Developing Climate-Resilient, Direct-Seeded, Adapted Multiple-Stress-Tolerant Rice Applying Genomics-Assisted Breeding

Abstract

There is an urgent need to breed dry direct-seeded adapted rice varieties in order to address the emerging scenario of water–labor shortage. The aim of this study was to develop high-yielding, direct-seeded adapted varieties utilizing biparental to multiparental crosses involving as many as six different parents in conventional breeding programs and 12 parents in genomics-assisted breeding programs. The rigorous single plant selections were followed from the F2 generation onwards utilizing phenotypic selection and quantitative trait locus (QTL)/gene-based/linked markers for tracking the presence of desirable alleles of targeted QTL/genes. In conventional breeding, multiparent lines had significantly higher yields (2,072–6,569 kg ha−1) than the biparental lines (1,493–6,326 kg ha−1). GAB lines derived from multiparent crosses had significantly higher (3,293–6,719 kg ha−1) yields than the multiparent lines from conventional breeding (2,072–6,569 kg ha−1). Eleven promising lines from genomics-assisted breeding carrying 7–11 QTL/genes and eight lines from conventional breeding with grain-yield improvement from 727 to 1,705 kg ha−1 and 68 to 902 kg ha−1, respectively, over the best check were selected. The developed lines may be released as varieties/parental lines to develop better rice varieties for direct-seeded situations or as novel breeding material to study genetic interactions.

Genetic Trends Estimation in IRRIs Rice Drought Breeding Program and Identification of High Yielding Drought-Tolerant Lines

“…Different crossing strategies (Additional file 2 : Figure S9) single, complex, double, and backcrosses have been used by the rice breeders to integrate these QTLs into the elite genetic backgrounds and develop the new breeding lines. Diverse materials, including landraces, and donors have been extensively used to diversify the gene pool and develop climate-resilient varieties (Sandhu et al 2021 ; Yadav et al 2021 ). However, this strategy of diversifying the elite gene pool with limited focus on recurrent selection and early re-cycling of high-value breeding lines may have limited genetic gain to a large extent and has not been sufficient to maintain the higher genetic gains over time.…”

“…Under this project, imperative efforts were made to incorporate the major drought-tolerant QTLs ( qDTY1.1, qDTY2.1, qDTY2.2, qDTY3.1, qDTY4.1, qDTY12.1 qDTY6.3, etc . ) into the background of the mega rice varieties like IR64, Swarna, and TDK-1, which led to the development of several high yielding drought-tolerant rice varieties (Bernier et al 2007 ; Venuprasad et al 2009 ; Vikram et al 2011 ; Mishra et al 2013 ; Yadaw et al 2013 ; Sandhu et al 2014 , 2019 , 2021 ; Kumar et al 2014 , 2020 ; Henry et al 2015 , 2019 ; Dixit et al 2017 , 2020 ; Sandhu and Kumar 2017 ; Bhandari et al 2020 ; Majumder et al 2021 ; Yadav et al 2021 ). The most popular drought-tolerant rice varieties include—DRR dhan 42, CR Dhan 801, Sahbhagi dhan in India, Sukha dhan 4, Bahuguni dhan 11 in Nepal, and Katihan 2, Katihan 3, Sahod Ulan 15, Sahod Ulan 19 in the Philippines, Yaenelo 4 in Myanmar, MPTSA and ATETE in Malawi, CAR 14 in Cambodia, and BRRI Dhan66, BRRI Dhan 71 in Bangladesh ( https://strasa.irri.org/varietal-releases/drought ).…”

Genetic Trends Estimation in IRRIs Rice Drought Breeding Program and Identification of High Yielding Drought-Tolerant Lines

“…Similarly, enhanced CF demarcates a plant's capabilities to withstand drought stress effectively. Furthermore, two multiparent conventional bred lines namely, IR 115844-B-B-281-1-2 and IR 115844-B-342-1-1-1 present in the selected panel have been reported to yield more than 7000 kg/ha under dry direct-seeded conditions, with higher yields under non-stress and reproductive stage drought stress conditions (Sandhu et al 2021). In our study, these lines showed the breeding values between 3200 to 3368.14, which form a valuable resource for the breeding programs to be utilized for drought-prone areas with major cultivation under dry seeded conditions having limited water and labor availability.…”

“…S8) single, complex, double, and backcrosses have been used by the rice breeders to integrate these QTLs into the elite genetic backgrounds and develop the new breeding lines. Diverse materials, including landraces, and donors have been extensively used to diversify the gene pool and develop climate-resilient varieties (Sandhu et al 2021). However, this strategy of diversifying the elite gene pool with limited focus on recurrent selection and early re-cycling of high-value breeding lines may have limited genetic gain to a large extent and has not been sufficient to maintain the higher genetic gains over time.…”

“…STRASA (Stress Tolerant Rice for Africa and South Asia) Project (2005)(2006)(2007)(2008)(2009)(2010)(2011)(2012)(2013)(2014)(2015)(2016)(2017)(2018)(2019) at IRRI, funded by the Bill and Melinda Gates Foundation (BMGF) was one of the most successful research programs that led to the successful development and release of more than 30 high-yielding drought-tolerant rice varieties in Asia and Africa (https://strasa.irri.org/). Under this project, imperative efforts were made to incorporate the major drought-tolerant QTLs (qDTY1.1,qDTY2.1,qDTY2.2,qDTY3.1,qDTY4.1,qDTY12.1 qDTY6.3,etc.,) into the background of the mega rice varieties like IR64, Swarna, and TDK-1 which led to the development of several high yielding drought-tolerant rice varieties (Bernier et al 2007;Venuprasad et al 2009;Vikram et al 2011;Mishra et al 2013;Yadaw et al 2013;Sandhu et al 2014;Kumar et al 2014;Henry et al 2015;Dixit et al 2017;Sandhu and Kumar 2017;Henry et al 2019;Sandhu et al 2019;Bhandari et al 2020;Dixit et al 2020;Kumar et al 2020;Majumder et al 2021;Sandhu et al 2021;Yadav et al 2021). The most popular drought-tolerant rice varieties include -DRR dhan 42, CR Dhan 801, Sahbhagi dhan in India, Sukha dhan 4, Bahuguni dhan 11 in Nepal, and Katihan 2, Katihan 3, Sahod Ulan 15, Sahod Ulan 19 in the Philippines, Yaenelo 4 in Myanmar, MPTSA ...…”