Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae
Allium vegetables, such as garlic and onion, have understudied genomes and limited molecular resources, hindering advances in genetic research and breeding of these species. In this study, we characterized and compared the simple sequence repeats (SSR) landscape in the transcriptomes of garlic and r...
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| Veröffentlicht in: | Molecular genetics and genomics : MGG 2018-10, Vol.293 (5), p.1091-1106 |
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| creator | Barboza, Karina Beretta, Vanesa Kozub, Perla C. Salinas, Cecilia Morgenfeld, Mauro M. Galmarini, Claudio R. Cavagnaro, Pablo F. |
| description | Allium
vegetables, such as garlic and onion, have understudied genomes and limited molecular resources, hindering advances in genetic research and breeding of these species. In this study, we characterized and compared the simple sequence repeats (SSR) landscape in the transcriptomes of garlic and related
Allium
(
A. cepa, A. fistulosum, and A. tuberosum
) and non-
Allium
monocot species. In addition, 110 SSR markers were developed from garlic ESTs, and they were characterized—along with 112 previously developed SSRs—at various levels, including transferability across Alliaceae species, and their usefulness for genetic diversity analysis. Among the
Allium
species analyzed, garlic ESTs had the highest overall SSR density, the lowest frequency of trinucleotides, and the highest of di- and tetranucleotides. When compared to more distantly related monocots, outside the Asparagales order, it was evident that ESTs of
Allium
species shared major commonalities with regards to SSR density, frequency distribution, sequence motifs, and GC content. A significant fraction of the SSR markers were successfully transferred across
Allium
species, including crops for which no SSR markers have been developed yet, such as leek, shallot, chives, and elephant garlic. Diversity analysis of garlic cultivars with selected SSRs revealed 36 alleles, with 2–5 alleles/locus, and PIC = 0.38. Cluster analysis grouped the accessions according to their flowering behavior, botanical variety, and ecophysiological characteristics. Results from this study contribute to the characterization of
Allium
transcriptomes. The new SSR markers developed, along with the data from the polymorphism and transferability analyses, will aid in assisting genetic research and breeding in garlic and other
Allium
. |
| doi_str_mv | 10.1007/s00438-018-1442-5 |
| format | Article |
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vegetables, such as garlic and onion, have understudied genomes and limited molecular resources, hindering advances in genetic research and breeding of these species. In this study, we characterized and compared the simple sequence repeats (SSR) landscape in the transcriptomes of garlic and related
Allium
(
A. cepa, A. fistulosum, and A. tuberosum
) and non-
Allium
monocot species. In addition, 110 SSR markers were developed from garlic ESTs, and they were characterized—along with 112 previously developed SSRs—at various levels, including transferability across Alliaceae species, and their usefulness for genetic diversity analysis. Among the
Allium
species analyzed, garlic ESTs had the highest overall SSR density, the lowest frequency of trinucleotides, and the highest of di- and tetranucleotides. When compared to more distantly related monocots, outside the Asparagales order, it was evident that ESTs of
Allium
species shared major commonalities with regards to SSR density, frequency distribution, sequence motifs, and GC content. A significant fraction of the SSR markers were successfully transferred across
Allium
species, including crops for which no SSR markers have been developed yet, such as leek, shallot, chives, and elephant garlic. Diversity analysis of garlic cultivars with selected SSRs revealed 36 alleles, with 2–5 alleles/locus, and PIC = 0.38. Cluster analysis grouped the accessions according to their flowering behavior, botanical variety, and ecophysiological characteristics. Results from this study contribute to the characterization of
Allium
