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Large‑scale transcriptomic and genomic analyses reveal a novel functional gene SERPINB6 for chicken carcass traits

Journal of Animal Science and Biotechnology 2024年第4期15卷 1466-1481页

作者： Di Zhao Ranran Liu Xiaodong Tan Huimin Kang Jie Wang Zheng Ma Haiquan Zhao Hai Xiang Zhengfen Zhang Hua Li Guiping Zhao Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding School of Life Science and EngineeringFoshan UniversityFoshanChina State Key Laboratory of Animal Biotech Breeding Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijingChina Guangdong Tinoo’s Foods Group Co. Ltd.QingyuanChina

Background Carcass traits are crucial indicators of meat production ***,the molecular regulatory mechanisms associated with these traits remain *** In this study,we conducted comprehensive transcriptomic and genomic analyses on 399 Tiannong partridge chickens to identify key genes and variants associated with carcass traits and to elucidate the underlying regulatory *** on association analyses with the elastic net(EN)model,we identified 12 candidate genes(AMY1A,AP3B2,CEBPG,EEF2,EIF4EBP1,FGFR1,FOXD3,GOLM1,LOC107052698,PABPC1,SERPINB6 and TBC1D16)for 4 carcass-related traits,namely live weight,dressed weight,eviscerated weight,and breast muscle ***6 was identified as the only overlapping gene by 3 analyses,EN model analysis,weighted gene co-expression network analysis and differential expression ***-level experiments confirmed that SERPINB6 promotes the proliferation of chicken DF1 cells and primary *** expression genome-wide association study and association analysis indicated that rs317934171 is the critical site that enhances SERPINB6 ***,a dual-luciferase reporter assay proved that gga-miR-1615 targets the 3′UTR of *** Collectively,our findings reveal that SERPINB6 serves as a novel gene for chicken carcass traits by promoting fibroblast and myoblast ***,the downstream variant rs317934171 regulates SERPINB6 *** results identify a new target gene and molecular marker for the molecular mechanisms of chicken carcass traits.

关键词： Carcass traits Chicken Genome SERPINB6 Transcriptome

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Engineering high amylose and resistant starch in maize by CRISPR/Cas9-mediated editing of starch branching enzymes

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The Crop Journal 2024年第4期12卷 1252-1258页

作者： Mingzheng Ma Shanqiu Sun Jinjie Zhu Xiantao Qi Gaoke Li Jianguang Hu Chuanxiao Xie Changlin Liu State Key Laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Hainan Yazhou Bay Seed Lab Sanya 572024HainanChina Anhui Agricultural University Hefei 230036AnhuiChina Crops research Institute Guangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina

To improve the amylose content(AC)and resistant starch content(RSC)of maize kernel starch,we employed the CRISPR/Cas9 system to create mutants of starch branching enzyme I(SBEI)and starch branching enzyme IIb(SBEIIb).A frameshift mutation in SBEI(E1,a nucleotide insertion in exon 6)led to plants with higher RSC(1.07%),lower hundred-kernel weight(HKW,24.71±0.14 g),and lower plant height(PH,218.50±9.42 cm)compared to the wild type(WT).Like the WT,E1 kernel starch had irregular,polygonal shapes with sharp edges.A frameshift mutation in SBEIIb(E2,a four-nucleotide deletion in exon 8)led to higher AC(53.48%)and higher RSC(26.93%)than that for the WT.E2 kernel starch was significantly different from the WT regarding granule morphology,chain length distribution pattern,X-ray diffraction pattern,and thermal characteristics;the starch granules were more irregular in shape and comprised typical B-type *** SBEI and SBEIIb(E12)had a synergistic effect on RSC,HKW,PH,starch properties,and starch biosynthesis-associated gene ***,SS1,SSIIa,SSIIIa,and SSIIIb were upregulated in E12 endosperm compared to WT *** study lays the foundation for rapidly improving the starch properties of elite maize lines.

关键词： Maize Gene editing Starch branching enzyme I Starch branching enzyme IIb

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Dynamic transcriptome profiles and novel markers in bovine spermatogenesis revealed by single-cell sequencing

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Journal of Integrative agriculture 2024年第7期23卷 2362-2378页

作者： Yuan Gao Fuxia Bai Qi Zhang Xiaoya An Zhaofei Wang Chuzhao Lei Ruihua Dang Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China College of Life Sciences Northwestern Polytechnical UniversityXi’an 710072China

