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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

Comparison of MegaBlast analysis of an unduplicated region and a twice duplicated region as inferred by the fingerprint physical map (a). Analysis of the BESs from H53F21 in quadruplicated contig 9077. These BESs contained a very common repeat with 400 copies per haploid genome. Sequence analysis supported the inference of four copies of the region per haploid genome made from BAC fingerprint data (a). MegaBlast of H53F21 (Build4MTP8A23, gi89261445) against 7.3 million reads with repeated masking gave 7 identical matches among 24 homoeologous sequences. Cluster 1 was composed of traces ending in …822,…160,…569,…607,…662,…749, and …105 that shared A at position 172 (circled). Homoeolog specific variations (polymorphisms) were evident among the 4 clusters inferred. Cluster 2 was composed of clones ending in 749, 850, and 601 that shared C at position 172. Cluster 3 was composed of clones ending in 100, 117, and 535 that shared G at position 172. Cluster 4 also had G at that position. TreeCluster analysis showed the most similar homoeologs clustered into 4 separate sets as expected for regions duplicated twice (circled) (b). Analysis of the BESs from B47P08 in contig 321 from an unduplicated region. Sequence analysis supported the inferrence of an  unduplicated region made from fingerprints at 90% sequence identity (c). The sequences found among BACs resequenced from contig 9077 showing a set of SNHs (HSVs) separated two groups of the four inferred to be present: the A cluster and the G cluster (adapted from [29]).
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fig2: Comparison of MegaBlast analysis of an unduplicated region and a twice duplicated region as inferred by the fingerprint physical map (a). Analysis of the BESs from H53F21 in quadruplicated contig 9077. These BESs contained a very common repeat with 400 copies per haploid genome. Sequence analysis supported the inference of four copies of the region per haploid genome made from BAC fingerprint data (a). MegaBlast of H53F21 (Build4MTP8A23, gi89261445) against 7.3 million reads with repeated masking gave 7 identical matches among 24 homoeologous sequences. Cluster 1 was composed of traces ending in …822,…160,…569,…607,…662,…749, and …105 that shared A at position 172 (circled). Homoeolog specific variations (polymorphisms) were evident among the 4 clusters inferred. Cluster 2 was composed of clones ending in 749, 850, and 601 that shared C at position 172. Cluster 3 was composed of clones ending in 100, 117, and 535 that shared G at position 172. Cluster 4 also had G at that position. TreeCluster analysis showed the most similar homoeologs clustered into 4 separate sets as expected for regions duplicated twice (circled) (b). Analysis of the BESs from B47P08 in contig 321 from an unduplicated region. Sequence analysis supported the inferrence of an unduplicated region made from fingerprints at 90% sequence identity (c). The sequences found among BACs resequenced from contig 9077 showing a set of SNHs (HSVs) separated two groups of the four inferred to be present: the A cluster and the G cluster (adapted from [29]).

Mentions: An important question that received the attention of soybean researchers in thepast is how much sequence variation one can expect between Forrest and othercultivars, if many are to be sequenced. This variation is extensive (about 1 bpdifference per 100–300 bp), when judged by using the criteria like thefollowing: (i) the coefficient of parentage [25], (ii) the number of sharedRFLP bands [26], (iii) polymorphism among microsatellite markers [27], and (iv)DNA sequence comparisons (Figure 2). In soybean, the degree of linkage disequilibria among loci is high,extending over distances that range from 50 kbp to 150 kbp [28]. Few meioseshave occurred within these regions to reshuffle the gene or DNA sequences, becausesoybean is largely an inbreeding crop. In recent times, only seven or eightcrosses have been made, starting from the time when the PIs were collected to thedevelopment of most modern US cultivars (Figure 3). Therefore, in different parts of the genome, LD encompasses large segments and sets of genes.


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

Lightfoot DA - Int J Plant Genomics (2008)

Comparison of MegaBlast analysis of an unduplicated region and a twice duplicated region as inferred by the fingerprint physical map (a). Analysis of the BESs from H53F21 in quadruplicated contig 9077. These BESs contained a very common repeat with 400 copies per haploid genome. Sequence analysis supported the inference of four copies of the region per haploid genome made from BAC fingerprint data (a). MegaBlast of H53F21 (Build4MTP8A23, gi89261445) against 7.3 million reads with repeated masking gave 7 identical matches among 24 homoeologous sequences. Cluster 1 was composed of traces ending in …822,…160,…569,…607,…662,…749, and …105 that shared A at position 172 (circled). Homoeolog specific variations (polymorphisms) were evident among the 4 clusters inferred. Cluster 2 was composed of clones ending in 749, 850, and 601 that shared C at position 172. Cluster 3 was composed of clones ending in 100, 117, and 535 that shared G at position 172. Cluster 4 also had G at that position. TreeCluster analysis showed the most similar homoeologs clustered into 4 separate sets as expected for regions duplicated twice (circled) (b). Analysis of the BESs from B47P08 in contig 321 from an unduplicated region. Sequence analysis supported the inferrence of an  unduplicated region made from fingerprints at 90% sequence identity (c). The sequences found among BACs resequenced from contig 9077 showing a set of SNHs (HSVs) separated two groups of the four inferred to be present: the A cluster and the G cluster (adapted from [29]).
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2376204&req=5

fig2: Comparison of MegaBlast analysis of an unduplicated region and a twice duplicated region as inferred by the fingerprint physical map (a). Analysis of the BESs from H53F21 in quadruplicated contig 9077. These BESs contained a very common repeat with 400 copies per haploid genome. Sequence analysis supported the inference of four copies of the region per haploid genome made from BAC fingerprint data (a). MegaBlast of H53F21 (Build4MTP8A23, gi89261445) against 7.3 million reads with repeated masking gave 7 identical matches among 24 homoeologous sequences. Cluster 1 was composed of traces ending in …822,…160,…569,…607,…662,…749, and …105 that shared A at position 172 (circled). Homoeolog specific variations (polymorphisms) were evident among the 4 clusters inferred. Cluster 2 was composed of clones ending in 749, 850, and 601 that shared C at position 172. Cluster 3 was composed of clones ending in 100, 117, and 535 that shared G at position 172. Cluster 4 also had G at that position. TreeCluster analysis showed the most similar homoeologs clustered into 4 separate sets as expected for regions duplicated twice (circled) (b). Analysis of the BESs from B47P08 in contig 321 from an unduplicated region. Sequence analysis supported the inferrence of an unduplicated region made from fingerprints at 90% sequence identity (c). The sequences found among BACs resequenced from contig 9077 showing a set of SNHs (HSVs) separated two groups of the four inferred to be present: the A cluster and the G cluster (adapted from [29]).
Mentions: An important question that received the attention of soybean researchers in thepast is how much sequence variation one can expect between Forrest and othercultivars, if many are to be sequenced. This variation is extensive (about 1 bpdifference per 100–300 bp), when judged by using the criteria like thefollowing: (i) the coefficient of parentage [25], (ii) the number of sharedRFLP bands [26], (iii) polymorphism among microsatellite markers [27], and (iv)DNA sequence comparisons (Figure 2). In soybean, the degree of linkage disequilibria among loci is high,extending over distances that range from 50 kbp to 150 kbp [28]. Few meioseshave occurred within these regions to reshuffle the gene or DNA sequences, becausesoybean is largely an inbreeding crop. In recent times, only seven or eightcrosses have been made, starting from the time when the PIs were collected to thedevelopment of most modern US cultivars (Figure 3). Therefore, in different parts of the genome, LD encompasses large segments and sets of genes.

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