Article
Gastroenterology & Hepatology
Yucan Zheng, Hongmei Guo, Leilei Chen, Weixia Cheng, Kunlong Yan, Zhihua Zhang, Mei Li, Yu Jin, Guorui Hu, Chunli Wang, Chunlei Zhou, Wei Zhou, Zhanjun Jia, Bixia Zheng, Zhifeng Liu
Summary: This retrospective study characterized the genotype and phenotype of 166 participants with intrahepatic cholestasis, and re-analyzed phenotype and whole-exome sequencing (WES) data from patients with previously undetermined genetic etiology. Disease-causing variants were identified in 31% of the participants. Regular re-evaluation of well-phenotyped patients' WES data can increase the diagnostic yield for cholestatic liver disease in children.
HEPATOLOGY INTERNATIONAL
(2023)
Article
Developmental Biology
T. Yammine, N. Reynaud, H. Lejeune, F. Diguet, P. A. Rollat-Farnier, A. Labalme, I Plotton, C. Farra, D. Sanlaville, E. Chouery, C. Schluth-Bolard
Summary: Male infertility affects about 7% of the male population, with balanced chromosomal rearrangements being a well-established cause but with unclear underlying pathophysiological mechanisms. This study used a combination of cytogenetic and molecular techniques to identify candidate genes implicated in spermatogenesis defects in three male carriers of different balanced translocations. Breakpoints were characterized at the molecular level, revealing gene disruptions and variations that need further validation for their roles in male infertility. This study emphasizes the importance of combining cytogenetic and molecular techniques to investigate spermatogenesis disorders in patients with structural rearrangements on a genomic scale.
MOLECULAR HUMAN REPRODUCTION
(2021)
Article
Plant Sciences
Jun Qin, Fengmin Wang, Qingsong Zhao, Ainong Shi, Tiantian Zhao, Qijian Song, Waltram Ravelombola, Hongzhou An, Long Yan, Chunyan Yang, Mengchen Zhang
Summary: In this study, the quantitative trait locus (QTL) controlling protein content in soybean was investigated using genome-wide association studies (GWAS) and linkage mapping approaches. The study identified major QTLs on chromosomes 6 and 20 and detected single nucleotide polymorphism (SNP) markers associated with protein content. Genomic selection methods were applied to improve soybean protein content based on these markers.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Stephanie Karhoff, Christian Vargas-Garcia, Sungwoo Lee, M. A. Rouf Mian, Michelle A. Graham, Anne E. Dorrance, Leah K. McHale
Summary: This study identified a gene associated with resistance to Phytophthora root and stem rot and suggested its role as a susceptibility factor in disease development. The findings will facilitate further functional analyses and marker-assisted breeding efforts.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Dennis N. Lozada, Guillermo Nunez, Phillip Lujan, Srijana Dura, Danise Coon, Derek W. Barchenger, Soumaila Sanogo, Paul W. Bosland
Summary: A genetic linkage map was constructed using GBS-derived SNP markers in a RIL population, identifying genomic regions associated with P. capsici resistance and candidate genes. The study revealed the genetic complexity of the P. capsici-Capsicum pathosystem and the potential role of epigenetics in conferring resistance to Phytophthora root rot. Significant genomic regions and candidate genes associated with disease response were identified, providing a deeper understanding of Phytophthora root rot resistance in chile pepper.
Article
Plant Sciences
Suprio Ghosh, Shengrui Zhang, Muhammad Azam, Kwadwo Gyapong Agyenim-Boateng, Jie Qi, Yue Feng, Yecheng Li, Jing Li, Bin Li, Junming Sun
Summary: In this study, genomic loci and candidate genes controlling tocopherol content in soybean seeds were identified using bulked-segregant analysis. Multiple genes related to tocopherol content were annotated and enriched functional terms were detected. A key candidate gene with significant variations in tocopherol content across multiple experimental locations was identified. These findings provide valuable gene resources and potential targets for further research in soybean breeding.
Article
Biotechnology & Applied Microbiology
Jingjing Liu, Yu Xiao, Pengwei Ren, Shuer Zhang, Yang Liu, Mingxia Zhu
Summary: This study identified candidate genes associated with high egg production in Wulong geese through genome-wide selection signal analysis and transcriptome analysis. A total of 132 genomic regions and 130 genes related to high egg production were identified. These genes were enriched in pathways related to egg production, and two genes (GCG and FAP) were common to both selected genes and differentially expressed genes. This research provides insights into breeding high egg production in Wulong geese and understanding the mechanisms of reproductive regulation in poultry.