transcriptomes. The new SSR markers developed, along with the data from the polymorphism and transferability analyses, will aid in assisting genetic research and breeding in garlic and other
Allium
.</description><identifier>ISSN: 1617-4615</identifier><identifier>EISSN: 1617-4623</identifier><identifier>DOI: 10.1007/s00438-018-1442-5</identifier><identifier>PMID: 29705936</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Alleles ; Alliaceae ; Allium ; Animal Genetics and Genomics ; Biochemistry ; Biomedical and Life Sciences ; Flowering ; Garlic ; Gene polymorphism ; Genetic analysis ; Genetic diversity ; Genetic research ; Genomes ; Genotype & phenotype ; Human Genetics ; Life Sciences ; Microbial Genetics and Genomics ; Original Article ; Plant breeding ; Plant Genetics and Genomics ; Simple sequence repeats ; Species ; Vegetables</subject><ispartof>Molecular genetics and genomics : MGG, 2018-10, Vol.293 (5), p.1091-1106</ispartof><rights>Springer-Verlag GmbH Germany, part of Springer Nature 2018</rights><rights>Molecular Genetics and Genomics is a copyright of Springer, (2018). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c372t-9c9afdb6a05f242776ae3b47da6d221299ea78a8d6f0dc1247cf99d17f598a993</citedby><cites>FETCH-LOGICAL-c372t-9c9afdb6a05f242776ae3b47da6d221299ea78a8d6f0dc1247cf99d17f598a993</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00438-018-1442-5$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00438-018-1442-5$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27903,27904,41467,42536,51297</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29705936$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Barboza, Karina</creatorcontrib><creatorcontrib>Beretta, Vanesa</creatorcontrib><creatorcontrib>Kozub, Perla C.</creatorcontrib><creatorcontrib>Salinas, Cecilia</creatorcontrib><creatorcontrib>Morgenfeld, Mauro M.</creatorcontrib><creatorcontrib>Galmarini, Claudio R.</creatorcontrib><creatorcontrib>Cavagnaro, Pablo F.</creatorcontrib><title>Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae</title><title>Molecular genetics and genomics : MGG</title><addtitle>Mol Genet Genomics</addtitle><addtitle>Mol Genet Genomics</addtitle><description>Allium
vegetables, such as garlic and onion, have understudied genomes and limited molecular resources, hindering advances in genetic research and breeding of these species. In this study, we characterized and compared the simple sequence repeats (SSR) landscape in the transcriptomes of garlic and related
Allium
(
A. cepa, A. fistulosum, and A. tuberosum
) and non-
Allium
monocot species. In addition, 110 SSR markers were developed from garlic ESTs, and they were characterized—along with 112 previously developed SSRs—at various levels, including transferability across Alliaceae species, and their usefulness for genetic diversity analysis. Among the
Allium
species analyzed, garlic ESTs had the highest overall SSR density, the lowest frequency of trinucleotides, and the highest of di- and tetranucleotides. When compared to more distantly related monocots, outside the Asparagales order, it was evident that ESTs of
Allium
species shared major commonalities with regards to SSR density, frequency distribution, sequence motifs, and GC content. A significant fraction of the SSR markers were successfully transferred across
Allium
species, including crops for which no SSR markers have been developed yet, such as leek, shallot, chives, and elephant garlic. Diversity analysis of garlic cultivars with selected SSRs revealed 36 alleles, with 2–5 alleles/locus, and PIC = 0.38. Cluster analysis grouped the accessions according to their flowering behavior, botanical variety, and ecophysiological characteristics. Results from this study contribute to the characterization of
Allium
transcriptomes. The new SSR markers developed, along with the data from the polymorphism and transferability analyses, will aid in assisting genetic research and breeding in garlic and other
Allium
