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Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.).

Wang H, Penmetsa RV, Yuan M, Gong L, Zhao Y, Guo B, Farmer AD, Rosen BD, Gao J, Isobe S, Bertioli DJ, Varshney RK, Cook DR, He G - BMC Plant Biol. (2012)

Bottom Line: The new set of 1,152 SSRs as well as about 4,000 published or unpublished SSRs were screened against two parents of a mapping population, generating 385 polymorphic loci.The SSRs mined from BESs will be of use in further molecular analysis of the peanut genome, providing a novel set of markers, genetically anchoring BAC clones, and incorporating gene sequences into a linkage map.This will aid in the identification of markers linked to genes of interest and map-based cloning.

View Article: PubMed Central - HTML - PubMed

Affiliation: Tuskegee University, Tuskegee, AL 36088, USA.

ABSTRACT

Background: Cultivated peanut (Arachis hypogaea L.) is an important crop worldwide, valued for its edible oil and digestible protein. It has a very narrow genetic base that may well derive from a relatively recent single polyploidization event. Accordingly molecular markers have low levels of polymorphism and the number of polymorphic molecular markers available for cultivated peanut is still limiting.

Results: Here, we report a large set of BAC-end sequences (BES), use them for developing SSR (BES-SSR) markers, and apply them in genetic linkage mapping. The majority of BESs had no detectable homology to known genes (49.5%) followed by sequences with similarity to known genes (44.3%), and miscellaneous sequences (6.2%) such as transposable element, retroelement, and organelle sequences. A total of 1,424 SSRs were identified from 36,435 BESs. Among these identified SSRs, dinucleotide (47.4%) and trinucleotide (37.1%) SSRs were predominant. The new set of 1,152 SSRs as well as about 4,000 published or unpublished SSRs were screened against two parents of a mapping population, generating 385 polymorphic loci. A genetic linkage map was constructed, consisting of 318 loci onto 21 linkage groups and covering a total of 1,674.4 cM, with an average distance of 5.3 cM between adjacent loci. Two markers related to resistance gene homologs (RGH) were mapped to two different groups, thus anchoring 1 RGH-BAC contig and 1 singleton.

Conclusions: The SSRs mined from BESs will be of use in further molecular analysis of the peanut genome, providing a novel set of markers, genetically anchoring BAC clones, and incorporating gene sequences into a linkage map. This will aid in the identification of markers linked to genes of interest and map-based cloning.

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Comparison of marker colinear in present and previous linkage maps.
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Figure 4: Comparison of marker colinear in present and previous linkage maps.

Mentions: The use of common markers between the present map and previous maps allows a comparison of recombination frequency and marker order among mapping populations. Five linkage groups in the present map were chosen to compare with the first SSR-based peanut map [30], because there were several markers incommon between two maps (Figure 4). Comparison of these two maps reveals both conservation of marker order and rearranged order the between two populations. For instance, LG7 and LG10 in present map had the same marker order as LG_AhIII and LG_AhVI in previous map. Three other linkage groups, however, revealed rearrangements in marker order between two mapping populations (Figure 4).


Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.).

Wang H, Penmetsa RV, Yuan M, Gong L, Zhao Y, Guo B, Farmer AD, Rosen BD, Gao J, Isobe S, Bertioli DJ, Varshney RK, Cook DR, He G - BMC Plant Biol. (2012)

Comparison of marker colinear in present and previous linkage maps.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3298471&req=5

Figure 4: Comparison of marker colinear in present and previous linkage maps.
Mentions: The use of common markers between the present map and previous maps allows a comparison of recombination frequency and marker order among mapping populations. Five linkage groups in the present map were chosen to compare with the first SSR-based peanut map [30], because there were several markers incommon between two maps (Figure 4). Comparison of these two maps reveals both conservation of marker order and rearranged order the between two populations. For instance, LG7 and LG10 in present map had the same marker order as LG_AhIII and LG_AhVI in previous map. Three other linkage groups, however, revealed rearrangements in marker order between two mapping populations (Figure 4).

Bottom Line: The new set of 1,152 SSRs as well as about 4,000 published or unpublished SSRs were screened against two parents of a mapping population, generating 385 polymorphic loci.The SSRs mined from BESs will be of use in further molecular analysis of the peanut genome, providing a novel set of markers, genetically anchoring BAC clones, and incorporating gene sequences into a linkage map.This will aid in the identification of markers linked to genes of interest and map-based cloning.

View Article: PubMed Central - HTML - PubMed

Affiliation: Tuskegee University, Tuskegee, AL 36088, USA.

ABSTRACT

Background: Cultivated peanut (Arachis hypogaea L.) is an important crop worldwide, valued for its edible oil and digestible protein. It has a very narrow genetic base that may well derive from a relatively recent single polyploidization event. Accordingly molecular markers have low levels of polymorphism and the number of polymorphic molecular markers available for cultivated peanut is still limiting.

Results: Here, we report a large set of BAC-end sequences (BES), use them for developing SSR (BES-SSR) markers, and apply them in genetic linkage mapping. The majority of BESs had no detectable homology to known genes (49.5%) followed by sequences with similarity to known genes (44.3%), and miscellaneous sequences (6.2%) such as transposable element, retroelement, and organelle sequences. A total of 1,424 SSRs were identified from 36,435 BESs. Among these identified SSRs, dinucleotide (47.4%) and trinucleotide (37.1%) SSRs were predominant. The new set of 1,152 SSRs as well as about 4,000 published or unpublished SSRs were screened against two parents of a mapping population, generating 385 polymorphic loci. A genetic linkage map was constructed, consisting of 318 loci onto 21 linkage groups and covering a total of 1,674.4 cM, with an average distance of 5.3 cM between adjacent loci. Two markers related to resistance gene homologs (RGH) were mapped to two different groups, thus anchoring 1 RGH-BAC contig and 1 singleton.

Conclusions: The SSRs mined from BESs will be of use in further molecular analysis of the peanut genome, providing a novel set of markers, genetically anchoring BAC clones, and incorporating gene sequences into a linkage map. This will aid in the identification of markers linked to genes of interest and map-based cloning.

Show MeSH
Related in: MedlinePlus