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He R, Wang S, Li Q, Wang Z, Mei Y, Li F. Phylogenomic analysis and molecular identification of true fruit flies. Front Genet 2024; 15:1414074. [PMID: 38974385 PMCID: PMC11224437 DOI: 10.3389/fgene.2024.1414074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/30/2024] [Indexed: 07/09/2024] Open
Abstract
The family Tephritidae in the order Diptera, known as true fruit flies, are agriculturally important insect pests. However, the phylogenetic relationships of true fruit flies, remain controversial. Moreover, rapid identification of important invasive true fruit flies is essential for plant quarantine but is still challenging. To this end, we sequenced the genome of 16 true fruit fly species at coverage of 47-228×. Together with the previously reported genomes of nine species, we reconstructed phylogenetic trees of the Tephritidae using benchmarking universal single-copy ortholog (BUSCO), ultraconserved element (UCE) and anchored hybrid enrichment (AHE) gene sets, respectively. The resulting trees of 50% taxon-occupancy dataset for each marker type were generally congruent at 88% nodes for both concatenation and coalescent analyses. At the subfamily level, both Dacinae and Trypetinae are monophyletic. At the species level, Bactrocera dorsalis is more closely related to Bactrocera latifrons than Bactrocera tryoni. This is inconsistent with previous conclusions based on mitochondrial genes but consistent with recent studies based on nuclear data. By analyzing these genome data, we screened ten pairs of species-specific primers for molecular identification of ten invasive fruit flies, which PCR validated. In summary, our work provides draft genome data of 16 true fruit fly species, addressing the long-standing taxonomic controversies and providing species-specific primers for molecular identification of invasive fruit flies.
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Affiliation(s)
- Rong He
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shuping Wang
- Technical Centre for Animal, Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai, China
| | - Qiang Li
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zuoqi Wang
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Li
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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Malik G, Jabeen A, Mir JI, Shah RA, Shah MA, Dinkar V, Sheikh MA, Kumar R, Sharma OC, Verma MK. Genetic diversity, population structure and marker-trait associations in Indian kale ( Brassica oleracea L. gp. acephala) using cross-species microsatellite markers. Heliyon 2024; 10:e29521. [PMID: 38681616 PMCID: PMC11046235 DOI: 10.1016/j.heliyon.2024.e29521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 05/01/2024] Open
Abstract
Kale is known for its exceptional nourishing and functional benefits to human body. However, it is an understudied species from genomic as well as agronomic aspects. It is important to characterize niche kale germplasms around the world to systematically conserve and utilize its genetic variability, especially for commercial traits in the interest of growers, consumers and industry. With this view, genomic and phenotypic characterizations of 62 Kashmiri kale accessions including popular landraces were done to estimate and partition genetic diversity, understand trait relationships, develop population structure and divulge marker-trait associations of economic significance. Sixty-six cross species microsatellite (SSR) markers within Brassica genus amplified 269 alleles in the germplasm. Their polymorphic information content (PIC) ranged from 0.00078 to 0.953 with an average of 0.407. The population structure analysis and neighbour joining tree clustering categorized the germplasm into three sub-populations. AMOVA revealed more within-population variance (67.73 %) than among-populations (32.27 %) variance. The principal component analysis (PCA) involving 24 agronomical traits revealed seven PCs (PC1 to PC7) having Eigen values more than 1, which explained a cumulative variation of 69.21 %. Association mapping with respect to these 24 agronomical traits using mixed linear model and general linear model revealed six overlapping significant marker-trait relationships with five being significant at probability value of 0.001/0.0001. The highly significant associations of two SSRs with economically important traits (siliqua length and seed weight) significantly correlated/related with leaf yield and seed yield were revealed for their possible utilization in marker assisted breeding for higher leaf and seed yields.
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Affiliation(s)
- Geetika Malik
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
| | - Asma Jabeen
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
| | - Javid Iqbal Mir
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
| | - Rafiq Ahmad Shah
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
| | - Mohd Abas Shah
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
| | - Vishal Dinkar
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
| | - Muneer Ahmad Sheikh
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
| | - Ravinder Kumar
- Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India, 110012
| | - Om Chand Sharma
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
| | - Mahendra Kumar Verma
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
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Rios-Willars E, Chirinos-Arias MC. Mfind: a tool for DNA barcode analysis in angiosperms and its relationship with microsatellites using a sliding window algorithm. PLANTA 2024; 259:134. [PMID: 38671234 DOI: 10.1007/s00425-024-04420-3] [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: 10/12/2023] [Accepted: 04/17/2024] [Indexed: 04/28/2024]
Abstract
MAIN CONCLUSION Mfind is a tool to analyze the impact of microsatellite presence on DNA barcode specificity. We found a significant correlation between barcode entropy and microsatellite count in angiosperm. Genetic barcodes and microsatellites are some of the identification methods in taxonomy and biodiversity research. It is important to establish a relationship between microsatellite quantification and genetic information in barcodes. In order to clarify the association between the genetic information in barcodes (expressed as Shannon's Measure of Information, SMI) and microsatellites count, a total of 330,809 DNA barcodes from the BOLD database (Barcode of Life Data System) were analyzed. A parallel sliding-window algorithm was developed to compute the Shannon entropy of the barcodes, and this was compared with the quantification of microsatellites like (AT)n, (AC)n, and (AG)n. The microsatellite search method utilized an algorithm developed in the Java programming language, which systematically examined the genetic barcodes from an angiosperm database. For this purpose, a computational tool named Mfind was developed, and its search methodology is detailed. This comprehensive study revealed a broad overview of microsatellites within barcodes, unveiling an inverse correlation between the sumz of microsatellites count and barcodes information. The utilization of the Mfind tool demonstrated that the presence of microsatellites impacts the barcode information when considering entropy as a metric. This effect might be attributed to the concise length of DNA barcodes and the repetitive nature of microsatellites, resulting in a direct influence on the entropy of the barcodes.
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Affiliation(s)
- Ernesto Rios-Willars
- Faculty of Systems, Autonomous University of Coahuila (UAdeC), 25350, Saltillo, Coahuila, México.
| | - Michelle C Chirinos-Arias
- Molecular Biology and Bioinformatics Area, Instituto de Genetica Barbara McClintock (IGBM), Lima, 15022, Peru
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Li G, Xu Z, Wang J, Mu C, Zhou Z, Li M, Hao Z, Zhang D, Yong H, Han J, Li X, Zhao J, Weng J. Gene pyramiding of ZmGLK36 and ZmGDIα-hel for rough dwarf disease resistance in maize. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:25. [PMID: 38516203 PMCID: PMC10951195 DOI: 10.1007/s11032-024-01466-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024]
Abstract
Maize rough dwarf disease (MRDD) caused by pathogenic viruses in the genus Fijivirus in the family Reoviridae is one of the most destructive diseases in maize. The pyramiding of effective resistance genes into maize varieties is a potential approach to reduce the damage resulting from the disease. Two major quantitative trait loci (QTLs) (qMrdd2 and qMrdd8) have been previously identified. The resistance genes ZmGLK36 and ZmGDIα-hel have also been cloned with the functional markers Indel-26 and IDP25K, respectively. In this study, ZmGLK36 and ZmGDIα-hel were introgressed to improve MRDD resistance of maize lines (Zheng58, Chang7-2, B73, Mo17, and their derived hybrids Zhengdan958 and B73 × Mo17) via marker-assisted selection (MAS). The converted lines and their derived hybrids, carrying one or two genes, were evaluated for MRDD resistance using artificial inoculation methods. The double-gene pyramiding lines and their derived hybrids exhibited increased resistance to MRDD compared to the monogenic lines and the respective hybrids. The genetic backgrounds of the converted lines were highly similar (90.85-98.58%) to the recurrent parents. In addition, agronomic trait evaluation demonstrated that pyramiding lines with one or two genes and their derived hybrids were not significantly different from the recurrent parents and their hybrids under nonpathogenic stress, including period traits (tasseling, pollen shedding, and silking), yield traits (ear length, grain weight per ear and 100-kernel weight) and quality traits (protein and starch content). There were differences in plant architecture traits between the improved lines and their hybrids. This study illustrated the successful development of gene pyramiding for improving MRDD resistance by advancing the breeding process. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01466-9.
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Affiliation(s)
- Gongjian Li
- Key Laboratory of Plant Molecular & Developmental Biology, College of Life Sciences, Yantai University, Yantai, 264000 Shandong China
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Zhennan Xu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jianjun Wang
- Corn Research Institute, Shanxi Agricultural University, Xinzhou, 030031 Shanxi China
| | - Chunhua Mu
- Shandong Academy of Agricultural Sciences, Jinan, 250000 Shandong China
| | - Zhiqiang Zhou
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Mingshun Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Zhuanfang Hao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Degui Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hongjun Yong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jienan Han
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xinhai Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jiqiang Zhao
- Key Laboratory of Plant Molecular & Developmental Biology, College of Life Sciences, Yantai University, Yantai, 264000 Shandong China
| | - Jianfeng Weng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Cai Q, Feng S, Zheng X. The complete chloroplast genome of Aristolochia fangchi provided insights into the phylogeny and species identification of Aristolochia. Genome 2024; 67:90-98. [PMID: 38091583 DOI: 10.1139/gen-2023-0068] [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] [Indexed: 03/02/2024]
Abstract
Aristolochia fangchi is an important species within the family Aristolochiaceae, most of which contain nephrotoxic aristolochic acid. The inadvertent use of Aristolochiaceae plants as raw ingredients in the manufacturing of patent medicine poses a significant risk warranting considerable attention. In this study, we assembled and analyzed the complete chloroplast genome of Aristolochia fangchi, which is a 159 867 bp long circular molecule. Functional annotation of the A. fangchi plastome unveiled a total of 113 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Subsequently, a series of genome structure and characteristic evaluations were conducted against the A. fangchi plastome. Further phylogenetic analysis suggested that a plausible phylogenetic relationship among Aristolochiaceae derived from the concatenated sequences of shared conserved genes rather than from the entire chloroplast genome with one IR copy. Finally, a DNA polymorphism assessment against a dozen Aristolochia plastomes yielded multiple potential regions for biomarker designation. Six pairs of primers were generated and underwent both in silico and actual PCR validations. In conclusion, this study identified the unique characteristics of the A. fangchi plastome, providing invaluable insights for further investigations on species identification and the phylogeny evolution between A. fangchi and its related species.
