Di Jin, Chao-Yue Yang, Xiao Liu, Jin-Song Lan, Tao Jiang, Hao Chen, Jia-Ying Zhang, Yu-Tong Jiang, Bo-Ran Peng, Liu-Jing Wang, Guang-Hua He, Nan Wang, Yun-Feng Li, Hui Zhuang
{"title":"PALEA AND GRAIN SHRUNKEN encoding OsMADS15 determines palea identity to affect rice grain yield and quality.","authors":"Di Jin, Chao-Yue Yang, Xiao Liu, Jin-Song Lan, Tao Jiang, Hao Chen, Jia-Ying Zhang, Yu-Tong Jiang, Bo-Ran Peng, Liu-Jing Wang, Guang-Hua He, Nan Wang, Yun-Feng Li, Hui Zhuang","doi":"10.1016/j.jgg.2026.04.019","DOIUrl":"https://doi.org/10.1016/j.jgg.2026.04.019","url":null,"abstract":"<p><p>The hull, composed of the lemma and palea, defines rice grain morphology and influences endosperm filling and quality. However, how palea development affects grain filling and quality remains poorly understood. Here, we identify a rice mutant, palea and grain shrunken 1 (pgs1), which exhibits a markedly reduced palea and elongated sterile lemmas. MutMap-based cloning reveals that PGS1 encodes the MADS-box transcription factor OsMADS15. The pgs1 mutant shows smaller but denser grains with substantially reduced chalkiness, and the expression of several palea identity genes, including G1, OsMADS1, and SL1, is significantly decreased. PGS1 is expressed in multiple floral organs, localizes to the nucleus, and lacks intrinsic transcriptional activation activity. Protein interaction assays show that PGS1 physically interacts with the histone demethylase JMJ706, and JMJ706 knockout lines exhibit floral and grain phenotypes similar to those of pgs1. Together, these results support a functional association between PGS1 and JMJ706 in the regulation of palea development and further suggest that defective palea development affects grain filling and grain quality in rice.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":7.1,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147823545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Risheng Li, Yamei Ma, Shuai Nie, Jingbo Zhou, Yunmeng Cao, Ke Zheng, Hui Wang, Tifeng Yang, Jingfang Dong, Jiansong Chen, Jian Wang, Lian Zhou, Lei Zhao, Shaochuan Zhou, Chongrong Wang, Junliang Zhao, Ziqiang Liu, Haifei Hu
{"title":"Population genomics reveals selection signatures and favorable haplotypes for low chalkiness in indica rice.","authors":"Risheng Li, Yamei Ma, Shuai Nie, Jingbo Zhou, Yunmeng Cao, Ke Zheng, Hui Wang, Tifeng Yang, Jingfang Dong, Jiansong Chen, Jian Wang, Lian Zhou, Lei Zhao, Shaochuan Zhou, Chongrong Wang, Junliang Zhao, Ziqiang Liu, Haifei Hu","doi":"10.1016/j.jgg.2026.04.013","DOIUrl":"https://doi.org/10.1016/j.jgg.2026.04.013","url":null,"abstract":"<p><p>Grain chalkiness compromises rice appearance quality and market value. The genetic basis of chalkiness reduction in indica rice remains less well understood than that in japonica. Modern Guangdong indica varieties released since the 1980s have long, translucent grains with low chalkiness, making them a suitable system to dissect quality improvement in indica. Here, we analyse whole-genome variation in 154 Guangdong indica varieties and 229 genetically diverse international indica accessions. Integrating population genomics, haplotype association analysis, and endosperm expression profiling, we identify four major chalkiness-associated genes, Wx, Chalk5, OsDER1, and OsATG8b, showing strong genetic differentiation consistent with breeding selection in Guangdong germplasm. Superior haplotypes at all four loci are significantly associated with reduced chalkiness in multi-year phenotyping in Guangzhou and in independent trials from the Philippines. Analysis of HuangHuaZhan pedigree further reveals stepwise pyramiding and fixation of these haplotypes during grain-quality improvement. Across other indica-growing provinces in southern China, favourable haplotypes at Wx and OsDER1 are largely fixed in cultivated varieties, whereas those at Chalk5 and OsATG8b remain less deployed. Variants in these four genes also enable efficient prediction of chalkiness across multiple machine learning models. Together, these results illustrate how breeding enriched favourable haplotypes for low chalkiness in indica rice.