Pooled analysis of data from multiple quantitative trait locus mapping populations

Quantitative trait locus (QTL) analysis on pooled data from multiple populations (pooled analysis) provides a means for evaluating, as a whole, evidence for existence of a QTL from different studies and examining differences in gene effect of a QTL among different populations. Objectives of this study were to: (1) develop a method for pooled analysis and (2) conduct pooled analysis on data from two soybean mapping populations. Least square interval mapping was extended for pooled analysis by inclusion of populations and cofactor markers as indicator variables and covariate variables separately in the multiple linear models. The general linear test approach was applied for detecting a QTL. Single population-based and pooled analyses were conducted on data from two F_2:3 mapping populations, Hamilton (susceptible) × PI 90763 (resistant) and Magellan (susceptible) × PI 404198A (resistant), for resistance to soybean cyst nematode (SCN) in soybean. It was demonstrated that where a QTL was shared among populations, pooled analysis showed increased LOD values on the QTL candidate region over single population analyses. Where a QTL was not shared among populations, however, the pooled analysis showed decreased LOD values on the QTL candidate region over single population analyses. Pooled analysis on data from genetically similar populations may have higher power of QTL detection than single population-based analyses. QTLs were identified by pooled analysis on linkage groups (LGs) G, B1 and J for resistance to SCN race 2 whereas QTLs on LGs G, B1 and E for resistance to SCN race 5 in soybean PI 90763 and PI 404198A. QTLs on LG G and B1 were identified in both PI 90763 and PI 404198A whereas QTLs on LG E and J were identified in PI 90763 only. QTLs on LGs G and B1 for resistance to race 2 may be the same or closely linked with QTLs on LG G and B1 for resistance to race 5, respectively. It was further demonstrated that QTLs on G and B1 carried by PI 90763 were not significantly different in gene effect from QTLs on LGs G and B1 in PI 404198A, respectively.     

QTL, additive and epistatic effects for SCN resistance in PI 437654

PI 437654 is a unique accession because of its resistance to nearly all HG types (races) of soybean cyst nematode (Heterodera glycines Ichinohe; SCN). Objectives of this study were to confirm and refine the locations and gene action associated with SCN resistance previously discovered in PI 437654, and to identify new QTLs that may have been missed because of low coverage with genetic markers used in previous studies. Using 205 F_7:9 RILs and 276 SSR and AFLP molecular markers covering 2,406.5 cM of 20 linkage groups (LGs), we confirmed and refined the locations of major SCN resistance QTLs on LG-A2, -B1, and -G previously identified in PI 437654 or other resistant sources. We found that these major QTLs have epistatic effects among them or with other loci for SCN resistance. We also detected some new QTLs with additive or epistatic effects for SCN resistance to different HG types (races) on all LGs except LGs-B2 and -D1b. The QTL on LG-G was associated with resistance to HG types 2.5.7, 1.2.5.7, 0, and 2.7 (races 1, 2, 3, and 5), and it contributed a large proportion of the additive effects. The QTL on LG-A2 was associated with resistance to HG types 2.5.7 and 0 (races 1 and 3). The QTL on LG-B1, associated with resistance to HG types 2.5.7, 0, 2.7 (races 1, 3, and 5), was the similar QTL found in PI 90763 and PI 404198B. In addition to QTL on LGs-A2, -B1 and -G, a novel additive QTL associated with SCN resistance to HG types 0, 2.7, and 1.3.5.6.7 (race 3, 5, and 14) was identified on LG-I flanked by Sat_299 and Sat_189. Several minor QTLs on LGs-C1, D1a, H, and K were also found to be associated with SCN resistance. Confirmation of the new resistance QTL is underway by evaluating another RIL population with a different genetic background.     

Molecular characterization of resistance to Heterodera glycines in soybean PI 438489B

Soybean (Glycine max L. Merr.) plant introduction (PI) 438489B is a newly found germplasm source that has resistance to multiple soybean cyst nematode (Heterodera glycines Ichinohe, SCN) races. We studied the inheritance of resistance to SCN races 1, 2, 3, 5 and 14 in PI 438489B using F₂ and F_2:3 families, which were generated by crossing to the susceptible cultivar ’Hamilton.’ The objectives of this study were to investigate the inheritance for resistance to SCN races in PI 438489B, to find molecular markers associated with resistances, and to study the allelic relationships among resistance loci for different SCN races. The results showed that the responses to SCN races were approximately normally distributed with large environmental effects, and were also highly correlated, which implied that genes giving resistance to different races were similar. The narrow-sense heritabilities of resistance to all five SCN races ranged from 0.55 to 0.88. Fifty one restriction fragment length polymorphism (RFLP) markers and 64 simple sequence repeat (SSR) markers were found to be polymorphic in the F₂ population. Quantitative trait loci (QTLs) associated with resistance to SCN races were anchored on soybean linkage groups (LGs) A1, A2, B1, B2, C1, C2, D1a, E and G. These QTLs explained 47.3%, 45.8%, 51.5%, 34.5% and 37.2% of the total phenotypic variances, respectively, for each race we investigated. Some QTLs for different races encompassed the same region of flanking markers; therefore, QTLs for multiple races may be linked or pleiotropic effects may be involved. Some loci provided resistance in a race-specific manner. Resistance to SCN race 14 had a different pattern compared to other races. Our results indicated that resistance to race 14 did not include loci on LGs A2 and G. These flanking markers associated with QTLs could be used to select for resistance to multiple SCN races in soybean breeding programs. Received: 25 March 2000 / Accepted: 4 August 2000     