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Affiliation(s)
- Qingqun Cai
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Guangdong Clinical Research Academy of Chinese Medicine, Guangzhou 510405, China
| | - Shiyin Feng
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Guangdong Clinical Research Academy of Chinese Medicine, Guangzhou 510405, China
| | - Xiasheng Zheng
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
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Kim KR, Park SY, Kim H, Kim J, Hong JM, Kim SY, Yu JN. Genome assembly and microsatellite marker development using Illumina and PacBio sequencing in Persicaria maackiana (Polygonaceae) from Korea. Genes Genomics 2024; 46:187-202. [PMID: 38240922 DOI: 10.1007/s13258-023-01479-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/23/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND Persicaria maackiana (Regel) is a potential medicinal plant that exerts anti-diabetic effects. However, the lack of genomic information on P. maackiana hinders research at the molecular level. OBJECTIVE Herein, we aimed to construct a draft genome assembly and obtain comprehensive genomic information on P. maackiana using high-throughput sequencing tools PacBio Sequel II and Illumina. METHODS Persicaria maackiana samples from three natural populations in Gaecheon, Gichi, and Uiryeong reservoirs in South Korea were used to generate genomic DNA libraries, perform genome de novo assembly, gene ontology analysis, phylogenetic tree analysis, genotyping, and identify microsatellite markers. RESULTS The assembled P. maackiana genome yielded 32,179 contigs. Assessment of assembly integrity revealed 1503 (93.12%) complete Benchmarking Universal Single-Copy Orthologs. A total of 64,712 protein-coding genes were predicted and annotated successfully in the protein database. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs, 13,778 genes were annotated into 18 categories. Genes that activated AMPK were identified in the KEGG pathway. A total of 316,992 microsatellite loci were identified, and primers targeting the flanking regions were developed for 292,059 microsatellite loci. Of these, 150 primer sets were randomly selected for amplification, and 30 of these primer sets were identified as polymorphic. These primers amplified 3-9 alleles. The mean observed and expected heterozygosity were 0.189 and 0.593, respectively. Polymorphism information content values of the markers were 0.361-0.754. CONCLUSION Collectively, our study provides a valuable resource for future comparative genomics, phylogeny, and population studies of P. maackiana.
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Affiliation(s)
- Kang-Rae Kim
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - So Young Park
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Heesoo Kim
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Jiyeon Kim
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Jeong Min Hong
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Sun-Yu Kim
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Jeong-Nam Yu
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea.
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Bhat S, Sharma A, Sharma P, Singh K, Kundan M, Fayaz M, Wajid MA, Gairola S, Misra P. Development and analysis of de novo transcriptome assemblies of multiple genotypes of Cymbopogon spp. reveal candidate genes involved in the biosynthesis of aromatic monoterpenes. Int J Biol Macromol 2023; 253:127508. [PMID: 37865377 DOI: 10.1016/j.ijbiomac.2023.127508] [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: 05/18/2023] [Revised: 09/25/2023] [Accepted: 10/07/2023] [Indexed: 10/23/2023]
Abstract
Despite the high economic value of the monoterpene-rich essential oils from different genotypes of Cymbopogon, the knowledge about the genes and metabolic route(s) involved in the biosynthesis of aromatic monoterpenes in this genus is limited. In the present study, a comprehensive transcriptome analysis of four genotypes of Cymbopogon, displaying diverse quantitative and qualitative profiles of volatile monoterpenes in their essential oils has been carried out. The comparative analysis of the deduced protein sequences corresponding to the transcriptomes of the four genotypes revealed 4609 genotype-specific orthogroups, which might contribute in defining genotype-specific phenotypes. The transcriptome data mining led to the identification of unigenes involved in the isoprenogenesis. The homology searches, combined with the phylogenetic and expression analyses provided information about candidate genes concerning the biosynthesis of monoterpene aldehyde, monoterpene alcohol, and monoterpene esters. In addition, the present study suggests a potential role of geranial reductase like enzyme in the biosynthesis of monoterpene aldehyde in Cymbopogon spp. The detailed analysis of the candidate pathway genes suggested that multiple enzymatic routes might be involved in the biosynthesis of aromatic monoterpenes in the genus Cymbopogon. The present study provides deeper insights into the biosynthesis of monoterpenes, which will be useful for the genetic improvement of these aromatic grasses.
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Affiliation(s)
- Sheetal Bhat
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Arti Sharma
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Priyanka Sharma
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kanwaljeet Singh
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Maridul Kundan
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohd Fayaz
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mir Abdul Wajid
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sumeet Gairola
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Department of Botany and Microbiology, HNB Garhwal University, Srinagar, Garhwal 246174, Uttarakhand, India.
| | - Prashant Misra
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Singh G, Singh N, Ellur RK, Balamurugan A, Prakash G, Rathour R, Mondal KK, Bhowmick PK, Gopala Krishnan S, Nagarajan M, Seth R, Vinod KK, Singh V, Bollinedi H, Singh AK. Genetic Enhancement for Biotic Stress Resistance in Basmati Rice through Marker-Assisted Backcross Breeding. Int J Mol Sci 2023; 24:16081. [PMID: 38003271 PMCID: PMC10671030 DOI: 10.3390/ijms242216081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/11/2023] [Accepted: 08/17/2023] [Indexed: 11/26/2023] Open
Abstract
Pusa Basmati 1509 (PB1509) is one of the major foreign-exchange-earning varieties of Basmati rice; it is semi-dwarf and early maturing with exceptional cooking quality and strong aroma. However, it is highly susceptible to various biotic stresses including bacterial blight and blast. Therefore, bacterial blight resistance genes, namely, xa13 + Xa21 and Xa38, and fungal blast resistance genes Pi9 + Pib and Pita were incorporated into the genetic background of recurrent parent (RP) PB1509 using donor parents, namely, Pusa Basmati 1718 (PB1718), Pusa 1927 (P1927), Pusa 1929 (P1929) and Tetep, respectively. Foreground selection was carried out with respective gene-linked markers, stringent phenotypic selection for recurrent parent phenotype, early generation background selection with Simple sequence repeat (SSR) markers, and background analysis at advanced generations with Rice Pan Genome Array comprising 80K SNPs. This has led to the development of Near isogenic lines (NILs), namely, Pusa 3037, Pusa 3054, Pusa 3060 and Pusa 3066 carrying genes xa13 + Xa21, Xa38, Pi9 + Pib and Pita with genomic similarity of 98.25%, 98.92%, 97.38% and 97.69%, respectively, as compared to the RP. Based on GGE-biplot analysis, Pusa 3037-1-44-3-164-20-249-2 carrying xa13 + Xa21, Pusa 3054-2-47-7-166-24-261-3 carrying Xa38, Pusa 3060-3-55-17-157-4-124-1 carrying Pi9 + Pib, and Pusa 3066-4-56-20-159-8-174-1 carrying Pita were identified to be relatively stable and better-performing individuals in the tested environments. Intercrossing between the best BC3F1s has led to the generation of Pusa 3122 (xa13 + Xa21 + Xa38), Pusa 3124 (Xa38 + Pi9 + Pib) and Pusa 3123 (Pi9 + Pib + Pita) with agronomy, grain and cooking quality parameters at par with PB1509. Cultivation of such improved varieties will help farmers reduce the cost of cultivation with decreased pesticide use and improve productivity with ensured safety to consumers.
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Affiliation(s)
- Gagandeep Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
| | - Niraj Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
| | - Ranjith Kumar Ellur
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
| | - Alexander Balamurugan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (G.P.)
| | - G. Prakash
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (G.P.)
| | - Rajeev Rathour
- Department of Agriculture Biotechnology, CSKHPKV, Palampur 176062, Himachal Pradesh, India
| | - Kalyan Kumar Mondal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (G.P.)
| | - Prolay Kumar Bhowmick
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
| | - S. Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
| | - Mariappan Nagarajan
- Rice Breeding and Genetics Research Centre, ICAR-Indian Agricultural Research Institute, Aduthurai 612101, Tamil Nadu, India
| | - Rakesh Seth
- Regional Station, ICAR-Indian Agricultural Research Institute, Karnal 132001, Haryana, India;
| | - K. K. Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
| | - Varsha Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
| | - Haritha Bollinedi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
| | - Ashok Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
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Zhao P, Zhang L, Liu Y, Wang Z, Guo H, Li J, Wu S, Gao Z, Yuan H. Genetic diversity and phylogenetic relationship estimation of Shanxi indigenous goat breeds using microsatellite markers. Anim Biotechnol 2023; 35:2276717. [PMID: 37934003 DOI: 10.1080/10495398.2023.2276717] [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] [Indexed: 11/08/2023]
Abstract
The objective of this study was to assess the genetic diversity, phylogenetic relationship and population structure of five goat breeds in Shanxi, China. High genetic diversities were found in the five populations, among which, Licheng big green goat (LCBG) has the highest genetic diversity, while Jinlan cashmere goat (JLCG) population has the lowest genetic diversity. Bottleneck analysis showed the absence of recent genetic bottlenecks in the five goat populations. Genetic differentiation analysis shows that the closest genetic relationship between LCBG and LLBG (Lvliang black goat) was found, and the genetic distance between JLCG and the other four populations is the largest. The population structure of JLCG is different from the other four populations with K = 2, while LCBG and LLBG have high similarity population structure as the K value changes. Knowledge about genetic diversity and population structure of indigenous goats is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of goat breeds.
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Affiliation(s)
- Peng Zhao
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - Li Zhang
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - Yin Liu
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - Zhengkun Wang
- Shanxi Animal Husbandry Technology Popularization Service Center, Taiyuan, China
| | - Hongyu Guo
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - Jun Li
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - Shuai Wu
- Agriculture and Rural Bureau of Lvliang City, Lvliang, Shanxi Province, China
| | - Zefeng Gao
- Agriculture and Rural Bureau of Lvliang City, Lvliang, Shanxi Province, China
| | - Hao Yuan
- Animal Husbandry Center of Yangcheng County, Jincheng, Shanxi Province, China
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10
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Rahim MS, Sharma V, Pragati Yadav, Parveen A, Kumar A, Roy J, Kumar V. Rethinking underutilized cereal crops: pan-omics integration and green system biology. PLANTA 2023; 258:91. [PMID: 37777666 DOI: 10.1007/s00425-023-04242-9] [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: 06/15/2023] [Accepted: 09/12/2023] [Indexed: 10/02/2023]
Abstract
MAIN CONCLUSION Due to harsh lifestyle changes, in the present era, nutritional security is needed along with food security so it is necessary to include underutilized cereal crops (UCCs) in our daily diet to counteract the rising danger of human metabolic illness. We can attain both the goal of zero hunger and nutritional security by developing improved UCCs using advanced pan-omics (genomics, transcriptomics, proteomics, metabolomics, nutrigenomics, phenomics and ionomics) practices. Plant sciences research progressed profoundly since the last few decades with the introduction of advanced technologies and approaches, addressing issues of food demand of the growing population, nutritional security challenges and climate change. However, throughout the expansion and popularization of commonly consumed major cereal crops such as wheat and rice, other cereal crops such as millet, rye, sorghum, and others were impeded, despite their potential medicinal and nutraceutical qualities. Undoubtedly neglected underutilized cereal crops (UCCs) also have the capability to withstand diverse climate change. To relieve the burden of major crops, it is necessary to introduce the new crops in our diet in the way of UCCs. Introgression of agronomically and nutritionally important traits by pan-omics approaches in UCCs could be a defining moment for the population's well-being on the globe. This review discusses the importance of underutilized cereal crops, as well as the application of contemporary omics techniques and advanced bioinformatics tools that could open up new avenues for future study and be valuable assets in the development and usage of UCCs in the perspective of green system biology. The increased and improved use of UCCs is dependent on number of factors that necessitate a concerted research effort in agricultural sciences. The emergence of functional genomics with molecular genetics might gear toward the reawakening of interest in underutilized cereals crops. The need of this era is to focus on potential UCCs in advanced agriculture and breeding programmes. Hence, targeting the UCCs, might provide a bright future for better health and scientific rationale for its use.
