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Hsiao C, Lin HH, Kang SR, Hung CY, Sun PY, Yu CC, Toh KL, Yu PJ, Ju YT. Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer. PLoS One 2022; 17:e0265311. [PMID: 35363791 PMCID: PMC8975116 DOI: 10.1371/journal.pone.0265311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 03/01/2022] [Indexed: 11/19/2022] Open
Abstract
Deer genera around the globe are threatened by anthropogenic interference. The translocation of alien species and their subsequent genetic introgression into indigenous deer populations is particularly harmful to the species of greatest conservation concern. Products derived from deer, including venison and antler velvet, are also at risk of fraudulent labeling. The current molecular markers used to genetically identify deer species were developed from genome sequences and have limited applicability for cross-species amplification. The absence of efficacious diagnostic techniques for identifying deer species has hampered conservation and wildlife crime investigation efforts. Expressed sequence tag-simple sequence repeat (EST-SSR) markers are reliable tools for individual and species identification, especially in terms of cross-species genotyping. We conducted transcriptome sequencing of sambar (Rusa unicolor) antler velvet and acquired 11,190 EST-SSRs from 65,074 newly assembled unigenes. We identified a total of 55 unambiguous amplicons in sambar (n = 45), which were selected as markers to evaluate cross-species genotyping in sika deer (Cervus nippon, n = 30) and red deer (Cervus elaphus, n = 46), resulting in cross-species amplification rates of 94.5% and 89.1%, respectively. Based on polymorphic information content (>0.25) and genotyping fidelity, we selected 16 of these EST-SSRs for species identification. This marker set revealed significant genetic differentiation based on the fixation index and genetic distance values. Principal coordinate analysis and STRUCTURE analysis revealed distinct clusters of species and clearly identified red-sika hybrids. These markers showed applicability across different genera and proved suitable for identification and phylogenetic analyses across deer species.
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Affiliation(s)
- Chen Hsiao
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Hsin-Hung Lin
- Kaohsiung Animal Propagation Station, Pingdong, Taiwan
| | | | - Chien-Yi Hung
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Pei-Yu Sun
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Chieh-Cheng Yu
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Kok-Lin Toh
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Pei-Ju Yu
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Yu-Ten Ju
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
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Koshiishi Y, Uchiyama H, Murata-Okubo M, Tanaka K, Kameyama Y, Hirayama H, Wada K. Development of 49 novel microsatellite markers from Next-generation sequencing data and a robust method for parentage tests in the emu (Dromaius novaehollandiae). Gene 2020; 769:145238. [PMID: 33068676 DOI: 10.1016/j.gene.2020.145238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/16/2020] [Accepted: 10/11/2020] [Indexed: 10/23/2022]
Abstract
The emu is a useful and new breed of poultry, but their genetic improvement has not advanced yet due to their very recent domestication. Pedigree information is difficult to record because of their complex reproduction system (polyandry). To identify parent-offspring relationships in the emu, parentage test based on polymorphic DNA markers have to be developed. In this study, we isolated more than 25,000 microsatellite (simple sequence repeat, SSR) regions from Next-generation sequencing data via the QDD pipeline and developed 49 SSR markers with polymorphism in the Japanese farmed emu. The dinucleotide motifs, (AC)n, (AT)n and (AG)n, were the most frequently detected and were found on 10,167 (38.55%), 8,114 (30.76%) and 4,796 (18.18%) contigs, respectively. Forty-nine novel SSR markers were characterized in 20 individuals and showed NA ranged from 2 to 12, with an average of 4.2. HE/HO ranged from 0.389/0.071 to 0.702/1.000 with an average of 0.601/0.515. PIC value ranged from 0.059 to 0.886 with an average of 0.528, and 17 of 49 markers showed a higher polymorphism than 0.500. Thirty-four individuals were genotyped using 12 markers, and CERVUS simulations based on genotype showed that parents of all offspring were identified with 0.9995-1.0 probability. Thus, 49 novel SSR markers and a robust method for parentage test for the Japanese emu were developed.
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Affiliation(s)
- Yuichi Koshiishi
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan
| | - Hironobu Uchiyama
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Michiko Murata-Okubo
- Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yuichi Kameyama
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan
| | - Hiroki Hirayama
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan
| | - Kenta Wada
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan.
