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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

An example of the useof Forrest genomics resources for soybean germplasm improvement (a). Summaryof the map locations of the known loci for resistance to SDS. A black rectangleindicates that the allele is segregating in that population. Nonsegregatingalleles may be either fixed to the resistance or susceptibility forms (b). An example of quantitative variationfor disease resistance identified in lines derived from Forrest. The resistantline RIL23, left of the line, has beneficial alleles for six QTL for resistanceto Fusarium virguliforme. The leafscorch associated with the fungal infection is evident in the neighboring RIL80to the right of the white line.
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fig4: An example of the useof Forrest genomics resources for soybean germplasm improvement (a). Summaryof the map locations of the known loci for resistance to SDS. A black rectangleindicates that the allele is segregating in that population. Nonsegregatingalleles may be either fixed to the resistance or susceptibility forms (b). An example of quantitative variationfor disease resistance identified in lines derived from Forrest. The resistantline RIL23, left of the line, has beneficial alleles for six QTL for resistanceto Fusarium virguliforme. The leafscorch associated with the fungal infection is evident in the neighboring RIL80to the right of the white line.

Mentions: Selected lines from the E × F population that contrast for mapped QTL werealso used for a variety of studies including the following: (i) to validateassays of pathogenicity [32, 53–55], (ii) to examine the effects of resistancegenes on gene expression [34, 56, 57], (iii) to analyze components of droughttolerance [24, 31, 36, 42, 46, 58], (iv) to validate methods of marker assistedselection [6, 31, 59–62], and (v) to provide for germplasm releases (Figure 4)and cultivars [6, 63]. New cultivars and new methods for selection of improvedsoybean genotypes are among the most important spin-offs from the genomicsresearch involving Forrest soybean. Among the selected lines, E × F78later became LS-G96 [63] and then “Gateway 512” (Gateway Seeds, Nashville, Ill, USA). This line together with the line E × F55 was used as parents that combined moderateresistance (carrying resistance alleles at six loci) to SDS with high yield.The RIL E × F23 wasreleased as SD-X for very high resistance to SDS [34] and good yield potentialunder license from Access Plant Technologies (Plymouth, Ind, USA), because it containedbeneficial alleles at all eight known resistance loci. In contrast, E × F85 issusceptible to SDS as it contained no beneficial alleles at the knownresistance loci. It makes a great entry for sentinel plots. For animal feed andhuman food, E × F52 has been used as a parent to provide veryhigh phytoestrogen contents to progeny (unpublished), since it containedbeneficial alleles at all the known loci underlying phytoestrogen content. Lowphytoestrogen contents are also required for estrogen sensitive consumers; E × F89 andE × F92 wereused as parents to provide parents for low phytoestrogen in the progeny(unpublished).


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

Lightfoot DA - Int J Plant Genomics (2008)

An example of the useof Forrest genomics resources for soybean germplasm improvement (a). Summaryof the map locations of the known loci for resistance to SDS. A black rectangleindicates that the allele is segregating in that population. Nonsegregatingalleles may be either fixed to the resistance or susceptibility forms (b). An example of quantitative variationfor disease resistance identified in lines derived from Forrest. The resistantline RIL23, left of the line, has beneficial alleles for six QTL for resistanceto Fusarium virguliforme. The leafscorch associated with the fungal infection is evident in the neighboring RIL80to the right of the white line.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig4: An example of the useof Forrest genomics resources for soybean germplasm improvement (a). Summaryof the map locations of the known loci for resistance to SDS. A black rectangleindicates that the allele is segregating in that population. Nonsegregatingalleles may be either fixed to the resistance or susceptibility forms (b). An example of quantitative variationfor disease resistance identified in lines derived from Forrest. The resistantline RIL23, left of the line, has beneficial alleles for six QTL for resistanceto Fusarium virguliforme. The leafscorch associated with the fungal infection is evident in the neighboring RIL80to the right of the white line.
Mentions: Selected lines from the E × F population that contrast for mapped QTL werealso used for a variety of studies including the following: (i) to validateassays of pathogenicity [32, 53–55], (ii) to examine the effects of resistancegenes on gene expression [34, 56, 57], (iii) to analyze components of droughttolerance [24, 31, 36, 42, 46, 58], (iv) to validate methods of marker assistedselection [6, 31, 59–62], and (v) to provide for germplasm releases (Figure 4)and cultivars [6, 63]. New cultivars and new methods for selection of improvedsoybean genotypes are among the most important spin-offs from the genomicsresearch involving Forrest soybean. Among the selected lines, E × F78later became LS-G96 [63] and then “Gateway 512” (Gateway Seeds, Nashville, Ill, USA). This line together with the line E × F55 was used as parents that combined moderateresistance (carrying resistance alleles at six loci) to SDS with high yield.The RIL E × F23 wasreleased as SD-X for very high resistance to SDS [34] and good yield potentialunder license from Access Plant Technologies (Plymouth, Ind, USA), because it containedbeneficial alleles at all eight known resistance loci. In contrast, E × F85 issusceptible to SDS as it contained no beneficial alleles at the knownresistance loci. It makes a great entry for sentinel plots. For animal feed andhuman food, E × F52 has been used as a parent to provide veryhigh phytoestrogen contents to progeny (unpublished), since it containedbeneficial alleles at all the known loci underlying phytoestrogen content. Lowphytoestrogen contents are also required for estrogen sensitive consumers; E × F89 andE × F92 wereused as parents to provide parents for low phytoestrogen in the progeny(unpublished).

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