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Affiliation(s)
- Mohammed Saba Rahim
- Department of Botany, School of Basic Sciences, Central University of Punjab, Punjab, 151401, India
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali, Punjab, 140 306, India
| | - Vinita Sharma
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali, Punjab, 140 306, India
| | - Pragati Yadav
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali, Punjab, 140 306, India
| | - Afsana Parveen
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali, Punjab, 140 306, India
| | - Adarsh Kumar
- Department of Botany, School of Basic Sciences, Central University of Punjab, Punjab, 151401, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali, Punjab, 140 306, India.
| | - Vinay Kumar
- Department of Botany, School of Basic Sciences, Central University of Punjab, Punjab, 151401, India.
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11
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Yin B, Wang H, Weng S, Li S, He J, Li C. A simple sequence repeats marker of disease resistance in shrimp Litopenaeus vannamei and its application in selective breeding. Front Genet 2023; 14:1144361. [PMID: 37576558 PMCID: PMC10415038 DOI: 10.3389/fgene.2023.1144361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 04/18/2023] [Indexed: 08/15/2023] Open
Abstract
The polymorphism of the simple sequence repeat (SSR) in the 5' untranslated coding region (5'-UTR) of the antiviral gene IRF (LvIRF) has been shown to be implicated in the resistance to viral pathogens in shrimp Litopenaeus vannamei (L. vannamei). In this study, we explored the potential of this (CT)n-SSR marker in disease resistance breeding and the hereditary property of disease resistance traits in offspring. From 2018 to 2021, eight populations were generated through crossbreeding by selecting individuals according to microsatellite genotyping. Our results demonstrated that shrimp with the shorter (CT)n repeat exhibited higher resistance to white spot syndrome virus (WSSV) or Decapod iridescent virus 1 (DIV1); meanwhile, these resistance traits could be inherited in offspring. Interestingly, we observed that the longer (CT)n repeats were associated with bacterial resistance traits. Accordingly, shrimp with longer (CT)n repeats exhibited higher tolerance to Vibrio parahaemolyticus infection. Taken together, these results indicate that the single (CT)n-SSR marker could be used to selective breeding for both resistance to virus and bacteria in shrimps.
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Affiliation(s)
- Bin Yin
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Guangzhou, China
- China-ASEAN Belt and Road Joint Laboratory on Marine Aquaculture Technology, Guangzhou, China
| | - Haiyang Wang
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Guangzhou, China
- China-ASEAN Belt and Road Joint Laboratory on Marine Aquaculture Technology, Guangzhou, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Guangzhou, China
- China-ASEAN Belt and Road Joint Laboratory on Marine Aquaculture Technology, Guangzhou, China
| | - Sedong Li
- Guangdong Evergreen Feed Industry Co., Ltd., Zhanjiang, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Guangzhou, China
- China-ASEAN Belt and Road Joint Laboratory on Marine Aquaculture Technology, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
| | - Chaozheng Li
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Guangzhou, China
- China-ASEAN Belt and Road Joint Laboratory on Marine Aquaculture Technology, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
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12
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Population genetic structure of a recent insect invasion: a gall midge, Asynapta groverae (Diptera: Cecidomyiidae) in South Korea since the first outbreak in 2008. Sci Rep 2023; 13:2812. [PMID: 36797385 PMCID: PMC9935521 DOI: 10.1038/s41598-023-29782-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
Outbreaks of Asynapta groverae, an invasive mycophagous gall midge, in South Korea have been repeatedly reported since the first occurrence in 2008. This species is a nuisance to residents owing to its mass emergence from newly built and furnished apartments. Here, the levels of genetic diversity, divergence, and structure of invasive A. groverae populations were investigated to understand their ability to survive in novel locations. Population genetic analyses were performed on seven invasive populations, including the first outbreak, sporadically emerged, and two laboratory-isolated (quarantined) populations, using the mitochondrial COI sequences and the ten novel microsatellite markers developed in this study. Non-indigenous A. groverae managed to maintain their populations for 12 years despite decreased genetic polymorphisms resulting from multiple incidences of founder effects by a small number of colonists. Additionally, the advantageous sustainability of A. groverae in the particle boards from which they emerge suggests that human-mediated dispersal is plausible, which may allow for the successful spread or invasion of A. groverae to new locations. This study is one of the few examples to demonstrate that an insect species successfully invaded new regions despite exhibiting decreased genetic diversity that was maintained for a decade. These findings indicate that the high genetic diversity of the initial founding population and asexual reproduction would contribute to the successful invasion of A. groverae in novel environments.
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13
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Whole Genome Wide SSR Markers Identification Based on ddRADseq Data. Methods Mol Biol 2023; 2638:59-66. [PMID: 36781635 DOI: 10.1007/978-1-0716-3024-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The advent of advanced NGS technologies have led to the generation of enormous amount of sequence data which further aid in the discovery of the various type of markers such as SSRs, SNPs, InDels, etc. Among all these markers, microsatellite SSR markers can be mined from the ddRADseq data as certain properties of SSR markers make them ideal markers for study. These assist researchers and breeders in diversity analysis and producing new varieties with desired traits. To extract the markers, first, the ddRADseq data is assembled into consensus sequences using STACKS program which are further assembled for mining microsatellites using QDD along with MISA tool.
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14
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Zampieri E, Volante A, Marè C, Orasen G, Desiderio F, Biselli C, Canella M, Carmagnola L, Milazzo J, Adreit H, Tharreau D, Poncelet N, Vaccino P, Valè G. Marker-Assisted Pyramiding of Blast-Resistance Genes in a japonica Elite Rice Cultivar through Forward and Background Selection. PLANTS (BASEL, SWITZERLAND) 2023; 12:757. [PMID: 36840105 PMCID: PMC9963729 DOI: 10.3390/plants12040757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Rice blast, caused by Pyricularia oryzae, is one of the main rice diseases worldwide. The pyramiding of blast-resistance (Pi) genes, coupled to Marker-Assisted BackCrossing (MABC), provides broad-spectrum and potentially durable resistance while limiting the donor genome in the background of an elite cultivar. In this work, MABC coupled to foreground and background selections based on KASP marker assays has been applied to introgress four Pi genes (Piz, Pib, Pita, and Pik) in a renowned japonica Italian rice variety, highly susceptible to blast. Molecular analyses on the backcross (BC) lines highlighted the presence of an additional blast-resistance gene, the Pita-linked Pita2/Ptr gene, therefore increasing the number of blast-resistance introgressed genes to five. The recurrent genome was recovered up to 95.65%. Several lines carrying four (including Pita2) Pi genes with high recovery percentage levels were also obtained. Phenotypic evaluations confirmed the effectiveness of the pyramided lines against multivirulent strains, which also had broad patterns of resistance in comparison to those expected based on the pyramided Pi genes. The developed blast-resistant japonica lines represent useful donors of multiple blast-resistance genes for future rice-breeding programs related to the japonica group.
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Affiliation(s)
- Elisa Zampieri
- Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, VC, Italy
- Institute for Sustainable Plant Protection, National Research Council, Strada Delle Cacce 73, 10135 Turin, TO, Italy
| | - Andrea Volante
- Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, VC, Italy
- Council for Agricultural Research and Economics—Research Centre for Vegetable and Ornamental Crops, Corso Inglesi 508, 18038 Sanremo, IM, Italy
| | - Caterina Marè
- Council for Agricultural Research and Economics—Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017 Fiorenzuola d’Arda, PC, Italy
| | - Gabriele Orasen
- Bertone Sementi S.P.A., Strada Cacciolo, 15030 Terruggia, AL, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics—Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017 Fiorenzuola d’Arda, PC, Italy
| | - Chiara Biselli
- Council for Agricultural Research and Economics—Viticulture and Oenology, Viale Santa Margherita 80, 52100 Arezzo, AR, Italy
| | - Marco Canella
- Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, VC, Italy
| | - Lorena Carmagnola
- Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, VC, Italy
| | - Joëlle Milazzo
- CIRAD, UMR PHIM TA A 120/K, Campus de Baillarguet, 34, CEDEX 5, 34398 Montpellier, France
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, 34, 34398 Montpellier, France
| | - Henri Adreit
- CIRAD, UMR PHIM TA A 120/K, Campus de Baillarguet, 34, CEDEX 5, 34398 Montpellier, France
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, 34, 34398 Montpellier, France
| | - Didier Tharreau
- CIRAD, UMR PHIM TA A 120/K, Campus de Baillarguet, 34, CEDEX 5, 34398 Montpellier, France
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, 34, 34398 Montpellier, France
| | - Nicolas Poncelet
- CIRAD, UMR PHIM TA A 120/K, Campus de Baillarguet, 34, CEDEX 5, 34398 Montpellier, France
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, 34, 34398 Montpellier, France
| | - Patrizia Vaccino
- Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, VC, Italy
| | - Giampiero Valè
- Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, VC, Italy
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica, Università del Piemonte Orientale, Piazza San Eusebio 5, 13100 Vercelli, VC, Italy
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15
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Characterization of highly polymorphic microsatellite markers for the chinese monal (Lophophorus lhuysii, Galliformes) using Illumina MiSeq sequencing. Mol Biol Rep 2023; 50:3903-3908. [PMID: 36652153 DOI: 10.1007/s11033-022-08151-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/23/2022] [Indexed: 01/19/2023]
Abstract
BACKGROUND The Chinese monal (Lophophorus lhuysii, Galliformes) is a vulnerable and endemic bird from southwestern China. To better protect this species and increase its population size, genetic markers are urgently needed for investigation and conservation of both wild and captive populations. METHODS AND RESULTS By using next-generation sequencing, we developed and characterized markers for seven microsatellite loci of the Chinese monal. PCR examination and statistical analysis indicated that these microsatellites exhibited moderate to high levels of polymorphism, with the expected heterozygosity and polymorphic information content ranging from 0.578 to 0.858 and from 0.540 to 0.841, respectively. Cross-species genome comparison further suggests that these microsatellites are a feature of certain galliform species rather than being specific to the Chinese monal. CONCLUSION A combination of the seven highly polymorphic loci may provide a fundamental genetic toolkit to assess genetic backgrounds and will contribute to design conservation plan, breeding management and other possible studies of the Chinese monal and other evolutionarily related species in the future.
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16
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Jeanjean SI, Renault V, Daunay A, Shen Y, Hardy LM, Deleuze JF, How-Kit A. LT-RPA: An Isothermal DNA Amplification Approach for Improved Microsatellite Genotyping and Microsatellite Instability Detection. Methods Mol Biol 2023; 2621:91-109. [PMID: 37041442 DOI: 10.1007/978-1-0716-2950-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Microsatellites are short tandem repeats of one to six nucleotides that are highly polymorphic and extensively used as genetic markers in numerous biomedical applications, including the detection of microsatellite instability (MSI) in cancer. The standard analytical method for microsatellite analysis relies on PCR amplification followed by capillary electrophoresis or, more recently, next-generation sequencing (NGS). However, their amplification during PCR generates undesirable frameshift products known as stutter peaks caused by polymerase slippage, complicating data analysis and interpretation, while very few alternative methods for microsatellite amplification have been developed to reduce the formation of these artifacts. In this context, the recently developed low-temperature recombinase polymerase amplification (LT-RPA) is an isothermal DNA amplification method at low temperature (32 °C) that drastically reduces and sometimes completely abolishes the formation of stutter peaks. LT-RPA greatly simplifies the genotyping of microsatellites and improves the detection of MSI in cancer. In this chapter, we describe in detail all the experimental steps necessary for the development of LT-RPA simplex and multiplex assays for microsatellite genotyping and MSI detection, including the design, optimization, and validation of the assays combined with capillary electrophoresis or NGS.