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Devadasan MJ, Kumar DR, Vineeth MR, Choudhary A, Surya T, Niranjan SK, Verma A, Sivalingam J. Reduced representation approach for identification of genome-wide SNPs and their annotation for economically important traits in Indian Tharparkar cattle. 3 Biotech 2020; 10:309. [PMID: 32582506 DOI: 10.1007/s13205-020-02297-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/09/2020] [Indexed: 11/24/2022] Open
Abstract
The present study was carried out in Tharparkar cattle for identification of genome-wide SNPs and microsatellites, and then annotate the identified high-quality SNPs to milk production, fertility, carcass, adaptability and immune response of economically important traits. A total of 146,011 SNPs were identified with respect to Bos taurus reference genome which are indicus specific, out of which 10,519 SNPs were found to be novel. Similarly, a total of 87,047 SNPs were identified with respect to Bos indicus reference genome. After final annotation of SNPs identified with respect to Bos indicus reference genome, 2871 SNPs were found to be associated in 383 candidate genes having to do with milk production, fertility, carcass, immune response and adaptability traits. Following that, 2571 microsatellites were identified. The information mined from the data might be of importance for the future breed improvement programs, conservation efforts and for enhancing the SNPs density of the existing bovine SNP chips.
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Affiliation(s)
| | - D Ravi Kumar
- ICAR-National Dairy Research Institute, Karnal, India
| | - M R Vineeth
- ICAR-National Dairy Research Institute, Karnal, India
| | | | - T Surya
- ICAR-National Dairy Research Institute, Karnal, India
| | - S K Niranjan
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Archana Verma
- ICAR-National Dairy Research Institute, Karnal, India
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Sen S, Dehury B, Sahu J, Rathi S, Yadav RNS. Mining and comparative survey of EST-SSR markers among members of Euphorbiaceae family. Mol Biol Rep 2018; 45:453-468. [PMID: 29626317 DOI: 10.1007/s11033-018-4181-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 04/02/2018] [Indexed: 11/30/2022]
Abstract
Euphorbiaceae represents flowering plants family of tropical and sub-tropical region rich in secondary metabolites of economic importance. To understand and assess the genetic makeup among the members, this study was undertaken to characterize and compare SSR markers from publicly available ESTs and GSSs of nine selected species of the family. Mining of SSRs was performed by MISA, primer designing by Primer3, while functional annotation, gene ontology (GO) and enrichment analysis were performed by Blast2GO. A total 12,878 number of SSRs were detected from 101,701 number of EST sequences. SSR density ranged from 1 SSR/3.22 kb to 1 SSR/15.65 kb. A total of 1873 primer pairs were designed for the annotated SSR-Contigs. About 77.07% SSR-ESTs could be assigned a significant match to the protein database. 3037 unique SSR-FDM were assigned and IPR003657 (WRKY Domain) was found to be the most dominant FDM among the members. 1810 unique GO terms obtained were further subjected to enrichment analysis to obtain 513 statistically significant GO terms mapped to the SSR containing ESTs. Most frequent enriched GO terms were, GO:0003824 for molecular function, GO:0006350 for biological process and GO:0005886 for cellular component, justifying the richness of defensive secondary metabolites and phytomedicine within the family. The results from this study provides tangible insight to genetic make-up and distribution of SSRs. Functional annotation corresponded many genes of unknown functions which may be considered as novel genes or genes responsible for stress specific secondary metabolites. Further studies are required to understand stress specific genes accountable for leveraging the synthesis of secondary metabolites.
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Affiliation(s)
- Surojit Sen
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam, India.
| | - Budheswar Dehury
- Biomedical Informatics Centre, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
| | - Jagajjit Sahu
- Distributed Information Center, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Sunayana Rathi
- Department of Biochemistry and Agricultural Chemistry, Assam Agricultural University, Jorhat, Assam, 785013, India
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Li Z, Chen F, Huang C, Zheng W, Yu C, Cheng H, Zhou R. Genome-wide mapping and characterization of microsatellites in the swamp eel genome. Sci Rep 2017; 7:3157. [PMID: 28600492 PMCID: PMC5466649 DOI: 10.1038/s41598-017-03330-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/26/2017] [Indexed: 11/09/2022] Open
Abstract
We described genome-wide screening and characterization of microsatellites in the swamp eel genome. A total of 99,293 microsatellite loci were identified in the genome with an overall density of 179 microsatellites per megabase of genomic sequences. The dinucleotide microsatellites were the most abundant type representing 71% of the total microsatellite loci and the AC-rich motifs were the most recurrent in all repeat types. Microsatellite frequency decreased as numbers of repeat units increased, which was more obvious in long than short microsatellite motifs. Most of microsatellites were located in non-coding regions, whereas only approximately 1% of the microsatellites were detected in coding regions. Trinucleotide repeats were most abundant microsatellites in the coding regions, which represented amino acid repeats in proteins. There was a chromosome-biased distribution of microsatellites in non-coding regions, with the highest density of 203.95/Mb on chromosome 8 and the least on chromosome 7 (164.06/Mb). The most abundant dinucleotides (AC)n was mainly located on chromosome 8. Notably, genomic mapping showed that there was a chromosome-biased association of genomic distributions between microsatellites and transposon elements. Thus, the novel dataset of microsatellites in swamp eel provides a valuable resource for further studies on QTL-based selection breeding, genetic resource conservation and evolutionary genetics.
