Multi-environment GWAS identifies genomic regions underlying grain nutrient traits in foxtail millet (Setaria italica).

Regulated cell death (RCD) plays key roles during essential processes along the plant life cycle. It takes part of specific developmental programs and maintains the organism homeostasis in response to unfavourable environments. Bryophytes could provide with valuable models to study developmental RCD processes as well as those triggered by biotic and abiotic stresses. Some pathways analogous to the ones present in angiosperms occur in the gametophytic haploid generation of bryophytes, allowing direct genetic studies. In this review, we focus on such RCD programs, identifying core conserved mechanisms and raising new key questions to analyse RCD from an evolutionary perspective. 

Cell death in bryophytes: emerging models to study core regulatory modules and conserved pathways

As nutrient allocation trade-offs occur between reproductive and vegetative development in crops, optimizing their partitioning holds promise for improving agricultural productivity and quality. Herein, we characterize the phenotypic diversity of the fruitfulness trait and identify associated genes in tea plants (Camellia sinensis). Over three consecutive years, we monitored the fruitfulness of an F1 hybrid population (n = 206) derived from crosses of ‘Emei Wenchun’ and ‘Chuanmu 217’. A marked variation was observed in the yield of individual plants, ranging from complete sterility (zero fruits) to exceptionally high fertility (1612 fruits). Using the high-resolution genetic linkage map and the fruitfulness data, we identified a stable major QTL designated as qFN5. To fine-map the underlying gene(s), artificial pollination experiments were conducted with extreme phenotype individuals (with the highest vs. lowest fruit numbers). Bulked segregant RNA sequencing (BSR-Seq) with ovules collected at two and seven days post-pollination (DPP) identified the genomic intervals that exhibit a high degree of overlap with qFN5. Analysis of expression dynamics combined with functional genomics data revealed a prominent candidate gene, CsETR2 (TGY048509), which encodes an ethylene receptor protein. When CsETR2 was overexpressed in Arabidopsis thaliana, the transgenic lines exhibited significantly decreased reproductive performance relative to the wild-type plants. Relative to the wild type, the transgenic lines exhibited a significant decline in several key traits: the number of effective panicles decreased by 72.5%, the seed setting rate dropped by 67.7%, and the silique length shortened by 38%. These findings demonstrate its role in regulating plant fruitfulness. Furthermore, yeast one-hybrid and dual-luciferase assays verified that CsMYB15 (TGY110225) directly binds to the CsETR2 promoter, thus repressing its transcription. In summary, our findings expand the understanding of genetic regulation underlying fruitfulness in tea plants and provide candidate target loci for breeding. 

Integrating Genetic Mapping and BSR-Seq Analysis to Identify Candidate Genes Controlling Fruitfulness in Camellia sinensis

Abstract Apomixis, a reproductive mechanism that enables clonal seed production, generates progeny genetically identical to the maternal parent. In plant breeding, sexual reproduction can enhance traits through genetic recombination and hybrid vigor, yet trait segregation significantly raises breeding costs and complexity. Although apomixis occurs naturally across various plant species, it remains notably absent in major crops like rice and maize. Significant progress has been made in identifying the genes that govern this process. Recent breakthroughs in synthetic apomixis provide promising pathways for crop improvement. This review offers a comprehensive analysis of natural apomixis and its genetic regulators, with a focus on recent advances in synthetic apomictic systems. We also explore the current state and potential of apomixis in forage breeding, especially in addressing challenges related to self-incompatibility, polyploidy, and genomic complexity in forage species. Finally, we discuss the challenges in applying apomixis to forage breeding and future directions for this research.

Harnessing apomixis: natural mechanisms and synthetic innovations for advancing crop and forage breeding

Maize ( Zea mays ssp. mays ) is the most productive crop worldwide now, and it is widely used as food, feed and raw materials for various industrial products. The continuous increase of maize yield is a testament of the success of plant breeding and modern agriculture. During domestication and historical breeding, humans has imposed strong selection on its morphological and physiological traits that benefit ecological adaptation, increase in yield and nutritional value, and harvesting. Recent advance in maize functional genomics studies has greatly deepened and expanded our understanding of the molecular and genetic bases of maize domestication and genetic improvement. In this article, we summarize the key traits and regulatory genes that underlie domestication and post-domestication genetic improvement of maize, and provide a forward outlook at how the knowledge can be harnessed to accelerate future maize breeding.