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Affiliation(s)
- Sophie I Jeanjean
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Victor Renault
- Laboratoire de Bio-informatique Clinique, Institut Curie, Paris, France
| | - Antoine Daunay
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Yimin Shen
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Lise M Hardy
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
- Laboratory of Excellence GenMed, Paris, France
| | - Jean-François Deleuze
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
- Laboratory of Excellence GenMed, Paris, France
- Centre National de Recherche en Génomique Humaine, CEA- Institut François Jacob, Evry, France
| | - Alexandre How-Kit
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand.
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17
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Moya-Moraga MR, Pérez-Ruíz C. Application of MaxEnt Modeling and HRM Analysis to Support the Conservation and Domestication of Gevuina avellana Mol. in Central Chile. PLANTS (BASEL, SWITZERLAND) 2022; 11:2803. [PMID: 36297827 PMCID: PMC9607360 DOI: 10.3390/plants11202803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
The Chilean hazelnut (Gevuina avellana Mol., Proteaceae) is a native tree of Chile and Argentina of edible fruit-type nut. We applied two approaches to contribute to the development of strategies for mitigation of the effects of climate change and anthropic activities in G. avellana. It corresponds to the first report where both tools are integrated, the MaxEnt model to predict the current and future potential distribution coupled with High-Resolution Melting Analysis (HRM) to assess its genetic diversity and understand how the species would respond to these changes. Two global climate models: CNRM-CM6-1 and MIROC-ES2L for four Shared Socioeconomic Pathways: 126, 245, 370, and 585 (2021−2040; 2061−2080) were evaluated. The annual mean temperature (43.7%) and water steam (23.4%) were the key factors for the distribution current of G. avellana (AUC = 0.953). The future prediction model shows to the year 2040 those habitat range decreases at 50% (AUC = 0.918). The genetic structure was investigated in seven natural populations using eight EST-SSR markers, showing a percentage of polymorphic loci between 18.69 and 55.14% and low genetic differentiation between populations (Fst = 0.052; p < 0.001). According to the discriminant analysis of principal components (DAPC) we identified 10 genetic populations. We conclude that high-priority areas for protection correspond to Los Avellanos and Punta de Águila populations due to their greater genetic diversity and allelic richness.
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Affiliation(s)
- Mario René Moya-Moraga
- Doctoral Program in Biotechnology and Genetic Resources of Plants and Associated Microorganisms (02E4), Polytechnic University of Madrid (UPM), University City, 28040 Madrid, Spain
- Department of Biotechnology, Faculty of Natural Sciences, Mathematics and the Environment (FCNMM), Metropolitan Technological University (UTEM), Ñuñoa 7750000, Chile
| | - César Pérez-Ruíz
- Department of Biotechnology and Plant Biology, School of Agricultural, Food and Biosystems Engineering, Polytechnic University of Madrid (UPM), University City, 28040 Madrid, Spain
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18
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Antunes AM, Nunes Stival JG, Targueta CP, de Campos Telles MP, Soares TN. A Pipeline for the Development of Microsatellite Markers using Next Generation Sequencing Data. Curr Genomics 2022; 23:175-181. [PMID: 36777003 PMCID: PMC9878831 DOI: 10.2174/1389202923666220428101350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/27/2022] [Accepted: 02/14/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Also known as Simple Sequence Repetitions (SSRs), microsatellites are profoundly informative molecular markers and powerful tools in genetics and ecology studies on plants. Objective: This research presents a workflow for developing microsatellite markers using genome skimming. Methods: The pipeline was proposed in several stages that must be performed sequentially: obtaining DNA sequences, identifying microsatellite regions, designing primers, and selecting candidate microsatellite regions to develop the markers. Our pipeline efficiency was analyzed using Illumina sequencing data from the non-model tree species Pterodon emarginatus Vog. Results: The pipeline revealed 4,382 microsatellite regions and drew 7,411 pairs of primers for P. emarginatus. However, a much larger number of microsatellite regions with the potential to develop markers were discovered from our pipeline. We selected 50 microsatellite regions with high potential for developing markers and organized 29 microsatellite regions in sets for multiplex PCR. Conclusion: The proposed pipeline is a powerful tool for fast and efficient development of microsatellite markers on a large scale in several species, especially nonmodel plant species.
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Affiliation(s)
- Adriana Maria Antunes
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Programa de Pós Graduação em Genética e Melhoramento de Plantas, Escola de Agronomia, Universidade Federal de Goias, Goiânia, Goiás, Brasil;,Address correspondence to this author at the Department of Genetics, Institute of Biological Sciences, Goias Federal University, Goiânia, Brazil; Tel/Fax: +55 62 981660987; E-mail:
| | - Júlio Gabriel Nunes Stival
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil
| | - Cíntia Pelegrineti Targueta
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil
| | - Mariana Pires de Campos Telles
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brasil
| | - Thannya Nascimentos Soares
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Programa de Pós Graduação em Genética e Melhoramento de Plantas, Escola de Agronomia, Universidade Federal de Goias, Goiânia, Goiás, Brasil
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19
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Liu Y, Fang X, Tang T, Wang Y, Wu Y, Luo J, Wu H, Wang Y, Zhang J, Ruan R, Zhou M, Zhang K, Yi Z. Inflorescence Transcriptome Sequencing and Development of New EST-SSR Markers in Common Buckwheat ( Fagopyrum esculentum). PLANTS (BASEL, SWITZERLAND) 2022; 11:742. [PMID: 35336623 PMCID: PMC8950064 DOI: 10.3390/plants11060742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Common buckwheat (Fagopyrum esculentum M.) is known for its adaptability, good nutrition, and medicinal and health care value. However, genetic studies of buckwheat have been hindered by limited genomic resources and genetic markers. In this study, Illumina HiSeq 4000 high-throughput sequencing technology was used to sequence the transcriptome of green-flower common buckwheat (Gr) with coarse pedicels and white-flower Ukrainian daliqiao (UD) with fine pedicels. A total of 118,448 unigenes were obtained, with an average length of 1248 bp and an N50 of 1850 bp. A total of 39,432 differentially expressed genes (DEGs) were identified, and the DEGs of the porphyrins and chlorophyll metabolic pathway had significantly upregulated expression in Gr. Then, a total of 17,579 sequences containing SSR loci were detected, and 20,756 EST-SSR loci were found. The distribution frequency of EST-SSR in the transcriptome was 17.52%, and the average distribution density was 8.21 kb. A total of 224 pairs of primers were randomly selected for synthesis; 35 varieties of common buckwheat and 13 varieties of Tartary buckwheat were verified through these primers. The clustering results well verified the previous conclusion that common buckwheat and Tartary buckwheat had a distant genetic relationship. The EST-SSR markers identified and developed in this study will be helpful to enrich the transcriptome information and marker-assisted selection breeding of buckwheat.
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Affiliation(s)
- Yang Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Xiaomei Fang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Tian Tang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Yudong Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Yinhuan Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Jinyu Luo
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Haotian Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Yingqian Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Jian Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Renwu Ruan
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Zelin Yi
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
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20
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Back to the wild: mining maize (Zea mays L.) disease resistance using advanced breeding tools. Mol Biol Rep 2022; 49:5787-5803. [PMID: 35064401 DOI: 10.1007/s11033-021-06815-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/06/2021] [Indexed: 10/19/2022]
Abstract
Cultivated modern maize (Zea mays L.) originated through the continuous process of domestication from its wild progenitors. Today, maize is considered as the most important cereal crop which is extensively cultivated in all parts of the world. Maize shows remarkable genotypic and phenotypic diversity which makes it an ideal model species for crop genetic research. However, intensive breeding and artificial selection of desired agronomic traits greatly narrow down the genetic bases of maize. This reduction in genetic diversity among cultivated maize led to increase the chance of more attack of biotic stress as climate changes hampering the maize grain production globally. Maize germplasm requires to integrate both durable multiple-diseases and multiple insect-pathogen resistance through tapping the unexplored resources of maize landraces. Revisiting the landraces seed banks will provide effective opportunities to transfer the resistant genes into the modern cultivars. Here, we describe the maize domestication process and discuss the unique genes from wild progenitors which potentially can be utilized for disease resistant in maize. We also focus on the genetics and disease resistance mechanism of various genes against maize biotic stresses and then considered the different molecular breeding tools for gene transfer and advanced high resolution mapping for gene pyramiding in maize lines. At last, we provide an insight for targeting identified key genes through CRISPR/Cas9 genome editing system to enhance the maize resilience towards biotic stress.
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21
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DNA-Based Tools to Certify Authenticity of Rice Varieties—An Overview. Foods 2022; 11:foods11030258. [PMID: 35159410 PMCID: PMC8834242 DOI: 10.3390/foods11030258] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/04/2022] [Accepted: 01/12/2022] [Indexed: 02/07/2023] Open
Abstract
Rice (Oryza sativa L.) is one of the most cultivated and consumed crops worldwide. It is mainly produced in Asia but, due to its large genetic pool, it has expanded to several ecosystems, latitudes and climatic conditions. Europe is a rice producing region, especially in the Mediterranean countries, that grow mostly typical japonica varieties. The European consumer interest in rice has increased over the last decades towards more exotic types, often more expensive (e.g., aromatic rice) and Europe is a net importer of this commodity. This has increased food fraud opportunities in the rice supply chain, which may deliver mixtures with lower quality rice, a problem that is now global. The development of tools to clearly identify undesirable mixtures thus became urgent. Among the various tools available, DNA-based markers are considered particularly reliable and stable for discrimination of rice varieties. This review covers aspects ranging from rice diversity and fraud issues to the DNA-based methods used to distinguish varieties and detect unwanted mixtures. Although not exhaustive, the review covers the diversity of strategies and ongoing improvements already tested, highlighting important advantages and disadvantages in terms of costs, reliability, labor-effort and potential scalability for routine fraud detection.
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22
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Management for Paddy, Oil Palm, and Pineapple Plantations in Malaysia: Current Status and Reviews. JOURNAL OF APPLIED SCIENCE & PROCESS ENGINEERING 2021. [DOI: 10.33736/jaspe.3438.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heavy rainfall causes a loss of fertiliser to the environment, and it leads to environmental issues such as eutrophication. Replenishment of fertiliser to replace the loss imposes a financial impact since frequent applications are costly and labour intensive. Therefore, investigations on proper fertiliser application in maintaining good soil pH, improving plant growth, and increasing crop yield from various plantations across Malaysia are of paramount importance. Meanwhile, limited agricultural-related studies about crop management in Malaysia have been done. This study presents a state-of-the-art review of Malaysia’s paddy, oil palm, pineapple plantations, and the existing nutrient management and fertilisation practices throughout the crop cycle. A systematic study of the existing crop management in terms of farming practices, nutrient management, and fertiliser application on the plantations of paddy, oil palm, and pineapple in Malaysia was carried out. Industry overviews for these three crop types based on past situations and future directions are also included. Recommendations on how to better manage these plantations are also outlined to promote a better understanding of the past, current, and future direction of the agricultural activities and management for principal edible crops like paddy, oil palm, and pineapple in Malaysia.
