LsNRL4 enhances photosynthesis and decreases leaf angles in lettuce

DNA methylation variations underlie lettuce domestication and divergence

BACKGROUND

Lettuce (Lactuca sativa L.) is an economically important vegetable crop worldwide. Lettuce is believed to be domesticated from a single wild ancestor Lactuca serriola and subsequently diverged into two major morphologically distinct vegetable types: leafy lettuce and stem lettuce. However, the role of epigenetic variation in lettuce domestication and divergence remains largely unknown.

RESULTS

To understand the genetic and epigenetic basis underlying lettuce domestication and divergence, we generate single-base resolution DNA methylomes from 52 Lactuca accessions, including major lettuce cultivars and wild relatives. We find a significant increase of DNA methylation during lettuce domestication and uncover abundant epigenetic variations associated with lettuce domestication and divergence. Interestingly, DNA methylation variations specifically associated with leafy and stem lettuce are related to regulation and metabolic processes, respectively, while those associated with both types are enriched in stress responses. Moreover, we reveal that domestication-induced DNA methylation changes could influence expression levels of nearby and distal genes possibly through affecting chromatin accessibility and chromatin loop.

CONCLUSION

Our study provides population epigenomic insights into crop domestication and divergence and valuable resources for further domestication for diversity and epigenetic breeding to boost crop improvement.

Photosynthesis promotion mechanisms of artificial humic acid depend on plant types: A hydroponic study on C3 and C4 plants

It is feasible to improve plant photosynthesis to address the global climate goals of carbon neutrality. The application of artificial humic acid (AHA) is a promising approach to promote plant photosynthesis, however, the associated mechanisms for C3 and C4 plants are still unclear. In this study, the real-time chlorophyll synthesis and microscopic physiological changes in plant leave cells with the application of AHA were first revealed using the real-time chlorophyll fluorescence parameters and Non-invasive Micro-test Technique. The transcriptomics suggested that the AHA application up-regulated the genes in photosynthesis, especially related to chlorophyll synthesis and light energy capture, in maize and the genes in photosynthetic vitality and carbohydrate metabolic process in lettuce. Structural equation model suggested that the photodegradable substances and growth hormones in AHA directly contributes to photosynthesis of C4 plants (0.37). AHA indirectly promotes the photosynthesis in the C4 plants by upregulating functional genes (e.g., Mg-CHLI and Chlorophyllase) involved in light capture and transformation (0.96). In contrast, AHA mainly indirectly promotes C3 plants photosynthesis by increasing chlorophyll synthesis, and the Rubisco activity and the ZmRbcS expression in the dark reaction of lettuce (0.55). In addition, Mg2+ transfer and flux in C3 plant leaves was significantly improved by AHA, indirectly contributes to plant photosynthesis (0.24). Finally, the AHA increased the net photosynthetic rate of maize by 46.50 % and that of lettuce by 88.00 %. Application of the nutrients- and hormone-rich AHA improves plant growth and photosynthesis even better than traditional Hoagland solution. The revelation of the different photosynthetic promotion mechanisms on C3 and C4 plant in this work guides the synthesis and efficient application of AHA in green agriculture and will propose the development of AHA technology to against climate change resulting from CO2 emissions in near future.

Yellow-Green Leaf 19 Encoding a Specific and Conservative Protein for Photosynthetic Organisms Affects Tetrapyrrole Biosynthesis, Photosynthesis, and Reactive Oxygen Species Metabolism in Rice