.</description><subject>Alleles</subject><subject>Alliaceae</subject><subject>Allium</subject><subject>Animal Genetics and Genomics</subject><subject>Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>Flowering</subject><subject>Garlic</subject><subject>Gene polymorphism</subject><subject>Genetic analysis</subject><subject>Genetic diversity</subject><subject>Genetic research</subject><subject>Genomes</subject><subject>Genotype & phenotype</subject><subject>Human Genetics</subject><subject>Life Sciences</subject><subject>Microbial Genetics and Genomics</subject><subject>Original Article</subject><subject>Plant breeding</subject><subject>Plant Genetics and Genomics</subject><subject>Simple sequence repeats</subject><subject>Species</subject><subject>Vegetables</subject><issn>1617-4615</issn><issn>1617-4623</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>BENPR</sourceid><recordid>eNp1kctOHDEQRS2UKBCSD2ATWWLDgg62--E2O4TIQwKxgKytart6ZNLjnthupPkafhX3DJkgpKxcsk_dqutLyBFnXzlj8iwyVpVtwXhb8KoSRb1HDnjDZVE1ony3q3m9Tz7G-MAYl42QH8i-UJLVqmwOyNONM2GMkHAYXEIKHoZ1dDEXli4h_MZALT7iMK6W6BN1ni4gDM6cU-tiCq6bkhv9fH91d08j_pnQGzylC_SYnMnUI4bo0nonffpaOwXwsccAnRs20LxNpBd5GzAI-Im872GI-PnlPCS_vl3dX_4orm-__7y8uC5MKUUqlFHQ264BVveiElI2gGVXSQuNFYILpRBkC61temYNF5U0vVKWy75WLShVHpKTre4qjNlCTHrposmfAh7HKWrBSiFVLTnP6PEb9GGcQja3oXgr27qtM8W31MZQwF6vgsum15ozPaent-npnJ6e09Nzz5cX5albot11_I0rA2ILxPzkFxj-jf6_6jO2xqg8</recordid><startdate>20181001</startdate><enddate>20181001</enddate><creator>Barboza, Karina</creator><creator>Beretta, Vanesa</creator><creator>Kozub, Perla C.</creator><creator>Salinas, Cecilia</creator><creator>Morgenfeld, Mauro M.</creator><creator>Galmarini, Claudio R.</creator><creator>Cavagnaro, Pablo F.</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20181001</creationdate><title>Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae</title><author>Barboza, Karina ; 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vegetables, such as garlic and onion, have understudied genomes and limited molecular resources, hindering advances in genetic research and breeding of these species. In this study, we characterized and compared the simple sequence repeats (SSR) landscape in the transcriptomes of garlic and related
Allium
(
A. cepa, A. fistulosum, and A. tuberosum
) and non-
Allium
monocot species. In addition, 110 SSR markers were developed from garlic ESTs, and they were characterized—along with 112 previously developed SSRs—at various levels, including transferability across Alliaceae species, and their usefulness for genetic diversity analysis. Among the
Allium
species analyzed, garlic ESTs had the highest overall SSR density, the lowest frequency of trinucleotides, and the highest of di- and tetranucleotides. When compared to more distantly related monocots, outside the Asparagales order, it was evident that ESTs of
Allium
species shared major commonalities with regards to SSR density, frequency distribution, sequence motifs, and GC content. A significant fraction of the SSR markers were successfully transferred across
Allium
species, including crops for which no SSR markers have been developed yet, such as leek, shallot, chives, and elephant garlic. Diversity analysis of garlic cultivars with selected SSRs revealed 36 alleles, with 2–5 alleles/locus, and PIC = 0.38. Cluster analysis grouped the accessions according to their flowering behavior, botanical variety, and ecophysiological characteristics. Results from this study contribute to the characterization of
Allium
transcriptomes. The new SSR markers developed, along with the data from the polymorphism and transferability analyses, will aid in assisting genetic research and breeding in garlic and other
Allium
.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>29705936</pmid><doi>10.1007/s00438-018-1442-5</doi><tpages>16</tpages></addata></record> |
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| source | SpringerLink Journals - AutoHoldings |
| subjects | Alleles Alliaceae Allium Animal Genetics and Genomics Biochemistry Biomedical and Life Sciences Flowering Garlic Gene polymorphism Genetic analysis Genetic diversity Genetic research Genomes Genotype & phenotype Human Genetics Life Sciences Microbial Genetics and Genomics Original Article Plant breeding Plant Genetics and Genomics Simple sequence repeats Species Vegetables |
| title | Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae |
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