Wild species have acquired many elite alleles for resistance to biotic and abiotic stresses during the long period of natural selection (Atwell et al., 2014; Mammadov et al., 2018). A large number of IL libraries constructed from wild and cultivated rice were used to detect QTLs for cold (Yuan R. et al., 2020), heat (Lei et al., 2013; Prasanth et al., 2016; Cao et al., 2020), drought (Zhang et al., 2006; Zhou et al., 2006), and salt (Tian et al., 2011; Yang et al., 2012) tolerance. For example, a set of 132 CSSLs were developed from a cultivated rice, 93–11, and the Guangxi common wild rice (GXCWR), and the cold-tolerance QTL qCT2.1 on chromosome 2 was identified using the secondary mapping population (Yuan R. et al., 2020). Using a set of 90 ILs derived from the cross between Teqing and Yuanjiang common wild rice (YJCWR), five QTLs related to heat response (qHST1-1, qHST1-2, qHST2, qHST3, and qHST8) in the seedling stage were detected, and O. rufipogon-derived alleles at one locus reduced sensitivity to heat (Lei et al., 2013). QTLs for resistance to biotic stress, such as that imposed by the green rice leafhopper (Thein et al., 2019), rice stripe necrosis virus (Gutiérrez et al., 2010) and rice blast fungus (Xu et al., 2015), were also mapped using ILs carrying wild rice donor fragments in cultivated rice backgrounds.

ILs developed from wild and cultivated rice are valuable materials for the genetic dissection of domestication-related traits such as an erect growth habit, inflorescence architecture, and awn length. Several domestication genes have been cloned using such IL-derived populations (Table 2). PROG1, a prostrate growth gene, was identified in a set of ILs developed from Teqing and YJCWR. Its non-functional allele determines the critical transition of rice from prostrate to erect growth (Tan et al., 2007, 2008). Using the same IL sets, a domestication gene, OsLG1, controlling inflorescence architecture was cloned (Zhu et al., 2013). Using a set of 354 ILs derived from the cross between 93 and 11 and YJCWR, an IL with long and barbed awns was identified. Further fine-mapping indicated that a frameshift deletion in LABA1 of cultivated rice reduces the cytokinin concentration in awn primordia, disrupting barb formation and awn elongation (Fu et al., 2010; Hua et al., 2015). Another domestication gene controlling plant architecture, TIG1, was also cloned in an IL population with the wild rice (W2014) segments in the 93–11 background (Zhang et al., 2019d).

There has also been a burst of studies on mapping novel genomic regions and QTLs for yield-related traits (Furuta et al., 2014, 2016; Ma et al., 2016; Qiao et al., 2016; Rao et al., 2018) and quality traits (Garcia-Oliveira et al., 2009; Fasahat et al., 2012; Yun et al., 2016; Qi et al., 2017) by using IL populations derived from the crosses between wild and cultivated rice, generally with the elite varieties as RPs. For example, using 33 CSSLs of O. rufipogon (W0106) in the background of the elite japonica rice variety Koshihikari, a total of 15 major QTLs for eight yield-related traits were detected, and a novel QTL controlling the number of grains per panicle were identified on chromosome 10 (Furuta et al., 2014). In the same background of Koshihikari, a set of 26 CSSLs with segments from O. nivara were constructed, and new QTLs associated with yield-related traits were identified (Furuta et al., 2016). A set of 198 CSSLs were developed by introgressing O. rufipogon segments into the background of the elite indica rice variety 93–11, and a new QTL associated with the heading date was detected in a 78-kb region on chromosome 10 (Qiao et al., 2016). Similarly, a set of 131 ILs were developed by introducing O. nivara segments into the 93–11 background, and 65 QTLs for 13 yield-related traits were detected by bin-map, with ∼36.9% of the alleles at the detected QTLs from O. nivara leading to improved yield-associated traits (Ma et al., 2016). QTLs associated with 12 grain quality traits were detected using 96 ILs developed from an interspecific cross between the Korean elite japonica rice variety Hwaseong and O. rufipogon (IRGC 105491). A total of 48 QTLs for these traits were identified, and most wild alleles of these detected QTLs had negative effects on the traits (Yun et al., 2016).

In addition to the traits mentioned above, IL sets developed from wild and cultivated rice have also been used for genetic dissection of other traits, such as interspecific hybrid sterility (Yang et al., 2016; Li et al., 2018a; Zhang et al., 2018), anther length (Ogami et al., 2019), the stigma exsertion rate (Tan et al., 2020), out-crossing rate (Prahalada et al., 2021), and photosynthetic efficiency (Rao et al., 2018).

