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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Bottom Line: The new set of 1,152 SSRs as well as about 4,000 published or unpublished SSRs were screened against two parents of a mapping population, generating 385 polymorphic loci.The SSRs mined from BESs will be of use in further molecular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 The new set of 1,152 SSRs as well as about 4,000 published or unpublished SSRs were screened against two parents of a mapping population, generating 385 polymorphic loci.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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Distribution of repeat number in trinucleotide AAT and AAG SSRs.
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Figure 2: Distribution of repeat number in trinucleotide AAT and AAG SSRs.

Mentions: To enlarge the pool of SSRs in peanut, BES sequences were used for mining SSRs. One hundred twenty eight and 1,296 SSRs were identified from BES sequences in the cultivated (tetraploid A. hypogaea) and wild (diploid A. duranensis) BAC clones, respectively (Table 2). For both wild and cultivated species, SSRs were more frequent in the non-annotated fraction of BES. As expected, among these SSRs dinucleotide (47.4%) and trinucleotide (37.1%) SSRs were predominant (Table 3). Survey of EST-SSRs in peanut [40] revealed a similar trend, with 59.5% dinucleotide and 33.7% trinucleotide SSRs. Dinucleotide SSRs composed of AT repeats accounted for 27.4% of all SSRs, followed by SSRs with AG repeats (15.0%). For trinucleotide SSRs, the AAG SSRs occurred at slightly higher frequency (15.2%) than AAT SSRs (12.0%) (Table 4). Moretzsohn et al. [21] also reported an abundance of AAT SSRs in EST sequences, with only AAG SSRs at a higher frequency. Because AT, AG, AAG, and AAT SSRs represented 67% of all SSRs in the BES data set, SSRs with these four motifs were compared for their quantity and frequency of polymorphism. For purposes of this analysis, SSRs were further subdivided into two classes based on length (in the sense of Temnykh et al. [41]), with Class I SSRs ≥ 20 bp and Class II SSRs ≤ 19 bp in length. For dinucleotide SSRs, the number of SSRs with AT motif in Class I was higher than those in Class II, while SSRs with AG motif were less frequent in Class I than in Class II (Figure 1, Table 5). For trinucleotide SSRs, both SSRs with AAT and AAG motifs in Class II were more frequent than in Class I (Figure 2, Table 6).


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)

Distribution of repeat number in trinucleotide AAT and AAG SSRs.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Distribution of repeat number in trinucleotide AAT and AAG SSRs.
Mentions: To enlarge the pool of SSRs in peanut, BES sequences were used for mining SSRs. One hundred twenty eight and 1,296 SSRs were identified from BES sequences in the cultivated (tetraploid A. hypogaea) and wild (diploid A. duranensis) BAC clones, respectively (Table 2). For both wild and cultivated species, SSRs were more frequent in the non-annotated fraction of BES. As expected, among these SSRs dinucleotide (47.4%) and trinucleotide (37.1%) SSRs were predominant (Table 3). Survey of EST-SSRs in peanut [40] revealed a similar trend, with 59.5% dinucleotide and 33.7% trinucleotide SSRs. Dinucleotide SSRs composed of AT repeats accounted for 27.4% of all SSRs, followed by SSRs with AG repeats (15.0%). For trinucleotide SSRs, the AAG SSRs occurred at slightly higher frequency (15.2%) than AAT SSRs (12.0%) (Table 4). Moretzsohn et al. [21] also reported an abundance of AAT SSRs in EST sequences, with only AAG SSRs at a higher frequency. Because AT, AG, AAG, and AAT SSRs represented 67% of all SSRs in the BES data set, SSRs with these four motifs were compared for their quantity and frequency of polymorphism. For purposes of this analysis, SSRs were further subdivided into two classes based on length (in the sense of Temnykh et al. [41]), with Class I SSRs ≥ 20 bp and Class II SSRs ≤ 19 bp in length. For dinucleotide SSRs, the number of SSRs with AT motif in Class I was higher than those in Class II, while SSRs with AG motif were less frequent in Class I than in Class II (Figure 1, Table 5). For trinucleotide SSRs, both SSRs with AAT and AAG motifs in Class II were more frequent than in Class I (Figure 2, Table 6).

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