Research work is needed in breeding rice varieties with high grain yield potential, good yield under drought, yield stability, resistance to existing biotic stresses, good grain and cooking quality, and good relative performance in multiple locations and environmental (managed under drought-stress and non-stress environments) conditions.
4.2.1. Donor Identification
The preliminary and important step of any breeding program involves the identification of suitable donors. Selection of a specific donor from a large germplasm collection is a crucial step. The use of a specific donor with special characteristics for a specific environment may lead to the success of any varietal and trait development program. Most of the traditional donors have several undesirable traits and therefore are not suitable for direct use in any breeding program. These landraces have undesirable traits such as little ground cover, tall plant height, low yield potential, and poor grain and eating quality, but they have a desirable drought tolerance trait. On the other hand, modern rice varieties have desirable traits such as high yield, improved plant type (early vigor, medium height, and lodging resistance), tolerance of biotic stress, and good grain type (medium to long slender). However, they are drought-susceptible. Breeding for any desired trait to get new gene combinations requires exploitation of genetic variation (intra-specific, inter-specific, or inter-generic) that exist in traditional landraces carrying desirable characteristics and modern improved varieties with high yield potential [153
]. The genotype at par performance in the target environment [154
] and the trait with high heritability [155
] can account for further high-throughput screening. The identified drought-tolerant donors such as PSBRc68, PSBRc80, PSBRc82, Aday Sel, Dagaddeshi, Kali Aus, Aus276, Kalia, N22, Apo, Dular, and IR77298-14-1-2 have been used in conventional breeding and QTL mapping studies at IRRI. Among these, improved donors such as PSBRc68, PSBRc80, PSBRc82, and IR77298-14-1-2 have been directly used in conventional breeding programs, whereas improved drought-tolerant lines free from undesirable linkages were derived from the mapping populations that involve traditional donors such as Aday Sel, Dagaddeshi, Kali Aus, Aus 276, Kalia, N22, Apo, and Dular and used in conventional breeding programs. In marker-assisted breeding programs, lines possessing the identified QTLs for grain yield under drought, which come from mapping populations that involve traditional donors, were used to improve mega-varieties.
A model drought-resistant rice variety for drought-prone environments can be considered as having better yields than any other presently available cultivar, not only under drought stress but also under irrigated conditions across different seasons and environments, being less sensitive to variable conditions [83
], and possessing good grain quality and resistance to biotic stresses.
4.2.3. Marker-Assisted Breeding: Identification, Introgression, and Pyramiding of QTLs
Marker-assisted breeding adopted at IRRI involves: the development of mapping populations involving traditional drought-tolerant donors and modern high-yielding varieties; precise phenotyping in multi-environment, controlled, and drought-stress conditions; repeated years; identification of polymorphic markers; genotyping with polymorphic markers; linkage map construction; and QTL mapping using genotypic and phenotypic data.
Large-scale systematic study with several mapping populations for identification of major quantitative trait loci (QTLs) using yield as a selection criterion [89
] led to the identification of several QTLs for grain yield under drought, followed by introgression of identified QTLs to develop drought-tolerant rice cultivars.
The success of screening strategies with careful assessment of size and structure of population has led to the development and release of several drought-tolerant lines with high yield under irrigated conditions [89
]. Identification of genetic regions linked to drought tolerance using genotyping strategies such as selective genotyping (SG), whole-genome genotyping (WGG), bulk segregant analysis (BSA) [50
], genome-wide association studies (GWAS, an improved version of marker-assisted selection) [169
], and successful introgression in different genetic backgrounds using marker-assisted backcrossing [42
], marker-assisted recurrent selection [175
], and marker-assisted QTL pyramiding [89
] has been reported. Mapping populations segregating for drought-tolerance-related traits led to the identification of 12 quantitative trait loci (QTLs) (Table 6
) showing a large effect against high-yielding, drought-susceptible popular varieties: Swarna, IR64, MTU1010, TDK1, Sabitri, and Vandana [49
] (Table 6
). Gathering all data on the donors/recipients, factors, traits, genes, mechanisms, and technologies that sustain yield under drought and accumulating them into elite genotypes without negative effects on yield potential could be the best solution for rainfed environments.
