Enhancement of rice (Oryza sativa L.) productivity under rainfed ecosystems is important to food security. Efforts to increase yield have had little success, mainly due to the complexity of inheritance of abiotic stress tolerance traits and the technical challenges of phenotyping these traits. The study was conducted to pyramid quantitative trait loci (QTLs) governing tolerance to moisture and heat stress from cv. Nagina22 and QTLs for high yield traits from variety IR64, with the aid of marker-assisted pedigree breeding. From the IR64/N22 cross, we identified 14 pyramided lines with various combinations of targeted QTLs (5–11 QTLs). The three best lines that performed well under moisture stress conditions were PL76 with two water-use efficiency (WUE) QTLs (Mr19a, SLA 9.1), three drought-tolerant yield (DTY) QTLs (qDTY1.2, qDTY3.2, qDTY6.1), one heat-tolerance (HT) QTL (qSSPF10) and four yield QTLs (qFLW4.1, qFLL9, LP1, GW5); PL476 with two WUE QTLs (%N11.1, qWue7a), two DTY QTLs (qDTY6.1, qDTY12.1), two HT QTLs (qSSPF10, qHT6) and three yield QTLs (qFLW4.1, qFLL9, LP1); and PL130 with two WUE QTLs (Mr19a, qWue7a), four DTY QTLs (qDTY1.2, qDTY3.2, qDTY4.1, qDTY12.1), two HT QTLs (qSSPF10, qHT6) and two yield QTLs (qFLW4.1, LP1). These three lines shown a yield advantage of 51.93%, 55.93% and 60.30%, respectively, over high-yielding IR64. Under heat stress, PL457 and PL130 with HT QTLs qSSPF10 and qHT6 showed 85.02% and 61.55% yield advantage, respectively, over IR64. In conclusion, we have demonstrated that the systematic combination of important QTLs from two contrasting parents through marker-assisted pedigree breeding is an outstanding approach to supplement conventional phenotype-based pedigree breeding, especially to improve complex traits such as yield and tolerance to moisture stress and heat.

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Context Regular genetic monitoring of rice diversity provides informed direction for plant breeders when selecting parents in breeding programs. Aims The investigation was conducted to assess the trends of decade-wise genetic diversity in popular Indian rice (Oryza sativa L.) genotypes. Methods We screened 62 genotypes including popular rice varieties released from the 1970s to 2010s in India along with landraces, using gene-specific markers and some of the key yield and yield-contributing traits. Key results Using gene-specific markers, genetic diversity has shown a downward trend from landraces to the 2010s. Qualitative analysis revealed that more alleles were present in landraces than released varieties. The disappearance of alleles was prominently observed in varieties released in the 1970s and even more so in the 2010s, which suggests that present-day cultivars are losing several valuable alleles of the key yield genes. Genetic diversity assessed using phenotypic data also exhibited a downward trend towards the 2010s. Molecular and phenotypic data on genetic diversity were used to group the rice genotypes, revealing that genotypes with common parents grouped together. Conclusions Genetic diversity has shown a downward trend from landraces to the 2010s, as assessed using both gene-specific markers and phenotypic data, although with slight deviations among various decades. Implications This study reinforces the fact that assessment of temporal trends in genetic diversity at regular intervals is warranted to meet future food demands while conserving on-farm crop diversity.

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