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Chen Y, Zhang Q, Liu W, Xu W, Wang J, Li Z, Geng F. Research Note: Analysis of microbial diversity on the shell surface of eggs collected from geographically distinct farms in China. Poult Sci 2024; 103:103659. [PMID: 38537401 PMCID: PMC11067731 DOI: 10.1016/j.psj.2024.103659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 05/01/2024] Open
Abstract
Micro-organisms on the eggshell surface of affect the quality of the egg. Sometimes, these microbes even pose a serious threat to the health of the egg's consumer. Bacterial 16S rDNA and fungal internal transcribed spacer region were sequenced to analyze the microbial diversity on the shell surface of the eggs collected from 4 distinct regions of China: Guyuan (GY; 1.5 million hens), Langfang (LF; 0.1 million hens), Beihai (BH; 1.2 million hens), and Dongguan (DG; 0.2 million hens). The results showed a higher bacterial and fungal abundance on the eggs collected from the northern and southern China farms, respectively. The dominant bacterial phylum detected across all egg samples was Firmicutes. In addition, the shell surfaces of the DG and LF samples harbored abundant levels of Proteobacteria. The dominant fungal phyla detected across all egg samples were Ascomycota and Basidiomycota. The bacterial compositions on eggshell surfaces differed significantly across all geographic regions, and the fungal composition differed significantly between samples collected from the southern and northern farms (P < 0.05). The abundance and composition of microbial colonies on the eggshell surface varied based on their geographical location (climate and environment) and farming scale (management). Our findings provide an important reference for optimizing the cleaning and disinfection methods for fresh eggs collected from different sources.
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Affiliation(s)
- Yan Chen
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Qionglian Zhang
- Southwest University of Science and Technology, Mianyang, 621010, China; Fengji Food Group Co., Ltd., Mianyang, 621000, China
| | - Wenbing Liu
- Fengji Food Group Co., Ltd., Mianyang, 621000, China
| | - Wenlong Xu
- Fengji Food Group Co., Ltd., Mianyang, 621000, China
| | - Jinqiu Wang
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Zhihua Li
- Institute of Agro-Products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, China
| | - Fang Geng
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, China.
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Poljak I, Vidaković A, Benić L, Tumpa K, Idžojtić M, Šatović Z. Patterns of Leaf and Fruit Morphological Variation in Marginal Populations of Acer tataricum L. subsp. tataricum. PLANTS (BASEL, SWITZERLAND) 2024; 13:320. [PMID: 38276777 PMCID: PMC10818317 DOI: 10.3390/plants13020320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
Marginal populations are usually smaller and more isolated and grow in less favourable conditions than those at the distribution centre. The variability of these populations is of high importance, as it can support the adaptations needed for the conditions that they grow in. In this research, the morphological variability of eight Tatar maple (Acer tataricum L. subsp. tataricum) populations was analysed. Tatar maple is an insect-pollinated and wind-dispersed shrub/tree, whose northwestern distribution edge is in southeastern Europe. Morphometric methods were used to analyse the variability of the populations using leaf and fruit morphology. The research revealed significant differences between and within populations. Furthermore, differences in the distribution of the total variability were noted, which suggest that different evolutionarily factors affect different plant traits. Correlation analysis confirmed a weak dependency between the vegetative and generative traits. In addition, no evidence was found for the presence of isolation by environment (IBE). However, the Mantel test for isolation by distance (IBD) was significant for the leaf morphometric traits and non-significant for the fruit morphometric traits. Being the marginal leading-edge populations, they are younger and were less likely to have had time for adaptation to local environments, which would have resulted in the development of IBE. Overall, edge populations of Tatar maple were characterised by great morphological variability, which helps these populations in their response to the intensive selective pressures they face in their environment.
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Affiliation(s)
- Igor Poljak
- Institute of Forest Genetics, Dendrology and Botany, Faculty of Forestry and Wood Technology, University of Zagreb, Svetošimunska cesta 23, HR-10000 Zagreb, Croatia; (I.P.); (A.V.); (L.B.); (K.T.); (M.I.)
| | - Antonio Vidaković
- Institute of Forest Genetics, Dendrology and Botany, Faculty of Forestry and Wood Technology, University of Zagreb, Svetošimunska cesta 23, HR-10000 Zagreb, Croatia; (I.P.); (A.V.); (L.B.); (K.T.); (M.I.)
| | - Luka Benić
- Institute of Forest Genetics, Dendrology and Botany, Faculty of Forestry and Wood Technology, University of Zagreb, Svetošimunska cesta 23, HR-10000 Zagreb, Croatia; (I.P.); (A.V.); (L.B.); (K.T.); (M.I.)
| | - Katarina Tumpa
- Institute of Forest Genetics, Dendrology and Botany, Faculty of Forestry and Wood Technology, University of Zagreb, Svetošimunska cesta 23, HR-10000 Zagreb, Croatia; (I.P.); (A.V.); (L.B.); (K.T.); (M.I.)
| | - Marilena Idžojtić
- Institute of Forest Genetics, Dendrology and Botany, Faculty of Forestry and Wood Technology, University of Zagreb, Svetošimunska cesta 23, HR-10000 Zagreb, Croatia; (I.P.); (A.V.); (L.B.); (K.T.); (M.I.)
