression: the TaGSNOR1 showed little change, whereas TaGSNOR2 showed higher expression during the incompatible response. TaGSNOR3 showed a rise of expression both in compatible and incompatible reactions. Before inoculation and after 72 h of pathogen inoculation, NO localization was studied in both compatible and incompatible reactions. The S-nitrosothiol accumulation, NR, and glutathione reductase activity showed a consistent increase in the incompatible interactions. The results demonstrate that both NR and GSNOR plays significant role in defence against the leaf rust pathogen in wheat by modulating NO homeostasis or signalling.

Chickpea is the most important nutrient-rich grain legume crop in the world. A diverse core set of 147 chickpea genotypes was genotyped with a Axiom(®)50K CicerSNP array and trait phenotyped in two different environments for four seed micronutrients (Zn, Cu, Fe and Mn). The trait data and high-throughput 50K SNP genotypic data were used for the genome-wide association study (GWAS). The study led to the discovery of genes/QTLs for seed Zn, Cu, Fe and Mn, concentrations in chickpea. The analysis of seed micronutrient data revealed significant differences for all four micronutrient concentrations (P ≤ 0.05). The mean concentrations of seed Zn, Cu, Fe and Mn pooled over the 2 years were 45.9 ppm, 63.8 ppm 146.1 ppm, and 27.0 ppm, respectively. The analysis of results led to the identification of 35 SNPs significantly associated with seed Zn, Cu, Fe and Mn concentrations. Among these 35 marker-trait associations (MTAs), 5 were stable (consistently identified in different environments), 6 were major (explaining more than 15% of the phenotypic variation for an individual trait) and 3 were both major and stable MTAs. A set of 6 MTAs, MTAs (3 for Mn, 2 for Fe, and 1 for Cu) reported by us during the present study have been also reported in the same/almost same genomic regions in earlier studies and therefore declared as validated MTAs. The stable, major and validated MTAs identified during the present study will prove useful in future chickpea molecular breeding programs aimed at enhancing the seed nutrient density of chickpea.

Wheat leaf rust caused by Puccinia triticina Eriks is an important disease that causes yield losses of up to 40% in susceptible varieties. Tetraploid emmer wheat (T. turgidum ssp. Dicoccum), commonly called Khapli wheat in India, is known to have evolved from wild emmer (Triticum turgidum var. dicoccoides), and harbors a good number of leaf rust resistance genes. In the present study, we are reporting on the screening of one hundred and twenty-three dicoccum wheat germplasm accessions against the leaf rust pathotype 77-5. Among these, an average of 45.50% of the germplasms were resistant, 46.74% were susceptible, and 8.53% had mesothetic reactions. Further, selected germplasm lines with accession numbers IC138898, IC47022, IC535116, IC535133, IC535139, IC551396, and IC534144 showed high level of resistance against the eighteen prevalent pathotypes. The infection type varied from “;”, “;N”, “;N1” to “;NC”. PCR-based analysis of the resistant dicoccum lines with SSR marker gwm508 linked to the Lr53 gene, a leaf rust resistance gene effective against all the prevalent pathotypes of leaf rust in India and identified from a T. turgidum var. dicoccoides germplasm, indicated that Lr53 is not present in the selected accessions. Moreover, we have also generated 35K SNP genotyping data of seven lines and the susceptible control, Mandsaur Local, to study their relationships. The GDIRT tool based on homozygous genotypic differences revealed that the seven genotypes are unique to each other and may carry different resistance genes for leaf rust.

Abstract The present study was undertaken for developing pre-harvest sprouting tolerant (PHST) wheat genotypes using marker-assisted backcross breeding (MABB). A major QTL for PHST was introgressed into an elite Indian wheat cv. Lok1 that is PHS susceptible. These PHST lines were also pyramided with one gene each for high grain protein content (Gpc-B1) and leaf rust resistance (Lr24). For introgression of PHST QTL, initially Lok1 was separately crossed with each of the two donors (PHS tolerant white-grained AUS1408 and CN19055). Backcrossing in each generation was followed by foreground and background selections using SSR markers. In advanced lines, KASP assay was also carried out for the candidate gene TaMKK3-A underlying the PHST QTL. The MAS derived lines homozygous for PHST QTL were screened for PHS using simulated rain chambers resulting in the selection of 10 PHST lines. For pyramiding of three QTL/genes (PHST QTL, Gpc-B1, and Lr24), MABB derived BC4F2 plants (from the cross Lok1/CN19055) were crossed with a MAS derived BC2F5 line [Lok1 (Gpc-B1 + Lr24)] developed earlier by us in the same background of Lok1. After foreground MAS followed by PHS screening, four advanced lines carrying all the three QTL/genes in homozygous condition were selected. These lines exhibited high level of PHST (PHS score 2–3) associated with significant improvement in GPC with no yield penalty and resistance against leaf rust under artificial epiphytotic conditions.