Testicular development is an important biological process in male and requires interaction between the male germ cells and somatic ***,the mechanisms of testicular development in livestock,particularly in cattle,are poorly ***,cellular heterogeneity hinders the profiling of different cell types at different developmental *** this study,we first performed a single-cell transcriptomic study of the bovine testis development during puberty by using 10×genomics single-cell RNA sequencing(scRNA-seq).By collecting the scRNA-seq data from 11,083 cells from prepubertal and pubertal bovine testes,a high-resolution scRNA-seq atlas was described,identifying 9 somatic and 13 spermatogenic *** also distinguished several stage-specific marker genes for bovine germ cells and somatic cells,such as GRAF2 and MORC1 for SSC(spermatogonial stem cells),HJURP and TCF19 for differentiating spermatogonia,ARSE for immature Sertoli,CLEC12B for mature Sertoli,LOC112441470 for *** conclusion,we have examined the transcription levels and constructed the single-cell developmental maps of germ cells and somatic cells during testicular development in Angus *** datasets provided new insights into spermatogenesis and testicular somatic cell development in cattle.

关键词： scRNA-seq cattle spermatogenesis testis development

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Amino acids in piglet diarrhea:Effects,mechanisms and insights

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Animal Nutrition 2024年第1期16卷 267-274页

作者： Xihong Zhou Jing Liang Xia Xiong Yulong Yin Key Laboratory of Agro-ecological Processes in Subtropical Region Institute of Subtropical AgricultureThe Chinese Academy of SciencesChangsha 410125China College of Advanced Agricultural Sciences University of Chinese Academy of SciencesBeijing 100049China

Piglet diarrhea is among one of the most serious health problems faced by the pig industry,resulting in significant economic *** disease in piglets has a multifactorial etiology that is affected by physiology,environment,and management *** is the most apparent symptom of intestinal *** a key class of essential nutrients in the piglet diet,amino acids confer a variety of beneficial effects on piglets in addition to being used as a substrate for protein synthesis,including maintaining appropriate intestinal integrity,permeability and epithelial renewal,and alleviating morphological damage and inflammatory and oxidative ***,provision of appropriate levels of amino acids could alleviate piglet *** amino acid effects are mediated by metabolites,gut microbes,and related signaling *** this review,we summarize the current understanding of dietary amino acid effects on gut health and diarrhea incidence in piglets,and reveal the mechanisms *** also provide ideas for using amino acid blends and emphasize the importance of amino acid balance in the diet to prevent diarrhea in piglets.

关键词： Piglet Amino acid Diarrhea Gut microbe Immune

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Fine mapping of two recessive genes TaFLA1 and TaSPL8 controlling flag leaf angle in bread wheat

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The Crop Journal 2024年第4期12卷 1159-1167页

作者： Qiushi Wang Jiaxing Bai Hongchun Xiong Yongdun Xie Chaojie Wang Jiayu Gu Linshu Zhao Huiyuan Li Jinfeng Zhang Shirong Zhao Yuping Ding Zhengwu Fang Huijun Guo Luxiang Liu College of agriculture Yangtze University/MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River(Co-Construction by Ministry and Province)Jingzhou 434000HubeiChina State Key Laboratory of Crop Gene Resources and Breeding/National Engineering Laboratory of Crop Molecular Breeding/CAEA research and Development Centre on Nuclear Technology Applications for Irradiation Mutation Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Flag leaf angle is one of the key target traits in high yield wheat breeding.A smaller flag leaf angle reduces shading and enables plants to grow at a higher density,which increases *** we identified a mutant,je0407,with an 84.34%-89.35%smaller flag leaf angle compared with the wild *** mutant also had an abnormal lamina joint and no ligule or *** analysis indicated that the ligule was controlled by two recessive genes,which were mapped to chromosomes 2AS and *** mutant allele on chromosome 2AS was named Tafla1b,and it was fine mapped to a 1 Mb physical *** mutant allele on chr.2DL was identified as Taspl8b,a novel allele of TaSPL8 with a missense mutation in the second exon,which was used to develop a cleaved amplified polymorphic sequence marker.F3 and F4 lines derived from crosses between Jing411 and je0407 were genotyped to investigate interactions between the Tafla1b and Taspl8b *** with the Tafla1b/Taspl8a genotype had 58.41%-82.76%smaller flag leaf angles,6.4%-24.9%shorter spikes,and a greater spikelet density(0.382 more spikelets per cm)compared with the wild *** with the Tafla1a/Taspl8b genotype had 52.62%-82.24%smaller flag leaf angles and no differences in plant height or spikelet density compared with the wild ***1b/Taspl8b plants produced erect leaves with an abnormal lamina *** two alleles had dosage effects on ligule formation and flag leaf angle,but no significant effect on thousand-grain *** mutant alleles provide novel resources for improvement of wheat plant architecture.

