MORE PANICLES 3, a natural allele of OsTB1/FC1, impacts rice yield in paddy fields at elevated CO2 levels

Variation in a single allele drives divergent yield responses to elevated CO2 between rice subspecies

Rising atmospheric CO2 generally increases yield of indica rice, one of the two main Asian cultivated rice subspecies, more strongly than japonica rice, the other main subspecies. The molecular mechanisms driving this difference remain unclear, limiting the potential of future rice yield increases through breeding efforts. Here, we show that between-species variation in the DNR1 (DULL NITROGEN RESPONSE1) allele, a regulator of nitrate-use efficiency in rice plants, explains the divergent response to elevated atmospheric CO2 (eCO2) conditions. eCO2 increased rice yield by 22.8-32.3% in plants carrying or mimicking the indica DNR1 allele, but only by 3.6-11.1% in plants carrying the japonica DNR1 allele. Rice plants carrying or mimicking the indica DNR1 allele exhibit decreased eCO2-responsive transcription and protein abundance of DNR1, which activates genes involved in nitrate transport and assimilation, driving the increase in plant growth. Our findings identify the indica DNR1 gene as a key breeding resource for sustainably enhancing nitrate uptake and rice yields in japonica varieties, potentially contributing to global food security as atmospheric CO2 levels continue to increase.

Regulation of tillering and panicle branching in rice and wheat

Branching is a critical aspect of plant architecture that significantly impacts the yield and adaptability of staple cereal crops like rice and wheat. Cereal crops develop tillers during the vegetative stage and panicle or spike branches during the reproductive stage, respectively, both of which are significantly impacted by hormones and genetic factors. Tillering and panicle branching are closely interconnected and exhibit high environmental plasticity. Here, we summarize the recent progress in genetic, hormonal, and environmental factors regulation in the branching of rice and wheat. This review not only provides a comprehensive overview of the current knowledge on branching mechanisms in rice and wheat, but also explores the prospects for future research aimed at optimizing crop architecture for enhanced productivity.

Genome-wide association study reveals novel QTLs and candidate genes for panicle number in rice

Introduction

Panicle number (PN) is one of the three key yield components in rice, maintaining stable tiller and PN is a crucial characteristic of an ideal plant architecture. Understanding the molecular mechanisms underlying PN is essential for breeders aiming to improve rice yield.

Methods

To dissect the genetic architecture of panicle number, a genome-wide association study (GWAS) was conducted in 411 japonica rice varieties. GWAS analysis was carried out with the mixed linear model using 743,678 high-quality SNPs.

Results

Over two experimental years, we detected a total of seven quantitative trait loci (QTLs), located on chromosomes 1, 4, 6, 8, 11, and 12; notably, qPN1.1 and qPN8 were detected consistently in both years. By combining haplotype and expression analyses, OsCKX11 was identified as the candidate gene for qPN8, while LOC_Os01g07870 and LOC_Os01g07950 were identified as candidate genes for qPN1.1. Significant differences were observed among the haplotypes of these candidate genes. Additionally, qRT-PCR results showed that LOC_Os01g07870 expression levels were significantly lower in accessions with high panicle numbers compared to those with low panicle numbers.

Discussion

To understand the natural biological function of these candidate genes, further research involving overexpression or silencing in rice is needed. Despite these challenges, our results will lay the foundation for further study of panicle development and provide valuable genetic resources for developing high-panicle-number rice cultivars using genetic engineering and molecular breeding.