Cicer arietinum L. (chickpea) is one of the most significant legume crops domesticated in the Fertile Crescent. This study was aimed to characterize a diverse composite set of 384 Cicer genotypes using unlinked simple sequence repeat (SSR) markers. The genotypes grown under the temperate conditions of Western-Himalayas included cultivated and wild relatives from primary (Cicer reticulatum Ladiz.), secondary (Cicer echinospermum P.H. Davis) and tertiary (Cicer microphyllum Benth.) gene pools. The analysis of genotypic data of eight SSR markers from eight linkage groups led to the identification of 63 alleles, ranging from 2 to 6 with an average value of 3.7 alleles per locus. The polymorphic information content of SSR markers ranged from 0.46 to 0.79 with an average value of 0.77 and the gene diversity ranged from 0.47 to 0.79 with an average of 0.64. The clustering of genotypes in the form of dendrogram discriminated all 384 genotypes into four major clusters. The wild genotypes belonging to different gene pools got clustered uniformly in different clusters along with cultivated chickpea genotypes. The analysis of data also led to the selection of core set of 192 genotypes. The core set was found to possess same diversity (63 alleles; average alleles per locus: 3.7; gene diversity: 0.65) as that of composite set of 384 genotypes. The development of core set in chickpea shall prove useful in gene discovery for variety of traits through genome-wide association studies. The results also provide an insight into gene/allele diversity available in our chickpea germplasm collection grown under agro-climatic conditions of the North Western-Himalayas.

Habitat loss due to climate change may cause the extinction of the clonal species with a limited distribution range. Thus, determining the genetic diversity required for adaptability by these species in sensitive ecosystems can help infer the chances of their survival and spread in changing climate. We studied the genetic diversity and population structure of Sambucus wightiana-a clonal endemic plant species of the Himalayan region for understanding its possible survival chances in anticipated climate change. Eight polymorphic microsatellite markers were used to study the allelic/genetic diversity and population structure. In addition, ITS1-ITS4 Sanger sequencing was used for phylogeny and SNP detection. A total number of 73 alleles were scored for 37 genotypes at 17 loci for 8 SSRs markers. The population structural analysis using the SSR marker data led to identifying two sub-populations in our collection of 37 S. wightiana genotypes, with 11 genotypes having mixed ancestry. The ITS sequence data show a specific allele in higher frequency in a particular sub-population, indicating variation in different S. wightiana accessions at the sequence level. The genotypic data of SSR markers and trait data of 11 traits of S. wightiana, when analyzed together, revealed five significant Marker-Trait Associations (MTAs) through Single Marker Analysis (SMA) or regression analysis. Most of the SSR markers were found to be associated with more than one trait, indicating the usefulness of these markers for working out marker-trait associations. Moderate to high genetic diversity observed in the present study may provide insurance against climate change to S. wightiana and help its further spread.

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.

Blumeria graminis (DC). E.U. Speer f.sp. tritici Em. Marchal (Syn. Erysiphe graminis DC f.sp. tritici, Em. Marchal), a causal organism of powdery mildew (PM), is one of the important diseases of wheat worldwide. A comprehensive evaluation of wheat germplasm accessions (19,460) conserved in the National Genebank of ICAR-National Bureau of Plant Genetic Resources was conducted to identify sources of resistance to PM. Accessions belonging to the three wheat species-bread wheat (Triticum aestivum L. subsp. aestivum) (15,944), durum wheat (T. durum Desf.) (3,359), and emmer wheat (T. dicoccum Schrank ex Schubl.) (157)-were screened at Wellington, a hotspot location for PM, for two consecutive seasons. Screening results indicated that 7271 (45%) from bread wheat, 756 (22%) from durum wheat, and 22 (14%) from emmer were resistant. Out of 8094 PM-resistant accessions, 60% were indigenous, while majority of the 40% exotic were from CIMMYT. Focused identification of germplasm strategy (FIGS), which identifies a set of similar plant genotypes with a greater possibility of containing specific target traits, was used to form a subset of 52 accessions (from 19,460) that have the potential to contain new PM resistance genes. Resistant accessions identified in the study have enriched the existing gene pool for PM resistance in wheat and will serve as a potential source for resistance in future.

