[Show abstract][Hide abstract] ABSTRACT: Sudden death syndrome (SDS) is a serious threat to soybean production that can be managed with host plant resistance. To dissect the genetic architecture of quantitative resistance to the disease in soybean, two independent association panels of elite soybean cultivars, consisting of 392 and 300 unique accessions, respectively, were evaluated for SDS resistance in multiple environments and years. The two association panels were genotyped with 52,041 and 5,361 single nucleotide polymorphisms (SNPs), respectively. Genome-wide association mapping was carried out using a mixed linear model that accounted for population structure and cryptic relatedness.Result: A total of 20 loci underlying SDS resistance were identified in the two independent studies, including 7 loci localized in previously mapped QTL intervals and 13 novel loci. One strong peak of association on chromosome 18, associated with all disease assessment criteria across the two panels, spanned a physical region of 1.2 Mb around a previously cloned SDS resistance gene (GmRLK18-1) in locus Rfs2. An additional variant independently associated with SDS resistance was also found in this genomic region. Other peaks were within, or close to, sequences annotated as homologous to genes previously shown to be involved in plant disease resistance. The identified loci explained an average of 54.5% of the phenotypic variance measured by different disease assessment criteria.
[Show abstract][Hide abstract] ABSTRACT: Isoflavones from soybeans [ Glycine max (L.) Merr.] have a significant impact on human health to reduce the risk of several major diseases. Breeding soybean for high isoflavone content in the seed is possible through marker-assisted selection (MAS) which can be based on quantitative trait loci (QTL). The objective of this study was to identify QTL controlling isoflavone content in a set of 'MD96-5722' by 'Spencer' recombinant inbred line (RIL) populations of soybean. Wide variations were found for seed concentrations of daidzein, glycitein, genistein, and total isoflavones among the RIL populations. Three QTL were identified on three different linkage groups (LG) represented by three different chromosomes (Chr). One QTL that controlled daidzein content was identified on LG A1 (Chr 5), and two QTL that underlay glycitein content were identified on LG K (Chr 9) and LG B2 (Chr 14). Identified QTL could be functional in developing soybean with preferable isoflavone concentrations in the seeds through MAS.
Journal of Agricultural and Food Chemistry 02/2014; · 3.11 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: This study reports a high density genetic linkage map based on the ‘Maryland 96-5722’ by ‘Spencer’ recombinant inbred line (RIL) population of soybean [Glycine max (L.) Merr.] and constructed exclusively with single nucleotide polymorphism (SNP) markers. The Illumina Infinium SoySNP6K BeadChip genotyping array produced 5,376 SNPs in the mapping population, with a 96.75% success rate. Significant level of goodness-of-fit for each locus was tested based on the observed vs. expected ratio (1:1). Out of 5,376 markers, 1,465 SNPs fit the 1:1 segregation rate having ≤20% missing data plus heterozygosity among the RILs. Among this 1,456 just 657 were polymorphic between the parents DNAs tested. These 657 SNPs were mapped using the JoinMap 4.0 software and 550 SNPs were distributed on 16 linkage groups (LGs) among the 20 chromosomes of the soybean genome. The total map length was just 201.57 centiMorgans (cM) with an average marker density of 0.37 cM. This is one of the high density SNP-based genetic linkage maps of soybean that will be used by the scientific community to map quantitative trait loci (QTL) and identify candidate genes for important agronomic traits in soybean.
Journal of Plant Genome Sciences. 11/2013; 1:80-89.
