Journal of Genetics and Genomics

The CLAVATA signaling: a roadmap to optimize grain shape in rice

Shaoyan Shen, Bingyang Jiao, Yunhai Li

2024, 51(7): 677-679. doi: 10.1016/j.jgg.2024.06.003

Abstract (0) PDF (0)

Abstract:

From molecule to cell: the expanding frontiers of plant immunity

Lei Li, Jing Liu, Jian-Min Zhou

2024, 51(7): 680-690. doi: 10.1016/j.jgg.2024.02.005

Abstract (0) PDF (0)

Abstract:
In recent years, the field of plant immunity has witnessed remarkable breakthroughs. During the co-evolution between plants and pathogens, plants have developed a wealth of intricate defense mechanisms to safeguard their survival. Newly identified immune receptors have added unexpected complexity to the surface and intracellular sensor networks, enriching our understanding of the ongoing plant-pathogen interplay. Deciphering the molecular mechanisms of resistosome shapes our understanding of these mysterious molecules in plant immunity. Moreover, technological innovations are expanding the horizon of the plant-pathogen battlefield into spatial and temporal scales. While the development provides new opportunities for untangling the complex realm of plant immunity, challenges remain in uncovering plant immunity across spatiotemporal dimensions from both molecular and cellular levels.

The OsCLV2s-OsCRN1 co-receptor regulates grain shape in rice

Xingxing Li, Meng-en Wu, Juncheng Zhang, Jingyue Xu, Yuanfei Diao, Yibo Li

2024, 51(7): 691-702. doi: 10.1016/j.jgg.2024.03.011

Abstract (0) PDF (0)

Abstract:
The highly conserved CLV-WUS negative feedback pathway plays a decisive role in regulating stem cell maintenance in shoot and floral meristems in higher plants, including Arabidopsis, rice, maize, and tomato. Here, we find significant natural variations in the OsCLV2c, OsCLV2d, and OsCRN1 loci in a genome-wide association study of grain shape in rice. OsCLV2a, OsCLV2c, OsCLV2d, and OsCRN1 negatively regulate grain length-width ratio and show distinctive geographical distribution, indica-japonica differentiation, and artificial selection signatures. Notably, OsCLV2a and OsCRN1 interact biochemically and genetically, suggesting that the two components function in a complex to regulate grain shape of rice. Furthermore, the genetic contributions of the haplotypes combining OsCLV2a, OsCLV2c, and OsCRN1 are significantly higher than those of each single gene alone in controlling key yield traits. These findings identify two groups of receptor-like kinases that may function as distinct co-receptors to control grain size in rice, thereby revealing a previously unrecognized role of the CLV class genes in regulating seed development and proposing a framework to understand the molecular mechanisms of the CLV-WUS pathway in rice and other crops.

Weakened tanning ability is an important mechanism for evolutionary skin lightening in East Asians

Youwei Pu, Siyu Pu, Yanyan Chen, Qinghong Kong, Xuyang Liu, Qi Zhao, Ke Xu, Jiuming Liu, Mengyuan Li, Xiaoyu Xu, Xiaoyang Qiao, Bing Su, Jing Chen, Zhaohui Yang

2024, 51(7): 703-713. doi: 10.1016/j.jgg.2024.03.001

Abstract (0) PDF (0)

Abstract:
The evolution of light-skin pigmentation among Eurasians is considered as an adaptation to the high-latitude environments. East Asians are ideal populations for studying skin color evolution because of the complex environment of East Asia. Here, we report a strong selection signal for the pigmentation gene phenylalanine hydroxylase (PAH) in light-skinned Han Chinese individuals. The intron mutation rs10778203 in PAH is enriched in East Asians and is significantly associated with skin color of the back of the hand in Han Chinese males (P < 0.05). In vitro luciferase and transcription factor binding assays show that the ancestral allele of rs10778203 could bind to SMAD2 and has a significant enhancer activity for PAH. However, the derived T allele (the major allele in East Asians) of rs10778203 decreases the binding activity of transcription factors and enhancer activity. Meanwhile, the derived T allele of rs10778203 shows a weaker ultraviolet radiation response in A375 cells and zebrafish embryos. Furthermore, rs10778203 decreases melanin production in transgenic zebrafish embryos after ultraviolet B (UVB) treatment. Collectively, PAH is a potential pigmentation gene that regulates skin tanning ability. Natural selection has enriched the adaptive allele, resulting in weakened tanning ability in East Asians, suggesting a unique genetic mechanism for evolutionary skin lightening in East Asians.

