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Soybean genomics: Developments through the use of cultivar "Forrest".

Lightfoot DA - Int J Plant Genomics (2008)

Bottom Line: Investment in Forrest genomics resulted in the development of the following research tools: (i) a genetic map, (ii) three RIL populations (96 > n > 975), (iii) approximately 200 NILs, (iv) 115 220 BACs and BIBACs, (v) a physical map, (vi) 4 different minimum tiling path (MTP) sets, (vii) 25 123 BAC end sequences (BESs) that encompass 18.5 Mbp spaced out from the MTPs, and 2 000 microsatellite markers within them (viii) a map of 2408 regions each found at a single position in the genome and 2104 regions found in 2 or 4 similar copies at different genomic locations (each of >150 kbp), (ix) a map of homoeologous regions among both sets of regions, (x) a set of transcript abundance measurements that address biotic stress resistance, (xi) methods for transformation, (xii) methods for RNAi, (xiii) a TILLING resource for directed mutant isolation, and (xiv) analyses of conserved synteny with other sequenced genomes.The SoyGD portal at sprovides access to the data.To date these resources assisted in the genomic analysis of soybean nodulation and disease resistance.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Soil and General Agriculture, Center for Excellence, The Illinois Soybean Center, Southern Illinois University at Carbondale, 62901-4415, USA. ga4082@siu.edu <ga4082@siu.edu>

ABSTRACT
Legume crops are particularly important due to their ability to support symbiotic nitrogen fixation, a key to sustainable crop production and reduced carbon emissions. Soybean (Glycine max) has a special position as a major source of increased protein and oil production in the common grass-legume rotation. The cultivar "Forrest" has saved US growers billions of dollars in crop losses due to resistances programmed into the genome. Moreover, since Forrest grows well in the north-south transition zone, breeders have used this cultivar as a bridge between the southern and northern US gene pools. Investment in Forrest genomics resulted in the development of the following research tools: (i) a genetic map, (ii) three RIL populations (96 > n > 975), (iii) approximately 200 NILs, (iv) 115 220 BACs and BIBACs, (v) a physical map, (vi) 4 different minimum tiling path (MTP) sets, (vii) 25 123 BAC end sequences (BESs) that encompass 18.5 Mbp spaced out from the MTPs, and 2 000 microsatellite markers within them (viii) a map of 2408 regions each found at a single position in the genome and 2104 regions found in 2 or 4 similar copies at different genomic locations (each of >150 kbp), (ix) a map of homoeologous regions among both sets of regions, (x) a set of transcript abundance measurements that address biotic stress resistance, (xi) methods for transformation, (xii) methods for RNAi, (xiii) a TILLING resource for directed mutant isolation, and (xiv) analyses of conserved synteny with other sequenced genomes. The SoyGD portal at sprovides access to the data. To date these resources assisted in the genomic analysis of soybean nodulation and disease resistance. This review summarizes the resources and their uses.

No MeSH data available.


Related in: MedlinePlus

Description of chromosome 18 resources at SoyGD (a). Thecurrent GMOD representation of 50 Mbp of the 51.5 Mbp chromosome 18 (linkagegroup G) in SoyGD (a). shows the build 3 version of the chromosome(cursor), anchored contigs (top row, blue), DNA markers (second row of features,red), QTL in the region (third row, burgundy), MTP2 clones (B, H, and E fourthrow, dark blue). Not shown here were BAC clones, ESTs, BAC end sequences, andgene models (b) shows the build 4 representation of 10 Mbp of the 51.5 Mbpchromosome 18 in SoyGD. Shown are the chromosome (cursor), DNA markers (top rowof features, red); QTL in the region (second row, blue); coalesced clones(purple) comprising the anchored contigs (third row, green); BAC end sequences(fourth row black); BESs encoding gene fragments (fifth row, puce);EST hybridizations to MTP2BH (sixth row gold); MTP4BH clones (seventh row, darkblue); BESs derived SSR (eighth row, green); ESThybridizations inferred on build 4 from clones also in MTP2BH (ninth row,blue); WGS trace file matches from MegaBlast (tenth and last row, light blue).It is recommended for readers to visit updated sitehttp://bioinformatics.siu.edu/ to see a full detailed color version and a build5 view. The gaps between contigs will be filled in build 5 by contig mergessuggested by BESs-SSRs and contig end overlap data.
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fig6: Description of chromosome 18 resources at SoyGD (a). Thecurrent GMOD representation of 50 Mbp of the 51.5 Mbp chromosome 18 (linkagegroup G) in SoyGD (a). shows the build 3 version of the chromosome(cursor), anchored contigs (top row, blue), DNA markers (second row of features,red), QTL in the region (third row, burgundy), MTP2 clones (B, H, and E fourthrow, dark blue). Not shown here were BAC clones, ESTs, BAC end sequences, andgene models (b) shows the build 4 representation of 10 Mbp of the 51.5 Mbpchromosome 18 in SoyGD. Shown are the chromosome (cursor), DNA markers (top rowof features, red); QTL in the region (second row, blue); coalesced clones(purple) comprising the anchored contigs (third row, green); BAC end sequences(fourth row black); BESs encoding gene fragments (fifth row, puce);EST hybridizations to MTP2BH (sixth row gold); MTP4BH clones (seventh row, darkblue); BESs derived SSR (eighth row, green); ESThybridizations inferred on build 4 from clones also in MTP2BH (ninth row,blue); WGS trace file matches from MegaBlast (tenth and last row, light blue).It is recommended for readers to visit updated sitehttp://bioinformatics.siu.edu/ to see a full detailed color version and a build5 view. The gaps between contigs will be filled in build 5 by contig mergessuggested by BESs-SSRs and contig end overlap data.