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23
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Ghosh A, Jangra S, Dietzgen RG, Yeh WB. Frontiers Approaches to the Diagnosis of Thrips (Thysanoptera): How Effective Are the Molecular and Electronic Detection Platforms? INSECTS 2021; 12:insects12100920. [PMID: 34680689 PMCID: PMC8540714 DOI: 10.3390/insects12100920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 11/23/2022]
Abstract
Simple Summary Thrips are important agricultural and forest pests. They cause damage by sucking plant sap and transmitting several plant viruses. Correct identification is the key for epidemiological studies and formulating appropriate management strategies. The application of molecular and electronic detection platforms has improved the morphological character-based diagnosis of thrips species. This article reviews research on molecular and automated identification of thrips species and discusses future research strategies for rapid and high throughput thrips diagnosis. Abstract Thrips are insect pests of economically important agricultural, horticultural, and forest crops. They cause damage by sucking plant sap and by transmitting several tospoviruses, ilarviruses, carmoviruses, sobemoviruses, and machlomoviruses. Accurate and timely identification is the key to successful management of thrips species. However, their small size, cryptic nature, presence of color and reproductive morphs, and intraspecies genetic variability make the identification of thrips species challenging. The use of molecular and electronic detection platforms has made thrips identification rapid, precise, sensitive, high throughput, and independent of developmental stages. Multi-locus phylogeny based on mitochondrial, nuclear, and other markers has resolved ambiguities in morphologically indistinguishable thrips species. Microsatellite, RFLP, RAPD, AFLP, and CAPS markers have helped to explain population structure, gene flow, and intraspecies heterogeneity. Recent techniques such as LAMP and RPA have been employed for sensitive and on-site identification of thrips. Artificial neural networks and high throughput diagnostics facilitate automated identification. This review also discusses the potential of pyrosequencing, microarrays, high throughput sequencing, and electronic sensors in delimiting thrips species.
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Affiliation(s)
- Amalendu Ghosh
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (A.G.); (S.J.)
| | - Sumit Jangra
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (A.G.); (S.J.)
| | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
- Correspondence:
| | - Wen-Bin Yeh
- Department of Entomology, National Chung Hsing University, Taichung City 402, Taiwan;
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Hasan N, Choudhary S, Naaz N, Sharma N, Laskar RA. Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. J Genet Eng Biotechnol 2021; 19:128. [PMID: 34448979 PMCID: PMC8397809 DOI: 10.1186/s43141-021-00231-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 08/17/2021] [Indexed: 11/28/2022]
Abstract
Background DNA markers improved the productivity and accuracy of classical plant breeding by means of marker-assisted selection (MAS). The enormous number of quantitative trait loci (QTLs) mapping read for different plant species have given a plenitude of molecular marker-gene associations. Main body of the abstract In this review, we have discussed the positive aspects of molecular marker-assisted selection and its precise applications in plant breeding programmes. Molecular marker-assisted selection has considerably shortened the time for new crop varieties to be brought to the market. To explore the information about DNA markers, many reviews have been published in the last few decades; all these reviews were intended by plant breeders to obtain information on molecular genetics. In this review, we intended to be a synopsis of recent developments of DNA markers and their application in plant breeding programmes and devoted to early breeders with little or no knowledge about the DNA markers. The progress made in molecular plant breeding, plant genetics, genomics selection, and editing of genome contributed to the comprehensive understanding of DNA markers and provides several proofs on the genetic diversity available in crop plants and greatly complemented plant breeding devices. Short conclusion MAS has revolutionized the process of plant breeding with acceleration and accuracy, which is continuously empowering plant breeders around the world.
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Affiliation(s)
- Nazarul Hasan
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India.
| | - Sana Choudhary
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India
| | - Neha Naaz
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India
| | - Nidhi Sharma
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India
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25
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An H, Lee HY, Shin H, Bang JH, Han S, Oh YL, Jang KY, Cho H, Hyun TK, Sung J, So YS, Jo IH, Chung JW. Evaluation of Genetic Diversity and Population Structure Analysis among Germplasm of Agaricus bisporus by SSR Markers. MYCOBIOLOGY 2021; 49:376-384. [PMID: 34512081 PMCID: PMC8409946 DOI: 10.1080/12298093.2021.1940746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
Agaricus bisporus is a popular edible mushroom that is cultivated worldwide. Due to its secondary homothallic nature, cultivated A. bisporus strains have low genetic diversity, and breeding novel strains is challenging. The aim of this study was to investigate the genetic diversity and population structure of globally collected A. bisporus strains using simple sequence repeat (SSR) markers. Agaricus bisporus strains were divided based on genetic distance-based groups and model-based subpopulations. The major allele frequency (MAF), number of genotypes (NG), number of alleles (NA), observed heterozygosity (HO), expected heterozygosity (HE), and polymorphic information content (PIC) were calculated, and genetic distance, population structure, genetic differentiation, and Hardy-Weinberg equilibrium (HWE) were assessed. Strains were divided into two groups by distance-based analysis and into three subpopulations by model-based analysis. Strains in subpopulations POP A and POP B were included in Group I, and strains in subpopulation POP C were included in Group II. Genetic differentiation between strains was 99%. Marker AB-gSSR-1057 in Group II and subpopulation POP C was confirmed to be in HWE. These results will enhance A. bisporus breeding programs and support the protection of genetic resources.
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Affiliation(s)
- Hyejin An
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Hwa-Yong Lee
- Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Hyeran Shin
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Jun Hyoung Bang
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Seahee Han
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Youn-Lee Oh
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Eumseong, Republic of Korea
| | - Kab-Yeul Jang
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Eumseong, Republic of Korea
| | - Hyunwoo Cho
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Tae Kyung Hyun
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Jwakyung Sung
- Department of Crop Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Yoon-Sup So
- Department of Crop Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Ick-Hyun Jo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Eumseong, Republic of Korea
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
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Beşer N, Mutafçılar ZÇ, Hasançebi S. Diversity analysis of the rice cultivars (
Oryza sativa
L.) by utilizing SSRs rice diversity by SSRs. J FOOD PROCESS PRES 2021. [DOI: 10.1111/jfpp.15232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Necmi Beşer
- Department of Genetics and Bioengineering Engineering Faculty Trakya University Edirne Turkey
| | - Zeynep Çisem Mutafçılar
- Department of Biotechnology and Genetics Institute of Science Trakya University Edirne Turkey
| | - Semra Hasançebi
- Department of Genetics and Bioengineering Engineering Faculty Trakya University Edirne Turkey
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27
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Raza Q, Riaz A, Saher H, Bibi A, Raza MA, Ali SS, Sabar M. Grain Fe and Zn contents linked SSR markers based genetic diversity in rice. PLoS One 2020; 15:e0239739. [PMID: 32986755 PMCID: PMC7521695 DOI: 10.1371/journal.pone.0239739] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/12/2020] [Indexed: 12/15/2022] Open
Abstract
Rice is critical for sustainable food and nutritional security; however, nominal micronutrient quantities in grains aggravate malnutrition in rice-eating poor populations. In this study, we evaluated genetic diversity in grain iron (Fe) and zinc (Zn) contents using trait-linked simple sequence repeat (SSR) markers in the representative subset of a large collection of local and exotic rice germplasm. Results demonstrated that aromatic fine grain accessions contained relatively higher Fe and Zn contents in brown rice (BR) than coarse grain accessions and a strong positive correlation between both mineral elements. Genotyping with 24 trait-linked SSR markers identified 21 polymorphic markers, among which 17 demonstrated higher gene diversity and polymorphism information content (PIC) values, strongly indicating that markers used in current research were moderate to highly informative for evaluating the genetic diversity. Population structure, principal coordinate and phylogenetic analyses classified studied rice accessions into two fine grain specific and one fine and coarse grain admixture subpopulations. Single marker analysis recognized four ZnBR and single FeBR significant marker-trait associations (MTAs) contributing 15.41-39.72% in total observed phenotypic variance. Furthermore, high grain Fe and Zn contents linked marker alleles from significant MTAs were also identified. Collectively, these results indicate a wide genetic diversity exist in grain Fe and Zn contents of studied rice accessions and reveal perspective for marker-assisted biofortification breeding.
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Affiliation(s)
- Qasim Raza
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
| | - Awais Riaz
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
| | - Hira Saher
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
| | - Ayesha Bibi
- Plant Pathology Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
| | - Mohsin Ali Raza
- Rice Technology Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab Pakistan
| | - Syed Sultan Ali
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
| | - Muhammad Sabar
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
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28
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Gene Pyramiding for Sustainable Crop Improvement against Biotic and Abiotic Stresses. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10091255] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Sustainable agricultural production is endangered by several ecological factors, such as drought, extreme temperatures, excessive salts, parasitic ailments, and insect pest infestation. These challenging environmental factors may have adverse effects on future agriculture production in many countries. In modern agriculture, conventional crop-breeding techniques alone are inadequate for achieving the increasing population’s food demand on a sustainable basis. The advancement of molecular genetics and related technologies are promising tools for the selection of new crop species. Gene pyramiding through marker-assisted selection (MAS) and other techniques have accelerated the development of durable resistant/tolerant lines with high accuracy in the shortest period of time for agricultural sustainability. Gene stacking has not been fully utilized for biotic stress resistance development and quality improvement in most of the major cultivated crops. This review emphasizes on gene pyramiding techniques that are being successfully deployed in modern agriculture for improving crop tolerance to biotic and abiotic stresses for sustainable crop improvement.
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29
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Ngernmuen A, Suktrakul W, Kate-Ngam S, Jantasuriyarat C. Transcriptome Comparison of Defense Responses in the Rice Variety 'Jao Hom Nin' Regarding Two Blast Resistant Genes, Pish and Pik. PLANTS 2020; 9:plants9060694. [PMID: 32485961 PMCID: PMC7356797 DOI: 10.3390/plants9060694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 11/24/2022]
Abstract
Jao Hom Nin (JHN) is a Thai rice variety with broad-spectrum resistant against rice blast fungus. JHN contains two rice blast resistant genes, Pish and Pik, located on chromosome 1 and on chromosome 11, respectively. To understand the blast resistance in JHN, the study of the defense mechanism related to the Pish and Pik genes is crucial. This study aimed to dissect defense response genes between the Pish and Pik genes using the RNA-seq technique. Differentially expressed genes (DEGs) of Pish and Pik backcross inbred lines were identified between 0 and 24 h after inoculation with rice blast spore suspension. The results showed that 1248 and 858 DEGs were unique to the Pish and Pik lines, respectively. The wall-associated kinase gene was unique to the Pish line and the zinc-finger-containing protein gene was unique to the Pik line. Pathogenicity-related proteins PR-4 and PR-10 were commonly found in both Pish and Pik lines. Moreover, DEGs functionally categorized in brassinosteriod, jasmonic acid, and salicylic acid pathways were detected in both Pish and Pik lines. These unique and shared genes in the Pish and Pik rice blast defense responses will help to dissect the mechanisms of plant defense and facilitate rice blast breeding programs.