Constructing the metabolic network of wheat kernels based on structure-guided chemical modification and multi-omics data

Zhitao Tian, Jingqi Jia, Bo Yin, Wei Chen

2024, 51(7): 714-722. doi: 10.1016/j.jgg.2024.02.008

Abstract (0) PDF (0)

Abstract:
Metabolic network construction plays a pivotal role in unraveling the regulatory mechanism of biological activities, although it often proves to be challenging and labor-intensive, particularly with non-model organisms. In this study, we develop a computational approach that employs reaction models based on the structure-guided chemical modification and related compounds to construct a metabolic network in wheat. This construction results in a comprehensive structure-guided network, including 625 identified metabolites and additional 333 putative reactions compared with the Kyoto Encyclopedia of Genes and Genomes database. Using a combination of gene annotation, reaction classification, structure similarity, and correlations from transcriptome and metabolome analysis, a total of 229 potential genes related to these reactions are identified within this network. To validate the network, the functionality of a hydroxycinnamoyltransferase (TraesCS3D01G314900) for the synthesis of polyphenols and a rhamnosyltransferase (TraesCS2D01G078700) for the modification of flavonoids are verified through in vitro enzymatic studies and wheat mutant tests, respectively. Our research thus supports the utility of structure-guided chemical modification as an effective tool in identifying causal candidate genes for constructing metabolic networks and further in metabolomic genetic studies.

Recombination and repeat-induced point mutation landscapes reveal trade-offs between the sexual and asexual cycles of Magnaporthe oryzae

Xifang Zong, Yaxin Lou, Mengshuang Xia, Kunyang Zhao, Jingxuan Chen, Ju Huang, Sihai Yang, Long Wang

2024, 51(7): 723-734. doi: 10.1016/j.jgg.2024.03.003

Abstract (0) PDF (0)

Abstract:
The fungal disease caused by Magnaporthe oryzae is one of the most devastating diseases that endanger many crops worldwide. Evidence shows that sexual reproduction can be advantageous for fungal diseases as hybridization facilitates host-jumping. However, the pervasive clonal lineages of M. oryzae observed in natural fields contradict this expectation. A better understanding of the roles of recombination and the fungi-specific repeat-induced point mutation (RIP) in shaping its evolutionary trajectory is essential to bridge this knowledge gap. Here we systematically investigate the RIP and recombination landscapes in M. oryzae using a whole genome sequencing data from 252 population samples and 92 cross progenies. Our data reveal that the RIP can robustly capture the population history of M. oryzae, and we provide accurate estimations of the recombination and RIP rates across different M. oryzae clades. Significantly, our results highlight a parent-of-origin bias in both recombination and RIP rates, tightly associating with their sexual potential and variations of effector proteins. This bias suggests a critical trade-off between generating novel allelic combinations in the sexual cycle to facilitate host-jumping and stimulating transposon-associated diversification of effectors in the asexual cycle to facilitate host coevolution. These findings provide unique insights into understanding the evolution of blast fungus.

The characterization of protein lactylation in relation to cardiac metabolic reprogramming in neonatal mouse hearts

Tongyu Zhang, Yingxi Zhu, Xiaochen Wang, Danyang Chong, Haiquan Wang, Dandan Bu, Mengfei Zhao, Lei Fang, Chaojun Li

2024, 51(7): 735-748. doi: 10.1016/j.jgg.2024.02.009

Abstract (0) PDF (0)

Abstract:
In mammals, the neonatal heart can regenerate upon injury within a short time after birth, while adults lose this ability. Metabolic reprogramming has been demonstrated to be critical for cardiomyocyte proliferation in the neonatal heart. Here, we reveal that cardiac metabolic reprogramming could be regulated by altering global protein lactylation. By performing 4D label-free proteomics and lysine lactylation (Kla) omics analyses in mouse hearts at postnatal days 1, 5, and 7, 2297 Kla sites from 980 proteins are identified, among which 1262 Kla sites from 409 proteins are quantified. Functional clustering analysis reveals that the proteins with altered Kla sites are mainly involved in metabolic processes. The expression and Kla levels of proteins in glycolysis show a positive correlation while a negative correlation in fatty acid oxidation. Furthermore, we verify the Kla levels of several differentially modified proteins, including ACAT1, ACADL, ACADVL, PFKM, PKM, and NPM1. Overall, our study reports a comprehensive Kla map in the neonatal mouse heart, which will help to understand the regulatory network of metabolic reprogramming and cardiac regeneration.