Mentions: Subsequently, the publiclyavailable soybean BAC fingerprint database was used to create build 4 [16] withthe following specific aims: (i) to increase the number of genetic markers inthe map, (ii) to reduce the frequency of clone contamination, (iii) to rebuildthe physical map at high stringency, (iv) to examine clone density per contig,and (v) to examine the effectiveness of the generic genome browser inrepresenting duplicated homoeologous regions (Table 6). Clones suspected ofcontamination were listed, fingerprintswere examined, and contaminated clones removed from the FPC database.Many (7134 about 10%) well-to-well contaminated clones were removed from thefingerprint database. The edited database produced 2854 contigs and encompassed1050 Mbp. In addition, homoeologous regions that might cause separate contigsto coalesce were detected in several ways. First, contigs with high clonedensity (23%) were inferred to represent two copy (240) or four copy (406)conserved genomic regions per haploid genome (Table 6). If the polyploidregions could all be split using HSVs (Figure 1) [29], there would be 1624regions with two copies and 480 regions with four copies in the soybean genome.A second proof of this genome structure was that pairs of separate contigs thatcontained the same marker anchors (69%) were inferred to represent homoeologousbut diverged genomic regions (Figure 6) [16]. A third proof came from ESThybridizations to BAC libraries where gene families with 1, 2, 4, and 8 memberswere more common than those with 3 or 5 members [57]. Finally, similaritysearch within the whole genome sequence at 90% similarity showed that thesequences that map to the contigs withduplicated regions do have homoeologs in the sequence, whereas sequencesfrom single copy regions do not (Figure 2) [29, 93].


Soybean genomics: Developments through the use of cultivar "Forrest".

Lightfoot DA - Int J Plant Genomics (2008)

Description of chromosome 18 resources at SoyGD (a). Thecurrent GMOD representation of 50 Mbp of the 51.5 Mbp chromosome 18 (linkagegroup G) in SoyGD (a). shows the build 3 version of the chromosome(cursor), anchored contigs (top row, blue), DNA markers (second row of features,red), QTL in the region (third row, burgundy), MTP2 clones (B, H, and E fourthrow, dark blue). Not shown here were BAC clones, ESTs, BAC end sequences, andgene models (b) shows the build 4 representation of 10 Mbp of the 51.5 Mbpchromosome 18 in SoyGD. Shown are the chromosome (cursor), DNA markers (top rowof features, red); QTL in the region (second row, blue); coalesced clones(purple) comprising the anchored contigs (third row, green); BAC end sequences(fourth row black); BESs encoding gene fragments (fifth row, puce);EST hybridizations to MTP2BH (sixth row gold); MTP4BH clones (seventh row, darkblue); BESs derived SSR (eighth row, green); ESThybridizations inferred on build 4 from clones also in MTP2BH (ninth row,blue); WGS trace file matches from MegaBlast (tenth and last row, light blue).It is recommended for readers to visit updated sitehttp://bioinformatics.siu.edu/ to see a full detailed color version and a build5 view. The gaps between contigs will be filled in build 5 by contig mergessuggested by BESs-SSRs and contig end overlap data.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2376204&req=5