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Affiliation(s)
- Zhigang Li
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Feng Chen
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Chunhua Huang
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Weixin Zheng
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Chunlai Yu
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Hanhua Cheng
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China.
| | - Rongjia Zhou
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China.
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Thatikunta R, Siva Sankar A, Sreelakshmi J, Palle G, Leela C, Durga Rani CV, Gouri Shankar V, Lavanya B, Narayana Reddy P, Dudhe MY. Utilization of in silico EST-SSR markers for diversity studies in castor ( Ricinus communis L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2016; 22:535-545. [PMID: 27924126 PMCID: PMC5120032 DOI: 10.1007/s12298-016-0367-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 07/13/2016] [Accepted: 07/25/2016] [Indexed: 05/06/2023]
Abstract
Castor (Ricinus communis L.) a chief non-edible oilseed crop has numerous industrial applications. Systematic genetic diversity analysis utilizing DNA based markers has been quick and reliable method that ensures selection of diverse parents for exploitation of higher levels of heterosis in breeding programs. From NCBI database, 63,852 EST sequences of castor were mined. One thousand one hundred and five (1105) EST-SSRs and 1652 repeat motifs sequences were identified from 20,495 non-redundant unigene sequences. Repeat motifs consisted of 29.7 % mono nucleotide repeats, 24.8 % di nucleotide repeats, 27.27 % tri nucleotide repeats and 3.94 % tetra nucleotide repeats. Twenty eight primer pairs were chosen from SSR-containing ESTs to determine genetic diversity among 27 castor accessions. Twelve EST-SSRs showed polymorphism. Number of alleles detected were 2-3 with an average of 2.33 per locus. 150-400 bp was the size of an allele. Dendrogram analysis grouped the 27 accessions into two separate clusters. Genetic similarity coefficient of dendrogram ranged from 0.24 to 0.83. The polymorphic information content value of 0.28-0.49 revealed medium level of diversity in castor. Results of present study indicated that EST-SSRs to be efficient markers for genetic diversity studies. Knowledge on level of diversity existing in castor genotypes would be useful for breeders to plan efficient hybrid breeding programme.
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Affiliation(s)
- Ramesh Thatikunta
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - A. Siva Sankar
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - J. Sreelakshmi
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - Gouthami Palle
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - C. Leela
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - Ch. V. Durga Rani
- Institute of Biotechnology, PJTSAU, Rajendranagar, Hyderabad, 500030 India
| | | | - B. Lavanya
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - P. Narayana Reddy
- Department of Plant Pathology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - M. Y. Dudhe
- ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad, 500030 India
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Deng T, Pang C, Lu X, Zhu P, Duan A, Tan Z, Huang J, Li H, Chen M, Liang X. De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery. PLoS One 2016; 11:e0147132. [PMID: 26766209 PMCID: PMC4713091 DOI: 10.1371/journal.pone.0147132] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/29/2015] [Indexed: 01/11/2023] Open
Abstract
The Chinese swamp buffalo (Bubalis bubalis) is vital to the lives of small farmers and has tremendous economic importance. However, a lack of genomic information has hampered research on augmenting marker assisted breeding programs in this species. Thus, a high-throughput transcriptomic sequencing of B. bubalis was conducted to generate transcriptomic sequence dataset for gene discovery and molecular marker development. Illumina paired-end sequencing generated a total of 54,109,173 raw reads. After trimming, de novo assembly was performed, which yielded 86,017 unigenes, with an average length of 972.41 bp, an N50 of 1,505 bp, and an average GC content of 49.92%. A total of 62,337 unigenes were successfully annotated. Among the annotated unigenes, 27,025 (43.35%) and 23,232 (37.27%) unigenes showed significant similarity to known proteins in NCBI non-redundant protein and Swiss-Prot databases (E-value < 1.0E-5), respectively. Of these annotated unigenes, 14,439 and 15,813 unigenes were assigned to the Gene Ontology (GO) categories and EuKaryotic Ortholog Group (KOG) cluster, respectively. In addition, a total of 14,167 unigenes were assigned to 331 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, 17,401 simple sequence repeats (SSRs) were identified as potential molecular markers. One hundred and fifteen primer pairs were randomly selected for amplification to detect polymorphisms. The results revealed that 110 primer pairs (95.65%) yielded PCR amplicons and 69 primer pairs (60.00%) presented polymorphisms in 35 individual buffaloes. A phylogenetic analysis showed that the five swamp buffalo populations were clustered together, whereas two river buffalo breeds clustered separately. In the present study, the Illumina RNA-seq technology was utilized to perform transcriptome analysis and SSR marker discovery in the swamp buffalo without using a reference genome. Our findings will enrich the current SSR markers resources and help spearhead molecular genetic research studies on the swamp buffalo.