[Show abstract][Hide abstract] ABSTRACT: The soybean aphid (Aphis glycines Matsumura) has been a major pest of soybean [Glycine max (L.) Merr.] in North America since it was first reported in 2000. Our previous study revealed that the strong aphid resistance of plant introduction (PI) 567598B was controlled by two recessive genes. The objective of this study was to locate these two genes on the soybean genetic linkage map using molecular markers. A mapping population of 282 F4:5 lines derived from IA2070 × E06902 was evaluated for aphid resistance in a field trial in 2009 and a greenhouse trial in 2010. Two quantitative trait loci (QTLs) were identified using the composite and multiple interval mapping methods, and were mapped on chromosomes 7 (linkage group M) and 16 (linkage group J), respectively. E06902, a parent derived from PI 567598B, conferred resistance at both loci. In the 2010 greenhouse trial, each of the two QTLs explained over 30 % of the phenotypic variation. Significant epistatic interaction was also found between these two QTLs. However, in the 2009 field trial, only the QTL on chromosome 16 was found and it explained 56.1 % of the phenotypic variation. These two QTLs and their interaction were confirmed with another population consisting of 94 F2:5 lines in the 2008 and 2009 greenhouse trials. For both trials in the alternative population, these two loci explained about 50 and 80.4 % of the total phenotypic variation, respectively. Our study shows that soybean aphid isolate used in the 2009 field trial defeated the QTL found on chromosome 7. Presence of the QTL on chromosome 16 conferred soybean aphid resistance in all trials. The markers linked to the aphid-resistant QTLs in PI 567598B or its derived lines can be used in marker-assisted breeding for aphid resistance.
Theoretical and Applied Genetics 05/2013; · 3.66 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The soybean aphid (Aphis glycines Matsumura) is a major pest on soybean [Glycine max (L.) Merr.] in North America. Aphid resistance has been found on plant introduction (PI) 567537, but its genetic characterization is unknown. The objectives of this study were to identify the resistance genes in PI 567537 using molecular markers and validate them in a different genetic background. A mapping population of 86 F4 lines from a cross between PI 567537 and a susceptible parent E00003 was investigated for aphid resistance in both greenhouse and field trials. A genomic region associated with the aphid resistance in PI 567537 was revealed on chromosome 16 (linkage group J) with molecular markers. This locus was coincidently located in the same region as Rag3 and explained most of the phenotypic variation, ranging from 87.4 % in the greenhouse trial to 78.9 % in the field trial. This resistance gene was further confirmed in an F2 population derived from a cross of PI 567537 × Skylla. The segregation of the F2 population indicated that the aphid resistance in PI 567537 was most likely controlled by a single dominant gene, which was the one we mapped in the F4-derived population. This gene was designated Rag3b since it is located in the same region as Rag3. The mapping of the aphid resistance gene in PI 567537 could be useful in marker-assisted selection when employing PI 567537 as an aphid resistance source.
[Show abstract][Hide abstract] ABSTRACT: The ecosystem services provided by natural enemies in soybean aphid (Aphis glycines) susceptible and resistant soybean (Glycine max) were studied in Michigan during the summer of 2010. We hypothesized that the lower population of aphids in resistant fields would lead to a corresponding reduction in the number and diversity of natural enemies in the same fields and therefore a reduction in the ecosystem services. Quarter acre blocks of SD01-76R (aphid susceptible), LD 16060 (single gene resistant) and Sparta (multiple gene resistant) soybean lines were planted. Within these blocks, sixteen aphid islands were planted. Each island consisted of a single susceptible (SD01-76R) plant infested with five aphids. Eight islands were caged to protect the aphids from predation while the remaining plants were left open. Aphid numbers on each of the islands were counted and after fourteen days the ecosystem services of predation was determined. The aphid and natural enemy population in the surrounding block was monitored weekly. Other indicators such as egg mass predation were used to detect any difference in predation and ecosystem services between the varieties. No significant differences were detected between the ecosystem services in resistant and susceptible fields.