Characterization of quantitative trait loci from DJ123 (aus) independently affecting panicle structure traits in indica rice cultivar IR64

The rice panicle is the principal organ to influence productivity and traits affecting panicle architecture determine sink size and yield potential. Improving panicle architecture may be effective in increasing yield under low-input conditions, but which traits are of importance under such conditions and how they are genetically controlled is not well understood. Using recombinant inbred lines (RILs) derived from a cross between a modern variety IR64 and a low fertility tolerant accession DJ123, quantitative trait locus (QTL) mapping was conducted under high soil fertility in Japan and low fertility in Madagascar. Among QTL for panicle length (PL) detected, the DJ123 allele increased rachis length at qCL1 and qPL9, while the IR64 allele increased primary branch length at qPL7. DJ123 further contributed two QTL for grain width whereas IR64 contributed two grain length QTL. Analysis of lines carrying different combinations of detected QTL indicates that rachis and primary branch lengths are independently regulated, explaining strong transgressive segregation for PL. The positive effects of PL-related QTL were further confirmed by a genome-wide analysis of allelic states in two breeding lines that had been selected repeatedly for total panicle weight per plant under low input conditions. This study provides the genetic basis for complex panicle architecture in rice and will aid in designing an ideal panicle architecture that leads to increased yield under low fertility conditions.

Supplementary information

The online version contains supplementary material available at 10.1007/s11032-024-01494-5.

The Function of Florigen in the Vegetative-to-Reproductive Phase Transition in and around the Shoot Apical Meristem

Plants undergo a series of developmental phases throughout their life-cycle, each characterized by specific processes. Three critical features distinguish these phases: the arrangement of primordia (phyllotaxis), the timing of their differentiation (plastochron) and the characteristics of the lateral organs and axillary meristems. Identifying the unique molecular features of each phase, determining the molecular triggers that cause transitions and understanding the molecular mechanisms underlying these transitions are keys to gleaning a complete understanding of plant development. During the vegetative phase, the shoot apical meristem (SAM) facilitates continuous leaf and stem formation, with leaf development as the hallmark. The transition to the reproductive phase induces significant changes in these processes, driven mainly by the protein FT (FLOWERING LOCUS T) in Arabidopsis and proteins encoded by FT orthologs, which are specified as 'florigen'. These proteins are synthesized in leaves and transported to the SAM, and act as the primary flowering signal, although its impact varies among species. Within the SAM, florigen integrates with other signals, culminating in developmental changes. This review explores the central question of how florigen induces developmental phase transition in the SAM. Future research may combine phase transition studies, potentially revealing the florigen-induced developmental phase transition in the SAM.

Potential of rice tillering for sustainable food production

Tillering, also known as shoot branching, is a fundamental trait for cereal crops such as rice to produce sufficient panicle numbers. Effective tillering that guarantees successful panicle production is essential for achieving high crop yields. Recent advances in molecular biology have revealed the mechanisms underlying rice tillering; however, in rice breeding and cultivation, there remain limited genes or alleles suitable for effective tillering and high yields. A recently identified quantitative trait locus (QTL) called MORE PANICLES 3 (MP3) has been cloned as a single gene and shown to promote tillering and to moderately increase panicle number. This gene is an ortholog of the maize domestication gene TB1, and it has the potential to increase grain yield under ongoing climate change and in nutrient-poor environments. This review reconsiders the potential and importance of tillering for sustainable food production. Thus, I provide an overview of rice tiller development and the currently understood molecular mechanisms that underly it, focusing primarily on the biosynthesis and signaling of strigolactones, effective QTLs, and the importance of MP3 (TB1). The possible future benefits in using promising QTLs such as MP3 to explore agronomic solutions under ongoing climate change and in nutrient-poor environments are also highlighted.

Cultivating potential: Harnessing plant stem cells for agricultural crop improvement

Meristems are stem cell-containing structures that produce all plant organs and are therefore important targets for crop improvement. Developmental regulators control the balance and rate of cell divisions within the meristem. Altering these regulators impacts meristem architecture and, as a consequence, plant form. In this review, we discuss genes involved in regulating the shoot apical meristem, inflorescence meristem, axillary meristem, root apical meristem, and vascular cambium in plants. We highlight several examples showing how crop breeders have manipulated developmental regulators to modify meristem growth and alter crop traits such as inflorescence size and branching patterns. Plant transformation techniques are another innovation related to plant meristem research because they make crop genome engineering possible. We discuss recent advances on plant transformation made possible by studying genes controlling meristem development. Finally, we conclude with discussions about how meristem research can contribute to crop improvement in the coming decades.