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Journal of Forestry Research 2022年第5期33卷 1593-1606页

作者： Zhongye Liu Wei Li Zhiru Xu Huihui Zhang Guangyu Sun Heng Zhang Chuanping Yang Guanjun Liu State Key Laboratory of Tree Genetics and Breeding Northeast Forestry UniversityHarbin 150040People’s Republic of China College of Life Science Northeast Forestry UniversityHarbin 150040People’s Republic of China

Numerous growth and physiological variables of 3-week-old Populus simonii × *** seedlings were assessed after treatment with either nitrate nitrogen(NO_(3)^(−)--N)(0.1,0.5,1,5,or 10 mmol·L^(−1)) or ammonium nitrogen(NH_(4)^(+)+-N)(0.1,0.5,1,5,or 10 mmol·L^(−1)) to determine the best nitrogen form and concentration to optimize growth,biomass allocation,pigment content,and photosynthetic *** results of combining membership function and an evaluation index suggested that,5 mmol·L^(−1) nitrogen,regardless of the form,yielded the highest comprehensive evaluation index and good *** addition,a Pearson correlation analysis and network visualization revealed that the total mass,shoot mass,root mass,leaf dry mass,plant height,leaf area,chlorophyll a and total chlorophyll had a physiological index connectivity degree≥15 for both nitrogen *** photosynthetic rate,stomatal conductance,transpiration rate,maximum photochemical efficiency of PSII,total nitrogen content,ground diameter,chlorophyll b,and carotenoid were unique indices for evaluating NH_(4)^(+)+-N-based nutrition,which could provide a theoretical basis for evaluating the effects of nitrogen fertilizer on seedlings,cultivation periods,and stress tolerance in ***× ***.

关键词： Nitrogen form Nitrogen concentration growth traits Physiological characteristics

Chicken chromatin accessibility atlas accelerates epigenetic annotation of birds and gene fine-mapping associated with growth traits

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Zoological Research 2023年第1期44卷 53-62页

作者： Xiao-Ning Zhu Yu-Zhe Wang Chong Li Han-Yu Wu Ran Zhang Xiao-Xiang Hu State Key Laboratory of Agrobiotechnology College of Biological SciencesChina Agricultural UniversityBeijing 100193China National Research Facility for Phenotypic and Genotypic Analysis of Model Animals(Beijing) China Agricultural UniversityBeijing 100193China

The development of epigenetic maps, such as the ENCODE project in humans, provides resources for gene regulation studies and a reference for research of disease-related regulatory elements. However,epigenetic information, such as a bird-specific chromatin accessibility atlas, is currently lacking for the thousands of bird species currently *** major genomic difference between birds and mammals is their shorter introns and intergenic distances, which seriously hinders the use of humans and mice as a reference for studying the function of important regulatory regions in birds. In this study, using chicken as a model bird species, we systematically compiled a chicken chromatin accessibility atlas using 53 Assay of Transposase Accessible Chromatin sequencing(ATAC-seq)samples across 11 tissues. An average of 50 ?796open chromatin regions were identified per sample,cumulatively accounting for 20.36% of the chicken genome. Tissue specificity was largely reflected by differences in intergenic and intronic peaks, with specific functional regulation achieved by two mechanisms: recruitment of several sequence-specific transcription factors and direct regulation of adjacent functional genes. By integrating data from genome-wide association studies, our results suggest that chicken body weight is driven by different regulatory variants active in growth-relevant tissues. We propose CAB39L(active in the duodenum), RCBTB1(muscle and liver), and novel long non-coding RNA ENSGALG00000053256(bone) as candidate genes regulating chicken body weight. Overall, this study demonstrates the value of epigenetic data in fine-mapping functional variants and provides a compendium of resources for further research on the epigenetics and evolution of birds and mammals.

关键词： Chicken Chromatin accessibility atlas ATAC-seq Tissue-specific OCRs GWAS growth traits

Predictive ability of genomic selection models for breeding value estimation on growth traits of Pacific white shrimp Litopenaeus vannamei

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Chinese Journal of Oceanology and Limnology 2017年第5期35卷 1221-1229页

作者：王全超于洋李富花张晓军相建海 Key Laboratory of Experimental Marine Biology Institute of Oceanology Chinese Academy of Sciences Qingdao 266071 China University of Chinese Academy of Sciences Beijing 100049 China Qingdao National Laboratory for Marine Science and Technology Qingdao 266071 China