Entomological Society of America Annual Meeting 2010; 12/2010
[Show abstract][Hide abstract] ABSTRACT: In conventional soybean (Glycine max), potassium (K) deficiency is associated with faster time to reproduction and greater nymph production in Aphis glycines (soybean aphid, SBA). Soybean lines with SBA resistance genes are nearing widespread commercialization; it is not known if resistance is maintained under K deficiency. Ten replicates of four soybean lines were planted in predator-proof cages in a K-deficient field in Montcalm County, Michigan. Two MSU lines carrying new Sparta genetics, E06902 (rag1b/ rag3 SBA resistant) and E07906-2 (rag1c/rag4 SBA resistant), were used along with LD16060 (Rag1 SBA resistant), and SD01-76R (SBA susceptible). Five cages were unfertilized, while five were amended with potash. Plants were infested with equal numbers of soybean aphids and populations were monitored weekly through the course of the growing season. No significant difference between aphid population numbers on plants in amended cages when compared to unfertilized cages even though significantly different plant K levels were detected. Aphid population numbers in cages exceeded the established 250 aphids/plant threshold, possibly explained by the discovery of a new aphid biotype.
Entomological Society of America Annual Meeting 2010; 12/2010
[Show abstract][Hide abstract] ABSTRACT: The soybean aphid (Aphis glycines Matsumura) is an important pest on soybean [Glycine max (L.) Merr.] in North America. Aphid resistance has recently been found on plant introduction (PI) 567543C, but little is known about its genetic control. The objectives of this study were to identify the resistance genes in PI 567543C with molecular markers and validate them in a different genetic background. A mapping population of 249 F(4) derived lines from a cross between PI 567543C and a susceptible parent was investigated for aphid resistance in both the greenhouse and the field. The broad sense heritability of aphid resistance in the field trial was over 0.95. The segregation of aphid resistance in this population suggests a major gene controlling the resistance. Bulked segregant analysis with molecular markers revealed a potential genomic region. After saturating this putative region with more markers, a genetic locus was mapped in an interval between Sat_339 and Satt414 on chromosome 16 (linkage group J) using the composite interval mapping method. This locus explained the majority of the phenotypic variation ranging from 84.7% in the field trial to 90.4% in the greenhouse trial. Therefore, the aphid resistance in PI 567543C could be mainly controlled by this gene. This aphid resistance gene was mapped on a different chromosome than the other resistance genes reported previously from other resistant germplasms. This gene appears to be additive based on the aphid resistance of the heterozygous lines at this locus. Thus, a new symbol Rag3 is used to designate this gene. Moreover, Rag3 was confirmed in a validation population. This new aphid-resistance gene could be valuable in breeding aphid resistant cultivars.
Theoretical and Applied Genetics 04/2010; 120(6):1183-91. · 3.66 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The soybean aphid, Aphis glycines Matsumura, first detected in the US in 2000 (Ostlie, 2002; Alleman et al. 2002) is a major pest of soybean. It has already evolved a new biotype (Ohio biotype) which is virulent to the Rag1 gene that confers resistance to soybean against the original Illinois biotype (Kim et al. 2008). This plant resistance study aims to achieve an understanding of induced resistance in soybean genotypes as a result of previous infestation by soybean aphids. Preliminary experiments with the genotypes K1621 and K1639 and the susceptible checks KS4202 and KO3-4686, exposed to 10 aphids for 2 days, suggested an induction of antibiotic resistance against the aphid (Illinois biotype) in all except KO3-4686. However, no significant induction of resistance affecting the reproductive performance of the aphid was observed in the same genotypes upon preconditioning with 10 aphids (Illinois biotype) over a range of time viz., 2, 4, 9 and 12 days respectively. Soybean genotypes like EO6902, EO7906-2 developed in MSU and some PIs have been found to be resistant to the Ohio biotype of the soybean aphid and currently, experiments are underway to study the effect of induced resistance on this biotype. The Electrical Penetration Graph (EPG) technique will give further insight on the effect of induced resistance, if any, on the feeding behavior of the soybean aphid.
Entomological Society of America Annual Meeting 2009; 12/2009
[Show abstract][Hide abstract] ABSTRACT: In conventional soybean (Glycine max), potassium (K) deficiency is associated with faster time to reproduction and greater nymph production in Aphis glycines (soybean aphid, SBA). Soybean lines with SBA resistance genes are nearing commercialization; it is not known if K deficiency affects them the same way. Eight replicated plantings of the Michigan State University soybean line E06906 with SBA resistance genes rag1b + rag3 were planted in predator-proof cages in a K-deficient field in Montcalm County, Michigan. Four cages were unfertilized, while four were amended with potash. Plants were infested with equal numbers of soybean aphids and populations were monitored weekly through the course of the growing season.