Article
Plant Sciences
He Wei, Yun Lian, Jinying Li, Haichao Li, Qijian Song, Yongkang Wu, Chenfang Lei, Shiwei Wang, Hui Zhang, Jinshe Wang, Weiguo Lu
Summary: This study identified three novel resistant quantitative trait loci (QTLs) for soybean cyst nematode (SCN) resistance in the soybean variety Handou 10. Candidate genes for these QTLs were predicted through functional analysis and transcriptome analysis. The study also emphasized the importance of plant-pathogen interaction in SCN resistance.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Chunli Wang, Wei Zhou, Luyan Zhang, Luhan Fu, Wei Shi, Yan Qing, Fen Lu, Jian Tang, Xiucheng Gao, Aihua Zhang, Zhanjun Jia, Yue Zhang, Xiaoke Zhao, Bixia Zheng
Summary: By performing whole exome sequencing on an unselected Chinese cohort of patients with microcephaly, we identified causative sequence variants in 65 families and discovered 8 potential novel candidate genes related to neurodevelopmental disorders/microcephaly. These results expand the morbid genome of monogenic neurodevelopmental disorders and support the adoption of whole exome sequencing as a first-tier test for individuals with microcephaly.
Article
Veterinary Sciences
Huaibing Yao, Xiaorui Liang, Zhihua Dou, Zhongkai Zhao, Wanpeng Ma, Zelin Hao, Hui Yan, Yuzhuo Wang, Zhuangyuan Wu, Gangliang Chen, Jie Yang
Summary: This study aimed to compare the morphological changes in mammary gland tissue and transcriptome expression profiles between young and adult female Bactrian camels, and explore the potential candidate genes and signaling pathways related to mammary gland development.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Emanuela Iovino, Luca Scapoli, Annalisa Palmieri, Rossella Sgarzani, Nayereh Nouri, Agnese Pellati, Francesco Carinci, Marco Seri, Tommaso Pippucci, Marcella Martinelli
Summary: In this study, whole exome sequencing data was used to explore the role of ultra-rare variants in non-syndromic cleft palate (nsCPO), a complex congenital disease. The analysis revealed an enrichment of ultra-rare variants in genes related to cytoskeletal protein binding, protein-containing complex binding, cell adhesion molecule binding, ECM-receptor interaction, and Integrin signaling pathways. Two genes implicated in nsCPO, COL2A1 and GLI3, were found to have significant overlap with the ultra-rare variant collapsing analysis. These findings provide insights into the pathobiology of nsCPO and potential candidate genes for the disease risk.
Article
Biochemistry & Molecular Biology
Yajie Liu, Pengzheng Chen, Wenshuo Li, Xinchun Liu, Guowu Yu, Hui Zhao, Shuhua Zeng, Mao Li, Genlou Sun, Zongyun Feng
Summary: Black barley seeds are a health-beneficial diet resource due to their special chemical composition and antioxidant properties. This study identified candidate genes for black pigmentation in barley through targeted metabolomics and conjunctive analyses of BSA-seq and BSR-seq. The results suggested that these candidate genes may regulate melanogenesis by manipulating the biosynthesis of black pigment precursors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Man Zhang, Qingqing Yang, Xi Yuan, Xiaolan Yan, Jia Wang, Tangren Cheng, Qixiang Zhang
Summary: Our study identified 1,445 candidate genes consistently linked with flowering time across multiple years through genome-wide association studies on 235 Prunus mume landraces. Transcriptome analysis revealed 617 genes differentially expressed during the flowering process, and co-expression network analysis identified 191 gene candidates with conserved transcriptional patterns during blooming across cultivars. Our findings will contribute to a greater understanding of flowering time control in woody perennials and facilitate molecular breeding of novel Prunus mume varieties.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Shikha Roy, Dinesh Gupta
Summary: In this study, we developed the DriverFuse package to integrate orthogonal data types and analyze fusion genes in cancer. The analysis of different datasets validated the usefulness of this package in identifying driver fusion genes and gaining insights into disease driver events.
Article
Biotechnology & Applied Microbiology
Ke Wang, Xinfeng Liu, Tang Qi, Yiqing Hui, Hailong Yan, Lei Qu, Xianyong Lan, Chuanying Pan
Summary: By managing goats and analyzing genes, candidate genes related to prolificacy were identified. The study revealed that some genes are significantly associated with fecundity, providing reference and assistance for artificial breeding of goats.