关键词： Wheat Ligule Flag leaf angle Fine mapping Tafla1 Taspl8

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Patterns of crop-specific fertilizer-nitrogen losses and opportunities for sustainable mitigation:A quantitative overview of 15N-tracing studies

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Soil Ecology Letters 2024年第2期6卷 71-81页

作者： Cong Xu Hanshen Zhu Haokuang Liu Cheng Ji Jie Yuan Guanlin Li Jidong Wang Yongchun Zhang National Agricultural Experimental Station for Agricultural Environment LuheInstitute of Agricultural Resources and EnvironmentJiangsu Academy of Agricultural SciencesNanjing210014China School of the Environment and Safety Engineering Jiangsu UniversityZhenjiang212013China

Pattern and mitigation potential of crop-specific fertilizer-N losses were *** showed high fertilizer-N losses due to high N application rates and low ***,SOC,and soil pH are key parameters affecting fertilizer-N *** a given application rate,soils with higher SOC have lower fertilizer-N *** N rate combined with SOC improvement could cut 34.8%-59.6%of N losses.

关键词： fertilizer-nitrogen loss crop-specific 15N tracing soil organic carbon meta-analysis

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Science china(Life Sciences) 2024年第9期67卷 1970-1988页

作者： Jiayi Yu Changbing Zheng Qiuping Guo Yulong Yin Yehui Duan Fengna Li CAS Key Laboratory of Agro-ecological Processes in Subtropical Region Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic ProcessNational Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry ProductionInstitute of Subtropical AgricultureChinese Academy of SciencesChangsha 410125China University of Chinese Academy of Sciences Beijing 100049China College of Animal Science and Technology Hunan Agricultural UniversityChangsha 410128China

We previously demonstrated that lipopolysaccharide(LPS)injection-induced immune stress could impair muscle growth in weaned piglets,but the precise mechanisms behind this remain ***,we found that chronic immune stress induced by LPS resulted in a significant reduction of 36.86%in the total muscle mass of piglets at 5 d post-treatment compared with the control *** 1 d,prior to muscle mass loss,multiple alterations were noted in response to LPS *** included a reduction in the abundance of Bacteroidetes,an increase in serum concentrations of pro-inflammatory cytokines,compromised mitochondrial morphology,and an upregulation in the expression of dynamin-related protein 1(Drp1),a critical protein involved in mitochondrial *** highlight a strong negative correlation between Bacteroidetes abundance and the levels of serum pro-inflammatory cytokines,corroborated by in vivo intervention strategies in the musculature of both pig and mouse ***,the effects of Bacteroidetes on inflammation and muscle mass loss may involve the signaling pathway of the tauro-β-muricholic acid-fibroblast growth factor ***,the induction of overexpression of inflammatory cytokines,achieved without LPS treatment through oral administration of recombinant human IL-6(rh IL-6),led to increased levels of circulating cytokines,subsequently causing a decrease in muscle ***,pre-treatment with Mdivi-1,an inhibitor of Drp-1,markedly attenuated the LPS-induced elevation in reactive oxygen species levels and rescued the associated decline in muscle ***,these data indicate that LPS-induced muscle mass loss was linked to the reduction of Bacteroidetes abundance,increased inflammation,and the disruption of mitochondrial *** insights offer promising avenues for the identification of potential therapeutic targets aimed at mitigating muscle mass loss.

关键词： Bacteroidetes inflammation mitochondrial morphology muscle mass loss piglets

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Anti-skin-aging effect of fish gelatin from Cynoscion acoupa by maintaining collagen matrix homeostasis on D-galactose induced aging mice

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Food Science and Human Wellness 2024年

作者： Jianxin Tian Jingru Liao Biluan Zhong Pan Li Xiaoqian Liu Bing Du Guanzhan Fish Maw Nutrition and Security research Center， College of Food Science， South china Agricultural University Guangdong Shenzhiyuan Health Technology Co.， Ltd.

Delaying skin-aging through diet is a hot research topic in recent years， but the anti-aging effects of fish gelatin and related mechanisms are not well understood. In this study， we prepared edible fish gelatin from the swim bladder of Cynoscion acoupa using three different processing methods， namely dried (DCM)， soaked (SCM) and instanted (ICM)， to investigate its anti-aging effects and mechanisms on D-galactose induced skin aging in mice， as well as its effects on the gut microbiota. The results demonstrated that fish gelatin significantly increased water content， collagen， hyaluronic acid (HA) and hyaluronic acid (HYP) content， and skin integrity of mice skin， as well as enhanced the antioxidative ability and anti-inflammatory capacity of the skin. In terms of protein and mRNA expression levels in skin tissue， CMs treated with different treatments can up-regulate the expression of EGFR and TIMP1， down-regulating the expression of MMP1 and MMP3， and increase the expression of COL3A1 and COL1A2. CMs attenuated the D-galactose-mediated inhibition collagen expression by stimulating the TGF-β/Smad signaling pathway， thereby maintaining collagen matrix homeostasis. In addition， we revealed that CMs reversed gut micribiota by increase the abundance of intestinal flora. In conclusion， we demonstrated that CMs， especially for ICM， as an effective dietary supplement， have potential anti-aging and skin health benefits.

