Genomics-Assisted Breeding of Climate-Smart Inbred and Hybrid Rice Varieties

Abstract

Global climatic alterations (GCA) such as drought, flood, salinity, submergence, and high/low temperature pose serious threats to crop productivity in several Asian and African countries. As a mitigation option to GCA, we need to develop and deploy climate-smart rice (inbred and hybrid) varieties (CSRVs) resilient to biotic and abiotic stresses. Genomics-assisted breeding (GAB) by integrating advanced genomics tools and an improved green super rice (GSR) breeding strategy (GSR-BT) is one of the leading reliable strategies to develop CSRVs. This provides a high-quality genome sequence and SNPs as allelic variants from the advanced genomics tools that help in understanding the molecular and physiological mechanisms underlying trait expression. It also plays a key role in the quick introgression of the desired genetic variants with the highest precision and less or no genetic drag through an innovative GSR-BT. Under the GSR program at the International Rice Research Institute (IRRI), first, BC1F2 populations derived from Huanghuazhan (HHZ), Weed Tolerant Rice 1 (WTR-1), and TME80518 (recipient parents) and 16 donors were developed. Later, these introgression lines (ILs) underwent simultaneous screenings over three rounds for different abiotic and biotic stresses as well as evaluation under normal irrigated conditions, resulting in the identification of trait-specific ILs. A total of 1333 (HHZ-ILs) + 2232 (WTR-1-ILs) + 1408 (TME80518-ILs) ILs were developed, which were further used either for varietal improvement or as parental lines for the development of pyramided lines (PDLs). Furthermore, a designed QTL pyramiding (DQP) approach began for stacking traits/genes derived from the generated trait-specific ILs. These more productive efforts resulted in the development of 1280 (HHZ-PDLs) + 850 (WTR-1-PDLs) PDLs that showed a significantly superior performance over the tolerant checks. Notably, we developed and distributed more than 240 CSRVs with multiple abiotic and biotic stress tolerance to Asia and Africa without compromising on grain yield and quality. A total of 26 IRRI-bred CSRVs were released, and 91 such cultivars were nominated into national cooperative yield trials from three recipient parents within a short span of 7 years. The released CSRVs are being cultivated on more than 2.7 million ha on a cumulative basis in Asia and Africa.