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Affiliation(s)
- Athipat Ngernmuen
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkhen Campus, Ladyao, Chatuchak, Bangkok 10900, Thailand; (A.N.); (W.S.)
| | - Worrawit Suktrakul
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkhen Campus, Ladyao, Chatuchak, Bangkok 10900, Thailand; (A.N.); (W.S.)
| | - Sureeporn Kate-Ngam
- Department of Agronomy, Faculty of Agriculture, Ubon Ratchathani University, Warinchamrap, Ubon Ratchathani 34190, Thailand;
| | - Chatchawan Jantasuriyarat
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkhen Campus, Ladyao, Chatuchak, Bangkok 10900, Thailand; (A.N.); (W.S.)
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Kasetsart University, Bangkok 10900, Thailand
- Correspondence: ; Tel.: +662-562-5444
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30
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Daunay A, Duval A, Baudrin LG, Buhard O, Renault V, Deleuze JF, How-Kit A. Low temperature isothermal amplification of microsatellites drastically reduces stutter artifact formation and improves microsatellite instability detection in cancer. Nucleic Acids Res 2020; 47:e141. [PMID: 31584085 PMCID: PMC6868440 DOI: 10.1093/nar/gkz811] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/03/2019] [Accepted: 09/11/2019] [Indexed: 12/28/2022] Open
Abstract
Microsatellites are polymorphic short tandem repeats of 1–6 nucleotides ubiquitously present in the genome that are extensively used in living organisms as genetic markers and in oncology to detect microsatellite instability (MSI). While the standard analysis method of microsatellites is based on PCR followed by capillary electrophoresis, it generates undesirable frameshift products known as ‘stutter peaks’ caused by the polymerase slippage that can greatly complicate the analysis and interpretation of the data. Here we present an easy multiplexable approach replacing PCR that is based on low temperature isothermal amplification using recombinase polymerase amplification (LT-RPA) that drastically reduces and sometimes completely abolishes the formation of stutter artifacts, thus greatly simplifying the calling of the alleles. Using HT17, a mononucleotide DNA repeat that was previously proposed as an optimal marker to detect MSI in tumor DNA, we showed that LT-RPA improves the limit of detection of MSI compared to PCR up to four times, notably for small deletions, and simplifies the identification of the mutant alleles. It was successfully applied to clinical colorectal cancer samples and enabled detection of MSI. This easy-to-handle, rapid and cost-effective approach may deeply improve the analysis of microsatellites in several biological and clinical applications.
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Affiliation(s)
- Antoine Daunay
- Laboratory for Genomics, Foundation Jean Dausset - CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France
| | - Alex Duval
- Sorbonne-Université, Université Pierre et Marie Curie - Paris 6, Paris, France, INSERM, UMRS 938-Centre de Recherche Saint-Antoine, Equipe 'Instabilité des Microsatellites et Cancers', Equipe labellisée par la Ligue Nationale contre le Cancer, and SIRIC CURAMUS, Paris, France Université Pierre et Marie Curie, Paris, France
| | - Laura G Baudrin
- Laboratory for Genomics, Foundation Jean Dausset - CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France.,Laboratory of Excellence GenMed, Paris, France
| | - Olivier Buhard
- Sorbonne-Université, Université Pierre et Marie Curie - Paris 6, Paris, France, INSERM, UMRS 938-Centre de Recherche Saint-Antoine, Equipe 'Instabilité des Microsatellites et Cancers', Equipe labellisée par la Ligue Nationale contre le Cancer, and SIRIC CURAMUS, Paris, France Université Pierre et Marie Curie, Paris, France
| | - Victor Renault
- Laboratory for Bioinformatics, Foundation Jean Dausset - CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France
| | - Jean-François Deleuze
- Laboratory for Genomics, Foundation Jean Dausset - CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France.,Centre National de Recherche en Génomique Humaine, CEA-Institut François Jacob, Evry, France
| | - Alexandre How-Kit
- Laboratory for Genomics, Foundation Jean Dausset - CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France
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31
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Aiello D, Ferradini N, Torelli L, Volpi C, Lambalk J, Russi L, Albertini E. Evaluation of Cross-Species Transferability of SSR Markers in Foeniculum vulgare. PLANTS (BASEL, SWITZERLAND) 2020; 9:E175. [PMID: 32024130 PMCID: PMC7076658 DOI: 10.3390/plants9020175] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/30/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Fennel (Foeniculum vulgare) is a species belonging to the Apiaceae family, well known for its nutritional and pharmacological properties. Despite the economic and agricultural relevance, its genomic and transcriptomic data remain poor. Microsatellites-also known as simple sequence repeats (SSRs)-are codominant markers widely used to perform cross-amplification tests starting from markers developed in related species. SSRs represent a powerful tool, especially for those species lacking genomic information. In this study, a set of primers previously designed in Daucus carota for polymorphic SSR loci was tested in commercial varieties and breeding lines of fennel in order to: (i) test their cross-genera transferability, (ii) look at their efficiency in assessing genetic diversity, and (iii) identify their usefulness for marker-assisted selection (MAS) in breeding programs. Thirty-nine SSR markers from carrot were selected and tested for their transferability score, and only 23% of them resulted suitable for fennel. The low rate of SSR transferability between the two species evidences the difficulties of the use of genomic SSR in cross-genera transferability.
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Affiliation(s)
- Domenico Aiello
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (D.A.); (N.F.); (L.T.); (L.R.)
| | - Nicoletta Ferradini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (D.A.); (N.F.); (L.T.); (L.R.)
| | - Lorenzo Torelli
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (D.A.); (N.F.); (L.T.); (L.R.)
| | - Chiara Volpi
- Enza Zaden Italia Research S.r.l. SS., 01016 Tarquinia, Italy;
| | - Joep Lambalk
- Enza Zaden, Research and Development B.V. P.O. Box 7, 1600AA Enkhuizen, The Netherlands;
| | - Luigi Russi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (D.A.); (N.F.); (L.T.); (L.R.)
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (D.A.); (N.F.); (L.T.); (L.R.)
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Tibihika PD, Curto M, Alemayehu E, Waidbacher H, Masembe C, Akoll P, Meimberg H. Molecular genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus, L. 1758) in East African natural and stocked populations. BMC Evol Biol 2020; 20:16. [PMID: 32000675 PMCID: PMC6990601 DOI: 10.1186/s12862-020-1583-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/16/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The need for enhancing the productivity of fisheries in Africa triggered the introduction of non-native fish, causing dramatic changes to local species. In East Africa, the extensive translocation of Nile tilapia (Oreochromis niloticus) is one of the major factors in this respect. Using 40 microsatellite loci with SSR-GBS techniques, we amplified a total of 664 individuals to investigate the genetic structure of O. niloticus from East Africa in comparison to Ethiopian and Burkina Faso populations. RESULTS All three African regions were characterized by independent gene-pools, however, the Ethiopian population from Lake Tana was genetically more divergent (Fst = 2.1) than expected suggesting that it might be a different sub-species. In East Africa, the genetic structure was congruent with both geographical location and anthropogenic activities (Isolation By Distance for East Africa, R2 = 0.67 and Uganda, R2 = 0.24). O. niloticus from Lake Turkana (Kenya) was isolated, while in Uganda, despite populations being rather similar to each other, two main natural catchments were able to be defined. We show that these two groups contributed to the gene-pool of different non-native populations. Moreover, admixture and possible hybridization with other tilapiine species may have contributed to the genetic divergence found in some populations such as Lake Victoria. We detected other factors that might be affecting Nile tilapia genetic variation. For example, most of the populations have gone through a reduction in genetic diversity, which can be a consequence of bottleneck (G-W, < 0.5) caused by overfishing, genetic erosion due to fragmentation or founder effect resulting from stocking activities. CONCLUSIONS The anthropogenic activities particularly in the East African O. niloticus translocations, promoted artificial admixture among Nile Tilapia populations. Translocations may also have triggered hybridization with the native congenerics, which needs to be further studied. These events may contribute to outbreeding depression and hence compromising the sustainability of the species in the region.
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Affiliation(s)
- Papius Dias Tibihika
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, 1180 Wien, Austria
- National Agricultural Research Organization, Kachwekano Zonal Agricultural Research and Development Institute, P.O. Box 421, Kabale, Uganda
| | - Manuel Curto
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, 1180 Wien, Austria
| | - Esayas Alemayehu
- National Agricultural Research Organization, Kachwekano Zonal Agricultural Research and Development Institute, P.O. Box 421, Kabale, Uganda
- Institute for Hydrobiology and Aquatic Ecosystems Management, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33/DG, 1180 Wien, Austria
| | - Herwig Waidbacher
- National Fishery and Aquatic Life Research Centre, P.O. Box 64, Addis Ababa, Sebeta Ethiopia
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences-Makerere University Kampala, P. O. Box, 7062 Kampala, Uganda
| | - Peter Akoll
- Department of Zoology, Entomology and Fisheries Sciences-Makerere University Kampala, P. O. Box, 7062 Kampala, Uganda
| | - Harald Meimberg
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, 1180 Wien, Austria
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Chukwu SC, Rafii MY, Ramlee SI, Ismail SI, Oladosu Y, Muhammad I, Ubi BE, Nwokwu G. Genetic analysis of microsatellites associated with resistance against bacterial leaf blight and blast diseases of rice ( Oryza sativa L.). BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1809520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Samuel Chibuike Chukwu
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Mohd Y. Rafii
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Shairul Izan Ramlee
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Siti Izera Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Yusuff Oladosu
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Isma’ila Muhammad
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Benjamin Ewa Ubi
- Department of Biotechnology, Faculty of Science, Ebonyi State University, Abakaliki, Nigeria
| | - Gilbert Nwokwu
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
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Gavhane DB, Kulwal PL, Kumbhar SD, Jadhav AS, Sarawate CD. Cataloguing of blast resistance genes in landraces and breeding lines of rice from India. J Genet 2019; 98:106. [PMID: 31819018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The rice blast caused by the fungus Magnaporthe oryzae is one of the most devastating diseases of rice and can lead to complete failure of the crop under severe cases. The first step in breeding for blast resistance in rice is therefore to identify the novel sources of resistance and cataloguing different blast resistant genes in these genotypes. In the present study, a set of 37 rice genotypes comprising of landraces, advanced breeding lines and released varieties were first characterized for blast resistance under epiphytotic conditions and subsequently different blast resistant genes were catalogued with the help of markers tightly linked to these genes. A total of 22 different blast resistant genes were catalogued in these genotypes. Lot of diversity was found to be present for different genes in the rice genotypes studied. In addition, a set of 2-3 markers were identified which could distinguish genotypes of a particular geographic area from each other.The results are useful for identifying the right combination of genotypes in the resistance breeding programme.
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Affiliation(s)
- Dnyaneshwar B Gavhane
- State Level Biotechnology Centre, Mahatma Phule Agricultural University, Rahuri 413 722, India.