Chlorophyll is the main photosynthetic pigment and is crucial for plant photosynthesis. Leaf color mutants are widely used to identify genes involved in the synthesis or metabolism of chlorophyll. In this study, a spontaneous mutant, yellow-green leaf 19 (ygl19), was isolated from rice (Oryza sativa). This ygl19 mutant showed yellow-green leaves and decreased chlorophyll level and net photosynthetic rate. Brown necrotic spots appeared on the surface of ygl19 leaves at the tillering stage. And the agronomic traits of the ygl19 mutant, including the plant height, tiller number per plant, and total number of grains per plant, were significantly reduced. Map-based cloning revealed that the candidate YGL19 gene was LOC_Os03g21370. Complementation of the ygl19 mutant with the wild-type CDS of LOC_Os03g21370 led to the restoration of the mutant to the normal phenotype. Evolutionary analysis revealed that YGL19 protein and its homologues were unique for photoautotrophs, containing a conserved Ycf54 functional domain. A conserved amino acid substitution from proline to serine on the Ycf54 domain led to the ygl19 mutation. Sequence analysis of the YGL19 gene in 4726 rice accessions found that the YGL19 gene was conserved in natural rice variants with no resulting amino acid variation. The YGL19 gene was mainly expressed in green tissues, especially in leaf organs. And the YGL19 protein was localized in the chloroplast for function. Gene expression analysis via qRT-PCR showed that the expression levels of tetrapyrrole synthesis-related genes and photosynthesis-related genes were regulated in the ygl19 mutant. Reactive oxygen species (ROS) such as superoxide anions and hydrogen peroxide accumulated in spotted leaves of the ygl19 mutant at the tillering stage, accompanied by the regulation of ROS scavenging enzyme-encoding genes and ROS-responsive defense signaling genes. This study demonstrates that a novel yellow-green leaf gene YGL19 affects tetrapyrrole biosynthesis, photosynthesis, and ROS metabolism in rice.

Genetic determinants of lettuce resistance to drop caused by Sclerotinia minor identified through genome-wide association mapping frequently co-locate with loci regulating anthocyanin content

KEY MESSAGE

GWAS identified 19 QTLs for resistance to Sclerotinia minor, 11 of them co-locating with red leaf color. Lower disease incidence was observed in red and dark red accessions. Lettuce (Lactuca sativa L.), one of the most economically important vegetables grown primarily in moderate climates around the world, is susceptible to many diseases including lettuce drop caused by the soilborne fungus Sclerotinia minor. Complete resistance to S. minor has not been identified in cultivated lettuce or its wild relatives. We conducted five experiments over 4 years with the diversity panel of almost 500 lettuce accessions to evaluate their response to the pathogen in an artificially infested field. The lowest disease incidence (DI) was observed in cultivars Eruption, Infantry, and Annapolis (median DI of 12.1-17.5%), while the highest DI was recorded for cultivars Reine des Glaces, Wayahead, and line FL. 43007 (median DI of 81.0-95.2%). Overall, significantly lower DI was observed in red and dark red accessions compared to those with a lower anthocyanin content. Genome-wide association mapping identified 19 QTLs for resistance to S. minor, 21 for the presence of red leaf color or its variations caused by the anthocyanin content, and one for the green color intensity. Eleven of the QTLs for disease resistance were located within 10 Mb of the loci associated with red color or anthocyanin content identified in this diversity panel. The frequent, non-random co-location of QTLs, together with the lower DI observed in red and dark red accessions suggests that lettuce interaction with S. minor may be partly influenced by anthocyanins. We have identified RLL2 and ANS, the genes of the anthocyanin biosynthesis pathway that co-locate with resistance QTLs, as candidates for functional studies to ascertain the involvement of anthocyanins in lettuce resistance against S. minor. Resistance QTLs closely linked with QTLs for anthocyanin content could be used to develop lettuce with a relatively high partial resistance and red color, while those not associated with anthocyanins could be used to develop partially resistant cultivars of green color.

Bioinformatics in Plant Breeding and Research on Disease Resistance

In the context of plant breeding, bioinformatics can empower genetic and genomic selection to determine the optimal combination of genotypes that will produce a desired phenotype and help expedite the isolation of these new varieties. Bioinformatics is also instrumental in collecting and processing plant phenotypes, which facilitates plant breeding. Robots that use automated and digital technologies to collect and analyze different types of information to monitor the environment in which plants grow, analyze the environmental stresses they face, and promptly optimize suboptimal and adverse growth conditions accordingly, have helped plant research and saved human resources. In this paper, we describe the use of various bioinformatics databases and algorithms and explore their potential applications in plant breeding and for research on plant disease resistance.