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Development of a 50K SNP Array for Japanese Flounder and Its Application in Genomic Selection for Disease Article

Qian Zhou, Ya-dong Chen, Sheng Lu, Yang Liu, Wen-teng Xu, Yang-zhen Li, Lei Wang, Na Wang, Ying-ming Yang, Song-lin Chen

Engineering 2021, Volume 7, Issue 3,   Pages 406-411 doi: 10.1016/j.eng.2020.06.017

Abstract:

Single nucleotide polymorphism (SNP) arrays are a powerful genotyping tool used in genetic researchWe developed a 50K Japanese flounder SNP array, "Yuxin No. 1," and report its utility in genomicbest linear unbiased prediction (ABLUP), suggesting good performance of the "Yuxin No. 1" SNPIn summary, we developed the "Yuxin No. 1" 50K SNP array, which provides a useful platform

Keywords： 牙鲆     单核苷酸多态性     SNP芯片     抗病性     基因组选择    

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Atomic Interface Catalytically Synthesizing SnP/CoP Hetero-Nanocrystals within Dual-Carbon Hybrids for Article

Chen Hu,Yanjie Hu,Aiping Chen,Xuezhi Duan,Hao Jiang,Chunzhong Li,

Engineering 2022, Volume 18, Issue 11,   Pages 154-160 doi: 10.1016/j.eng.2021.11.026

Abstract: Herein, an in situ catalytic phosphorization strategy is developed to synthesize SnP/CoP hetero-nanocrystalswithin reduced graphene oxide (rGO)-coated carbon frameworks, in which the SnP relative formation energyThe lithiation/delithiation mechanism is disclosed, showing that the 4.0 nm sized SnP/CoP nanocrystalsformed metallic Co of CoP at a relatively high potential accelerates the subsequent reaction kinetics of SnP

Keywords： Catalytic phosphorization     SnP     Hetero-nanocrystals     Fast charging     Li-ion batteries    

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Detection of genomic signatures for pig hairlessness using high-density SNP data

Ying SU,Yi LONG,Xinjun LIAO,Huashui AI,Zhiyan ZHANG,Bin YANG,Shijun XIAO,Jianhong TANG,Wenshui XIN,Lusheng HUANG,Jun REN,Nengshui DING

Frontiers of Agricultural Science and Engineering 2014, Volume 1, Issue 4,   Pages 307-313 doi: 10.15302/J-FASE-2014039

Abstract: conducted a genomic scan for genetically differentiated regions between hairy and hairless pigs using 60K SNP

Keywords： hairlessness     pig     selective sweeping    

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A genome-wide association study of five meat quality traits in Yorkshire pigs

Qian DONG,Huiying LIU,Xinyun LI,Wei WEI,Shuhong ZHAO,Jianhua CAO

Frontiers of Agricultural Science and Engineering 2014, Volume 1, Issue 2,   Pages 137-143 doi: 10.15302/J-FASE-2014014

Abstract: drip loss within 24 h and water-holding capacity in 231 Yorkshire barrows using illumina porcine 60k SNPThe results showed that a total of 344 single nucleotide polymorphisms (SNP) were significantly associatedIn addition, 25 haplotype blocks based on 116 SNPs were revealed with SNP combination patterns for fiveOur study added new SNP information for identification of meat quality traits in pigs and will help elucidate

Keywords： Pig     GWAS     meat quality trait     SNP    

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The genetic regulation of skeletal muscle development: insights from chicken studies

Wen LUO, Bahareldin A. ABDALLA, Qinghua NIE, Xiquan ZHANG

Frontiers of Agricultural Science and Engineering 2017, Volume 4, Issue 3,   Pages 295-304 doi: 10.15302/J-FASE-2017159

Abstract: Skeletal muscle development is a complex multi-process trait regulated by various genetic factors. The chicken embryo is an ideal model system for studying skeletal muscle development. However, only a small proportion of the genetic factors affecting skeletal muscle development have been identified in chicken. The aim of this review is to summarize recent knowledge about the genetic factors involved in the regulation of skeletal muscle development in the chicken, such as gene polymorphisms, epigenetic modification, noncoding RNAs and transcription factors, which can influence skeletal muscle development at the genome, epigenome, transcriptome and proteome levels. Research on the regulation of skeletal muscle development in chicken is not yet comprehensive and most of the candidate genes and single nucleotide polymorphisms related to chicken muscle growth remain to be verified in experimental studies. In addition, the data derived from transcriptome sequencing and genome-wide association studies still require further investigation and analysis and comprehensive studies on the regulation of chicken skeletal muscle development will continue as a major research focus.