Entomological Society of America Annual Meeting 2009; 12/2009
[Show abstract][Hide abstract] ABSTRACT: The soybean aphid (Aphis glycines Matsumura) is an important pest of soybean [Glycine max (L.) Merr.] in North America since it was first reported in 2000. PI 567541B is a newly discovered aphid resistance germplasm with early maturity characteristics. The objectives of this study were to map and validate the aphid resistance genes in PI 567541B using molecular markers. A mapping population of 228 F3 derived lines was investigated for the aphid resistance in both field and greenhouse trials. Two quantitative trait loci (QTLs) controlling the aphid resistance were found using the composite interval mapping method. These two QTLs were localized on linkage groups (LGs) F and M. PI 567541B conferred resistant alleles at both loci. An additive x additive interaction between these two QTLs was identified using the multiple interval mapping method. These two QTLs combined with their interaction explained most of the phenotypic variation in both field and greenhouse trials. In general, the QTL on LG F had less effect than the one on LG M, especially in the greenhouse trial. These two QTLs were further validated using an independent population. The effects of these two QTLs were also confirmed using 50 advanced breeding lines, which were all derived from PI 567541B and had various genetic backgrounds. Hence, these two QTLs identified and validated in this study could be useful in improving soybean aphid resistance by marker-assisted selection.
Theoretical and Applied Genetics 12/2008; 118(3):473-82. · 3.66 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Enhancing soybean germplasm by incorporating resistance to the soybean aphid,Aphis glycines Matsumura, (Hempitera: Aphididae) is important to reduce yield loss and insecticide costs for soybean production in the North Central States. Resistance to soybean aphid (SBA) was screened in three aphid-resistant lines developed by the MSU Soybean Breeding Program (E06901, E06905, E06906) compared to a commercial susceptible variety. Resistant and commercial lines were planted in replicated plots in two locations in MI. Weekly sampling for SBA using whole-plant counts indicated, fewer SBA abundance and lower infestations on resistant lines. Under no-choice conditions using plants infested then caged, resistant lines had lower SBA density than the susceptible line under pressure of natural enemies. In caged plants,when total SBA-abundance/plant after two weeks were counted,both nymphs and adults reproduced less on resistant lines. Within each resistant line, SBA numbers were significantly different between caged and open plants. Clip-cage experiments were conducted, to determine differences in SBA survival, fecundity and longevity on resistant and susceptible lines by restricting individual aphids (1-d-old viviparous aptera) to clip-cages in low, mid and, high positions of a plant. Leaf damage caused by Popillia japonica was assessed on these lines during out-breaks. Results of this study will assist the university Soybean Program, to further enhance these lines as aphid-resistant cultivars suitable for commercial release.
Entomological Society of America Annual Meeting 2008; 11/2008
[Show abstract][Hide abstract] ABSTRACT: Linkage maps of the sweet cherry cultivar ‘Emperor Francis’ (EF) and the wild forest cherry ‘New York 54’ (NY) were constructed
using primarily simple sequence repeat (SSR) markers and gene-derived markers with known positions on the Prunus reference map. The success rate for identifying SSR markers that could be placed on either the EF or NY maps was only 26%
due to two factors: a reduced transferability of other Prunus-species-derived markers and a low level of polymorphism in the mapping parents. To increase marker density, we developed
four cleaved amplified polymorphic sequence markers (CAPS), 19 derived CAPS markers, and four insertion–deletion markers for
cherry based on 101 Prunus expressed sequence tags. In addition, four gene-derived markers representing orthologs of a tomato vacuolar invertase and
fruit size gene and two sour cherry sorbitol transporters were developed. To complete the linkage analysis, 61 amplified fragment
length polymorphism and seven sequence-related amplified polymorphism markers were also used for map construction. This analysis
resulted in the expected eight linkage groups for both parents. The EF and NY maps were 711.1cM and 565.8cM, respectively,
with the average distance between markers of 4.94cM and 6.22cM. A total of 82 shared markers between the EF and NY maps
and the Prunus reference map showed that the majority of the marker orders were the same with the Prunus reference map suggesting that the cherry genome is colinear with that of the other diploid Prunus species.
