Journal of Genetics and Genomics

Engineering the future cereal crops with big biological data: toward intelligence-driven breeding by design

Lei Liu, Jimin Zhan, Jianbing Yan

2024, 51(8): 781-789. doi: 10.1016/j.jgg.2024.03.005

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How to feed 10 billion human populations is one of the challenges that need to be addressed in the following decades, especially under an unpredicted climate change. Crop breeding, initiating from the phenotype-based selection by local farmers and developing into current biotechnology-based breeding, has played a critical role in securing the global food supply. However, regarding the changing environment and ever-increasing human population, can we breed outstanding crop varieties fast enough to achieve high productivity, good quality, and widespread adaptability? This review outlines the recent achievements in understanding cereal crop breeding, including the current knowledge about crop agronomic traits, newly developed techniques, crop big biological data research, and the possibility of integrating them for intelligence-driven breeding by design, which ushers in a new era of crop breeding practice and shapes the novel architecture of future crops. This review focuses on the major cereal crops, including rice, maize, and wheat, to explain how intelligence-driven breeding by design is becoming a reality.

Modern phenomics to empower holistic crop science, agronomy, and breeding research

Ni Jiang, Xin-Guang Zhu

2024, 51(8): 790-800. doi: 10.1016/j.jgg.2024.04.016

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Crop phenomics enables the collection of diverse plant traits for a large number of samples along different time scales, representing a greater data collection throughput compared with traditional measurements. Most modern crop phenomics use different sensors to collect reflective, emitted, and fluorescence signals, etc., from plant organs at different spatial and temporal resolutions. Such multi-modal, high-dimensional data not only accelerates basic research on crop physiology, genetics, and whole plant systems modeling, but also supports the optimization of field agronomic practices, internal environments of plant factories, and ultimately crop breeding. Major challenges and opportunities facing the current crop phenomics research community include developing community consensus or standards for data collection, management, sharing, and processing, developing capabilities to measure physiological parameters, and enabling farmers and breeders to effectively use phenomics in the field to directly support agricultural production.

Both gain- and loss-of-function variants of KCNA1 are associated with paroxysmal kinesigenic dyskinesia

Wan-Bing Sun, Jing-Xin Fu, Yu-Lan Chen, Hong-Fu Li, Zhi-Ying Wu, Dian-Fu Chen

2024, 51(8): 801-810. doi: 10.1016/j.jgg.2024.03.013

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KCNA1 is the coding gene for Kv1.1 voltage-gated potassium-channel α subunit. Three variants of KCNA1 have been reported to manifest as paroxysmal kinesigenic dyskinesia (PKD), but the correlation between them remains unclear due to the phenotypic complexity of KCNA1 variants as well as the rarity of PKD cases. Using the whole exome sequencing followed by Sanger sequencing, we screen for potential pathogenic KCNA1 variants in patients clinically diagnosed with paroxysmal movement disorders and identify three previously unreported missense variants of KCNA1 in three unrelated Chinese families. The proband of one family (c.496G>A, p.A166T) manifests as episodic ataxia type 1, and the other two (c.877G>A, p.V293I and c.1112C>A, p.T371A) manifest as PKD. The pathogenicity of these variants is confirmed by functional studies, suggesting that p.A166T and p.T371A cause a loss-of-function of the channel, while p.V293I leads to a gain-of-function with the property of voltage-dependent gating and activation kinetic affected. By reviewing the locations of PKD-manifested KCNA1 variants in Kv1.1 protein, we find that these variants tend to cluster around the pore domain, which is similar to epilepsy. Thus, our study strengthens the correlation between KCNA1 variants and PKD and provides more information on genotype-phenotype correlations of KCNA1 channelopathy.

Cmtm4 deficiency exacerbates colitis by inducing gut dysbiosis and S100a8/9 expression

Qiao Meng, Jing Ning, Jingjing Lu, Jing Zhang, Ming Zu, Xiurui Han, Huiling Zheng, Yueqing Gong, Xinyu Hao, Ying Xiong, Fang Gu, Wenling Han, Weiwei Fu, Jun Wang, Shigang Ding

2024, 51(8): 811-823. doi: 10.1016/j.jgg.2024.03.009

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The dysfunction of innate immunity components is one of the major drivers for ulcerative colitis (UC), and increasing reports indicate that the gut microbiome serves as an intermediate between genetic mutations and UC development. Here, we find that the IL-17 receptor subunit, CMTM4, is reduced in UC patients and dextran sulfate sodium (DSS)-induced colitis. The deletion of CMTM4 (Cmtm4^-/-) in mice leads to a higher susceptibility to DSS-induced colitis than in wild-type, and the gut microbiome significantly changes in composition. The causal role of the gut microbiome is confirmed with a cohousing experiment. We further identify that S100a8/9 is significantly up-regulated in Cmtm4^-/- colitis, with the block of its receptor RAGE that reverses the phenotype associated with the CMTM4 deficiency. CMTM4 deficiency rather suppresses S100a8/9 expression in vitro via the IL17 pathway, further supporting that the elevation of S100a8/9 in vivo is most likely a result of microbial dysbiosis. Taken together, the results suggest that CMTM4 is involved in the maintenance of intestinal homeostasis, suppression of S100a8/9, and prevention of colitis development. Our study further shows CMTM4 as a crucial innate immunity component, confirming its important role in UC development and providing insights into potential targets for the development of future therapies.