Keywords： chicken     epigenetic modification     miRNAs     skeletal muscle development     SNP     transcription factor    

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The microRNA, miR-29c, participates in muscle development through targeting the

Weiya ZHANG,Wei WEI,Yuanyuan ZHAO,Shuhong ZHAO,Xinyun LI

Frontiers of Agricultural Science and Engineering 2015, Volume 2, Issue 4,   Pages 311-317 doi: 10.15302/J-FASE-2015075

Abstract: Previous studies indicated that miR-29c is important for muscle development in mice and human, but its role in pigs is unknown. In this study, we detected the expression of miR-29c in Meishan longissimus lumborum (LL) muscle. The results showed that miR-29c was gradually upregulated during development of skeletal muscle in pig. Moreover, the expression of and genes, which were confirmed to be targeted by miR-29c in mice, was decreased along with muscle development. Furthermore, the expression level of miR-29c was significantly higher in adult Meishan pigs than Large White pigs, while the expression of and genes was significantly lower in Meishan pigs. These results indicated that the expression pattern of miR-29c was opposite to that of and genes in pigs. Also, the luciferase assay indicated that miR-29s can target the gene in pigs. In addition, we identified a T to C mutation in the primary transcript of miR-29c, which was associated with the postmortem muscle pH in pigs. Based on these results, we concluded that miR-29c is also important in skeletal muscle development of pigs.

Keywords： pig     miR-29c     skeletal muscle     expression     SNP    

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Genome-wide association study of the backfat thickness trait in two pig populations

Dandan ZHU,Xiaolei LIU,Rothschild MAX,Zhiwu ZHANG,Shuhong ZHAO,Bin FAN

Frontiers of Agricultural Science and Engineering 2014, Volume 1, Issue 2,   Pages 91-95 doi: 10.15302/J-FASE-2014005

Abstract: identified in two independent pig populations, using a genome-wide association study of porcine 60K SNPFor each population, 30 most significant single-nucleotide polymorphisms (SNPs) were selected and SNPThe most significant SNP (ALGA0006623) was located on SSC1, upstream of the gene.

Keywords： backfat thickness     SNP chip     genome-wide association study     compressed mixed linear model     pig    

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UNREDUCED MEGAGAMETOPHYTE FORMATION VIA SECOND DIVISION RESTITUTION CONTRIBUTES TO TETRAPLOID PRODUCTION IN INTERPLOIDY CROSSES WITH ‘ORAH’ MANDARIN (CITRUS RETICULATA)

Frontiers of Agricultural Science and Engineering 2021, Volume 8, Issue 2,

Abstract: By analyzing their genetic origins using nine novel single nucleotide polymorphism (SNP) markers, allThese tetraploid plantlets were genotyped using eight pericentromeric SNP markers and nine centromeredistal SNP markers.Based on the genotypes of the 2n megagametophytes, the parental heterozygosity rates in 16 SNP loci and

Keywords： Citrus / 2n gamete / interploidy hybridization / pericentromeric SNP marker / second division restitution    

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UNREDUCED MEGAGAMETOPHYTE FORMATION VIA SECOND DIVISION RESTITUTION CONTRIBUTES TO TETRAPLOID PRODUCTION IN INTERPLOIDY CROSSES WITH ‘ORAH’ MANDARIN (

Qiangming XIA, Wei WANG, Kaidong XIE, Xiaomeng WU, Xiuxin DENG, Jude W. GROSSER, Wenwu GUO

Frontiers of Agricultural Science and Engineering   Pages 302-313 doi: 10.15302/J-FASE-2021385

Abstract: By analyzing their genetic origins using nine novel single nucleotide polymorphism (SNP) markers, allThese tetraploid plantlets were genotyped using eight pericentromeric SNP markers and nine centromeredistal SNP markers.Based on the genotypes of the 2n megagametophytes, the parental heterozygosity rates in 16 SNP loci and

Keywords： Citrus     2n gamete     interploidy hybridization     pericentromeric SNP marker     second division restitution    

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Study on the molecular characteristic in phlegm-dampness constitution

Wang Qi,Dong Jing,Wu Hongdong,Wang Dongpo,Yao Shilin,Ren Xiaojuan

Strategic Study of CAE 2008, Volume 10, Issue 7,   Pages 100-103

Abstract: results of prophase, sieve the related gene and characteristics of single nucleotide polymorphisms( SNP

Keywords： phlegm-dampness constitution     Genechip Mapping Array     Molecular characteristic    

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A systematic survey of LU domain-containing proteins reveals a novel human gene, LY6A, which encodes the candidate ortholog of mouse Ly-6A/Sca-1 and is aberrantly expressed in pituitary tumors

