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Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species.

Hill T, Ashrafi H, Chin-Wo SR, Stoffel K, Truco MJ, Kozik A, Michelmore R, Van Deynze A - G3 (Bethesda) (2015)

Bottom Line: Marker density was sufficient to locate the chromosomal breakpoint resulting in the P1/P8 translocation between C. frutescens and C. annuum to a single bin.There were extensive chromosomal regions with suppressed recombination and reduced intraspecific marker density.Similar to tomato, the extent of reduced recombination appears to be more pronounced in pepper than in other plant species.

View Article: PubMed Central - PubMed

Affiliation: Seed Biotechnology Center, University of California, Davis, California 95616 Department of Plant Sciences, University of California, Davis, California 95616.

No MeSH data available.


Pepper maps vs. tomato and potato genomes. Genetic and physical positions of FA (red circles) and NM (blue dots) markers matching tomato and potato genome sequences ≥ 80% ID and ≥75% unigene coverage. (A) Positions of 8267 mapped unigenes, 7660 FA and 1,755 NM found on tomato chromosomes. (B) Positions of 8131 mapped unigenes, 7551 FA and 1723 NM found on the potato chromosomes. Green circles represent previously identified translocations between pepper and tomato whereas the P4/Sl11 and St11 clusters (highlighted in yellow) represent a previously unmapped translocation event.
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fig9: Pepper maps vs. tomato and potato genomes. Genetic and physical positions of FA (red circles) and NM (blue dots) markers matching tomato and potato genome sequences ≥ 80% ID and ≥75% unigene coverage. (A) Positions of 8267 mapped unigenes, 7660 FA and 1,755 NM found on tomato chromosomes. (B) Positions of 8131 mapped unigenes, 7551 FA and 1723 NM found on the potato chromosomes. Green circles represent previously identified translocations between pepper and tomato whereas the P4/Sl11 and St11 clusters (highlighted in yellow) represent a previously unmapped translocation event.

Mentions: We analyzed synteny between each pepper map and the assembled genomes of pepper’s close solanaceous relatives, tomato and potato (File S5, Table S13, Table S14, Table S15, Table S16, and Figure 9). Alignment of the FA and NM maps to both genomes was similar, demonstrating good concordance between both pepper maps and the tomato and potato genomes. Dot plots showing relative pepper genetic positions vs. relative physical positions on each chromosome group are highly similar between the tomato and potato assemblies. These plots demonstrate several translocations in common between tomato and potato with pepper. In addition to the eight major translocations previously described (Tanksley et al. 1988; Livingstone et al. 1999; Wu et al. 2009; Wu and Tanksley 2010), there appears to be a translocation between the nonrecombining region on P4 and T11/S11 and possibly T12/S12 that has, to our knowledge, not been observed by syntenic analyses between pepper maps and tomato.


Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species.

Hill T, Ashrafi H, Chin-Wo SR, Stoffel K, Truco MJ, Kozik A, Michelmore R, Van Deynze A - G3 (Bethesda) (2015)

Pepper maps vs. tomato and potato genomes. Genetic and physical positions of FA (red circles) and NM (blue dots) markers matching tomato and potato genome sequences ≥ 80% ID and ≥75% unigene coverage. (A) Positions of 8267 mapped unigenes, 7660 FA and 1,755 NM found on tomato chromosomes. (B) Positions of 8131 mapped unigenes, 7551 FA and 1723 NM found on the potato chromosomes. Green circles represent previously identified translocations between pepper and tomato whereas the P4/Sl11 and St11 clusters (highlighted in yellow) represent a previously unmapped translocation event.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4632054&req=5

fig9: Pepper maps vs. tomato and potato genomes. Genetic and physical positions of FA (red circles) and NM (blue dots) markers matching tomato and potato genome sequences ≥ 80% ID and ≥75% unigene coverage. (A) Positions of 8267 mapped unigenes, 7660 FA and 1,755 NM found on tomato chromosomes. (B) Positions of 8131 mapped unigenes, 7551 FA and 1723 NM found on the potato chromosomes. Green circles represent previously identified translocations between pepper and tomato whereas the P4/Sl11 and St11 clusters (highlighted in yellow) represent a previously unmapped translocation event.
Mentions: We analyzed synteny between each pepper map and the assembled genomes of pepper’s close solanaceous relatives, tomato and potato (File S5, Table S13, Table S14, Table S15, Table S16, and Figure 9). Alignment of the FA and NM maps to both genomes was similar, demonstrating good concordance between both pepper maps and the tomato and potato genomes. Dot plots showing relative pepper genetic positions vs. relative physical positions on each chromosome group are highly similar between the tomato and potato assemblies. These plots demonstrate several translocations in common between tomato and potato with pepper. In addition to the eight major translocations previously described (Tanksley et al. 1988; Livingstone et al. 1999; Wu et al. 2009; Wu and Tanksley 2010), there appears to be a translocation between the nonrecombining region on P4 and T11/S11 and possibly T12/S12 that has, to our knowledge, not been observed by syntenic analyses between pepper maps and tomato.

Bottom Line: Marker density was sufficient to locate the chromosomal breakpoint resulting in the P1/P8 translocation between C. frutescens and C. annuum to a single bin.There were extensive chromosomal regions with suppressed recombination and reduced intraspecific marker density.Similar to tomato, the extent of reduced recombination appears to be more pronounced in pepper than in other plant species.

View Article: PubMed Central - PubMed

Affiliation: Seed Biotechnology Center, University of California, Davis, California 95616 Department of Plant Sciences, University of California, Davis, California 95616.

No MeSH data available.