Molecular markers for resistance to Heterodera glycines in advanced soybean germplasm

Germplasm line J87-233 is resistant to soybean cyst nematode (SCN) races 1, 2, 3, 5 and moderately resistant to race 14 with resistance derived from 3 primitive sources, Peking, PI 88788 and PI 90763. F_2:3 progeny of J87-233 and SCN-susceptible Hutcheson cross were evaluated for response to SCN races 1, 2, 3, 5 and 14. Linkage groups (LG) A, B, F, G, J, M, N, S were tested with 215 genomic clones and 45 decamers for parental genotypes. QTL for race 1 and QTL for race 3 were detected on LG A2, the region of BLT65V and SCAR 548/563_{1100/1025,975.} The cluster analysis of 12 soybean cultivars and 38 plant introductions confirmed association of SCAR_{1100/1025,975} with resistance to races 1 and 3, and suggested possible DNA rearrangements that might give rise to new resistance specificities in the region. The highly significant association of K69T marker with SCN race 1 resistance in conjunction with its location, 18.5 cM from the reported QTL, exemplifies the importance of the QTL locus on LG G and suggests expansion of the linkage map in the LG G-terminal region. Detected interaction between loci on LG A2 and LG G, and also with loci on LG F and LG M, may play a significant role in the genotype-specific response to SCN. Identification of two major regions on LG A2 and LG G for SCN resistance shows their applicability to advanced germplasm, however, transmission of molecular marker alleles indicates that applied markers are not yet reliable in revealing all possible recombination events in breeding for SCN resistance.     

Molecular mapping of soybean aphid resistance genes in PI 567541B

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 × 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.     

Novel quantitative trait loci for broad-based resistance to soybean cyst nematode (Heterodera glycines Ichinohe) in soybean PI 567516C

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most destructive pest of soybean worldwide. Host plant resistance is an effective approach to control this pest. Plant introduction PI 567516C has been reported to be highly resistant to multiple-HG types of SCN. The objectives of this study were to identify and map novel quantitative trait loci (QTL) for SCN resistance to six HG types (also known as races 1, 2, 3, 5, 14, and LY1). Mapping was conducted using 250 F_2:3 progeny derived from a Magellan (susceptible) × PI 567516C (resistant) cross. F_6:7 recombinant inbred lines (RILs) developed from the F_2:3 progeny were employed to confirm the putative QTL identified. A total of 927 polymorphic simple sequence repeats (SSR) and single nucleotide polymorphism (SNP) markers were genotyped. Following the genetic linkage analysis, permutation tests and composite interval mapping were performed to identify and map QTL. Four QTL were associated with resistance to either multiple- or single-SCN HG types. Two QTL for resistance to multiple-SCN HG types were mapped to Chromosomes 10 and 18 and have not been reported in other SCN resistance sources. New QTL were confirmed by analysis of 250 F_6:7 RILs from the same population. SSR and SNP markers closely associated with these QTL can be useful for the development of near-isogenic lines for fine-mapping and positional cloning of candidate genes for SCN resistance.     

Genetic mapping of soybean cyst nematode race-3 resistance loci in the soybean PI 437.654

Resistance to the soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is difficult to evaluate in soybean [Glycine max (L.) Merr.] breeding. PI 437.654 has resistance to more SCN race isolates than any other known soybean. We screened 298 F₆₇ recombinant-inbred lines from a cross between PI 437.654 and BSR101 for SCN race-3 resistance, genetically mapped 355 RFLP markers and the I locus, and tested these markers for association with resistance loci. The Rhg ₄ resistance locus was within 1 cM of the I locus on linkage group A. Two additional QTLs associated with SCN resistance were located within 3cM of markers on groups G and M. These two loci were not independent because 91 of 96 lines that had a resistant-parent marker type on group G also had a resistant-parent marker type on group M. Rhg ₄ and the QTL on G showed a significant interaction by together providing complete resistance to SCN race-3. Individually, the QTL on G had greater effect on resistance than did Rhg ₄, but neither locus alone provided a degree of resistance much different from the susceptible parent. The nearest markers to the mapped QTLs on groups A and G had allele frequencies from the resistant parent indicating 52 resistant lines in this population, a number not significantly different from the 55 resistant lines found. Therefore, no QTLs from PI 437.654 other than those mapped here are expected to be required for resistance to SCN race-3. All 50 lines that had the PI 437.654 marker type at the nearest marker to each of the QTLs on groups A and G were resistant to SCN race-3. We believe markers near to these QTLs can be used effectively to select for SCN race-3 resistance, thereby improving the ability to breed SCN-resistant soybean varieties.     