Tree Genetics & Genomes 09/2008; 4(4):897-910. · 2.40 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: S clerotinia stem rot, also called white mold, is caused by the fungal pathogen Sclerotinia sclerotiorum (Lib.) deBary and aff ects a large number of crops, including soybean [Glycine max (L.) Merr.]. This disease occurs more frequently in the Upper Midwest region of the United States and southern Canada in high-yield soybean production systems during cool, wet summers (Grau et al., 2004; Hoff man et al., 1998). The infection process begins with colonization of the soybean fl ower petals by S. sclero-tiorum ascospores. Infection then spreads to pods, nodes, and stems and may result in premature plant death (Grau, 1988). Symptoms of infection include wilting, dying plants, white tufts of myce-lium on the stems, leaves, and pods, and sclerotia on and in stems. Sclerotia are often harvested inadvertently along with the seed and may contribute to reduced seed quality as well as a broader distribution of the pathogen (Danielson et al., 2004; Grau et al., 2004). From controlled yield loss studies, for every 10% increase ABSTRACT Soybean [Glycine max (L.) Merr.] PI 391589B, a selection from PI 391589A was recently identi-fi ed as a new source of resistance to Sclero-tinia sclerotiorum (Lib.) deBary, which causes Sclerotinia stem rot. The objective of this study was to identify the quantitative trait loci (QTLs) associated with resistance to S. sclerotiorum in PIs 391589A and 391589B. BC 1 F 4:5 and BC 1 F 4:6 populations from a cross of 'Kottman'(2) × PI 391589A and a population of F 2 -derived lines from a cross of PI 391589B × IA2053 were evalu-ated for resistance to S. sclerotiorum in the fi eld and in the greenhouse from 2003 to 2005 and genotyped with simple sequence repeat mark-ers. Single factor analysis identifi ed 18 markers on nine linkage groups (LGs) signifi cantly (P < 0.05) associated with resistance to S. sclerotio-rum in the two populations. Four regions on LGs E, F, M, and O were signifi cantly associated with the disease resistance in both populations. The four regions are between Satt411 (12.9 cM) and Satt369 (56.2 cM) on LG E, between Satt269 (11.4 cM) and AW186493 (21.0 cM) on LG F, between Satt463 (50.1 cM) and Satt323 (60.1 cM) on LG M, and between Satt581 (106.0 cM) and Satt153 (118.14 cM) on LG O on the soybean composite map developed by Song and others in 2004. Composite interval mapping identifi ed seven QTLs (P < 0.10), each explaining 6.0 to 15.7% of the phenotypic variance. A QTL on LG M near marker Satt463 (50.1 cM) is unique to PI 391589A and B. Therefore, PIs 391589A and 391589B offer breeders a new allele for resis-tance to the disease.
[Show abstract][Hide abstract] ABSTRACT: The soybean aphid (Aphis glycines Matsumura) has become a major pest of soybean in North America since 2000. Seven aphid resistance sources, PI 71506, Dowling, Jackson, PI 567541B, PI 567598B, PI 567543C, and PI 567597C, have been identified. Knowledge of genetic relationships among these sources and their ancestral parents will help breeders develop new cultivars with different resistance genes. The objective of this research was to examine the genetic relationships among these resistance sources. Sixty-one lines were tested with 86 simple sequence repeat (SSR) markers from 20 linkage groups. Non-hierarchical (VARCLUS) and hierarchical (Ward's) clustering and multidimensional scaling (MDS) were used to determine relationships among the 61 lines. Two hundred and sixty-two alleles of the 86 SSR loci were detected with a mean polymorphism information content of 0.36. The 61 lines were grouped into 4 clusters by both clustering methods and the MDS results consistently corresponded to the assigned clusters. The 7 resistance sources were clustered into 3 different groups corresponding to their geographical origins and known pedigree information, indicating genetic differences among these sources. The largest variation was found among individuals within different clusters by analysis of molecular variance.
