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

Lightfoot DA - Int J Plant Genomics (2008)

Bottom Line: 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.

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

Genetic systems used with Forrestgermplasm and the inbred soybean crop (a). The ancestryof Forrest and Hartwig showing the known cultivars that were crossed and therelationship between Flyer and Williams 82 (b). A diagram showing how NILsderived from RILs fix most loci but allow the continued segregation ofheterozygous regions in inbred crops like soybean. The effect is to Mendelize afew of the loci contributing to QT while causing the majority to be fixed. A dark pod parent was crossed with a light colored pod parent; the F1 heterozygous type (shown as purple pods) was selfed; and F2 progeny was advanced to the F5 by selfing. Aheterozygous plant at any time or heterogeneous RIL at F5:7 or lateridentified is shown as purple pods. Single plants are extracted and seed increased. NILs thatresult may fix the heterogeneous region to the parent 1 allele, the parent 2allele, or are still heterogeneous. Occasionally heterozygous plants are foundwithin some heterogeneous NILs even at the F5:15 and the progeny ofsuch plants can be used to find new recombination events. Shown are the resultswith Satt309 and NIL11 plant 3 and eighteen of the progeny collected from it(adapted from [40]).
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fig3: Genetic systems used with Forrestgermplasm and the inbred soybean crop (a). The ancestryof Forrest and Hartwig showing the known cultivars that were crossed and therelationship between Flyer and Williams 82 (b). A diagram showing how NILsderived from RILs fix most loci but allow the continued segregation ofheterozygous regions in inbred crops like soybean. The effect is to Mendelize afew of the loci contributing to QT while causing the majority to be fixed. A dark pod parent was crossed with a light colored pod parent; the F1 heterozygous type (shown as purple pods) was selfed; and F2 progeny was advanced to the F5 by selfing. Aheterozygous plant at any time or heterogeneous RIL at F5:7 or lateridentified is shown as purple pods. Single plants are extracted and seed increased. NILs thatresult may fix the heterogeneous region to the parent 1 allele, the parent 2allele, or are still heterogeneous. Occasionally heterozygous plants are foundwithin some heterogeneous NILs even at the F5:15 and the progeny ofsuch plants can be used to find new recombination events. Shown are the resultswith Satt309 and NIL11 plant 3 and eighteen of the progeny collected from it(adapted from [40]).

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)

Genetic systems used with Forrestgermplasm and the inbred soybean crop (a). The ancestryof Forrest and Hartwig showing the known cultivars that were crossed and therelationship between Flyer and Williams 82 (b). A diagram showing how NILsderived from RILs fix most loci but allow the continued segregation ofheterozygous regions in inbred crops like soybean. The effect is to Mendelize afew of the loci contributing to QT while causing the majority to be fixed. A dark pod parent was crossed with a light colored pod parent; the F1 heterozygous type (shown as purple pods) was selfed; and F2 progeny was advanced to the F5 by selfing. Aheterozygous plant at any time or heterogeneous RIL at F5:7 or lateridentified is shown as purple pods. Single plants are extracted and seed increased. NILs thatresult may fix the heterogeneous region to the parent 1 allele, the parent 2allele, or are still heterogeneous. Occasionally heterozygous plants are foundwithin some heterogeneous NILs even at the F5:15 and the progeny ofsuch plants can be used to find new recombination events. Shown are the resultswith Satt309 and NIL11 plant 3 and eighteen of the progeny collected from it(adapted from [40]).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3: Genetic systems used with Forrestgermplasm and the inbred soybean crop (a). The ancestryof Forrest and Hartwig showing the known cultivars that were crossed and therelationship between Flyer and Williams 82 (b). A diagram showing how NILsderived from RILs fix most loci but allow the continued segregation ofheterozygous regions in inbred crops like soybean. The effect is to Mendelize afew of the loci contributing to QT while causing the majority to be fixed. A dark pod parent was crossed with a light colored pod parent; the F1 heterozygous type (shown as purple pods) was selfed; and F2 progeny was advanced to the F5 by selfing. Aheterozygous plant at any time or heterogeneous RIL at F5:7 or lateridentified is shown as purple pods. Single plants are extracted and seed increased. NILs thatresult may fix the heterogeneous region to the parent 1 allele, the parent 2allele, or are still heterogeneous. Occasionally heterozygous plants are foundwithin some heterogeneous NILs even at the F5:15 and the progeny ofsuch plants can be used to find new recombination events. Shown are the resultswith Satt309 and NIL11 plant 3 and eighteen of the progeny collected from it(adapted from [40]).
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: 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.

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