**3.2 Simple sequence repeat (SSR) and SNPs (third generation markers)**

Rice crop was recognized with more than 20,000 SSR markers and over one million SNPs and Indels, which include both functional and non-functional markers [39–41]. This has opened up huge opportunities for the use of molecular markers in diversity analysis, mapping genes/QTLs for various agronomic traits under drought, and their use in marker-assisted breeding (MAB) and also in positional cloning of QTLs to identify candidate genes for complex traits [42].

The accessibility of complete rice genomic sequence information, rice linkage maps, and molecular marker technology has made it possible to dissect complex traits into individual quantitative trait loci (QTLs) [43–46]. Linkage mapping, association mapping, nested association mapping, marker-aided recurrent selection (MARS), and genome-wide selection (GWS) are different approaches currently followed for the mapping and introgression of QTLs for drought tolerance. There are several sources of genomic variation such as QTL main effects, QTL × QTL interactions, and QTL × environment interactions. A thorough understanding of this variation is very important before embarking on marker-assisted selection (MAS) of drought QTLs. Several major-effect QTLs for grain yield under drought have been identified and are being used in marker-assisted breeding/ pyramiding. Courtois et al. [47] identified the meta-QTLs for root traits under drought stress. Meta-analysis of 53 grain yield associated QTLs identified from 15 previous studies bring about in 14 meta-QTLs. In general, rice varieties with deep and high-volume root system exhibits better adaptability under drought conditions [48]. Among the root traits, root length, volume, thickness and root growth angle (RGA) are playing key role in mitigating drought tolerance [49]. In turn, RGA determines the root depth. The deeper and profuse root architecture support plants to extract water from deeper soil layers. The three major QTLs governing root growth angle (RGA) in rice were reported by Uga et al. [49–51]. Among them, DEEPER ROOTING 1 (DRO1) is the significant one and this QTL has been fine mapped and the underlying gene, an early auxin responsive factor, has been cloned using IR64, a shallow rooted variety and Kinandang Patong (KP), a deeply rooted variety. The variation in the DRO1 gene in the major Indian rice genotypes used in drought tolerant breeding plans and their association with RGA is reported [52]. So far, 675 root QTLs and more than 85 genes related to 29 different root parameters have been reported in rice [47]; https://snp-seek.irri.org/). The introduction of deep rooting traits in high yielding varieties is a resourceful way of enlightening drought tolerance in rice.