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Quantitative trait loci identification reveals zinc finger protein CONSTANS-LIKE 4 as the key candidate gene of stigma color in watermelon(Citrullus lanatus)

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Journal of Integrative agriculture 2024年第7期23卷 2292-2305页

作者： Shuang Pei Zexu Wu Ziqiao Ji Zheng Liu Zicheng Zhu Feishi Luan Shi Liu Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(Northeast Region) Ministry of Agriculture and RuralAffairs/College of Horticulture and Landscape ArchitectureNortheast Agricultural UniversityHarbin 150030China Institute of Rural Revitalization Science and Technology Heilongjiang Academy of Agricultural SciencesHarbin 150028China

Stigma color is a critical agronomic trait in watermelon that plays an important role in ***,there are few reports on the regulation of stigma color in *** this study,a genetic analysis of the F2 population derived from ZXG1553(P1,with orange stigma)and W1-17(P2,with yellow stigma)indicated that stigma color is a quantitative trait and the orange stigma is recessive compared with the yellow *** segregant analysis sequencing(BSA-seq)revealed a 3.75 Mb segment on chromosome 6 that is related to stigma ***,a major stable effective QTL Clqsc6.1(QTL stigma color)was detected in two years between cleaved amplified polymorphic sequencing(CAPS)markers Chr06_8338913 and Chr06_9344593 spanning a~1.01 Mb interval that harbors 51 annotated ***97C06G117020(annotated as zinc finger protein CONSTANS-LIKE 4)was identified as the best candidate gene for the stigma color trait through RNA-seq,quantitative real-time PCR(qRT-PCR),and gene structure alignment analysis among the natural watermelon *** expression level of Cla97C06G117020 in the orange stigma accession was lower than in the yellow stigma accessions with a significant difference.A nonsynonymous SNP site of the Cla97C06G117020 coding region that causes amino acid variation was related to the stigma color variation among nine watermelon accessions according to their re-sequencing *** color formation is often related to carotenoids,and we also found that the expression trend of ClCHYB(annotated asβ-carotene hydroxylase)in the carotenoid metabolic pathway was consistent with Cla97C06G117020,and it was expressed in low amounts in the orange stigma *** data indicated that Cla97C06G117020 and ClCHYB may interact to form the stigma *** study provides a theoretical basis for gene fine mapping and mechanisms for the regulation of stigma color in watermelon.

关键词： watermelon stigma color gene mapping zinc finger protein CONSTANS-LIKE 4

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Asymmetric expression of CA2 and CA13 linked to calcification in the bilateral mandibular condyles cause crossed beaks in chickens

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Journal of Integrative agriculture 2024年第7期23卷 2379-2390页

作者： Lei Shi Yanyan Sun Yunlei Li Hao Bai Jingwei Yuan Hui Ma Yuanmei Wang Panlin Wang Aixin Ni Linlin Jiang Pingzhuang Ge Shixiong Bian Yunhe Zong Jinmeng Zhao Adamu MIsa Hailai HTesfay Jilan Chen State Key Laboratory of Animal Biotech Breeding/Key Laboratory of Animal(Poultry)Genetics Breeding and Reproduction of Ministry of agriculture and Rural Affairs/Institute of Animal Sciences Chinese Academy of Agricultural SciencesBeijing 100193China College of Animal Science and Technology Hebei Agricultural UniversityBaoding 071001China Joint International research Laboratory of agriculture and Agri-Product Safety Ministry of Education/Institutes of Agricultural Science and Technology DevelopmentYangzhou UniversityYangzhou 225009China

Crossed beak is a complex mode of inheritance with prevalence ranging from 0.2 to 7.4% in at least 12 chicken strains *** reveal the intrinsic factors causing crossed beaks,genes expression patterns in bilateral mandibular condyle between affected and normal birds were characterized by RNA sequencing analysis in the present *** beak was induced by short length of unilateral mandibular ramus,and a total of 110differentially expressed genes were up-or down-regulated in the affected(short)mandibular condyle side as compared to the normal *** anhydrase 2(CA2)and Carbonic anhydrase 13(CA13)were enriched in the carbonate dehydratase activity,and high-expressed in mandibular condyle and osteoblasts(Presearch suggested that CA2 and CA13 are down-calcified in shortside mandibular condyle,and caused mandibular ramus to grow ***2 and CA13 have the critical role in crossed beaks by regulating calcification of mandibular condyle.

关键词： chicken crossed beak carbonic anhydrase calcification CA2 CA13

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