Novel and Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice Created by Physiological Coupling-Uncoupling and Network Rewiring Effects.

Isaiah C M Pabuayon,Balpreet Dhatt,Ai Kitazumi,Rakesh Kumar Singh,Benildo G De Los Reyes,Harkamal Walia,Glenn B Gregorio,Kevin R Cushman,Masoud Zabet-Moghaddam

doi:10.3389/fpls.2021.615277

Abstract

The phenomenon of transgressive segregation, where a small minority of recombinants are outliers relative to the range of parental phenotypes, is commonly observed in plant breeding populations. While this phenomenon has been attributed to complementation and epistatic effects, the physiological and developmental synergism involved have not been fully illuminated by the QTL mapping approach alone, especially for stress-adaptive traits involving highly complex interactions. By systems-level profiling of the IR29 × Pokkali recombinant inbred population of rice, we addressed the hypothesis that novel salinity tolerance phenotypes are created by reconfigured physiological networks due to positive or negative coupling-uncoupling of developmental and physiological attributes of each parent. Real-time growth and hyperspectral profiling distinguished the transgressive individuals in terms of stress penalty to growth. Non-parental network signatures that led to either optimal or non-optimal integration of developmental with stress-related mechanisms were evident at the macro-physiological, biochemical, metabolic, and transcriptomic levels. Large positive net gain in super-tolerant progeny was due to ideal complementation of beneficial traits while shedding antagonistic traits. Super-sensitivity was explained by the stacking of multiple antagonistic traits and loss of major beneficial traits. The synergism uncovered by the phenomics approach in this study supports the modern views of the Omnigenic Theory, emphasizing the synergy or lack thereof between core and peripheral components. This study also supports a breeding paradigm rooted on genomic modeling from multi-dimensional genetic, physiological, and phenotypic profiles to create novel adaptive traits for new crop varieties of the 21st century.

Highlights

Plant breeding during the Green Revolution created the modern cultivars of rice, maize, and wheat with superior yields under well-managed environments with ideal water and nutrient conditions
We expected to identify outliers that perform worse than IR29 or better than Pokkali at V4 to V12 based on Standard Evaluation Score (SES) and results revealed clear outliers not identified at V1 to V5 (Supplementary Dataset 1)
We established the minimal comparative panel, consisting of thirty-seven recombinant inbred line (RIL) spanning the full range of tolerance at electrical conductivity (EC) = 9 dS m−1, and the outliers revealed at EC = 12 dS m−1, consisting of the super-sensitive FL499 and super-tolerant FL510 (Table 1 and Figure 1A)

Summary

Introduction

Plant breeding during the Green Revolution created the modern cultivars of rice, maize, and wheat with superior yields under well-managed environments with ideal water and nutrient conditions. Developing the generation of crops with minimal penalty to yield under marginalized environments is the new overarching goal. Key to this goal are new genetic variants and novel phenotypes that may not have been achieved in the past. Has plant breeding fully exhausted the combining potential of exotic germplasm to create adaptive phenotypes that are more relevant today? There is a strong optimism that strategic utilization of exotic germplasm could lead to further improvements in complex traits that define yield potential under marginal environments. Are further genetic gains on top of what had been achieved postGreen Revolution still possible? How can the power of genomics be used for additional genetic gains?

Methods

Results

Conclusion