Development of a Temperate Climate-Adapted indica Multi-stress Tolerant Rice Variety by Pyramiding Quantitative Trait Loci

Abstract

Successful cultivation of rice (Oryza sativa L.) in many Asian countries requires submergence stress tolerance at the germination and early establishment stages. Two quantitative trait loci, Sub1 (conferring submergence tolerance) and AG1 (conferring anaerobic germination), were recently pyramided into a single genetic background, without compromising any desirable agronomic traits, leading to the development of Ciherang-Sub1 + AG1 (CSA). However, little research has been conducted to enhance plant tolerance to abiotic stress (submergence) and biotic stress (rice blast), which occur in a damp climate following flooding. The BC₂F₅ breeding line was phenotypically characterized using the AvrPi9 isolate. The biotic and abiotic stress tolerance of selected lines was tested under submergence stress and anaerobic germination conditions, and lines tolerant to each stress condition were identified through phenotypic and gene expression analyses. The Ciherang-Sub1 + AG1 + Pi9 (CSA-Pi9) line showed similar agronomic performance to its recurrent parent, CSA, but had significantly reduced chalkiness in field trials conducted in temperate regions. Unexpectedly, the CSA-Pi9 line also showed salinity tolerance. Thus, the breeding line newly developed in this study, CSA-Pi9, functioned under stress conditions, in which Sub1, AG1, and Pi9 play a role and had superior grain quality traits compared to its recurrent parent in temperate regions. We speculate that CSA-Pi9 will enable the establishment of climate-resilient rice cropping systems, particularly in East Asia.

Keywords: AG1; Climate change; Pi9; QTL pyramiding; Rice; Rice blast disease; Sub1.

Fig. 1

Schematic representation of the breeding strategy used to develop CSA-Pi9 via marker-assisted backcrossing (MABC). CSA: recurrent parent; IRBL9-w: donor parent; BL isolates: blast isolates

Fig. 2

Analysis of the genetic background and foreground selection of CSA-Pi9. Foreground selection of CSA-Pi9 using Sub1A-, AG1- and Pi9-specific markers (a, b). Analysis of the genetic background of CSA-Pi9 using the KNU Axiom Oryza 580 K Genotyping Array containing SNPs designed on the basis of IRGSPv1.0 (left) and MH63 v.2 (right) (c). M: marker; bp: base pair; kbp: kilobase pair

Fig. 3

AvrPi9 phenotyping and validation of Pi9-mediated resistance. Photographs of lesions (a) and quantification of lesion length (b) in CSA-Pi9 and CSA leaves inoculated with PO6-6 (incompatible isolate). Photographs of lesions (c) and quantification of lesion length (d) in CSA-Pi9 and CSA leaves inoculated with RO1-1 (compatible isolate)

Fig. 4

Characterization of the CSA-Pi9 breeding line treated with submergence stress for 14 days. Growth phenotype of CSA-Pi9 and other genotypes during submergence stress (a) and at 7 days after de-submergence (b). Shoot elongation rate [calculated as (shoot height after submergence (S)/shoot height before S) × 100] (c) and SPAD value (d) of CSA-Pi9 before and after submergence. Expression levels of Sub1A (e), adh1 (f) and OsTPP7 (g) under submergence stress. Data represent mean ± standard error (SE). Lowercase letters above bars and lines indicate statistically significant differences (P < 0.01; Duncan's multiple range test). IR64: submergence susceptible variety; IR64-Sub1: submergence tolerant variety; yellow arrow: newly emerging leaves; red arrow: no new leaves; DAS: days after submergence; DAR: days after recovery

Fig. 5

Characterization of CSA-Pi9 under anaerobic germination conditions. Phenotype of CSA-Pi9 plants at 34 days after sowing (a), germination rate (b), coleoptile length (c) and shoot length (d). Expression levels of OsTPP7 (e) and adh1 (f). Data for IR64 were unavailable, as its seeds did not germinate. Lowercase letters above bars indicate statistically significant differences (P < 0.01; Duncan's multiple range test)

Fig. 6

Comparison of the panicle shape (a) and grain shape with and without the hull (b) of CSA-Pi9 and CSA plants grown in field A (normal irrigation condition) in 2019