Development of a large SNP genotyping array and generation of high-density genetic maps in tomato.

The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS) has increased the number and density of genetic markers, the efficiency of constructing detailed linkage maps, and our ability to overlay recombination and physical maps of the genome. We develope...

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Autores principales:	Sung-Chur Sim, Gregor Durstewitz, Jörg Plieske, Ralf Wieseke, Martin W Ganal, Allen Van Deynze, John P Hamilton, C Robin Buell, Mathilde Causse, Saranga Wijeratne, David M Francis
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0bd978bdf82a40ae8b464a0b05a7bca2
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spelling	oai:doaj.org-article:0bd978bdf82a40ae8b464a0b05a7bca22021-11-18T07:13:00ZDevelopment of a large SNP genotyping array and generation of high-density genetic maps in tomato.1932-620310.1371/journal.pone.0040563https://doaj.org/article/0bd978bdf82a40ae8b464a0b05a7bca22012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22802968/?tool=EBIhttps://doaj.org/toc/1932-6203The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS) has increased the number and density of genetic markers, the efficiency of constructing detailed linkage maps, and our ability to overlay recombination and physical maps of the genome. We developed an array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs) mainly discovered based on NGS-derived transcriptome sequences. Of the SNPs, 7,720 (88%) passed manufacturing quality control and could be scored in tomato germplasm. The array was used to generate high-density linkage maps for three interspecific F(2) populations: EXPEN 2000 (Solanum lycopersicum LA0925 x S. pennellii LA0716, 79 individuals), EXPEN 2012 (S. lycopersicum Moneymaker x S. pennellii LA0716, 160 individuals), and EXPIM 2012 (S. lycopersicum Moneymaker x S. pimpinellifolium LA0121, 183 individuals). The EXPEN 2000-SNP and EXPEN 2012 maps consisted of 3,503 and 3,687 markers representing 1,076 and 1,229 unique map positions (genetic bins), respectively. The EXPEN 2000-SNP map had an average marker bin interval of 1.6 cM, while the EXPEN 2012 map had an average bin interval of 0.9 cM. The EXPIM 2012 map was constructed with 4,491 markers (1,358 bins) and an average bin interval of 0.8 cM. All three linkage maps revealed an uneven distribution of markers across the genome. The dense EXPEN 2012 and EXPIM 2012 maps showed high levels of colinearity across all 12 chromosomes, and also revealed evidence of small inversions between LA0716 and LA0121. Physical positions of 7,666 SNPs were identified relative to the tomato genome sequence. The genetic and physical positions were mostly consistent. Exceptions were observed for chromosomes 3, 10 and 12. Comparing genetic positions relative to physical positions revealed that genomic regions with high recombination rates were consistent with the known distribution of euchromatin across the 12 chromosomes, while very low recombination rates were observed in the heterochromatic regions.Sung-Chur SimGregor DurstewitzJörg PlieskeRalf WiesekeMartin W GanalAllen Van DeynzeJohn P HamiltonC Robin BuellMathilde CausseSaranga WijeratneDavid M FrancisPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 7, p e40563 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sung-Chur Sim Gregor Durstewitz Jörg Plieske Ralf Wieseke Martin W Ganal Allen Van Deynze John P Hamilton C Robin Buell Mathilde Causse Saranga Wijeratne David M Francis Development of a large SNP genotyping array and generation of high-density genetic maps in tomato.
description	The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS) has increased the number and density of genetic markers, the efficiency of constructing detailed linkage maps, and our ability to overlay recombination and physical maps of the genome. We developed an array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs) mainly discovered based on NGS-derived transcriptome sequences. Of the SNPs, 7,720 (88%) passed manufacturing quality control and could be scored in tomato germplasm. The array was used to generate high-density linkage maps for three interspecific F(2) populations: EXPEN 2000 (Solanum lycopersicum LA0925 x S. pennellii LA0716, 79 individuals), EXPEN 2012 (S. lycopersicum Moneymaker x S. pennellii LA0716, 160 individuals), and EXPIM 2012 (S. lycopersicum Moneymaker x S. pimpinellifolium LA0121, 183 individuals). The EXPEN 2000-SNP and EXPEN 2012 maps consisted of 3,503 and 3,687 markers representing 1,076 and 1,229 unique map positions (genetic bins), respectively. The EXPEN 2000-SNP map had an average marker bin interval of 1.6 cM, while the EXPEN 2012 map had an average bin interval of 0.9 cM. The EXPIM 2012 map was constructed with 4,491 markers (1,358 bins) and an average bin interval of 0.8 cM. All three linkage maps revealed an uneven distribution of markers across the genome. The dense EXPEN 2012 and EXPIM 2012 maps showed high levels of colinearity across all 12 chromosomes, and also revealed evidence of small inversions between LA0716 and LA0121. Physical positions of 7,666 SNPs were identified relative to the tomato genome sequence. The genetic and physical positions were mostly consistent. Exceptions were observed for chromosomes 3, 10 and 12. Comparing genetic positions relative to physical positions revealed that genomic regions with high recombination rates were consistent with the known distribution of euchromatin across the 12 chromosomes, while very low recombination rates were observed in the heterochromatic regions.
format	article
author	Sung-Chur Sim Gregor Durstewitz Jörg Plieske Ralf Wieseke Martin W Ganal Allen Van Deynze John P Hamilton C Robin Buell Mathilde Causse Saranga Wijeratne David M Francis
author_facet	Sung-Chur Sim Gregor Durstewitz Jörg Plieske Ralf Wieseke Martin W Ganal Allen Van Deynze John P Hamilton C Robin Buell Mathilde Causse Saranga Wijeratne David M Francis
author_sort	Sung-Chur Sim
title	Development of a large SNP genotyping array and generation of high-density genetic maps in tomato.
title_short	Development of a large SNP genotyping array and generation of high-density genetic maps in tomato.
title_full	Development of a large SNP genotyping array and generation of high-density genetic maps in tomato.
title_fullStr	Development of a large SNP genotyping array and generation of high-density genetic maps in tomato.
title_full_unstemmed	Development of a large SNP genotyping array and generation of high-density genetic maps in tomato.
title_sort	development of a large snp genotyping array and generation of high-density genetic maps in tomato.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/0bd978bdf82a40ae8b464a0b05a7bca2
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Development of a large SNP genotyping array and generation of high-density genetic maps in tomato.

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