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":7.1,"publicationDate":"2026-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147789710","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genetic dissection of clinical heterogeneity in Hemoglobin H patients by targeted long-read sequencing.","authors":"Yuhua Ye, Chao Niu, Aiping Mao, Li Chen, Lang Qin, Weijie Chen, Zhentian Liu, Tiantian Xie, Yong Long, Xuan Shang, Yushan Huang, Qianqian Zhang, Libao Chen, Hualei Luo, Yihong Li, Yulin Lu, Yumeng Liu, Liuhua Liao, Junqin Cai, Riyang Liu, Xinhua Zhang, Lihong Zeng, Yaoyun Li, Jianhong Chen, Zeyan Zhong, Jianpei Fang, Xinyu Li, Xingkun Yang, Bin Lin, Kui Li, Xiaoyun Hua, Binbin Huang, Honggui Qin, Yueyan Huang, Zhijing Huang, Jinquan Lao, Xiang Qu, Juanjuan Chen, Xiaoqin Feng, Qiujun Liu, Wanying Lin, Xiaoman Zhou, Yidan Liang, Xingjiang Long, Jiaofeng Qin, Lixiang Yan, Weijian Zhu, Lian Yu, Chengwu Fan, Deguo Tang, Tianyu Zhong, Jufang Tan, Zhilin Ren, Yang Gao, Xiangmin Xu","doi":"10.1016/j.jgg.2026.04.011","DOIUrl":"https://doi.org/10.1016/j.jgg.2026.04.011","url":null,"abstract":"<p><p>Hemoglobin H (HbH) disease is a subtype of α-thalassemia typically caused by genetic defects in three out of four α-globin genes. To date, the genetic factors contributing to the highly heterogeneous clinical severity of HbH disease remain largely unknown. In this study, we perform targeted long-read sequencing (T-LRS) on a cohort of 591 HbH patients, aiming to profile the genomic variants and their haplotypes within the α/β-globin gene clusters and key erythroid genes. Phenotypic analysis confirms that non-deletional HbH patients generally exhibit more severe clinical manifestations compared to deletional ones. Moreover, we identify the co-inheritance of β-thalassemia mutations to be a mitigating factor for HbH patients, as reflected by higher hemoglobin levels and lower serum ferritin, suggesting the less imbalanced synthesis of α/β-globin among these patients. Furthermore, through haplotype phasing using long-sequencing reads, we find a haplotype of HS40 associated with milder clinical symptoms of HbH patients, validated by reporter gene assay, and that functional mutations in erythroid transcription factors BCL11A and MYB-HBS1L exert significant effects on β-thalassemia but not on HbH patients. This study presents the largest T-LRS study for α-thalassemia patients, which may provide insight into precise clinical diagnosis and phenotyping of HbH diseases.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":7.1,"publicationDate":"2026-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147789633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Fusing T7 exonuclease with the G-to-T base editor enhances the editing purity in rice.","authors":"Qiurong Ren, Xiaojuan Gao, Tao Shi, Jiangmei Cao","doi":"10.1016/j.jgg.2026.04.010","DOIUrl":"https://doi.org/10.1016/j.jgg.2026.04.010","url":null,"abstract":"<p><p>The G-to-T base editor (GTBE) is a genome editing tool that does not rely on deaminases. However, its application has been limited by low G-to-T editing efficiency and high insertion and deletion (InDel) byproduct rates. In this study, we develop a series of editors (GTBE1-GTBE7) using three strategies: modification of the Cas9 nickase (nCas9) variant, fusion with a transcriptional activation domain, and fusion with a 5'-3' exonuclease targeting nicked DNA. Both protoplast and stable rice transformant analyses reveal that the GTBE7 editor, which incorporates T7 exonuclease, significantly improves G-to-T editing purity compared to the previously reported GTBE1 editor. In stable transformants, the InDel efficiency of GTBE7 is reduced by 14%-27.7% compared to GTBE1. To further broaden the editing range of GTBE7, we develop the GTBE7_nSpRY editor, enabling G-to-T base editing at non-NGG protospacer adjacent motif (PAM) sequences. Using GTBE7_nSpRY, we successfully create herbicide-resistant rice and identify the G628A mutation site, generating Imazethapyr-resistant rice plants through G-to-C byproduct edits. In summary, the GTBE7 and GTBE7_nSpRY editors developed in this study enhance G-to-T editing purity, reduce InDel byproduct efficiency, and offer potential for expanding the application of G-to-T base editing in plants.