In plants, the enzyme CCD8 (carotenoid cleavage dioxygenase 8) is involved in the synthesis of an important hormone, strigolactone, and therefore, plays an important role in controlling growth and development. Using cDNA and protein sequence derived from the gene ZmCCD8 from maize, we identified putative orthologs of the gene encoding CCD8 in six other monocots and eight dicots; the sequence similarity ranged from 52-75.9% at the gene level and 60.9-93.7% at the protein level. The average length of the gene was ~3.3 kb (range: 2.08 to 3.98 kb), although the number of introns within the genes differed (4 or 5 in dicots and 3 or 4 in monocots, except in T. urartu with 6 introns). Several cis-acting regulatory elements were identified in the promoters of CCD8 genes, which are known to respond to biotic and abiotic stresses. The N-terminal end (up to ~70 amino acids) of CCD8 proteins was highly variable due to insertions, deletions and mismatches. The variation in genes and proteins were particularly conspicuous in T. urartu and Ae. tauschii among the monocots and A. thaliana and P. persica among the dicots. In CCD8 proteins, 12 motifs were also identified, of which 6 were novel; 4 of these novel motifs occurred in all the 15 species. The 3D structures of proteins had the characteristic features of the related enzyme apocarotenoid oxygenase (ACO) of Synechocystis (a representative of cyanobacteria). The results of qRT-PCR in wheat revealed that under phosphorous (P)-starved condition (relative to expression under optimum P used as control), the expression of TaCCD8 genes increased ~37 fold in root tissue of the cultivar C306 and ~33 fold in shoot tissue of the cultivar HUW468 (the two cultivars differed in their P-use efficiency). This suggested that expression of TaCCD8 genes is genotype-dependent and tissue-specific and is regulated under different levels of P supply.

Near isogenic lines (NILs) are ideal material for a variety of genetic studies including validation of specific QTL. In the present study, eight pairs of NILs for grain weight were developed, seven in the background of Raj3765, and one in the background of K9107. For this purpose, marker-assisted selection (MAS) was used for the transfer of three grain weight QTL (QGw.ccsu-1A.2, QGw.ccsu-1A.3 and QGw.ccsu-1B.1) that were earlier identified in our laboratory. Two genotypes of each of the eight pairs of NILs, differed for QTL alleles (QTL(Hgw) derived from the donor parent and the QTL(Lgw) derived from the recipient parent). Each pair of NILs involved a solitary QTL except one NIL, which differed for all the three QTL. The difference in thousand grain weight (TGW) in two NILs of an individual pair ranged from 2.8 to 7.5 g, thus validating the effect of the QTL for TGW, although the quantum of difference did not always match the phenotypic variance of the corresponding QTL. As expected, the NILs which involved all the three QTL had the maximum difference of 7.5 g in TGW, and the NILs which involved QTL, QGw.ccsu-1A.2 had minimum average difference of 2.8 g for TGW. The NILs produced during the present study may be used in future for MAS and for fine mapping of TGW QTL.

MicroRNAs (miRNAs) are tiny (20–24 nt bp) regulatory non-protein-coding RNA molecules that have been extensively characterized and found important for many physiological and developmental processes. The miss-expression of miRNAs leads to various defects in plants. MicroRNAs repress gene expression by directing mRNA degradation or translational arrest. Several proteins such as PP43A, HYL1, DCL, HST are indispensable role players in promoting miRNA biogenesis in plants. During miRNA biogenesis, lariat RNAs are produced as by-products of pre-mRNA splicing which have a negative role in regulation of miRNA homeostasis. By acting as a decoy and by sequestering to the dicing complex, lariat RNA can prevent the processing of miRNAs. A number of bioinformatic tools with different methodologies are available to identify and validate miRNAs and their targets. Many miRNAs have been reported in different crops for different traits; however, no reports are available on their use in plant breeding. Recently, researchers have developed trait specific miRNA-based molecular markers (miRNA-SSRs/SNP) for many quantitative traits in different plant species. In the future, these molecular markers can be used for plant breeding programs. In this review, a comprehensive up-to-date information is provided on the bioinformatic tools used for analysis of plant miRNAs and their targets, the number of miRNAs, their biogenesis, gene silencing mechanism and miRNA-based molecular markers.