Strong genotype by environment interactions in the rice Global MAGIC population across seedling stage drought

Abstract

Crop adaptation is required to sustainably increase the rate of yield gains to meet projected future needs under the challenging conditions of climate change and competition for resources. Future adaptation will likely need to harness both highly polygenic traits and genotype-by-environment interactions (GxE), the study of which is aided by complex recombinant populations. We used the diverse Oryza sativa Global Multiparent Advanced Generation InterCross (MAGIC) population to study the genetic architecture and contributions of seedling emergence, establishment, and development to yield components under dry-direct seeding and seedling stage drought across three growing seasons. Dry-direct seeding is an establishment practice that has the potential to reduce methane emissions, water use, and labor demands for rice farmers, but increases the possibility of early-season drought conditions. We found substantial evidence for large roles of environmental variation and GxE in controlling trait variation. Maintenance of shoot growth during seedling stage drought was positively correlated with crown root number and both directly and indirectly influenced agronomic traits. Other than the major green revolution locus sd1, most allelic effects were conditionally neutral (affecting trait values in some environments but not others) and most alleles had their strongest effect in an environmental extreme. This discovery is both a challenge and a potential opportunity: with variable genetic architecture, selection in any one environment may not result in stable trait gains across environments. However, conditionally neutral GxE is a potential route to sustainable yield stability through allele pyramiding.

Response of Southeast Asian rice root architecture and anatomy phenotypes to drought stress

“…Other shallow root phenotypes in our studycrown root number and crown roots per tillerwere not consistently related to productivity under drought in this study. Moyers et al (2022) reported crown root number to be correlated with growth and productivity under vegetative stage drought stress in the rice Global MAGIC population under dry direct-seeded conditions. Ruangsiri et al (2021) found that crown root number was reduced in KDML 105 chromosome segment substitution lines when planted in clay soil, but an increase in crown root number was found in the same population when planted in sandy soil condition.…”

“…Other shallow root phenotypes in our study – crown root number and crown roots per tiller – were not consistently related to productivity under drought in this study. Moyers et al. (2022) reported crown root number to be correlated with growth and productivity under vegetative stage drought stress in the rice Global MAGIC population under dry direct-seeded conditions.…”

Scanning the rice Global MAGIC population for dynamic genetic control of seed traits under vegetative drought

“…We used the genotyping data generated for the Global MAGIC lines (S6 generation) using genotyping × sequencing (GBS) (Elshire et al., 2011) as described in (Moyers et al., 2022; Zaw et al., 2019). Briefly, we built GBS libraries using the restriction enzyme ApeKI for each Global MAGIC line and six biological replicates of each parent.…”