fig6: Description of chromosome 18 resources at SoyGD (a). Thecurrent GMOD representation of 50 Mbp of the 51.5 Mbp chromosome 18 (linkagegroup G) in SoyGD (a). shows the build 3 version of the chromosome(cursor), anchored contigs (top row, blue), DNA markers (second row of features,red), QTL in the region (third row, burgundy), MTP2 clones (B, H, and E fourthrow, dark blue). Not shown here were BAC clones, ESTs, BAC end sequences, andgene models (b) shows the build 4 representation of 10 Mbp of the 51.5 Mbpchromosome 18 in SoyGD. Shown are the chromosome (cursor), DNA markers (top rowof features, red); QTL in the region (second row, blue); coalesced clones(purple) comprising the anchored contigs (third row, green); BAC end sequences(fourth row black); BESs encoding gene fragments (fifth row, puce);EST hybridizations to MTP2BH (sixth row gold); MTP4BH clones (seventh row, darkblue); BESs derived SSR (eighth row, green); ESThybridizations inferred on build 4 from clones also in MTP2BH (ninth row,blue); WGS trace file matches from MegaBlast (tenth and last row, light blue).It is recommended for readers to visit updated sitehttp://bioinformatics.siu.edu/ to see a full detailed color version and a build5 view. The gaps between contigs will be filled in build 5 by contig mergessuggested by BESs-SSRs and contig end overlap data.
Mentions: Subsequently, the publiclyavailable soybean BAC fingerprint database was used to create build 4 [16] withthe following specific aims: (i) to increase the number of genetic markers inthe map, (ii) to reduce the frequency of clone contamination, (iii) to rebuildthe physical map at high stringency, (iv) to examine clone density per contig,and (v) to examine the effectiveness of the generic genome browser inrepresenting duplicated homoeologous regions (Table 6). Clones suspected ofcontamination were listed, fingerprintswere examined, and contaminated clones removed from the FPC database.Many (7134 about 10%) well-to-well contaminated clones were removed from thefingerprint database. The edited database produced 2854 contigs and encompassed1050 Mbp. In addition, homoeologous regions that might cause separate contigsto coalesce were detected in several ways. First, contigs with high clonedensity (23%) were inferred to represent two copy (240) or four copy (406)conserved genomic regions per haploid genome (Table 6). If the polyploidregions could all be split using HSVs (Figure 1) [29], there would be 1624regions with two copies and 480 regions with four copies in the soybean genome.A second proof of this genome structure was that pairs of separate contigs thatcontained the same marker anchors (69%) were inferred to represent homoeologousbut diverged genomic regions (Figure 6) [16]. A third proof came from ESThybridizations to BAC libraries where gene families with 1, 2, 4, and 8 memberswere more common than those with 3 or 5 members [57]. Finally, similaritysearch within the whole genome sequence at 90% similarity showed that thesequences that map to the contigs withduplicated regions do have homoeologs in the sequence, whereas sequencesfrom single copy regions do not (Figure 2) [29, 93].

Bottom Line: Investment in Forrest genomics resulted in the development of the following research tools: (i) a genetic map, (ii) three RIL populations (96 > n > 975), (iii) approximately 200 NILs, (iv) 115 220 BACs and BIBACs, (v) a physical map, (vi) 4 different minimum tiling path (MTP) sets, (vii) 25 123 BAC end sequences (BESs) that encompass 18.5 Mbp spaced out from the MTPs, and 2 000 microsatellite markers within them (viii) a map of 2408 regions each found at a single position in the genome and 2104 regions found in 2 or 4 similar copies at different genomic locations (each of >150 kbp), (ix) a map of homoeologous regions among both sets of regions, (x) a set of transcript abundance measurements that address biotic stress resistance, (xi) methods for transformation, (xii) methods for RNAi, (xiii) a TILLING resource for directed mutant isolation, and (xiv) analyses of conserved synteny with other sequenced genomes.The SoyGD portal at sprovides access to the data.To date these resources assisted in the genomic analysis of soybean nodulation and disease resistance.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Soil and General Agriculture, Center for Excellence, The Illinois Soybean Center, Southern Illinois University at Carbondale, 62901-4415, USA. ga4082@siu.edu <ga4082@siu.edu>

ABSTRACT
Legume crops are particularly important due to their ability to support symbiotic nitrogen fixation, a key to sustainable crop production and reduced carbon emissions. Soybean (Glycine max) has a special position as a major source of increased protein and oil production in the common grass-legume rotation. The cultivar "Forrest" has saved US growers billions of dollars in crop losses due to resistances programmed into the genome. Moreover, since Forrest grows well in the north-south transition zone, breeders have used this cultivar as a bridge between the southern and northern US gene pools. Investment in Forrest genomics resulted in the development of the following research tools: (i) a genetic map, (ii) three RIL populations (96 > n > 975), (iii) approximately 200 NILs, (iv) 115 220 BACs and BIBACs, (v) a physical map, (vi) 4 different minimum tiling path (MTP) sets, (vii) 25 123 BAC end sequences (BESs) that encompass 18.5 Mbp spaced out from the MTPs, and 2 000 microsatellite markers within them (viii) a map of 2408 regions each found at a single position in the genome and 2104 regions found in 2 or 4 similar copies at different genomic locations (each of >150 kbp), (ix) a map of homoeologous regions among both sets of regions, (x) a set of transcript abundance measurements that address biotic stress resistance, (xi) methods for transformation, (xii) methods for RNAi, (xiii) a TILLING resource for directed mutant isolation, and (xiv) analyses of conserved synteny with other sequenced genomes. The SoyGD portal at sprovides access to the data. To date these resources assisted in the genomic analysis of soybean nodulation and disease resistance. This review summarizes the resources and their uses.

No MeSH data available.


Related in: MedlinePlus