Multiple IL sets derived from indica-japonica crosses have been developed to mine QTLs for rice yield-related traits (Ando et al., 2008; Sun et al., 2017; Mitsuya et al., 2019), quality-related traits (Hao et al., 2009; Sun et al., 2015; Wang et al., 2021), and resistance to biotic (Park et al., 2007) and abiotic (Zang et al., 2008; Zhao et al., 2016; Feng et al., 2018) stresses. Several QTLs for these traits have been detected and causal natural variations for the detected QTLs have been identified by using IL-derived F₂ populations (Table 2). For example, two sets of reciprocal ILs derived from a japonica rice variety Lemont and an indica variety Teqing were constructed, and multiple QTLs for grain number per panicle (GNP) were identified form these two ILs. Among these detected QTLs, a stable QTL GNP1 was further finely mapped to a 33.7-kb region and a GA biosynthesis gene GA20-oxidase 1 was identified as the candidate gene for GNP1 (Wu et al., 2016). QTL analysis of seven panicle- and grain-related traits was performed in a set of genotype-defined CSSLs derived from a cross of two genome-sequenced varieties, Nipponbare and Zhenshan 97, and a total of 43 QTLs for these traits were identified. Furthermore, the novel locus qGL11 for grain length and thousand-grain weight was finely mapped to a 25-kb region, and the IAA-amido synthetase gene OsGH3.13 was verified as the causal gene for qGL11 (Wang et al., 2021).

Heterosis is one of the most important characteristics of F₁ plants derived from indica-japonica crosses (Dan et al., 2014). Many ILs and IL-derived backcross and/or testcross populations have been used to dissect the genetic basis of heterosis (Xin et al., 2011; Wang Z. et al., 2012; Tao et al., 2016; Xiong et al., 2021; Yang et al., 2021c). For example, a set of 70 ILs and corresponding testcross F₁ populations were developed from a cross between the indica rice variety IR24 (RP) and japonica rice variety Asominori to investigate heterotic loci (HLs) associated with six yield-related traits (Xin et al., 2011). A total of 41 HLs were detected on the basis of mid-parent heterosis values with single-point analysis, and most of QTLs were overdominant, suggesting that heterotic effects at the single-locus level are mainly overdominant in rice (Xin et al., 2011). Tao et al. (2016) constructed a set of 128 CSSLs derived from a cross between the indica rice variety 93–11 and japonica rice variety Nipponbare to investigate the genetic basis of heterosis. Using the testcross populations derived from CSSLs and three P-TGMS lines, a total of 97 HLs associated with yield components were detected. Genetic analysis revealed that the contribution of different genetic effects to heterosis might vary among traits (Tao et al., 2016; Yang et al., 2021c). In a recent study, Ghd8 was identified and verified as a major HL for yield components by using a set of intersubspecific CSSLs and two test populations (Xiong et al., 2021). This HL has also been identified in the two-line rice hybrid system (Li et al., 2016), indicating its important role in hybrid breeding.

QTLs have been mapped in ILs derived from indica-japonica crosses for other traits, including hybrid sterility (Zhao et al., 2011), nutrient utilization (Kabange et al., 2021), seed germination and dormancy (Li et al., 2011; Zhang et al., 2020a), mature seed culturability (Zhao et al., 2009), carbon isotope discrimination (Takai et al., 2009), lodging resistance (Mulsanti et al., 2018), and cell wall characteristics (Xu et al., 2017).

ILs developed from intrasubspecific crosses are favored by breeders because there are no incompatibility barriers in these crosses. Although the genetic diversity within rice subspecies is lower than that between subspecies, there are still large phenotypic differences among varieties from different regions with different genealogical relationships in the same subspecies. Several IL libraries from intrasubspecific crosses have been developed in rice to genetically dissect complex traits such as yield-related traits (Shen and Xing, 2014; Hori et al., 2021a; Kato and Hirayama, 2021), quality-related traits (Yang et al., 2021b), root traits (Anis et al., 2019), resistance to preharvest sprouting (Hori et al., 2010; Mizuno et al., 2018), and heterosis (Lin et al., 2020). For example, a set of 202 CSSLs of an elite hybrid, Shanyou 63, were developed in the Zhenshan 97 background, and QTLs for heading date and plant height were detected (Shen and Xing, 2014; Shen et al., 2014). A total of 15 partial dominance QTLs for plant height were identified in 15 CSSL-derived F₂ populations, and these QTLs were further identified as HLs for plant height that acted dominantly and epistatically (Shen et al., 2014). Furthermore, multiple QTLs and HLs for yield and spikelets per panicle were identified in these CSSLs, and the hybrids pyramiding these detected HLs in the combined parental genome background showed yield performance similar to that of Shanyou 63, indicating that heterosis might be successfully achieved by manipulating several major dominant HLs (Shen et al., 2022).