Genomic selection(GS)can be used to accelerate genetic improvement by shortening the selection *** successful application of GS depends largely on the accuracy of the prediction of genomic estimated breeding value(GEBV).This study is a fi rst attempt to understand the practicality of GS in Litopenaeus vannamei and aims to evaluate models for GS on growth *** performance of GS models in *** was evaluated in a population consisting of 205 individuals,which were genotyped for 6 359 single nucleotide polymorphism(SNP)markers by specifi c length amplifi ed fragment sequencing(SLAF-seq)and phenotyped for body length and body *** GS models(RR-BLUP,Bayes A,and Bayesian LASSO)were used to obtain the GEBV,and their predictive ability was assessed by the reliability of the GEBV and the bias of the predicted *** mean reliability of the GEBVs for body length and body weight predicted by the dif ferent models was 0.296 and 0.411,*** each trait,the performances of the three models were very similar to each other with respect to *** regression coeffi cients estimated by the three models were close to one,suggesting near to zero bias for the ***,when GS was applied in a *** population for the studied scenarios,all three models appeared *** analyses suggested that improved estimation of the genomic prediction could be realized by increasing the size of the training population as well as the density of SNPs.

关键词： genomic selection model prediction growth traits penaeid shrimp

A genome-wide association study on growth traits in orangespotted grouper(Epinephelus coioides) with RAD-seq genotyping

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Science China(Life Sciences) 2018年第8期61卷 934-946页

作者： Hui Yu Xinxin You Jia Li Xinhui Zhang Shuai Zhang Shoujia Jiang Xueqiang Lin Hao-Ran Lin Zining Meng Qiong Shi BGI Education Center University of Chinese Academy of Sciences Shenzhen Key Lab of Marine Genomics Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals BGI Academy of Marine SciencesBGI Marine BGI State Key Laboratory of Biocontrol Institute of Aquatic Economic Animals and the Guangdong Province Key Laboratory for Aquatic Economic Animals Sun Yat-Sen University Laboratory of Aquatic Genomics College of Life Sciences and Oceanography Shenzhen University

The orange-spotted grouper, Epinephelus coioides, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a genome-wide association study （GWAS） on a natural population of 198 individuals aiming to screen the whole genome of orange-spotted grouper for identification of growth-related loci by restriction-site associated DNA sequencing. In this research, 261,366 single nucleotide polymorphisms （SNPs） were developed, in which 110 SNPs were identified to be correlated with growth and 20 SNPs were further confirmed to be associated with both body weight and total length. From these identified SNPs, we annotated a total of 34 genes, including adgrb2, csnkzal, cers5, co122al, creb5, dndl, dzankl, dnail, npy2r, fat3, lrrk2, lrp5, map3k9, and so on. Among these candidate genes, npy2r （neuropeptide Y receptor Y2） was reported to play a critical role in growth of the orange-spotted grouper. In addition, population structure, principal component analysis, kinship matrix and linkage disequilibrium were examined to verify the accuracy and reliability of our GWAS results. Our data will also provide a valuable genetic resource for further marker-assisted selection program to improve growth quality in groupers.

关键词： orange-spotted grouper genome-wide association study (GWAS) restriction-site associated DNA sequencing (RAD-scq) growth traits npy2r

G×E Analysis of growth traits of Betula platyphylla Clones at Three Separated Sites in Northeastern China

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Phyton-International Journal of Experimental Botany 2022年第9期91卷 2055-2068页

作者： Yuxi Li Xinxin Zhang Qinhui Zhang Luping Jiang Rui Han Siqi Sun Xiaoqing Hu Xiaona Pei Chunli Zhao Xiyang Zhao College of Forestry and Grassland Jilin Agricultural UniversityChangchun130118China State Key Laboratory of Tree Genetics and Breeding Northeast Forestry UniversityHarbin150040China

To select elite materials,the growth traits of 32 Betula platyphylla clones at three separated northern sites in Northeast China were investigated and *** results showed that there were significant differences among all variation sources in the different investigated traits(Ptraits were higher than 10%.The repeatability of different traits ranged from 0.760 to *** analysis showed that tree height were significantly correlated with diameter at breast height,but neither was significantly correlated with leaf traits nor element *** main effects and multiplicative interaction analysis showed that genotype,environment and genotype×environment interactions were significantly different in diameter at breast height,which indicated that environment had a significant effect on *** assessment results showed that three clones with high and stable diameters at breast height were selected,and the genetic gains of diameter at breast height on sites Maoershan,Qingan,and Yongji were 21.24%,20.58%,and 38.65%,*** results could provide a theoretical basis for elite clone selection in *** and other broad leaved species.