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":7.1,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147789556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Rapid and robust sex determination from ancient enamel proteomes using protSexInferer.","authors":"Fan Bai, Zhongyou Wu, Song Xing, Qiaomei Fu","doi":"10.1016/j.jgg.2026.04.012","DOIUrl":"https://doi.org/10.1016/j.jgg.2026.04.012","url":null,"abstract":"","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":7.1,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147789685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"ZmFBL41 variants enhance maize resistance to Rhizoctonia solani by attenuating ZmFAH degradation and increasing fumaric acid accumulation.","authors":"Jicheng Qu, Bao Lin, Tiantian Geng, Mingyue Lai, Yunya Bi, Fangyu Liang, Bin Yuan, Daolin Fu, Jiajie Wu, Haifeng Liu, Zhaohui Chu","doi":"10.1016/j.jgg.2026.04.009","DOIUrl":"https://doi.org/10.1016/j.jgg.2026.04.009","url":null,"abstract":"<p><p>The F-box protein ZmFBL41, which targets ZmCAD and ZmNCED6, increases susceptibility to maize banded leaf and sheath blight (BLSB). Here, we report significantly reduced BLSB resistance in maize expressing the susceptible haplotype ZmFBL41<sup>B73</sup>, and the identification of ZmFBL41<sup>B73</sup>-interacting protein, fumarylacetoacetate hydrolase (FAH). In contrast to ZmCAD, which interacts with the LRR3 motif, ZmFAH interacts with each LRR motif of ZmFBL41<sup>B73</sup>. ZmFAH positively regulates plant resistance to Rhizoctonia solani and decrease BLSB resistance in zmfah maize but increase sheath blight (ShB) resistance in ZmFAH-overexpressing rice. ZmFAH is involved in fumaric acid (FA) metabolism, which inhibits fungal growth and invasion in plants. Compared with the susceptible allele of ZmFBL41<sup>B73</sup>, the resistant haplotype ZmFBL41<sup>Chang7-2</sup>, with two amino acid substitutions, exhibits weaker interactions with and promotes the degradation of ZmFAH, thereby resulting in greater FA accumulation and increased resistance to BLSB in the inbred lines of the Chang7-2 haplotype than in those of the B73 haplotype. Additionally, field fumarate pretreatment significantly increases rice resistance to bacterial blight and ShB. Collectively, our findings reveal the dual functions of ZmFBL41<sup>Chang7-2</sup> in strengthening the host's chemical barrier through FA accumulation in addition to the previously identified physical barrier protection through lignin accumulation during fungal infection.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":7.1,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147789716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dan Tian, Fengcui Qian, Lehan Pan, Mingxue Yin, Bihan Liu, Yuxi Zhang, Xiaobao Yang, Lu Yang, Guangyong Sun, Zhongtao Zhang, Songlin Wang, Patrick S C Leung, M Eric Gershwin, Chunquan Li, Dong Zhang
{"title":"The heterogeneity and sexual-dimorphism of human TCRαβ<sup>+</sup>CD4<sup>-</sup>CD8<sup>-</sup>double negative T cells.","authors":"Dan Tian, Fengcui Qian, Lehan Pan, Mingxue Yin, Bihan Liu, Yuxi Zhang, Xiaobao Yang, Lu Yang, Guangyong Sun, Zhongtao Zhang, Songlin Wang, Patrick S C Leung, M Eric Gershwin, Chunquan Li, Dong Zhang","doi":"10.1016/j.jgg.2026.04.008","DOIUrl":"https://doi.org/10.1016/j.jgg.2026.04.008","url":null,"abstract":"<p><p>TCRαβ<sup>+</sup> double negative T (DNT) cells are increasingly being recognized for their critical roles in the progression of various diseases. However, the molecular and functional signatures remain poorly understood and controversial. In this study, we characterize the single-cell transcriptome, TCR repertoire, and chromatin accessibility of peripheral DNT cells from 10 healthy donors. Naïve, regulatory, cytotoxic, antibody-dependent cell-mediated cytotoxicity, and helper-like DNT cell subsets exhibit specific gene expression, transcriptome regulation, development signature, and sexual heterogeneity, respectively. Using publicly available data, we observe changes in the proportion and gene expression of DNT cell subsets, especially the helper subset, in patients with ulcerative colitis and type 1 diabetes. Overall, human DNT cells exhibit phenotypic and functional diversity, providing a valuable framework for understanding the development and progression of immune-related diseases.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":7.1,"publicationDate":"2026-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147730367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hongjia Zhang, Zhao Li, Hong Li, Yan Liu, Baoshuai Zhang, Sudi Li, Lei Zhang, Jiawei Zhao, Weiwei Zou, Yuxin Tu, Bin Hu, Chengcai Chu, Xinglin Du, Wenzhu Jiang, Soon-Wook Kwon, Zhihua Zhang
