Allele‐specific analysis of single parent backcross population identifies HOX10 transcription factor as a candidate gene regulating rice root growth

Abstract

Understanding the molecular and physiological mechanisms of trait diversity is crucial for crop improvement to achieve drought adaptation. Root traits such as high biomass and/or deep rootedness are undoubtedly important drought adaptive traits. The major aim of this investigation was to functionally characterize a set of ethyl methane sulfonate-induced rice mutants for root traits. We report the identification of a high-root biomass mutant through a novel screening strategy for yield and Δ C measurements. The high-root mutant (392-9-1) thus identified, had a 66% higher root biomass compared to wild-type (Nagina-22). Better maintenance of leaf turgor and carbon assimilation rates resulted in lower drought susceptibility index in 392-9-1. Targeted resequencing revealed three non-synonymous single nucleotide variations in 392-9-1 for the genes HOX10, CITRATE SYNTHASE and ZEAXANTHIN EPOXIDASE. Segregation pattern of phenotype and mutant alleles in a single parent backcross F population revealed a typical 3:1 segregation for each of the mutant alleles. The number of F progeny with root biomass equal to or greater than that of 392-9-1 represented approximately one-third of the population indicating a major role played by HOX10 gene in regulating root growth in rice. Allele-specific Sanger sequencing in contrasting F progenies confirmed the co-segregation of HOX10 allele with the root biomass. The non-synonymous mutations in the other two genes did not reveal any specific pattern of co-segregation with root phenotype, indicating a strong role of HOX10, an upstream transcription factor, in regulating root biomass in rice.

Leaf mass area determines water use efficiency through its influence on carbon gain in rice mutants

“…The high‐LMA mutant, 392‐9‐1, was one such type. We had earlier reported the mechanisms associated with root growth in this mutant that maintained higher tissue water relations and hence superior drought adaptation (Reddy et al ).…”

“…In this investigation, we utilized a large number of EMS induced mutant lines to examine the variations in LMA and to assess its role in regulating carbon gain under altered soil moisture conditions. The EMS induced mutagenized lines in the genetic background of a drought tolerant cultivar, Nagina‐22 (N22) displayed substantial variations in number of morpho‐physiological and yield associated traits (Mohapatra et al , Mithra et al , Reddy et al ). Significant variability was also observed in leaf characters such as leaf length (LL), leaf width (LW), total leaf weight, total leaf area (LA t ), leaf mass area (LMA), and DM ag /LA t in the stabilized M 6 population of mutants (Table ).…”

“…S4) would have counteracted the effect of leaf thickness, contributing to increased carboxylation efficiency. The high‐LMA mutant, especially 392‐9‐1, that incidentally had higher root biomass (Reddy et al ) was capable of maintaining relatively higher g s (Table ). On the other hand, the low‐LMA mutant had poor root traits and hence had lower g s and transpiration rate.…”

“…Single parent backcross populations were developed by crossing the high‐LMA mutant (392‐9‐1) and the low‐LMA mutant (380‐4‐3) separately with N22. Such populations have been effectively used to study the trait associations and in identification of candidate genes (Allen et al , Reddy et al ). Though segregating F 2 progenies of both the populations displayed considerable variability for LMA and other biometric parameters (Figs S8 and S9), only the progenies derived by crossing high‐LMA mutant displayed mendalian segregation for LMA, DM ag /LA t and Δ 13 C. Since there was no difference in LMA and DM ag /LA t between low‐LMA mutant and wild‐type, the progenies of this cross did not show specific segregation pattern (Table S1) for these traits.…”

Aerobic Rice with or without Strategic Irrigation in the Subtropics

“…Indeed, trait-based selection for enhanced water extraction and maintenance of positive tissue turgor through greater water extraction from where soil water is available is widely recognised as one approach to enhance yield under water-limited conditions for rice [19]. Close links between a deeper root system, photosynthetic efficiency, and lower drought susceptibility were evident using a large number of mutagenized rice lines [19], as was found among land races of rice [20] and other crop species (e.g., chickpea- [21]; maize- [22]). Likewise, use of canopy temperature [23] or high carbon isotope discrimination [24] as proxies for gains from deep rooting during drought stress has been reported.…”