Genomic landscape of maize domestication and breeding improvement

In maize, prolificacy, the number of ears per plant, is a trait of interest to maize breeders for breeding high grain-yielding cultivars or specialty corn, as well as being a model trait for decoding the molecular mechanism of maize evolution. Its genetic basis remains largely unknown. We identified a stable quantitative trait locus, qEN7, for ear number on chromosome 7 in both F2 and F2:3 populations derived from a single cross between the nonprolific inbred line Mo17 and the prolific inbred line LAN404 derived from the landrace PI217404. qEN7 explained 10.7%–11.9% of phenotypic variation, and the LAN404 allele at this locus was associated with an increase of around one ear per plant. qEN7 was confined by fine-mapping to a 0.56-Mb region containing eight annotated genes. Analysis of selection, gene expression patterns in various maize tissues, and sequence polymorphisms between the two parental lines suggested that Zm00001d020683, which encodes a putative INDETERMINATE DOMAIN (IDD) transcription factor, is the most likely candidate gene underlying qEN7. Zm00001d020683 is expressed mainly in the vegetative meristem, immature ears, and internodes and has undergone selection during maize improvement. The identification of qEN7 and the prediction of its candidate gene sheds some light on the evolution of maize ear number and provides a novel resource for breeding of multi-ear maize cultivars. 

Identifying QTL and candidate genes for prolificacy in maize

The transition from mitosis to meiosis is a critical event in the reproductive development of all sexually reproducing species. However, the mechanisms that regulate this process in plants remain largely unknown. Here, we find that the rice (Oryza sativa L.) protein RETINOBLASTOMA RELATED 1 (RBR1) is essential to the transition from mitosis to meiosis. Loss of RBR1 function results in hyper-proliferative sporogenous-cell-like cells (SCLs) in the anther locules during early stages of reproductive development. These hyper-proliferative SCLs are unable to initiate meiosis, eventually stagnating and degrading at late developmental stages to form pollen-free anthers. These results suggest that RBR1 acts as a gatekeeper of entry into meiosis. Furthermore, cytokinin content is significantly increased in rbr1 mutants, whereas the expression of type-B response factors, particularly LEPTO1, is significantly reduced. Given the known close association of cytokinins with cell proliferation, these findings imply that hyper-proliferative germ cells in the anther locules may be attributed to elevated cytokinin concentrations and disruptions in the cytokinin pathway. Using a genetic strategy, the association between germ cell hyper-proliferation and disturbed cytokinin signaling in rbr1 has been confirmed. In summary, we reveal a unique role of RBR1 in the initiation of meiosis; our results clearly demonstrate that the RBR1 regulatory module is connected to the cytokinin signaling pathway and switches mitosis to meiosis in rice. 

RETINOBLASTOMA RELATED 1 switches mitosis to meiosis in rice.

Cohesin is a multi-subunit protein responsible for holding sister chromatids together during mitosis and meiosis. Each subunit is functionally essential, and their deletion is always lethal. SCC3 is a highly conserved constituent of the cohesin complex. However, the exact mitotic and meiotic functions of SCC3 in rice remains to be elucidated. Here, we found null alleles of SCC3 cause embryo lethality. Only scc3 weak mutants could survive and show vegetative and reproductive defects. Specifically, the replication process of sister chromatids is disturbed in scc3 during interphase both in mitosis and meiosis. Moreover, SCC3 has distinct localization patterns between mitotic and meiotic cells. The numbers of DMC1, RAD51 and ZIP4 foci are significantly decreased in scc3, and ZEP1 displays as an abnormal punctate foci during zygotene. Importantly, the scc3 fails to synapse, but in this case chromosome fragmentation is absent. Thus, SCC3 seems to inhibit inter-sister chromatids repair (ISR), and this process is independent of DMC1-mediated ISR.

SCC3 acts as the cohesin and inhibits inter-sister chromatids repair during rice meiosis

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Identifying QTL and candidate genes for prolificacy in maize

RETINOBLASTOMA RELATED 1 switches mitosis to meiosis in rice.

SCC3 acts as the cohesin and inhibits inter-sister chromatids repair during rice meiosis