| | - Zlatko Šatović
- Department for Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
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Wu Q, Dong S, Zhao Y, Yang L, Qi X, Ren Z, Dong S, Cheng J. Genetic diversity, population genetic structure and gene flow in the rare and endangered wild plant Cypripedium macranthos revealed by genotyping-by-sequencing. BMC PLANT BIOLOGY 2023; 23:254. [PMID: 37189068 DOI: 10.1186/s12870-023-04212-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/03/2023] [Indexed: 05/17/2023]
Abstract
BACKGROUND Genetic diversity, genetic structure, and gene flow in plant populations and their influencing factors are important in conservation biology. Cypripedium macranthos is one of the few wild orchids with high ornamental value in northern China. However, over the past decade, excessive collection, trading, tourism development, habitat fragmentation, deceptive pollination, and seed germination difficulties have all caused a sharp decline in the number of C. macranthos individuals and its population. In order to propose a scientific and effective conservation strategy, the genetic diversity, genetic structure and gene flow of the current CM population are urgent scientific issues to be clarified. RESULTS Here, 99 individuals of C. macranthos from north and northeast China were analyzed to evaluate the genetic diversity, gene flow among populations, and genetic structure by genotyping-by-sequencing. More than 68.44 Gb high-quality clean reads and 41,154 SNPs were obtained. Our data based on bioinformatics methods revealed that C. macranthos has lower genetic diversity, high levels of historical gene flow, and moderate-to-high genetic differentiation between populations. The gene migration model revealed that the direction of gene flow was mainly from northeast populations to north populations in China. The results of genetic structure analysis showed that 11 C. macranthos populations can be considered as two groups, and further divided into four subgroups. Moreover, the Mantel test detected no significant "Isolation by Distance" between populations. CONCLUSIONS Our study demonstrates that the present genetic diversity and genetic structure of C. macranthos populations were mainly caused by biological characteristics, human interference, habitat fragmentation, and restricted gene flow. Finally, constructive measures, which can provide a basis for the proposal of conservation strategies, have been suggested.
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Affiliation(s)
- Qi Wu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shang Dong
- Department of Yichun, Heilongjiang Academy of Forestry, Yichun, Heilongjiang, China
| | - Yuxin Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lei Yang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiujin Qi
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhihe Ren
- Management Office of Hebei Dahaituo National Nature Reserve, Chicheng, Hebei, China
| | - Shubin Dong
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
| | - Jin Cheng
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
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Rai MK. Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects. PLANTA 2023; 257:34. [PMID: 36622439 DOI: 10.1007/s00425-023-04067-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
The present review illustrates a comprehensive overview of the start codon targeted (SCoT) polymorphism marker and their utilization in various applications related to genetic and genomic studies. Start codon targeted (SCoT) polymorphism marker, a targeted fingerprinting marker technique, has gained considerable importance in plant genetics, genomics, and molecular breeding due to its many desirable features. SCoT marker targets the region flanking the start codon, a highly conserved region in plant genes. Therefore, it can distinguish genetic variations in a specific gene that link to a specific trait. It is a simple, novel, cost-effective, highly polymorphic, and reproducible molecular marker for which there is no need for prior sequence information. In the recent past, SCoT markers have been employed in many commercially important and underutilized plant species for a variety of applications, including genetic diversity analysis, interspecific/generic genetic relationships, cultivar/hybrid/species identification, sex determination, construction of linkage map, association mapping/analysis, differential gene expression, and genetic fidelity analysis of tissue culture-raised plants. The main aim of this review is to provide up-to-date information on SCoT markers and their application in many commercially important and underutilized plant species, mainly progress made in the last 8-10 years.
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Affiliation(s)
- Manoj K Rai
- Department of Environmental Science, Indira Gandhi National Tribal University, Amarkantak, MP, 484887, India.
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Yang J, Hu G, Hu G. Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales. BMC Genomics 2022; 23:27. [PMID: 34991482 PMCID: PMC8734052 DOI: 10.1186/s12864-021-08259-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/13/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Handeliodendron Rehder and Eurycorymbus Hand.-Mazz. are the monotypic genera in the Sapindaceae family. The phylogenetic relationship of these endangered species Handeliodendron bodinieri (Lévl.) Rehd. and Eurycorymbus cavaleriei (Lévl.) Rehd. et Hand.-Mazz. with other members of Sapindaceae s.l. is not well resolved. A previous study concluded that the genus Aesculus might be paraphyletic because Handeliodendron was nested within it based on small DNA fragments. Thus, their chloroplast genomic information and comparative genomic analysis with other Sapindaceae species are necessary and crucial to understand the circumscription and plastome evolution of this family. RESULTS The chloroplast genome sizes of Handeliodendron bodinieri and Eurycorymbus cavaleriei are 151,271 and 158,690 bp, respectively. Results showed that a total of 114 unique genes were annotated in H. bodinieri and E. cavaleriei, and the ycf1 gene contained abundant SSRs in both genomes. Comparative analysis revealed that gene content, PCGs, and total GC content were remarkably similar or identical within 13 genera from Sapindaceae, and the chloroplast genome size of four genera was generally smaller within the family, including Acer, Dipteronia, Aesculus, and Handeliodendron. IR boundaries of the H. bodinieri showed a significant contraction, whereas it presented a notable expansion in E. cavaleriei cp genome. Ycf1, ndhC-trnV-UAC, and rpl32-trnL-UAG-ccsA were remarkably divergent regions in the Sapindaceae species. Analysis of selection pressure showed that there are a few positively selected genes. Phylogenetic analysis based on different datasets, including whole chloroplast genome sequences, coding sequences, large single-copy, small single-copy, and inverted repeat regions, consistently demonstrated that H. bodinieri was sister to the clade consisting of Aesculus chinensis and A. wangii and strongly support Eurycorymbus cavaleriei as sister to Dodonaea viscosa. CONCLUSION This study revealed that the cp genome size of the Hippocastanoideae was generally smaller compared to the other subfamilies within Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and Handeliodendron is not nested within the genus Aesculus.
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Affiliation(s)
- Jiaxin Yang
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Guoxiong Hu
- College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China.
| | - Guangwan Hu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
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