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

Abstract

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.

Assessment of molecular genetic diversity of 384 chickpea genotypes and development of core set of 192 genotypes for chickpea improvement programs

“…A variety of DNA based markers ''popularly also known as molecular markers'' have become available and are being used in crop improvement programs world-wide (Gupta et al 2008;Mir et al 2013a;Mir and Varshney 2013;Gupta et al 2013;Kumar et al 2021). Some of the most important type of markers still popular for molecular breeding programs includes SSR markers, SNP markers, Array-based markers and recently emerged microRNA based markers (Gupta et al 2008;Tyagi et al 2019;Tyagi et al 2021;Sihag et al 2021). In chickpea, a variety of molecular markers including AFLPs, RAPDs, SSRs have been already used to unravel and understand the genetic diversity available in chickpea (Talebi et al 2008a, b;Saeed et al 2011;Keneni et al 2012;Ghaffari et al 2014).…”

Transcriptional Regulation of Metabolic and Cellular Processes in Durum Wheat (Triticum turgidum subsp. durum) in the Face of Temperature Increasing

“…Additionally, the influence of post-transcriptional regulation through non-coding RNAs (miRNA, siRNA, lncRNA) is well known. It has been reported that the target genes of such RNAs are generally those with ontologies related to cell wall architecture, ROS regulation, and the development of the next phase, among others [40,41]. Similarly, epigenetic mechanisms have been found to be involved in the response to thermal stress, such as DNA methylation, histone modifications, and chromatin remodeling [42].…”

Genomics Associated Interventions for Heat Stress Tolerance in Cool Season Adapted Grain Legumes

“…The miR408 overexpression results plantacyanin transcript repression to regulate DREB and other drought responsive genes [ 186 ]. This tool can largely aid in future breeding programmes for various biotic and abiotic stresses in legumes as in wheat 70 miRNA based SSR markers have been identified and validated on a set of 20 terminal heat-tolerant and heat-susceptible genotypes for developing heat tolerant cultivars through marker assisted selection [ 215 ].…”