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GAVHANE DNYANESHWARB, KULWAL PAWANL, KUMBHAR SHAILESHD, JADHAV ASHOKS, SARAWATE CHANDRAKANTD. Cataloguing of blast resistance genes in landraces and breeding lines of rice from India. J Genet 2019. [DOI: 10.1007/s12041-019-1148-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Substantial enhancement of high polymorphic SSR marker development using in silico method from 18 available rice blast fungus genome sequences and its application in genetic diversity assessment. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00264-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Khade KA, Panigrahi M, Ahmad SF, Kumar P, Bhushan B. Genetic characterization and assessment of diversity in Pandharpuri buffalo breed of India using heterologous microsatellite markers. Anim Biotechnol 2019; 31:426-431. [PMID: 31092100 DOI: 10.1080/10495398.2019.1612757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The present study was aimed at genetic characterization and diversity analysis of Pandharpuri buffalo population using the Food and Agriculture Organization (FAO) recommended bovine microsatellite markers. Genomic DNA was isolated from blood samples of 50 unrelated animals and a total of 23 microsatellite loci were amplified using polymerase chain reaction. Among 23 recommended microsatellite markers, 14 markers (BM2113, BM1818, CSSM66, HEL13, INRA037, ILSTS05, HAUT27, INRA023, INRA035, HEL5, ETH3, NRA063, MM12 and ETH10) were found to be highly polymorphic in Pandharpuri population. The amplified products were run on polyacrylamide gel electrophoresis (PAGE) apparatus along with a ladder; subsequently, the allele typing was done based on silver staining of the gel. The effective and observed number of alleles, heterozygosity (expected and unbiased) estimates and polymorphic information content (PIC) levels were estimated for each locus. A total of 87 alleles were secured for 14 polymorphic loci studied giving an overall average of 6.21 alleles per locus. The number of alleles ranged from 2 (INRA063) to 9 (BM1818 and HEL13). The mean effective number of alleles across all polymorphic loci was found to be 4.28. The overall mean expected heterozygosity and unbiased expected heterozygosity values were 0.77 and 0.76, ranging from 0.50 (INRA063) to 0.88 (BM1818) and 0.50 (INRA063) to 0.88 (BM1818), respectively. The average PIC estimate across all polymorphic loci was 0.73 ranging from 0.373 (INRA063) to 0.864 (BM1818). In the present study, the characterization and diversity estimates are reported for Pandharpuri population. It was found to maintain optimum diversity based on 14 polymorphic microsatellite markers.
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Affiliation(s)
- Krishnadeo Ankush Khade
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Sheikh Firdous Ahmad
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Pushpendra Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
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Kitazawa N, Shomura A, Mizubayashi T, Ando T, Nagata K, Hayashi N, Takahashi A, Yamanouchi U, Fukuoka S. Rapid DNA-genotyping system targeting ten loci for resistance to blast disease in rice. BREEDING SCIENCE 2019; 69:68-83. [PMID: 31086485 PMCID: PMC6507720 DOI: 10.1270/jsbbs.18143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/13/2018] [Indexed: 06/09/2023]
Abstract
The fungal pathogen Pyricularia oryzae causes blast, a severe disease of rice (Oryza sativa L.). Improving blast resistance is important in rice breeding programs. Inoculation tests have been used to select for resistance genotypes, with DNA marker-based selection becoming an efficient alternative. No comprehensive DNA marker system for race-specific resistance alleles in the Japanese rice breeding program has been developed because some loci contain multiple resistance alleles. Here, we used the Fluidigm SNP genotyping platform to determine a set of 96 single nucleotide polymorphism (SNP) markers for 10 loci with race-specific resistance. The markers were then used to evaluate the presence or absence of 24 resistance alleles in 369 cultivars; results were 93.5% consistent with reported inoculation test-based genotypes in japonica varieties. The evaluation system was successfully applied to high-yield varieties with indica genetic backgrounds. The system includes polymorphisms that distinguish the resistant alleles at the tightly linked Pita and Pita-2 loci, thereby confirming that all the tested cultivars with Pita-2 allele carry Pita allele. We also developed and validated insertion/deletion (InDel) markers for ten resistance loci. Combining SNP and InDel markers is an accurate and efficient strategy for selection for race-specific resistance to blast in breeding programs.
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Affiliation(s)
- Noriyuki Kitazawa
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Ayahiko Shomura
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Tatsumi Mizubayashi
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Tsuyu Ando
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Kazufumi Nagata
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Nagao Hayashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Akira Takahashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Utako Yamanouchi
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Shuichi Fukuoka
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
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Ding Y, Xue L, Guo RX, Luo GJ, Song YT, Lei JJ. De Novo Assembled Transcriptome Analysis and Identification of Genic SSR Markers in Red-Flowered Strawberry. Biochem Genet 2019; 57:607-622. [PMID: 30825077 DOI: 10.1007/s10528-019-09912-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 02/19/2019] [Indexed: 10/27/2022]
Abstract
Red-flowered strawberry is a new ornamental flower derived from intergeneric hybridization (Fragaria × Potentilla). To date, few molecular markers have been reported for this plant. RNA sequencing provides a relatively fast and low-cost approach for large-scale detection of simple sequence repeats (SSRs). In the present study, we profiled the transcriptome of red-flowered strawberry by Illumina HiSeq 2500 to identify SSRs related to petal color. Based on 2 million clean reads of red and white flowers from red-flowered strawberry hybrids, we assembled 91,835 unigenes with an average length of 717 bp. After functional annotation and prediction, there were 47,058 unigenes; of these, 26,861 had a gene ontology annotation, with 14,264 SSR loci. Mononucleotide SSRs were the predominant repeat type (47.20%, n = 6724), followed by di- (32.50%, n = 4641), tri- (19.10%, n = 2729), tetra- (0.90%, n = 132), hexa- (0.2%, n = 21), and penta- (0.10%, n = 16) nucleotide repeats. The most frequent di-, tri-, and tetra-nucleotide repeats were AG/CT, AAG/CTT, and AAAG/CTTT, respectively. PCR amplification with 105 SSR primer pairs yielded four bands specific to red flowers, namely UgRFsr57622, UgRFsr94149, UgRFsr40142, and UgRFsr54608; corresponding 4 trait-specific markers were found to co-segregate with white and red flower color in hybrid population, demonstrating that the genic SSR marker is useful to discriminate between white and red flowers in strawberry. Markers to discriminate flower color in red-flowered strawberry will be useful for early selection of progeny and for breeding management.
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Affiliation(s)
- Yan Ding
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Li Xue
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Rui-Xue Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Gang-Jun Luo
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yu-Tong Song
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jia-Jun Lei
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
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40
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Kumar M, Rakesh Sharma V, Kumar V, Sirohi U, Chaudhary V, Sharma S, Saripalli G, Naresh RK, Yadav HK, Sharma S. Genetic diversity and population structure analysis of Indian garlic ( Allium sativum L.) collection using SSR markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:377-386. [PMID: 30956421 PMCID: PMC6419858 DOI: 10.1007/s12298-018-0628-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/07/2018] [Accepted: 11/16/2018] [Indexed: 05/03/2023]
Abstract
Genetic diversity was assessed among 53 Indian garlic accessions using SSR markers. Initially, 24 SSR primer pairs were used for screening three selected garlic accessions. Out of 24 SSR primer pairs, 10 primer pairs which consistently showed good amplification and polymorphism were selected for DNA profiling. SSR primer pairs showed PIC values ranging from 0.30 to 0.99. Based on AMOVA we found that the greater part of the genetic diversity was expected due to intra population with 84% variation and only 16% of variation was due to among populations suggesting presence of genetic structure. The results of cluster analysis and principal component analysis largely correspond to each other. Population structure analysis revealed genetic differentiation of accessions. The results of present study revealed existence of significant variability in Indian garlic germplasm.
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Affiliation(s)
- Mukesh Kumar
- Department of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, 250110 UP India
| | - V. Rakesh Sharma
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 UP India
| | - Vipin Kumar
- Department of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, 250110 UP India
| | - Ujjawal Sirohi
- Department of Agri. Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, 250110 UP India
| | - Veena Chaudhary
- Department of Chemistry, Meerut College, Meerut, 250003 UP India
| | - Shiveta Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 UP India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 UP India
| | - R. K. Naresh
- Department of Agronomy, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, 250110 UP India
| | - Hemant Kumar Yadav
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 UP India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 UP India
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Chukwu SC, Rafii MY, Ramlee SI, Ismail SI, Oladosu Y, Okporie E, Onyishi G, Utobo E, Ekwu L, Swaray S, Jalloh M. Marker-assisted selection and gene pyramiding for resistance to bacterial leaf blight disease of rice (Oryza sativa L.). BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1584054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Samuel Chibuike Chukwu
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Mohd Y. Rafii
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Shairul Izan Ramlee
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Siti Izera Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Yussuf Oladosu
- Department of Crop Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Emmanuel Okporie
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Godwin Onyishi
- Department of Crop Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Emeka Utobo
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Lynda Ekwu
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Senesie Swaray
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Momodu Jalloh
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
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Platten JD, Cobb JN, Zantua RE. Criteria for evaluating molecular markers: Comprehensive quality metrics to improve marker-assisted selection. PLoS One 2019; 14:e0210529. [PMID: 30645632 PMCID: PMC6333336 DOI: 10.1371/journal.pone.0210529] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 12/26/2018] [Indexed: 11/18/2022] Open
Abstract
Despite strong interest over many years, the usage of quantitative trait loci in plant breeding has often failed to live up to expectations. A key weak point in the utilisation of QTLs is the “quality” of markers used during marker-assisted selection (MAS): unreliable markers result in variable outcomes, leading to a perception that MAS products fail to achieve reliable improvement. Most reports of markers used for MAS focus on markers derived from the mapping population. There are very few studies that examine the reliability of these markers in other genetic backgrounds, and critically, no metrics exist to describe and quantify this reliability. To improve the MAS process, this work proposes five core metrics that fully describe the reliability of a marker. These metrics give a comprehensive and quantitative measure of the ability of a marker to correctly classify germplasm as QTL[+]/[–], particularly against a background of high allelic diversity. Markers that score well on these metrics will have far higher reliability in breeding, and deficiencies in specific metrics give information on circumstances under which a marker may not be reliable. The metrics are applicable across different marker types and platforms, allowing an objective comparison of the performance of different markers irrespective of the platform. Evaluating markers using these metrics demonstrates that trait-specific markers consistently out-perform markers designed for other purposes. These metrics also provide a superb set of criteria for designing superior marker systems for a target QTL, enabling the selection of an optimal marker set before committing to design.
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Tibihika PD, Curto M, Dornstauder-Schrammel E, Winter S, Alemayehu E, Waidbacher H, Meimberg H. Application of microsatellite genotyping by sequencing (SSR-GBS) to measure genetic diversity of the East African Oreochromis niloticus. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1136-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Song S, Tian D, Zhang Z, Hu S, Yu J. Rice Genomics: over the Past Two Decades and into the Future. GENOMICS, PROTEOMICS & BIOINFORMATICS 2018; 16:397-404. [PMID: 30771506 PMCID: PMC6411948 DOI: 10.1016/j.gpb.2019.01.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/14/2019] [Accepted: 01/23/2019] [Indexed: 01/08/2023]
Abstract
Domestic rice (Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct field applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we briefly review its achievements over the past two decades and present the potential for its bright future.