关键词： Betula platyphylla growth traits genetic variation AMMI stability

Polymorphisms in the Myostatin-1 gene and their association with growth traits in Ancherythroculter nigrocauda

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Chinese Journal of Oceanology and Limnology 2017年第3期35卷 597-602页

作者：孙艳红李清王贵英祝东梅陈见李佩童金苟 Wuhan Aquaculture Science Research Institute Wuhan 430207China State Key Laboratory of Freshwater Ecology and Biotechnology Institute of HydrobiologyChinese Academy of SciencesWuhan 430072China

Myostatin （MSTN） is a member of the transforming growth factor-β gene superfamily that negatively regulates skeletal muscle development and growth. In the present study, partial genomic fragments of Myostatin-1 （MSTN-1） in two commercial hatchery populations of Ancherythroculter nigrocauda, an economically important freshwater fish, were screened for single nucleotide polymorphisms （SNPs） and then genotyped by direct sequencing of PCR products. Five SNPs were identified in intron 1 and exon 2, including a non-synonymous mutation causing an amino acid change （Val to Ile） at position 180. Association analyses based on 300 individuals revealed that the g. 1129T〉C SNP locus was significantly associated with total length （TL）, body length （BL）, body height （BH） and body weight （BW） in 6- and 18-month-old populations, while the g. 1289G〉A locus was significantly associated with BH and BW in the 6-month-old population. Haplotype analyses revealed that fish with the genotype combinations TC/TC or TC/GA showed better growth performance. Our results suggest that g.l129T〉C and g.1289G〉A have positive effects on growth traits and may be candidate gene markers for marker-assisted selection in A. nigrocauda.

关键词： Myostatin-1 (MSTN-1) single nucleotide polymorphisms (SNPs) Ancherythroculter nigrocauda growth traits association analysis

Genetic parameter estimates for growth traits at early stage of Pacific abalone,Haliotis discus hannai Ino

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Acta Oceanologica Sinica 2007年第5期26卷 90-95页

作者： DENG Yuewen LIU Xiao ZHANG Guofan ZHAO Hongen Institute of Oceanology Chinese Academy of Sciences Qingdao 266071 China Fisheries College Guangdong Ocean University Zhanjiang 524025 China Dalian Institute of Fisheries Dalian 116013 China

Heritability and genetic and phenotypic correlations were estimated for juvenile growth traits of Pacific abalone Haliotis discus hannai Ino. The estimates were calculated from shell length and shell width measurements on progeny resulting from 12 half-sib families and 36 full-sib families obtained using artificial fertilization of mating three females to each male. The measurements were taken at 10, 20 and 30 d after fertilization. It was found that heritability estimates based on sire component ranged from 0.23 to 0.36 for shell length and 0.21 to 0.32 for shell width. Heritability estimates from dam component were larger than those from sire component at three ages, indicating presence of maternal effects, non-additive genetic effects and common environmental effects. Phenotypic correlations were significant at three ages （P 〈 0.05）, with values of 0.92, 0.93 and 0.92, respectively. Genetic correlations from the paternal half-sib correlation analysis were highly positive at three ages, with values of 0.50, 0.78 and 0.81, respectively. The results suggest that selective breeding is an effective approach to improving growth traits of Pacific abalone stocks.

关键词： Haliotis discus hannai Ino growth traits heritability genetic correlations

Polymorphisms in the FOXO gene are associated with growth traits in the Sanmen breeding population of the razor clam Sinonovacula constricta

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Aquaculture and Fisheries 2018年第5期3卷 177-183页

作者： Shumei Xie Donghong Niu Kanyun Wei Zhiguo Dong Jiale Li Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Ministry of EducationShanghai Ocean UniversityShanghai201306China National Demonstration Center for Experimental Fisheries Science Education Shanghai Ocean UniversityShanghai201306China Shanghai Engineering Research Center of Aquaculture Shanghai201306China Co-Innovation Center of Jiangsu Marine Bio-industry Technology Lianyungang222001China

