OsGADD45a1: a multifaceted regulator of rice architecture, grain yield, and blast resistance

KEY MESSAGE

The homolog gene of the Growth Arrest and DNA Damage-inducible 45 (GADD45) in rice functions in the regulation of plant architecture, grain yield, and blast resistance. The Growth Arrest and DNA Damage-inducible 45 (GADD45) family proteins, well-established stress sensors and tumor suppressors in mammals, serve as pivotal regulators of genotoxic stress responses and tumorigenesis. In contrast, the homolog and role of GADD45 in plants have remained unclear. Herein, using forward genetics, we identified an activation tagging mutant AC13 exhibited dwarf characteristics resulting from the loss-of-function of the rice GADD45α homolog, denoted as OsGADD45a1. osgadd45a1 mutants displayed reduced plant height, shortened panicle length, and decreased grain yield compared to the wild-type Kitaake. Conversely, no obvious differences in plant height, panicle length, or grain yield were observed between wild-type and OsGADD45a1 overexpression plants. OsGADD45a1 displayed relatively high expression in germinated seeds and panicles, with localization in both the nucleus and cytoplasm. RNA-sequencing analysis suggested a potential role for OsGADD45a1 in the regulation of photosynthesis, and binding partner identification indicates OsGADD45a1 interacts with OsRML1 to regulate rice growth. Intriguingly, our study unveiled a novel role for OsGADD45a1 in rice blast resistance, as osgadd45a1 mutant showed enhanced resistance to Magnaporthe oryzae, and the expression of OsGADD45a1 was diminished upon blast fungus treatment. The involvement of OsGADD45a1 in rice blast fungus resistance presents a groundbreaking finding. In summary, our results shed light on the multifaceted role of OsGADD45a1 in rice, encompassing biotic stress response and the modulation of several agricultural traits, including plant height, panicle length, and grain yield.

Fine mapping of the panicle length QTL qPL5 in rice

Panicle length is a crucial trait tightly associated with spikelets per panicle and grain yield in rice. To dissect the genetic basis of panicle length, a population of 161 recombinant inbred lines (RILs) was developed from the cross between an aus variety Chuan 7 (C7) and a tropical Geng variety Haoboka (HBK). C7 has a panicle length of 30 cm, 7 cm longer than that of HBK, and the panicle length was normally distributed in the RIL population. A total of six quantitative trait loci (QTLs) for panicle length were identified, and single QTLs explained the phenotypic variance from 4.9 to 18.1%. Among them, three QTLs were mapped to the regions harbored sd1, DLT, and Ehd1, respectively. To validate the genetic effect of a minor QTL qPL5, a near-isogenic F2 (NIF2) population segregated at qPL5 was developed. Interestingly, panicle length displayed bimodal distribution, and heading date also exhibited significant variation in the NIF2 population. qPL5 accounted for 66.5% of the panicle length variance. The C7 allele at qPL5 increased panicle length by 2.4 cm and promoted heading date by 5 days. Finally, qPL5 was narrowed down to an 80-kb region flanked by markers M2197 and M2205 using a large NIF2 population of 7600 plants. LOC_Os05g37540, encoding a phytochrome signal protein whose homolog in Arabidopsis enlarges panicle length, is regarded as the candidate gene because a single-nucleotide mutation (C1099T) caused a premature stop codon in HBK. The characterization of qPL5 with enlarging panicle length but promoting heading date makes its great value in breeding early mature varieties without yield penalty in rice.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01443-2.

Characterization of qPL5: a novel quantitative trait locus (QTL) that controls panicle length in rice (Oryza sativa L.)

Panicle length (PL) is an important trait that determines panicle architecture and strongly affects grain yield and quality in rice. However, this trait has not been well characterized genetically, and its contribution to yield improvement is not well understood. Characterization of novel genes related to PL is of great significance for breeding high-yielding rice varieties. In our previous research, we identified qPL5, a quantitative trait locus for PL. In this study, we aimed to determine the exact position of qPL5 in the rice genome and identify the candidate gene. Through substitution mapping, we mapped qPL5 to a region of 21.86 kb flanked by the molecular marker loci STS5-99 and STS5-106 in which two candidate genes were predicted. By sequence analysis and relative expression analysis, LOC-Os05g41230, which putatively encodes a BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 precursor, was considered to be the most likely candidate gene for qPL5. In addition, we successfully developed a pair of near-isogenic lines (NILs) for qPL5 in different genetic backgrounds to evaluate the genetic effects of qPL5. Agronomic trait analysis of the NILs indicated that qPL5 positively contributes to plant height, grain number per panicle, panicle length, grain yield per plant, and flag leaf length, but it had no influence on heading date and grain-size-related traits. Therefore, qPL5 and the markers tightly linked to it should be available for molecular breeding of high-yielding varieties.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01339-z.

Dissection of the Genetic Basis of Rice Panicle Architecture Using a Genome-wide Association Study

Panicle architecture is one of the major factors influencing productivity of rice crops. The regulatory mechanisms underlying this complex trait are still unclear and genetic resources for rice breeders to improve panicle architecture are limited. Here, we have performed a genome-wide association study (GWAS) to analyze and identify genetic determinants underlying three panicle architecture traits. A population of 340 rice accessions from the 3000 Rice Genomes Project was phenotyped for panicle length, primary panicle number and secondary branch number over two years; GWAS was performed across the whole panel, and also across the japonica and indica sub-panels. A total of 153 quantitative trait loci (QTLs) were detected, of which 5 were associated with multiple traits, 8 were unique to either indica or japonica sub-panels, while 37 QTLs were stable across both years. Using haplotype and expression analysis, we reveal that genetic variations in the OsSPL18 promoter significantly affect gene expression and correlate with panicle length phenotypes. Three new candidate genes with putative roles in determining panicle length were also identified. Haplotype analysis of OsGRRP and LOC_Os03g03480 revealed high association with panicle length variation. Gene expression of DSM2, involved in abscisic acid biosynthesis, was up-regulated in long panicle accessions. Our results provide valuable information and resources for further unravelling the genetic basis determining rice panicle architecture. Identified candidate genes and molecular markers can be used in marker-assisted selection to improve rice panicle architecture through molecular breeding.