{"title":"Natural variation of OsGATA16 contributes to differential immunity against Magnaporthe oryzae in rice.","authors":"Hongjia Zhang, Zhao Li, Hong Li, Yan Liu, Baoshuai Zhang, Sudi Li, Lei Zhang, Jiawei Zhao, Weiwei Zou, Yuxin Tu, Bin Hu, Chengcai Chu, Xinglin Du, Wenzhu Jiang, Soon-Wook Kwon, Zhihua Zhang","doi":"10.1016/j.jgg.2026.04.007","DOIUrl":"10.1016/j.jgg.2026.04.007","url":null,"abstract":"<p><p>Rice blast, caused by the fungal pathogen Magnaporthe oryzae, constitutes a critical threat to global rice production. Leveraging functional genes from germplasm resources to breed resistant varieties remains the most effective and sustainable strategy for blast control. Here, we identify a GATA transcription factor OsGATA16 as a candidate regulator of blast resistance by genome-wide association study (GWAS) using a diverse rice germplasm panel. Functional analysis shows that OsGATA16 overexpression significantly reduces blast resistance, whereas knockout lines exhibit enhanced resistance, establishing OsGATA16 as a negative regulator of rice immunity. Transcriptome, qRT-PCR, dual-luciferase, and DAP-seq assays reveal that OsGATA16 directly represses diterpenoid biosynthetic genes. UPLC-MS/MS reveals increased accumulation of pimarane-type diterpenoids in osgata16 mutants. Further analysis indicates that the key pimarane-type diterpenoid abietic acid promotes blast resistance but compromises cold tolerance. Given OsGATA16's known role in cold tolerance, haplotype analysis of 137 core-collection rice accessions uncovers a trade-off between blast resistance and cold tolerance. The japonica-dominant Hap1, featuring key residues Val292 and Gly333, shows stronger transcriptional repression activity than indica Hap2, with population genetics supporting divergent allele selection. Collectively, OsGATA16 negatively regulates blast resistance by repressing pimarane-type diterpenoid biosynthesis, serving as a valuable target for breeding dual stress-resilient rice.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":7.1,"publicationDate":"2026-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147724884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"OsMDS1 regulates cell elongation and thermotolerance in rice.","authors":"Menghan Fan, Junfeng Dai, Zhigang Wu, Yong Yang, Lisha Zhang","doi":"10.1016/j.jgg.2026.04.006","DOIUrl":"10.1016/j.jgg.2026.04.006","url":null,"abstract":"<p><p>Cereal crops often exhibit a tradeoff between thermotolerance, which is important for climate adaptation, and cell elongation, which is crucial for ideal plant architecture and yield. Here, we characterize the rice mutant with dwarfing and short roots/grains 1 (Osmds1), which shows dwarfism, shorter roots, and reduced grain size, along with enhanced thermosensitivity. OsMDS1 encodes a KNOTTED1-like homeobox (KNOX) transcription factor. A 15-bp deletion in the GSE domain of OsMDS1 is identified in Osmds1, which we show to be an allele of Osh15, d6, Oskn3, Shennong9816d, and rlb. OsMDS1 interacts with the chaperone LO9-177 and the transcription factor OsBC1, two components of the OsBUL1-LO9-177-OsBC1 complex, but not with OsBUL1, whereas Osmds1 binds to all three components. Further analysis indicates that OsMDS1 and OsBC1 synergistically activate the auxin biosynthesis genes OsYUCCA1 and OsTDD1, revealing a link between the KNOX and auxin pathways. OsMDS1 also interacts with the heat-shock protein OsDjC38 and regulates its expression. Genetic analysis shows that Osmds1 and OsDjC38 knockout plants have elevated sensitivity to prolonged heat stress and impaired antioxidant enzyme activity. Our results suggest that OsMDS1 coordinates both cell elongation and the heat-stress response, possibly through auxin pathways, providing a promising target for rice breeding.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":7.1,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147719068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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