The GW5-WRKY53-SGW5 module regulates grain size variation in rice

An intronic SNP in the Carotenoid Cleavage Dioxygenase 1 (CsCCD1) controls yellow flesh formation in cucumber fruit (Cucumis sativus L.)

Vitamin A is a crucial yet scarce vitamin essential for maintaining normal metabolism and bodily functions in humans and can only be obtained from food. Carotenoids represent a diverse group of functional pigments that act as precursors for vitamins, hormones, aroma volatiles and antioxidants. As a vital vegetable in the world, elevated carotenoid levels in cucumber fruit produce yellow flesh, enhancing both visual appeal and nutritional value. However, the genetic mechanisms and regulatory networks governing yellow flesh in cucumbers remain inadequately characterized. In this study, we employed map-based cloning to identify a Carotenoid Cleavage Dioxygenase 1 (CsCCD1) as a key genetic factor influencing yellow flesh in cucumbers. A causal single nucleotide polymorphism (SNP) in the eighth intron of CsCCD1 led to aberrant splicing, resulting in a truncated transcript. The truncated protein has significantly decreased enzyme activity and increased carotenoid accumulation in the fruit. CRISPR/Cas9-generated CsCCD1 knockout mutants exhibited yellow flesh and significantly higher carotenoid content compared to wild-type cucumbers. Metabolic profiling indicated a marked accumulation of β-cryptoxanthin in the flesh of these knockout mutants. The intronic SNP was shown to perfectly segregate with yellow flesh in 159 diverse cucumber germplasms, particularly within the semi-wild ecotype Xishuangbanna, known for its substantial carotenoid accumulation. Furthermore, transient overexpression of CsCCD1 in yellow-fleshed Xishuangbanna cucumbers restored a white flesh phenotype, underscoring the critical role of CsCCD1 in determining flesh colour in both cultivated and semi-wild cucumbers. These findings lay a theoretical foundation for breeding high-nutrient yellow-fleshed cucumber varieties.

The molecular mechanism of transcription factor regulation of grain size in rice

Rice is a crucial food crop in China, and the continuous and stable improvement of rice yield is of great significance for ensuring national food security. Grain size in rice is closely related to thousand-grain weight, making it a key factor influencing yield. Identifying genes associated with grain size and elucidating their molecular mechanisms are essential for breeding high-yield, high-quality rice varieties. Transcription factors play a vital role in regulating plant growth and development, and many transcription factor families are crucial in controlling grain size in rice. Here, we review the mechanisms by which transcription factors regulate rice grain size, summarize and evaluate the regulatory mechanisms of transcription factors that have been discovered in recent decades to regulate rice grain size, construct two possible super networks composed of transcription factors as links to regulate rice grain size, and points out the application of transcription factors regulating grain size in rice breeding. This review will provide a roadmap for understanding the regulatory mechanisms of rice grain size and applying these genes to rice breeding using molecular breeding techniques.

Cis-regulatory dynamics in plant domestication

Cis-regulatory elements (CREs) are critical sequence determinants for spatiotemporal control of gene expression. Genetic variants within CREs have driven phenotypic transitions from wild to cultivated plants during domestication. This review summarizes our current understanding of genetic variants within CREs involved in plant domestication. We also propose avenues for studies to expand our understanding of both CRE biology and domestication processes, such as examining primary mechanisms that generate CRE genetic variants during plant domestication and investigating the roles of CREs in domestication syndrome. Additionally, we discuss existing challenges and highlight future opportunities for exploring CREs in plant domestication, emphasizing the potential of modifying CREs to contribute to crop improvement.

Genetic Improvement of rice Grain size Using the CRISPR/Cas9 System

Rice grain size influences both grain yield and quality, making it a significant target for rice genetic improvement. In recent years, numerous genes related to grain size with differential effects have been cloned. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing system is a convenient tool for modifying genes. The use of the CRISPR/Cas9 tool for the genetic improvement of grain size-related genes is worth exploring. This paper summarizes the known grain size-related genes and the use of CRISPR/Cas9 for grain size modification and discusses the potential applications of CRISPR/Cas9 for improving rice grain size.

When Size Matters: New Insights on How Seed Size Can Contribute to the Early Stages of Plant Development

The seed habit is the most complex and successful method of sexual reproduction in vascular plants. It represents a remarkable moment in the evolution of plants that afterward spread on land. In particular, seed size had a pivotal role in evolutionary success and agronomic traits, especially in the field of crop domestication. Given that crop seeds constitute one of the primary products for consumption, it follows that seed size represents a fundamental determinant of crop yield. This adaptative feature is strictly controlled by genetic traits from both maternal and zygotic tissues, although seed development and growth are also affected by environmental cues. Despite being a highly exploited topic for both basic and applied research, there are still many issues to be elucidated for developmental biology as well as for agronomic science. This review addresses a number of open questions related to cues that influence seed growth and size and how they influence seed germination. Moreover, new insights on the genetic-molecular control of this adaptive trait are presented.