The transgenerational effects of maternal low-protein diet during lactation on offspring

Lin-Jian Gu, Li Li, Qian-Nan Li, Ke Xu, Wei Yue, Jing-Yi Qiao, Tie-Gang Meng, Ming-Zhe Dong, Wen-Long Lei, Jia-Ni Guo, Zhen-Bo Wang, Qing-Yuan Sun

2024, 51(8): 824-835. doi: 10.1016/j.jgg.2024.04.008

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Environmental factors such as diet and lifestyle can influence the health of both mothers and offspring. However, its transgenerational transmission and underlying mechanisms remain largely unknown. Here, using a maternal lactation-period low-protein diet (LPD) mouse model, we show that maternal LPD during lactation causes decreased survival and stunted growth, significantly reduces ovulation and litter size, and alters the gut microbiome in the female LPD-F1 offspring. The transcriptome of LPD-F1 metaphase II (MII) oocytes shows that differentially expressed genes are enriched in female pregnancy and multiple metabolic processes. Moreover, maternal LPD causes early stunted growth and impairs metabolic health, which is transmitted over two generations. The methylome alteration of LPD-F1 oocytes can be partly transmitted to the F2 oocytes. Together, our results reveal that LPD during lactation transgenerationally affects offspring health, probably via oocyte epigenetic changes.

A homing rescue gene drive with multiplexed gRNAs reaches high frequency in cage populations but generates functional resistance

Shibo Hou, Jingheng Chen, Ruobing Feng, Xuejiao Xu, Nan Liang, Jackson Champer

2024, 51(8): 836-843. doi: 10.1016/j.jgg.2024.04.001

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CRISPR homing gene drives have considerable potential for managing populations of medically and agriculturally significant insects. They operate by Cas9 cleavage followed by homology-directed repair, copying the drive allele to the wild-type chromosome and thus increasing in frequency and spreading throughout a population. However, resistance alleles formed by end-joining repair pose a significant obstacle. To address this, we create a homing drive targeting the essential hairy gene in Drosophila melanogaster. Nonfunctional resistance alleles are recessive lethal, while drive carriers have a recoded “rescue” version of hairy. The drive inheritance rate is moderate, and multigenerational cage studies show drive spread to 96%-97% of the population. However, the drive does not reach 100% due to the formation of functional resistance alleles despite using four gRNAs. These alleles have a large deletion but likely utilize an alternate start codon. Thus, revised designs targeting more essential regions of a gene may be necessary to avoid such functional resistance. Replacement of the rescue element’s native 3' UTR with a homolog from another species increases drive inheritance by 13%-24%. This was possibly because of reduced homology between the rescue element and surrounding genomic DNA, which could also be an important design consideration for rescue gene drives.

Functional role of circRNA CHRC through miR-431-5p/KLF15 signaling axis in the progression of heart failure

Yi Hu, Huaming Cao, Jie Sheng, Yizhuo Sun, Yuping Zhu, Qin Lin, Na Yi, Siyu He, Luying Peng, Li Li

2024, 51(8): 844-854. doi: 10.1016/j.jgg.2024.03.010

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Pathological myocardial hypertrophy is a common early clinical manifestation of heart failure, with noncoding RNAs exerting regulatory influence. However, the molecular function of circular RNAs (circRNAs) in the progression from cardiac hypertrophy to heart failure remains unclear. To uncover functional circRNAs and identify the core circRNA signaling pathway in heart failure, we construct a global triple network (microRNA, circRNA, and mRNA) based on the competitive endogenous RNA (ceRNA) theory. We observe that cardiac hypertrophy-related circRNA (circRNA CHRC), within the ceRNA network, is down-regulated in both transverse aortic constriction mice and Ang-II—treated primary mouse cardiomyocytes. Silencing circRNA CHRC increases cross-sectional cell area, atrial natriuretic peptide, and β-myosin heavy chain levels in primary mouse cardiomyocytes. Further screening shows that circRNA CHRC targets the miR-431-5p/KLF15 axis implicated in heart failure progression in vivo and in vitro. Immunoprecipitation with anti-Ago2-RNA confirms the interaction between circRNA CHRC and miR-431-5p, while miR-431-5p mimics reverse Klf15 activation caused by circRNA CHRC overexpression. In summary, circRNA CHRC attenuates cardiac hypertrophy via sponging miR-431-5p to maintain the normal level of Klf15 expression.