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Affiliation(s)
- Tingxian Deng
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Chunying Pang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Xingrong Lu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Peng Zhu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Anqin Duan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Zhengzhun Tan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Jian Huang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Hui Li
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Mingtan Chen
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Xianwei Liang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
- * E-mail:
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Xu S, Wang G, Mao W, Hu Q, Liu N, Ye L, Gong Y. Genetic diversity and population structure of common bean (Phaseolus vulgaris) landraces from China revealed by a new set of EST-SSR markers. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.08.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Li G, Ra WH, Park JW, Kwon SW, Lee JH, Park CB, Park YJ. Developing EST-SSR markers to study molecular diversity in Liriope and Ophiopogon. BIOCHEM SYST ECOL 2011. [DOI: 10.1016/j.bse.2011.08.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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GONG YM, XU SC, MAO WH, LI ZY, HU QZ, ZHANG GW, DING J. Genetic Diversity Analysis of Faba Bean (Vicia faba L.) Based on EST-SSR Markers. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/s1671-2927(11)60069-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Gong YM, Xu SC, Mao WH, Hu QZ, Zhang GW, Ding J, Li YD. Developing new SSR markers from ESTs of pea (Pisum sativum L.). J Zhejiang Univ Sci B 2010; 11:702-7. [PMID: 20803774 PMCID: PMC2932880 DOI: 10.1631/jzus.b1000004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2010] [Accepted: 04/16/2010] [Indexed: 11/11/2022]
Abstract
The development of expressed sequence tags (ESTs) from pea has provided a useful source for mining novel simple sequence repeat (SSR) markers. In the present research, in order to find EST-derived SSR markers, 18 552 pea ESTs from the National Center for Biotechnology Information (NCBI) database were downloaded and assembled into 10 086 unigenes. A total of 586 microsatellites in 530 unigenes were identified, indicating that merely 5.25% of sequences contained SSRs. The most abundant SSRs within pea were tri-nucleotide repeat motifs, and among all the tri-nucleotide repeats, the motif GAA was the most abundant type. In total, 49 SSRs were used for primer design. EST-SSR loci were subsequently screened on 10 widely adapted varieties in China. Of these, nine loci showed polymorphic profiles that revealed two to three alleles per locus. The polymorphism information content value ranged from 0.18 to 0.58 with an average of 0.41. Furthermore, transferable analysis revealed that some of these loci showed transferability to faba bean. Because of their polymorphism and transferability, these nine novel EST-SSRs will be valuable tools for marker-assisted breeding and comparative mapping of pea in the future.
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Affiliation(s)
- Ya-ming Gong
- Institute of Vegetables, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Sheng-chun Xu
- Institute of Vegetables, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Wei-hua Mao
- Center of Analysis and Measurement, Zhejiang University, Hangzhou 310029, China
| | - Qi-zan Hu
- Institute of Vegetables, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Gu-wen Zhang
- Institute of Vegetables, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Ju Ding
- Institute of Vegetables, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Ya-dan Li
- Center of Analysis and Measurement, Zhejiang University, Hangzhou 310029, China
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