Frontiers of Medicine 2023, Volume 17, Issue 3,   Pages 458-475 doi: 10.1007/s11684-022-0968-4

Abstract: The Ly-6 and uPAR (LU) domain-containing proteins represent a large family of cell-surface markers. In particular, mouse Ly-6A/Sca-1 is a widely used marker for various stem cells; however, its human ortholog is missing. In this study, based on a systematic survey and comparative genomic study of mouse and human LU domain-containing proteins, we identified a previously unannotated human gene encoding the candidate ortholog of mouse Ly-6A/Sca-1. This gene, hereby named LY6A, reversely overlaps with a lncRNA gene in the majority of exonic sequences. We found that LY6A is aberrantly expressed in pituitary tumors, but not in normal pituitary tissues, and may contribute to tumorigenesis. Similar to mouse Ly-6A/Sca-1, human LY6A is also upregulated by interferon, suggesting a conserved transcriptional regulatory mechanism between humans and mice. We cloned the full-length LY6A cDNA, whose encoded protein sequence, domain architecture, and exon‒intron structures are all well conserved with mouse Ly-6A/Sca-1. Ectopic expression of the LY6A protein in cells demonstrates that it acts the same as mouse Ly-6A/Sca-1 in their processing and glycosylphosphatidylinositol anchoring to the cell membrane. Collectively, these studies unveil a novel human gene encoding a candidate biomarker and provide an interesting model gene for studying gene regulatory and evolutionary mechanisms.

Keywords： domain-containing protein family     novel human gene     LY6A     pituitary tumor     biomarker     nonsynonymous SNP    

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Title Author Date Type Operation

Development of a 50K SNP Array for Japanese Flounder and Its Application in Genomic Selection for Disease

Qian Zhou, Ya-dong Chen, Sheng Lu, Yang Liu, Wen-teng Xu, Yang-zhen Li, Lei Wang, Na Wang, Ying-ming Yang, Song-lin Chen

Journal Article

Atomic Interface Catalytically Synthesizing SnP/CoP Hetero-Nanocrystals within Dual-Carbon Hybrids for

Chen Hu,Yanjie Hu,Aiping Chen,Xuezhi Duan,Hao Jiang,Chunzhong Li,

Journal Article

Detection of genomic signatures for pig hairlessness using high-density SNP data

Ying SU,Yi LONG,Xinjun LIAO,Huashui AI,Zhiyan ZHANG,Bin YANG,Shijun XIAO,Jianhong TANG,Wenshui XIN,Lusheng HUANG,Jun REN,Nengshui DING

Journal Article

A genome-wide association study of five meat quality traits in Yorkshire pigs

Qian DONG,Huiying LIU,Xinyun LI,Wei WEI,Shuhong ZHAO,Jianhua CAO

Journal Article

The genetic regulation of skeletal muscle development: insights from chicken studies

Wen LUO, Bahareldin A. ABDALLA, Qinghua NIE, Xiquan ZHANG

Journal Article

The microRNA, miR-29c, participates in muscle development through targeting the

Weiya ZHANG,Wei WEI,Yuanyuan ZHAO,Shuhong ZHAO,Xinyun LI

Journal Article

Genome-wide association study of the backfat thickness trait in two pig populations

Dandan ZHU,Xiaolei LIU,Rothschild MAX,Zhiwu ZHANG,Shuhong ZHAO,Bin FAN

Journal Article

UNREDUCED MEGAGAMETOPHYTE FORMATION VIA SECOND DIVISION RESTITUTION CONTRIBUTES TO TETRAPLOID PRODUCTION IN INTERPLOIDY CROSSES WITH ‘ORAH’ MANDARIN (CITRUS RETICULATA)

Journal Article

UNREDUCED MEGAGAMETOPHYTE FORMATION VIA SECOND DIVISION RESTITUTION CONTRIBUTES TO TETRAPLOID PRODUCTION IN INTERPLOIDY CROSSES WITH ‘ORAH’ MANDARIN (

Qiangming XIA, Wei WANG, Kaidong XIE, Xiaomeng WU, Xiuxin DENG, Jude W. GROSSER, Wenwu GUO

Journal Article

Study on the molecular characteristic in phlegm-dampness constitution

Wang Qi,Dong Jing,Wu Hongdong,Wang Dongpo,Yao Shilin,Ren Xiaojuan

Journal Article

A systematic survey of LU domain-containing proteins reveals a novel human gene, LY6A, which encodes the candidate ortholog of mouse Ly-6A/Sca-1 and is aberrantly expressed in pituitary tumors

Journal Article