Two imprinted genes primed by DEMETER in the central cell and activated by WRKY10 in the endosperm

Ke Yang, Yuling Tang, Yue Li, Wenbin Guo, Zhengdao Hu, Xuanpeng Wang, Frédéric Berger, Jing Li

2024, 51(8): 855-865. doi: 10.1016/j.jgg.2024.04.003

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The early development of the endosperm is crucial for balancing the allocation of maternal nutrients to offspring. This process is believed to be evolutionarily associated with genomic imprinting, resulting in parentally biased allelic gene expression. Beyond Fertilization Independent Seed (FIS) genes, the number of imprinted genes involved in early endosperm development and seed size determination remains limited. This study introduces early endosperm-expressed HAIKU (IKU) downstream Candidate F-box 1 (ICF1) and ICF2 as maternally expressed imprinted genes (MEGs) in Arabidopsis thaliana. Although these genes are also demethylated by DEMETER (DME) in the central cell, their activation differs from the direct DME-mediated activation seen in classical MEGs such as the FIS genes. Instead, ICF maternal alleles carry pre-established hypomethylation in their promoters, priming them for activation by the WRKY10 transcription factor in the endosperm. On the contrary, paternal alleles are predominantly suppressed by CG methylation. Furthermore, we find that ICF genes partially contribute to the small seed size observed in iku mutants. Our discovery reveals a two-step regulatory mechanism that highlights the important role of conventional transcription factors in the activation of imprinted genes, which was previously not fully recognized. Therefore, the mechanism provides a new dimension to understand the transcriptional regulation of imprinting in plant reproduction and development.

Whole-genome resequencing of Hu sheep identifies candidate genes associated with agronomic traits

Liming Zhao, Lvfeng Yuan, Fadi Li, Xiaoxue Zhang, Huibin Tian, Zongwu Ma, Deyin Zhang, Yukun Zhang, Yuan Zhao, Kai Huang, Xiaolong Li, Jiangbo Cheng, Dan Xu, Xiaobin Yang, Kunchao Han, Xiuxiu Weng, Weimin Wang

2024, 51(8): 866-876. doi: 10.1016/j.jgg.2024.03.015

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The phenotypic diversity resulting from artificial or natural selection of sheep has made a significant contribution to human civilization. Hu sheep are a local sheep breed unique to China with high reproductive rates and rapid growth. Genomic selection signatures have been widely used to investigate the genetic mechanisms underlying phenotypic variation in livestock. Here, we conduct whole-genome sequencing of 207 Hu sheep and compare them with the wild ancestors of domestic sheep (Asiatic mouflon) to investigate the genetic characteristics and selection signatures of Hu sheep. Based on six signatures of selection approaches, we detect genomic regions containing genes related to reproduction (BMPR1B, BMP2, PGFS, CYP19, CAMK4, GGT5, and GNAQ), vision (ALDH1A2, SAG, and PDE6B), nervous system (NAV1), and immune response (GPR35, SH2B2, PIK3R3, and HRAS). Association analysis with a population of 1299 Hu sheep reveals that those missense mutations in the GPR35 (GPR35 g.952651 A>G; GPR35 g.952496 C>T) and NAV1 (NAV1 g.84216190 C>T; NAV1 g.84227412 G>A) genes are significantly associated (P < 0.05) with immune and growth traits in Hu sheep, respectively. This research offers unique insights into the selection characteristics of Hu sheep and facilitates further genetic improvement and molecular investigations.

The origin of two divergent ovine β-globin haplotypes and their potential association with environmental adaptation

Yuxin Kang, Yilin Liang, Fengting Fan, Hojjat Asadollahpour Nanaei, Chunna Cao, Yu Jiang, Xianyong Lan, Chuanying Pan, Ran Li

2024, 51(8): 877-879. doi: 10.1016/j.jgg.2024.03.014

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Copy number variation of NAL23 causes narrow-leaf development in rice

Degui Zhou, Yajing Li, Xianrong Xie, Wenyan Ding, Libin Chen, Tie Li, Jianian Tang, Xiyu Tan, Weizhi Liu, Yueqin Heng, Yongyao Xie, Letian Chen, Qi Liu, Shaochuan Zhou, Jing Zhao, Gong Zhang, Jiantao Tan, Yaoguang Liu, Rongxin Shen

2024, 51(8): 880-883. doi: 10.1016/j.jgg.2024.04.006

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DAIS: a method for identifying spatial domains based on density clustering of spatial omics data

Qichao Yu, Ru Tian, Xin Jin, Liang Wu

2024, 51(8): 884-887. doi: 10.1016/j.jgg.2024.04.002

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Corrigendum to “Root-derived long-distance signals trigger ABA synthesis and enhance drought resistance in Arabidopsis” [Journal of Genetics and Genomics (2024) 51, 749-761]

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

2024, 51(8): 888-888. doi: 10.1016/j.jgg.2024.07.012

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2024 Vol. 51, No. 8