ILs derived from advanced backcrosses generally carry only one or a few chromosome fragments from the donor, which greatly minimizes the genetic background noise and facilitates the evaluations of the genetic effects of QTLs/genes on corresponding traits. The target introgressed segment of an IL is homozygous, conferring its genomic stability, so ILs can be repeatedly planted in multiple sites to evaluate the genetic effects of QTLs across different environments (Zhou et al., 2017). A set of ILs covering the entire DP genome can be applied to identify multiple QTLs associated with the trait of interest, and the genetic effects of these detected QTLs can be compared based on their additive effect in the same background, especially using single segment substitution lines (SSSLs) (Ye et al., 2010; Zhu et al., 2018). ILs are not only beneficial for comparing the genetic effects of different QTLs in the same background but also beneficial for comparing the effects of different alleles at one QTL in the fixed background, so as to identify the favorable alleles or allele combinations. For example, the heading date QTL qHD-3 was identified by using a library consisting of 1123 CSSLs from multiple donors in the same genetic background, Huajingxian 74 (HJX74). Compared with the HJX74 allele, the qHD-3 allele from donor variety Lemont delayed rice heading, while qHD-3 from another donor parent, IR64, promoted rice heading. Further sequencing analysis revealed that different variants of DTH3 were identified between Lemont and IR64 (Zhu et al., 2018). To investigate the interaction effect of Ghd8 on yield mid-parent heterosis (MPH), Xiong et al. (2021) constructed five near-isogenic lines (NILs) with each carrying an introgression segment covering Ghd8 from a particular donor in the same background of ZS97, and identified the combination (Ghd8^ACC10/Ghd8^MH63) with the highest MPH for both spikelet number and grain yield per plant using a half-diallel mating design.

Reciprocal ILs developed in both parental backgrounds have the advantage of enabling evaluation of differences in allelic effects of QTLs in both genetic backgrounds (Kubo et al., 2002). Reciprocal ILs are not only conducive to the detection and fine mapping of QTLs that have both large and small effects but also appropriate for evaluating gene activity as a single factor or in epistatic interactions (Takai et al., 2014). Reciprocal ILs have been used to identify background-independent QTLs (BI-QTLs) and epistatic QTLs (E-QTLs) for grain yield- and quality-related traits (Takai et al., 2014; Qiu et al., 2017; Hori et al., 2021b), salt tolerance (Cheng et al., 2012), lodging resistance (Ookawa et al., 2016), the leaf net photosynthetic rate (Adachi et al., 2019), and sink- and source-related traits (Wang et al., 2020). For example, using the reciprocal CSSLs derived from a cross between MH63 and 02428, a total of nine BI-QTLs for appearance quality were identified. Thirteen and 10 stably expressed QTLs (SE-QTLs) were also detected in the MH63 and 02428 backgrounds, respectively (Qiu et al., 2017). Compared with E-QTLs, BI-QTLs, and SE-QTLs are more easily applied for rice genetic improvement because their function does not depend on background or the environment.

Most agronomic traits of crops are complex traits controlled by multiple genes and affected by environmental factors. Understanding the genetic and environmental bases of QTL × QTL and gene-by-environment (G × E) interactions is of fundamental importance in plant breeding (Monteverde et al., 2019). As in recombinant inbred lines (RILs), genetic interactions between QTLs/genes, such as additive-by-dominance and dominance-by-dominance interactions, also cannot be analyzed using ILs because all sites in ILs are homozygous. However, the offspring-separated populations derived from the crosses between ILs or backcrosses between ILs and RPs are ideal populations for genetic interaction analysis due to their low genetic background noise. Genetic interaction analysis among four major rice heading date genes, Ghd7, Ghd8, OsPRR37, and Hd1, was performed in a 4-gene segregating population in the near-isogenic background under both natural long-day (NLD) and natural short-day (NSD) conditions (Zhang et al., 2019a). Tetragenic, trigenic and digenic interactions among these four genes for heading date were observed under both conditions but were more significant under NLD conditions. Further analysis showed that the differences in digenic interactions between Ghd7 and OsPRR37 under different conditions were essential to the alternative function of OsPRR37 (Zhang et al., 2019a). Genetic interaction analysis between QTLs for other agronomic traits, such as plant height (Shen et al., 2014), grain size (Xia et al., 2018), tillering (Zhou et al., 2020), cold tolerance (Liang et al., 2018), and drought tolerance (Yadav et al., 2019), was also performed in IL-derived populations.

