Abstract
Physical maps of chromosomes provide a framework for organizing and integrating diverse genetic information. DNA microarrays are a valuable technique for physical mapping and can also be used to facilitate the discovery of single feature polymorphisms (SFPs). Wheat chromosome arm 2BL was physically mapped using a Wheat Genome Array onto near-isogenic lines (NILs) with the aid of wheat-rice synteny and mapped wheat EST information. Using high variance probe set (HVP) analysis, 314 HVPs constituting genes present on 2BL were identified. The 314 HVPs were grouped into 3 categories: HVPs that match only rice chromosome 4 (298 HVPs), those that match only wheat ESTs mapped on 2BL (1), and those that match both rice chromosome 4 and wheat ESTs mapped on 2BL (15). All HVPs were converted into gene sets, which represented either unique rice gene models or mapped wheat ESTs that matched identified HVPs. Comparative physical maps were constructed for 16 wheat gene sets and 271 rice gene sets. Of the 271 rice gene sets, 257 were mapped to the 18-35 Mb regions on rice chromosome 4. Based on HVP analysis and sequence similarity between the gene models in the rice chromosomes and mapped wheat ESTs, the outermost rice gene model that limits the translocation breakpoint to orthologous regions was identified.
| Original language | English |
|---|---|
| Pages (from-to) | 1277-1296 |
| Number of pages | 20 |
| Journal | Genetica |
| Volume | 138 |
| Issue number | 11 |
| DOIs | |
| Publication status | Published - 2010 Nov 29 |
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Keywords
- Comparative physical mapping
- High variance probe (HVP)
- Wheat chromosome arm 2BL
ASJC Scopus subject areas
- Genetics
- Insect Science
- Animal Science and Zoology
- Plant Science
Cite this
Comparative physical mapping between wheat chromosome arm 2BL and rice chromosome 4. / Lee, Tong Geon; Lee, Yong Jin; Kim, Dae Yeon; Seo, Yong Weon.
In: Genetica, Vol. 138, No. 11, 29.11.2010, p. 1277-1296.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Comparative physical mapping between wheat chromosome arm 2BL and rice chromosome 4
AU - Lee, Tong Geon
AU - Lee, Yong Jin
AU - Kim, Dae Yeon
AU - Seo, Yong Weon
PY - 2010/11/29
Y1 - 2010/11/29
N2 - Physical maps of chromosomes provide a framework for organizing and integrating diverse genetic information. DNA microarrays are a valuable technique for physical mapping and can also be used to facilitate the discovery of single feature polymorphisms (SFPs). Wheat chromosome arm 2BL was physically mapped using a Wheat Genome Array onto near-isogenic lines (NILs) with the aid of wheat-rice synteny and mapped wheat EST information. Using high variance probe set (HVP) analysis, 314 HVPs constituting genes present on 2BL were identified. The 314 HVPs were grouped into 3 categories: HVPs that match only rice chromosome 4 (298 HVPs), those that match only wheat ESTs mapped on 2BL (1), and those that match both rice chromosome 4 and wheat ESTs mapped on 2BL (15). All HVPs were converted into gene sets, which represented either unique rice gene models or mapped wheat ESTs that matched identified HVPs. Comparative physical maps were constructed for 16 wheat gene sets and 271 rice gene sets. Of the 271 rice gene sets, 257 were mapped to the 18-35 Mb regions on rice chromosome 4. Based on HVP analysis and sequence similarity between the gene models in the rice chromosomes and mapped wheat ESTs, the outermost rice gene model that limits the translocation breakpoint to orthologous regions was identified.
AB - Physical maps of chromosomes provide a framework for organizing and integrating diverse genetic information. DNA microarrays are a valuable technique for physical mapping and can also be used to facilitate the discovery of single feature polymorphisms (SFPs). Wheat chromosome arm 2BL was physically mapped using a Wheat Genome Array onto near-isogenic lines (NILs) with the aid of wheat-rice synteny and mapped wheat EST information. Using high variance probe set (HVP) analysis, 314 HVPs constituting genes present on 2BL were identified. The 314 HVPs were grouped into 3 categories: HVPs that match only rice chromosome 4 (298 HVPs), those that match only wheat ESTs mapped on 2BL (1), and those that match both rice chromosome 4 and wheat ESTs mapped on 2BL (15). All HVPs were converted into gene sets, which represented either unique rice gene models or mapped wheat ESTs that matched identified HVPs. Comparative physical maps were constructed for 16 wheat gene sets and 271 rice gene sets. Of the 271 rice gene sets, 257 were mapped to the 18-35 Mb regions on rice chromosome 4. Based on HVP analysis and sequence similarity between the gene models in the rice chromosomes and mapped wheat ESTs, the outermost rice gene model that limits the translocation breakpoint to orthologous regions was identified.
KW - Comparative physical mapping
KW - High variance probe (HVP)
KW - Wheat chromosome arm 2BL
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U2 - 10.1007/s10709-010-9528-y
DO - 10.1007/s10709-010-9528-y
M3 - Article
C2 - 21113791
AN - SCOPUS:78650510777
VL - 138
SP - 1277
EP - 1296
JO - Genetica
JF - Genetica
SN - 0016-6707
IS - 11
ER -