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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

Soybean Tilling gel image of Gm_clavata1 pool ps33 screening,representing 768 individuals, 8 individuals per pool (LI-COR 700 channelmutations are marked in red boxes; blue boxes represent lane numbers) from http://www.soybeantilling.org/ (thanks to Dr. K. Meksem and Dr. B. Liu SIUC, unpublished data).
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fig8: Soybean Tilling gel image of Gm_clavata1 pool ps33 screening,representing 768 individuals, 8 individuals per pool (LI-COR 700 channelmutations are marked in red boxes; blue boxes represent lane numbers) from http://www.soybeantilling.org/ (thanks to Dr. K. Meksem and Dr. B. Liu SIUC, unpublished data).

Mentions: (iii) Study of gene function through TILLING. Twosoybean mutagenized M2 libraries are already available for TILLING [113], fromwhich ∼3000 of the 6000 available M2 lines were phenotyped visually. A soybean mutant database has been developed totrack and sort these mutants (http://www.soybeantilling.org/).While developing a database that would allow search for “TILLED” genes a searchengine was developed, so that the database can be searched for both phenotypeand gene. The mutations occurred at a rate of ∼1 mutation/170 kbp, so that a screeningof 6150 M2 families may provide a series of up to 40 to 60 alleles within each1.5 kbp fragment of a target gene. This approach led to the identification of a putative mutant for asoybean leucine rich repeat receptor like kinase gene Gm-Clavata1A (AF197946; Figure 8). In future, TILLING and crosses among TILLED mutants[100–102] will allow the testing of candidate genes and will provide newgenetic variation that may lead to germplasm enhancement.


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

Lightfoot DA - Int J Plant Genomics (2008)

Soybean Tilling gel image of Gm_clavata1 pool ps33 screening,representing 768 individuals, 8 individuals per pool (LI-COR 700 channelmutations are marked in red boxes; blue boxes represent lane numbers) from http://www.soybeantilling.org/ (thanks to Dr. K. Meksem and Dr. B. Liu SIUC, unpublished data).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig8: Soybean Tilling gel image of Gm_clavata1 pool ps33 screening,representing 768 individuals, 8 individuals per pool (LI-COR 700 channelmutations are marked in red boxes; blue boxes represent lane numbers) from http://www.soybeantilling.org/ (thanks to Dr. K. Meksem and Dr. B. Liu SIUC, unpublished data).
Mentions: (iii) Study of gene function through TILLING. Twosoybean mutagenized M2 libraries are already available for TILLING [113], fromwhich ∼3000 of the 6000 available M2 lines were phenotyped visually. A soybean mutant database has been developed totrack and sort these mutants (http://www.soybeantilling.org/).While developing a database that would allow search for “TILLED” genes a searchengine was developed, so that the database can be searched for both phenotypeand gene. The mutations occurred at a rate of ∼1 mutation/170 kbp, so that a screeningof 6150 M2 families may provide a series of up to 40 to 60 alleles within each1.5 kbp fragment of a target gene. This approach led to the identification of a putative mutant for asoybean leucine rich repeat receptor like kinase gene Gm-Clavata1A (AF197946; Figure 8). In future, TILLING and crosses among TILLED mutants[100–102] will allow the testing of candidate genes and will provide newgenetic variation that may lead to germplasm enhancement.

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