Most the traits with low heritability are easily affected by the environment, and there is an obvious interaction between gene and the environment. Understanding G × E interactions can help breeders in deciding which QTL to use in their breeding programs while tailoring crop cultivars for specific or more diverse environments (Liu et al., 2008). G × E interactions were analyzed in ILs or IL-derived populations planted in a variety of environments. To dissect the genetic basis of the genetic main effect (G) and G × E interaction effect (GE) for panicle number (PN) in rice, a population consisting of 35 SSSLs derived from originating from crosses between the RP, HJX74, and 17 DPs was grown in six cropping season environments (Liu et al., 2008). The total genetic effect was partitioned into G and GE by using the mixed linear-model approach, and then QTL analyses of these effects were conducted separately. A single QTL effect was divided into two components: The additive effect (a) and additive × environment interaction effect (ae). A total of 18 QTLs for PN were identified, and three types of QTLs were suggested according to their effects expressed. Two QTLs expressed stably across environments due to the association with only a, nine QTLs with only ae were unstable, and the remaining seven QTLs were identified with both a and ae, which were also unstable across environments (Liu et al., 2008). Notably, when QTLs have large ae values in opposing directions in different environments, selection for an allele with favorable effects in certain environments could lead to undesired results in other environments.

Each line of ILs carries only one or a few donor chromosome segments, which usually affects only one or a few traits of the RP. Therefore, using ILs to improve single-target trait in rice is efficient. In the elite genetic backgrounds, IL with improved agronomic performance can be released as a new variety.

Increasing rice yield to meet the need for a rapidly growing global population is one of the most important goals of rice breeding. Many yield-related QTLs/genes have been introgressed into elite backgrounds to increase rice yield. For example, GN4-1, a QTL for grain number per panicle, was introgressed into ZH8006 from WYJ6, and grain yield increased by more than 10% (Zhou et al., 2018). To achieve the high yield potential in Kongyu 131, a minute chromosome fragment carrying the favorable Gn1a allele from the donor parent GKBR was introgressed into the genome of Kongyu 131, which resulted in larger panicles and a subsequent yield increase in the new Kongyu 131 (Feng et al., 2017). In addition, introgression of a functional epigenetic OsSPL14^WFP allele into elite indica cultivars can greatly improve panicle traits and grain yield (Kim et al., 2018).

With the increasing development of people’s living standards, rice quality has received attention from both rice producers and consumers. There have been many successful cases of improving rice grain quality through ILs. For example, to improve the eating and cooking quality of Zhenshan 97 and its hybrid Shanyou 63, the Wx/Waxy gene region from Minghui 63, a restorer line with medium amylose content (AC), soft gel consistency (GC), and high gelatinization temperature (GT), was introgressed into Zhenshan 97B and then transferred into Zhenshan 97A (Zhou et al., 2003). In recent years, the discovery of different alleles of Wx and ALK has provided more choices for rice grain quality improvement via gene introgression (Chen et al., 2020; Huang et al., 2021; Zhang et al., 2021b; Zhou et al., 2021). GS9 is an important gene for both grain shape and chalkiness, and appearance quality could be largely improved by developing an IL for this gene (Zhao et al., 2018, 2021).

Biotic and abiotic stresses are large threats to rice production, leading to serious yield losses every year. ILs constructed by introgressing novel genes into modern varieties are an effective tool for solving this problem. For example, by combining a backcross breeding strategy combined with MAS, a total of 12 blast resistance genes were introgressed into one maintainer line of cytoplasmic male sterility (CMS) and three photo-thermo genetic male sterility (P-TGMS) lines. The blast resistance of these lines was significantly improved, while other traits were not changed (Jiang et al., 2012, 2015, 2019). Using the same strategy, brown planthopper resistance has been improved by introgressing Bph3, Bph14, Bph15, Bph18, Bph20, Bph21, and Bph33 into 93–11 and Jin23B (Hu et al., 2013, 2018; Jiang et al., 2018), and bacterial blight resistance has been improved by pyramiding Xa4, xa5, xa13, and Xa21 (Huang et al., 1997). In the two IL populations developed with C258 and ZGX1 as RPs and IR75861 as the DP, 12 and 8 lines had higher salt tolerance than the RPs, respectively, and they could be directly planted into environments characterized by salt stress (Qiu et al., 2015).