[Show abstract][Hide abstract] ABSTRACT: T he soybean aphid (SBA; Aphis glycines Matsumura) was fi rst discovered in eight midwestern U.S. states in 2000. Since then it has spread throughout the north-central United States and parts of Canada (North Central Soybean Research Program, 2004) and has become one of the major pests aff ecting soybean production in North America. Soybean aphid populations can double very quickly (McCornack et al., 2004), reaching thou-sands of aphids per plant. Aphid feeding reduces photosynthesis (Macedo et al., 2003) and reduces yield components including plant height, number of nodes and pods per plant, seed size, and bean quality (DiFonzo and Hines, 2002; Ostlie, 2001). In effi cacy trials conducted in Michigan during SBA outbreak years, yield in untreated plots was 18 to 40% less than yield in treated plots (DiFonzo, 2006; DiFonzo and Hines, 2002). Insecticides are still the primary means of controlling SBA, increasing production costs and human exposure. In 2005, an outbreak year for SBA across the Midwest, millions of acres were treated (USDA-National Agricultural Statistics Service, 2006). Insecticide applications also kill natural enemies of SBAs (Smith and Krischik, 1999) and may fl are populations of other soybean pests such as spider mites. Host-plant resistance is the most eff ective means of control of insects. Soybeans resistant to SBA colonization ABSTRACT In a previous study, two soybean [Glycine max (L.) Merr.] plant introductions (PIs), PI 567541B and PI 567598B, were found to possess anti-biosis-type resistance to the soybean aphid (Aphis glycines Matsumura). Plants with anti-biosis resistance negatively interfere with the reproduction of the aphid and thus control the insect effectively. Field studies were conducted to determine the inheritance of antibiosis resis-tance in PI 567541B and PI 567598B. The two resistant PIs were crossed with one or two sus-ceptible soybean lines and the F 1 and F 2 plants and F 2:3 families were evaluated for aphid resis-tance. All F 1 plants were found to be suscep-tible to soybean aphids. The plants in seven F 2 populations segregated in a 15:1 susceptible/ resistant ratio, which is the expected ratio for a trait controlled by two recessive genes. The F 2:3 families also segregated in a 15:1 suscep-tible/resistant ratio. Therefore, the segregation data suggest that two major recessive genes are involved in the resistance in PI 567541B and PI 567598B. This information will be use-ful to breeders for designing effi cient breeding schemes for developing soybean cultivars with antibiosis resistance to aphids.
[Show abstract][Hide abstract] ABSTRACT: Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe; HG) is one of the most destructive pests of soybean (Glycine max (L.) Merr.) in the United States. Over 100 SCN-resistant accessions within the USDA Soybean Germplasm Collection have been identified, but little is known about the genetic diversity of this SCN-resistant germplasm. The objective of this research was to evaluate the genetic variation and determine the genetic relationships among SCN-resistant accessions. One hundred twenty-two genotypes were evaluated by 85 simple sequence repeat (SSR) markers from 20 linkage groups. Non-hierarchical (VARCLUS) and hierarchical (Ward's) clustering were combined with multidimensional scaling (MDS) to determine relationships among tested lines. The 85 SSR markers produced 566 allelic fragments with a mean polymorphic information content (PIC) value of 0.35. The 122 lines were grouped into 7 clusters by 2 different clustering methods and the MDS results consistently corresponded to the assigned clusters. Assigned clusters were dominated by genotypes that possess one or more unique SCN resistance genes and were associated with geographical origins. The results of analysis of molecular variance (AMOVA) showed that the variation differences among clusters and individual lines were significant, but the differences among individuals within clusters were not significant.