Root-derived long-distance signals trigger ABA synthesis and enhance drought resistance in Arabidopsis

Qian-Qian Liu, Jin-Qiu Xia, Jie Wu, Yi Han, Gui-Quan Zhang, Ping-Xia Zhao, Cheng-Bin Xiang

2024, 51(7): 749-761. doi: 10.1016/j.jgg.2024.03.007

Abstract (0) PDF (0)

Abstract:
Vascular plants have evolved intricate long-distance signaling mechanisms to cope with environmental stress, with reactive oxygen species (ROS) emerging as pivotal systemic signals in plant stress responses. However, the exact role of ROS as root-to-shoot signals in the drought response has not been determined. In this study, we reveal that compared with wild-type plants, ferric reductase defective 3 (frd3) mutants exhibit enhanced drought resistance concomitant with elevated NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3) transcript levels and abscisic acid (ABA) contents in leaves as well as increased hydrogen peroxide (H₂O₂) levels in roots and leaves. Grafting experiments distinctly illustrate that drought resistance can be conferred by the frd3 rootstock regardless of the scion genotype, indicating that long-distance signals originating from frd3 roots promote an increase in ABA levels in leaves. Intriguingly, the drought resistance conferred by the frd3 mutant rootstock is weakened by the CAT2-overexpressing scion, suggesting that H₂O₂ may be involved in long-distance signaling. Moreover, the results of comparative transcriptome and proteome analyses support the drought resistance phenotype of the frd3 mutant. Taken together, our findings substantiate the notion that frd3 root-derived long-distance signals trigger ABA synthesis in leaves and enhance drought resistance, providing new evidence for root-to-shoot long-distance signaling in the drought response of plants.

shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals

Li Zhan, Xiao Luo, Wenqin Xie, Xuan-An Zhu, Zijing Xie, Jianfeng Lin, Lin Li, Wenli Tang, Rui Wang, Lin Deng, Yufan Liao, Bingdong Liu, Yantong Cai, Qianwen Wang, Shuangbin Xu, Guangchuang Yu

2024, 51(7): 762-768. doi: 10.1016/j.jgg.2024.02.004

Abstract (2) PDF (0)

Abstract:
The molecular clock model is fundamental for inferring species divergence times from molecular sequences. However, its direct application may introduce significant biases due to sequencing errors, recombination events, and inaccurately labeled sampling times. Improving accuracy necessitates rigorous quality control measures to identify and remove potentially erroneous sequences. Furthermore, while not all branches of a phylogenetic tree may exhibit a clear temporal signal, specific branches may still adhere to the assumptions, with varying evolutionary rates. Supporting a relaxed molecular clock model better aligns with the complexities of evolution. The root-to-tip regression method has been widely used to analyze the temporal signal in phylogenetic studies and can be generalized for detecting other phylogenetic signals. Despite its utility, there remains a lack of corresponding software implementations for broader applications. To address this gap, we present shinyTempSignal, an interactive web application implemented with the shiny framework, available as an R package and publicly accessible at https://github.com/YuLab-SMU/shinyTempSignal. This tool facilitates the analysis of temporal and other phylogenetic signals under both strict and relaxed models. By extending the root-to-tip regression method to diverse signals, shinyTempSignal helps in the detection of evolving features or traits, thereby laying the foundation for deeper insights and subsequent analyses.

The Iberian Roma Population Variant Server (IRPVS)

Fabiola Mavillard, Javier Perez-Florido, Francisco M. Ortuño, Amador Valladares, Miren L. Álvarez-Villegas, Gema Roldán, Rosario Carmona, Manuel Soriano, Santiago Susarte, Pilar Fuentes, Daniel López-López, Ana María Nuñez-Negrillo, Alejandra Carvajal, Yolanda Morgado, Daniel Arteaga, Rosa Ufano, Pablo Mir, Juan F. Gamella, Joaquín Dopazo, Carmen Paradas, Macarena Cabrera-Serrano

2024, 51(7): 769-773. doi: 10.1016/j.jgg.2024.03.006

Abstract (2) PDF (0)

Abstract:

Genetic mapping of plasma proteome on brain structure

Shengyi Ma, Fengzhe Xu, Yuanqing Fu, Ju-Sheng Zheng

2024, 51(7): 774-777. doi: 10.1016/j.jgg.2024.03.017

Abstract (0) PDF (0)

Abstract:

Chinese patients with adult onset leukodystrophy caused by CST3 variants

Yi Zhang, Zhi-Ying Wu

2024, 51(7): 778-780. doi: 10.1016/j.jgg.2024.05.002

Abstract (0) PDF (0)

Abstract:

2024 Vol. 51, No. 7