The excess application of fertilizers in rice production not only increases cost, but also causes severe environmental problems (Zhang et al., 2020c). Breeding rice varieties with high nitrogen-use efficiency (NUE) is of great significance to the practice of Green Super Rice (Yu et al., 2020). GRF4 promotes and integrates nitrogen assimilation, carbon fixation, and growth, whereas DELLA inhibits these processes. Introgression of GRF4 into the elite variety 93–11 carrying sd1 can significantly improve its NUE, thereby increasing yield (Li et al., 2018b). NAL1 and the gain-of-function mutation dep1-1 have been reported to play important roles in N-responsive tillering regulation, and pyramiding of the dep1-1 and NAL1^NJ6 alleles can achieve sustainable improvements in NUE and grain yield in japonica rice breeding (Sun et al., 2014; Xu et al., 2019). The introgression of favorable alleles of other NUE-related genes such as OsTCP19 and OsSBM1 also showed great potential for genetic improvement of high NUE in rice (Liu et al., 2021; Xu et al., 2021).

To meet people’s diverse demands for rice, modern rice varieties should be improved mainly by multiple locus introgression to improve the overall features of rice in terms of grain yield and quality, resistance to biotic and abiotic stresses and nitrogen use efficiency, etc. For example, Luan et al. (2019) used four SSSLs with HJX74 as the RP to develop a new maintainer named H131B with a suitable heading date, good appearance and eating and cooking quality, and fragrant smell by pyramiding MADS50, gs3, fgr, Wx^gl, and ALK. Dixit et al. (2020) developed seven ILs possessing a combination of seven to ten QTLs for resistance to different biotic and abiotic stresses by using the MAS breeding method in the background of Swarna. These ILs were superior to the respective RPs in terms of agronomic performance and possessed superior grain quality. Luo et al. (2016) successfully developed a new restorer line, WH6725, with disease resistance to rice blast and bacterial blight, tolerance to submergence and an aromatic fragrance by pyramiding Xa27, Pi9, Sub1A, and badh2.1. Through genotyping-based identification and backcrossing with MAS, Zeng et al. (2017) introgressed 21 favorable alleles from NIP and 9311 into Teqing and then developed three lines that exhibited higher yield potential and better grain quality than their parental varieties and the super-hybrid rice Liang-you-pei-jiu. Guangzhan 63-4S is an elite two-line thermos-sensitive genic male sterile line. However, it is highly susceptible to blast and bacterial blight. Two BC₂ ILs were developed to introgress Xa7 for bacterial blight and Pi-2 for blast resistance. Then, the ILs were crossed and pyramided with these two genes. A new two-line thermosensitive genic male-sterile line named Hua1228S that was resistant against both rice blast and bacterial blight was developed (Mi et al., 2018).

IL platform developed by multiple donors in an elite genetic background facilitates the discovery of new QTLs and identification of multiple alleles of a gene. IL platform can be used to identify the optimal allele or allele combination by evaluating their genetic effects in the fixed background and then improve varieties by QTL pyramiding (Zhang, 2021; Figure 1D). In addition, new varieties can be directly developed by screening transgressive lines of target traits in the IL platform (Figure 1D). HJX74 is an elite variety from South China. A single segment IL platform including more than 2000 ILs was developed with HJX74 as the RP and more than 40 varieties as DPs (Luan et al., 2019; Zhang, 2021). A large number of important genes were identified using this platform (Wang S. et al., 2012; Wang et al., 2015; Yang et al., 2021a). In addition, a series of varieties have been bred by pyramiding different favorable genes in this platform, such as three-line maintainer lines (H121B, H131B, HZB, HBB, E5-HXB, and E5-HBB) (Luan et al., 2019), black rice (Huaxiaohei1 and Huaxiaohei 2), red rice (Huaxiaohong1 and Huaxiaohong 2), and high-quality rice (Huabiao1 and Huabiao 3) (Zhang, 2021). Huanghuazhan (HHZ) is an elite rice variety widely planted in the middle and downstream regions of the Yangtze River and in South China. An IL platform including 496 ILs were developed using HHZ as the RP and 8 varieties as DPs (Ali et al., 2017). Most ILs showed significantly higher yields than the parents under both abiotic stress conditions (salt and drought) and non-abiotic stress conditions (submergence). Ultimately, at least six ILs were directly released as new green super rice varieties in the Philippines and Pakistan and have been grown on more than 1 million ha of land in different ecosystems (Ali et al., 2017).