We identified the FOXO gene and five single-nucleotide polymorphisms(SNPs)in its coding region in the Sanmen breeding population of the razor clam Sinonovacula *** ScFOXO gene encodes a protein of 625 amino acids in length that contains a conserved DNA-binding ***-time polymerase chain reaction analysis showed that ScFOXO mRNA is widely expressed in adult tissues,with higher expression in the siphons and *** the SNPs,c.879G>C(Val293Val)and c.1725A>G(Ser575Ser)are synonymous mutations,and c.543C>T(Phe181Leu),c.848A>G(Tyr283Cys),and c.1625G>C(Gly542Phe)are non-synonymous *** SNPs all show significant associations with total body weight,shell length,shell width,and shell height(SH)in this *** parameter analysis showed that all SNPs except c.848A>G(Tyr283Cys)exhibit complete *** SNP c.1625G>C(Gly542Phe)was used for genetic linkage mapping and demonstrates the strongest linkage(logarithm of the odds[LOD]value:41.46)with the marker 96616(37.02 cM)in the linkage group *** LOD value of this marker in relation to growth traits ranges from 1.04 to 1.53;only markers with a LOD value3 were considered to be linked with growth traits in the razor clam linkage *** summary,ScFOXO may be a growth trait-related gene and may represent a marker for Sanmen breeding group selection.

关键词： Sinonovacula constricta Single-nucleotide polymorphism(SNP) FOXO growth traits

Polymorphisms of the IGF1 gene and their association with growth traits, serum concentration and expression rate of IGF1 and IGF1R in buffalo

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2017年第12期18卷 1064-1074页

作者： Mohammed A.EL-MAGD Ayman A.SALEH Abeer A.NAFEAA Shymaa M.EL-KOMY Mohamed A.AFIFI Department of Anatomy&Embryology Faculty of Veterinary MedicineKafrelsheikh UniversityE1-Geish StreetKafrelsheikhEgypt Department of Animal Wealth Development Veterinary Genetics&Genetic EngineeringFaculty of Veterinary MedicineZagazig UniversityZagazigEgypt Department of Physiology Faculty of Veterinary MedicineBenha UniversityBenhaEgypt Department of Animal Production Faculty of AgricultureTanta UniversityTantaEgypt Department of Animal Wealth Development BiostatisticsFaculty of Veterinary MedicineZagazig UniversityZagazigEgypt Department of Health Management Atlantic Veterinary CollegeUniversity of Prince Edward IslandCharlottetownPE C1A 4P3Canada

The insulin-like growth factor 1（IGF1） gene is a member of the group of somatotropin axis genes that play a significant role in cell proliferation and growth of muscles. Here, we searched for polymorphisms in buffalo IGF1 and found two novel single nucleotide polymorphisms（SNPs）, G64 A and G280A, in the noncoding sequences of exon 1 and exon 4, respectively. Statistical analysis of different genotypes showed that the individuals with GG genotypes had significantly（P〈0.05） higher body weight（BW） and average daily gain（ADG） than those with other genotypes at ages of 3–6 months in G64A SNP and 6–9 months in G280A SNP. The combined genotypes of these two SNPs produced three haplotypes, GG/GG, AG/AG, and AA/AA, which were significantly associated（P〈0.0001） with BW and ADG at an age from 3 to 12 months. Buffaloes with the homozygous GG/GG haplotype showed higher growth performance than other buffaloes. The two SNPs were correlated with m RNA levels of IGF1 and IGF1 receptor（IGF1 R） in semitendinosus muscle as well as with the serum concentration level of IGF1. Also, buffaloes with GG/GG haplotype showed higher m RNA and serum concentration levels. The data revealed that these two SNPs could be valuable genetic markers for selection of Egyptian buffaloes for better performance in the population.

关键词： Insulin-like growth factor 1 (IGF1) IGFIR Single nucleotide polymorphism (SNP) growth traits Buffalo

Relationship Between Combined Genotypes of UCP Gene and growth traits in Chickens

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Journal of Northeast Agricultural University(English Edition) 2012年第2期19卷 47-53页

作者： Leng Li Li Hui Key Laboratory of Chicken Genetics and Breeding Ministry of Agriculture Northeast Agricultural University Harbin 150030 China College of Animal Science and Technology Northeast Agricultural University Harbin 150030 China

The uncoupling protein （UCP） is a member of the mitochondrial membrane transporter family, which plays an important role in energy metabolism. In the present study, the UCP gene was considered as a candidate gene for chicken growth traits, and the association of UCP gene SNPs with growth rate was investigated in the eighth generation of NEAUHLF broiler lines. Two SNPs were found in chicken UCP gene, and the association analysis results showed that both the individual and combination of chicken UCPgene SNPs were significantly associated with body weight of 7 weeks （BW7） and carcass weight （CW）（P〈0.05）, and the combination had much significant effects than the single SNP. This research suggested that the UCP gene could be a candidate gene or linked to a major gene which affected growth traits in chicken

关键词： chicken uncoupling protein gene SNPs genotype combination growth traits