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Affiliation(s)
- Shuhui Song
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Dongmei Tian
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhang Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Ridzuan R, Rafii MY, Ismail SI, Mohammad Yusoff M, Miah G, Usman M. Breeding for Anthracnose Disease Resistance in Chili: Progress and Prospects. Int J Mol Sci 2018; 19:E3122. [PMID: 30314374 PMCID: PMC6213496 DOI: 10.3390/ijms19103122] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/17/2018] [Accepted: 08/18/2018] [Indexed: 11/16/2022] Open
Abstract
Chili anthracnose is one of the most devastating fungal diseases affecting the quality and yield production of chili. The aim of this review is to summarize the current knowledge concerning the chili anthracnose disease, as well as to explore the use of marker-assisted breeding programs aimed at improving anthracnose disease resistance in this species. This disease is caused by the Colletotrichum species complex, and there have been ongoing screening methods of chili pepper genotypes with resistance to anthracnose in the field, as well as in laboratories. Conventional breeding involves phenotypic selection in the field, and it is more time-consuming compared to molecular breeding. The use of marker-assisted selection (MAS) on the basis of inheritance, the segregation ratio of resistance to susceptibility, and the gene-controlling resistance may contribute to the development of an improved chili variety and speed up the selection process, while also reducing genetic drag in the segregating population. More importantly, by using molecular markers, the linkage groups are determined dominantly and co-dominantly, meaning that the implementation of a reliable method to produce resistant varieties is crucial in future breeding programs. This updated information will offer a supportive direction for chili breeders to develop an anthracnose-resistant chili variety.
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Affiliation(s)
- Raihana Ridzuan
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Mohd Y Rafii
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Siti Izera Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Martini Mohammad Yusoff
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Gous Miah
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Magaji Usman
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
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Li SF, Wang BX, Guo YJ, Deng CL, Gao WJ. Genome-wide characterization of microsatellites and genetic diversity assessment of spinach in the Chinese germplasm collection. BREEDING SCIENCE 2018; 68:455-464. [PMID: 30369820 PMCID: PMC6198904 DOI: 10.1270/jsbbs.18032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/09/2018] [Indexed: 05/02/2023]
Abstract
Spinach is a nutritional leafy green vegetable, and it also serves as a model species for studying sex chromosome evolution. Genetic marker development and genome structure analysis are important in breeding practice and theoretical evolution studies of spinach. In this study, the frequency and distribution of different microsatellites in the recently released draft spinach genome were characterized. A total of 261,002 perfect microsatellites were identified (estimated frequency: ~262.1 loci/Mbp). The most abundant microsatellites were tetranucleotide and trinucleotide, accounting for 33.2% and 27.7% of the total number of microsatellites, respectively. A total of 105 primer pairs were designed and screened, and 34 were polymorphic among the detected spinach cultivars. Combined with seven primer sets developed previously, 41 primer pairs were used to investigate genetic diversity among 43 spinach cultivars in China. The average polymorphism information content value of the 41 markers was 0.43, representing an intermediate level. The spinach cultivars had a low genetic diversity, and no detectable common factors were shared by each group in the UPGMA dendrogram. This study's findings facilitate further investigations on the organization of the microsatellites in spinach genome and provide clues for future breeding applications of spinach in China.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University,
Xinxiang 453007,
China
| | - Bing-Xiao Wang
- College of Life Sciences, Henan Normal University,
Xinxiang 453007,
China
| | - Yu-Jiao Guo
- College of Life Sciences, Henan Normal University,
Xinxiang 453007,
China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University,
Xinxiang 453007,
China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University,
Xinxiang 453007,
China
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Wang X, Yang S, Chen Y, Zhang S, Zhao Q, Li M, Gao Y, Yang L, Bennetzen JL. Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana. BMC Genomics 2018; 19:500. [PMID: 29945549 PMCID: PMC6020451 DOI: 10.1186/s12864-018-4878-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 06/18/2018] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Simple sequence repeats (SSRs) are tandem repeats of DNA that have been used to develop robust genetic markers. These molecular markers are powerful tools for basic and applied studies such as molecular breeding. In the model plants in Nicotiana genus e.g. N. benthamiana, a comprehensive assessment of SSR content has become possible now because several Nicotiana genomes have been sequenced. We conducted a genome-wide SSR characterization and marker development across seven Nicotiana genomes. RESULTS Here, we initially characterized 2,483,032 SSRs (repeat units of 1-10 bp) from seven genomic sequences of Nicotiana and developed SSR markers using the GMATA® software package. Of investigated repeat units, mono-, di- and tri-nucleotide SSRs account for 98% of all SSRs in Nicotiana. More complex SSR motifs, although rare, are highly variable between Nicotiana genomes. A total of 1,224,048 non-redundant Nicotiana (NIX) markers were developed, of which 99.98% are novel. An efficient and uniform genotyping protocol for NIX markers was developed and validated. We created a web-based database of NIX marker information including amplicon sizes of alleles in each genome for downloading and online analysis. CONCLUSIONS The present work constitutes the first deep characterization of SSRs in seven genomes of Nicotiana, and the development of NIX markers for these SSRs. Our online marker database and an efficient genotyping protocol facilitate the application of these markers. The NIX markers greatly expand Nicotiana marker resources, thus providing a useful tool for future research and breeding. We demonstrate a novel protocol for SSR marker development and utilization at the whole genome scale that can be applied to any lineage of organisms. The Tobacco Markers & Primers Database (TMPD) is available at http://biodb.sdau.edu.cn/tmpd/index.html.
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Affiliation(s)
- Xuewen Wang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201 People’s Republic of China
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
| | - Shuai Yang
- Agricultural Big-Data Research Center, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 China
| | - Yongdui Chen
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650223 People’s Republic of China
| | - Shumeng Zhang
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
| | - Qingshi Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201 People’s Republic of China
| | - Meng Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201 People’s Republic of China
| | - Yulong Gao
- Tobacco Breeding Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021 Yunnan China
| | - Long Yang
- Agricultural Big-Data Research Center, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 China
| | - Jeffrey L. Bennetzen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201 People’s Republic of China
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
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48
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la Bastide PYD, Naumann C, Hintz WE. Assessment of intra-specific variability in Saprolegnia parasitica populations of aquaculture facilities in British Columbia, Canada. DISEASES OF AQUATIC ORGANISMS 2018; 128:235-248. [PMID: 29862981 DOI: 10.3354/dao03224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Among the Saprolegnia species found in aquaculture facilities, S. parasitica is recognized as the primary fish pathogen and remains an ongoing concern in fish health management. Until recently, these pathogens were kept in check by use of malachite green; due to its toxicity, this chemical has now been banned from use in many countries. It is difficult to predict and control S. parasitica outbreaks in freshwater systems and there is a need to understand the population genetic structure of this pathogen. Genetic characterization of this species in aquaculture systems would provide information to track introductions and determine possible sources of inoculum. Degenerate PCR primers containing short sequence repeats were used to create microsatellite-associated genetic markers (random amplified microsatellites) for the comparison of S. parasitica isolates collected primarily from commercial Atlantic salmon aquaculture systems in British Columbia, Canada, over a 15 mo period to describe their spatial and temporal variability. The frequencies of amplified products were compared and the population genetic diversity was measured using Nei's genetic distance and Shannon's information index, while the species population structure was evaluated by phylogenetic analysis. S. parasitica was detected in all facilities sampled. Genetic diversity was low but not clonal, most likely due to repeated introduction events and a low level of sexual recombination over time. A better understanding of pathogen population structure will assist the development of effective preventative measures and targeted treatments for disease outbreaks.
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Affiliation(s)
- Paul Y de la Bastide
- Department of Biology, Centre for Forest Biology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
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Beier S, Thiel T, Münch T, Scholz U, Mascher M. MISA-web: a web server for microsatellite prediction. Bioinformatics 2018; 33:2583-2585. [PMID: 28398459 PMCID: PMC5870701 DOI: 10.1093/bioinformatics/btx198] [Citation(s) in RCA: 1032] [Impact Index Per Article: 172.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/06/2017] [Indexed: 12/27/2022] Open
Abstract
Motivation Microsatellites are a widely-used marker system in plant genetics and forensics. The development of reliable microsatellite markers from resequencing data is challenging. Results We extended MISA, a computational tool assisting the development of microsatellite markers, and reimplemented it as a web-based application. We improved compound microsatellite detection and added the possibility to display and export MISA results in GFF3 format for downstream analysis. Availability and Implementation MISA-web can be accessed under http://misaweb.ipk-gatersleben.de/. The website provides tutorials, usage note as well as download links to the source code. Contact scholz@ipk-gatersleben.de.
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Affiliation(s)
- Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Thomas Thiel
- KWS Saat SE, Grimsehlstr. 31, 37555 Einbeck, Germany
| | - Thomas Münch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany
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50
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Zhao Z, Tseng YC, Peng Z, Lopez Y, Chen CY, Tillman BL, Dang P, Wang J. Refining a major QTL controlling spotted wilt disease resistance in cultivated peanut (Arachis hypogaea L.) and evaluating its contribution to the resistance variations in peanut germplasm. BMC Genet 2018; 19:17. [PMID: 29571286 PMCID: PMC5865372 DOI: 10.1186/s12863-018-0601-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 03/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spotted wilt, caused by tomato spotted wilt virus (TSWV), has been one of major diseases in cultivated peanut grown in the southeastern United States (US) since 1990. Previously a major quantitative trait locus (QTL) controlling spotted wilt disease resistance was mapped to an interval of 2.55 cM genetic distance corresponding to a physical distance of 14.4 Mb on chromosome A01 of peanut by using a segregating F2 population. The current study focuses on refining this major QTL region and evaluating its contributions in the US peanut mini-core germplasm. RESULTS Two simple sequence repeat (SSR) markers associated with the major QTL were used to genotype F5 individuals, and 25 heterozygous individuals were selected and developed into an F6 segregating population. Based on visual evaluation in the field, a total of 194 susceptible F6 individuals were selected and planted into F7 generation for phenotyping. Nine SSR markers were used to genotype the 194 F6 individuals, and QTL analysis revealed that a confidence interval of 15.2 Mb region had the QTL with 22.8% phenotypic variation explained (PVE). This QTL interval was further genotyped using the Amplicon-seq method. A total of 81 non-redundant single nucleotide polymorphism (SNP) and eight InDel markers were detected. No recombinant was detected among the F6 individuals. Two InDel markers were integrated into the linkage group and helped to refine the confidence interval of this QTL into a 0.8 Mb region. To test the QTL contributes to the resistance variance in US peanut mini-core germplasm, two flanking SSR markers were used to genotype 107 mini-core germplasm accessions. No statistically significant association was observed between the genotype at the QTL region and spotted wilt resistance in the mini-core germplasm, which indicated that the resistance allelic region at this QTL didn't contribute to the resistance variance in the US peanut mini-core germplasm, thus was a unique resistance source. CONCLUSION A major QTL related to spotted wilt disease resistance in peanut was refined to a 0.8 Mb region on A01 chromosome, which didn't relate to spotted wilt disease resistance in the US peanut mini-core germplasm and might be a unique genetic source.
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Affiliation(s)
- Zifan Zhao
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Yu-Chien Tseng
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.,North Florida Research and Education Center, University of Florida, Marianna, FL, 32446, USA
| | - Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Yolanda Lopez
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Charles Y Chen
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Barry L Tillman
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.,North Florida Research and Education Center, University of Florida, Marianna, FL, 32446, USA
| | - Phat Dang
- USDA-ARS National Peanut Research Laboratory, Dawson, GA, 39842, USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA. .,Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
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