The drought marker-assisted breeding program at IRRI has led to the development and release of high-yielding drought-tolerant lines (Table 7
The major and consistent drought grain yield (GY) QTLs were reported to be collocated with QTLs for plant height and/or days to flowering [50
]. The developed drought-tolerant lines possessed earliness, root plasticity traits, greater root length density, better water-use efficiency mechanism, better regulation of shoot growth [106
], and a yield advantage of 0.8–1.0 t·ha−1
under severe drought. These short-duration varieties of 105–110 days without any yield decline possessed better adaptability to less water and variable environmental growing conditions. QTLs related to traits enhancing drought tolerance have been reported in cotton [136
], pearl millet [182
], maize [156
], Sorghum [91
], and barley [183
]. Fine-mapping of QTLs to facilitate exact introgression devoid of undesirable linkages; identification of useful candidate genes; effectiveness in various genetic backgrounds and variable environment; and effective use, pyramiding, and interaction studies may now open new windows to the development of drought-tolerant rice cultivars. Fine-mapping of qDTY12.1
resulted in the partitioning of the qDTY12.1
into sub-QTLs and multiple intra-QTL genes (OsNAM12.1
transcription factor and co-localized target genes). This strengthened the view of more than a single gene underneath the functionality of one QTL and reiterate grain yield under drought, a complex trait [124
]. Insertion mutants in the co-localized target genes in the qDTY12.1
region lead to an increase in the lateral roots compared to the wild type [124
]. Fine-mapping of qDTY1.1
shows that qDTY1.1
harbors the green revolution gene ‘sd1
Genetic linkages; complex gene network; QTL × QTL, QTL × background, QTL × environment interactions [175
]; and pleiotropy are the most important aspects in breeding when studying the complexity of genetic regions related to drought biotic and abiotic stress traits. The linkage of qDTY1.1
supports the fact that during the green revolution era the drought-tolerant alleles were not maintained properly during the development of dwarf varieties for the irrigated ecosystem. The debate continued on the pleiotropic effect of dominant allele of sd1
on drought vs. linkage of dominant allele of sd1
with drought tolerance. The possibility of a pleiotrophic effect indicated the separation of the drought-susceptible allele and dwarfness is impossible. Vikram et al. [121
] have successfully demonstrated the linkage of qDTY1.1
with the sd1
gene, nullifying the debate on the linkages or pleiotropic effects of the sd1
gene. The development of new drought-tolerant dwarf lines is a successful example of breakage of linkages between qDTY1.1
loci. Many studies reported the collocation of major and consistent drought grain yield (GY) QTLs such as qDTY1.1
, with QTLs for days to flowering and plant height [50
]. The linkages of the drought QTLs were successfully broken and drought-tolerant lines in Swarna, IR64, and Vandana background were developed [74
Pyramiding QTLs for a quantitative trait such as grain yield may be an effective approach to combine superior alleles and achieve the desirable phenotypic level of variation [185
]. QTL pyramiding may be an appropriate approach to improve the efficiency of marker-assisted selection for desirable loci in rice breeding programs and to understand the interactions among genetic loci. Under severe reproductive-stage drought stress, grain yield advantage of 0.8–1.0 t·ha−1
was reported in QTL introgression programs involving popular high-yielding varieties IR64 and Swarna [144
]. The QTL pyramiding program ongoing at IRRI in the background of popular rice varieties Swarna, IR64, Vandana, Sabitri, TDK1, Anjali, Samba Mahsuri, MRQ74, MR219, and some Korean lines (Jinmibyeo, Gayabyeo, Hanarumbyeo, and Sangnambatbyeo) uses the different marker-assisted breeding approaches shown in Table 8
. It is evident from Table 8
that, even for the same QTL, researchers may have to find and use different sets of peak and flanking markers depending on the polymorphism of the donor and recipient and the identification of such polymorphic markers within the QTL region. Fine mapping, physiological and molecular characterization of the QTL interval to capture all the desirable genes with positive interactions contributing to drought tolerance is an important step before initiating a QTL introgression program.