RFLP markers associated with soybean cyst nematode resistance and seed composition in a ‘Peking’בEssex’ population

 Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, causes severe damage to soybean [Glycine max (L.) Merr] throughout North America and worldwide. Molecular markers associated with loci conferring SCN resistance would be useful in breeding programs using marker-assisted selection (MAS). In this study, 200 F_2:3 families derived from two contrasting parents, SCN-resistant ‘Peking’ with relatively low protein and oil concentrations, and SCN-susceptible ‘Essex’ with high protein and oil concentrations, were used to determine loci underlying the SCN resistance and seed composition. Three different SCN Race isolates (1, 3, and 5) were used to screen both parents and F_2:3 families. The parents were surveyed with 216 restriction fragment length polymorphism (RFLP) probes with five different restriction enzymes. Fifty-six were polymorphic and contrasted with trait data from bioassays to identify molecular markers associated with loci controlling resistance to SCN and seed composition. Five RFLP markers, A593 and T005 on linkage group (LG) B, A018 on LG E, and K014 and B072 on LG H, were significantly linked to resistance loci for Race 1 isolate, which jointly explained 57.7% of the total phenotypic variation. Three markers (B072 and K014, both on LG H; T005 on LG B) were associated with resistance to the Race 3 isolate and jointly explained 21.4% of the total phenotypic variation. Two markers (K011 on LG I, A963 on LG E) associated with resistance to the Race 5 isolate together explained 14.0% of the total phenotypic variation. In the same population we also identified two RFLP markers (B072 on LG H, B148 on LG F) associated with loci conferring protein concentration, which jointly explained 32.3% of the total phenotypic variation. Marker B072 was also linked to loci controlling the concentration of seed oil, which explained 21% of the total phenotypic variation. Clustering among quantitative trait loci (QTLs) conditioning resistance to different SCN Race isolates and seed protein and oil concentrations may exist in this population. We believe that markers located near these QTLs could be used to select for new SCN resistance and higher levels of seed protein and oil concentrations in breeding improved soybean cultivars. Received: 3 March 1998 / Accepted: 18 August 1998     

Changes in the Reproduction of Heterodera glycines on Different Lines of Glycine max

Selection for ability of soybean cyst nematode (SCN), Heterodera glycines, to reproduce on soybeans with different sources of resistance divides some SCN race 4 field populations into two distinct subpopulations. These subpopulations reproduce well on ''Bedford'' and plant introduction (PI) 88788 or PI 89772 and PI 90763 but not on both pairs of soybean lines. The ability of these subpopulations to reproduce on the four soybean lines was reversed by changing the soybean line used as a host during a second cycle of selection. When SCN populations previously selected for reproduction on Bedford and PI 88788 were selected for their ability to reproduce on D72-8927 and J74-88, the ability of these populations to reproduce on Bedford and PI 88788 decreased significantly and their ability to reproduce on PI 89772 and PI 90763 increased significantly. Conversely, when SCN populations, previously selected for reproduction on P189772 and P190763, were selected for their ability to reproduce on Bedford, the reproduction of these populations on Bedford increased significantly and reproduction on PI 89772 and PI 90763 decreased significantly. Selection for ability of a SCN race 4 field population to reproduce on soybean lines derived from SCN race 4 resistant PIs resulted in the same division of the field population into two distinct subpopulations. These data substantiate earlier proposals to rotate cultivars with different genes for SCN resistance as a means of managing SCN populations.     

Transgenic soybean overexpressing GmSAMT1 exhibits resistance to multiple‐HG types of soybean cyst nematode Heterodera glycines

Soybean (Glycine max (L.) Merr.) salicylic acid methyl transferase (GmSAMT1) catalyses the conversion of salicylic acid to methyl salicylate. Prior results showed that when GmSAMT1 was overexpressed in transgenic soybean hairy roots, resistance is conferred against soybean cyst nematode (SCN), Heterodera glycines Ichinohe. In this study, we produced transgenic soybean overexpressing GmSAMT1 and characterized their response to various SCN races. Transgenic plants conferred a significant reduction in the development of SCN HG type 1.2.5.7 (race 2), HG type 0 (race 3) and HG type 2.5.7 (race 5). Among transgenic lines, GmSAMT1 expression in roots was positively associated with SCN resistance. In some transgenic lines, there was a significant decrease in salicylic acid titer relative to control plants. No significant seed yield differences were observed between transgenics and control soybean plants grown in one greenhouse with 22 °C day/night temperature, whereas transgenic soybean had higher yield than controls grown a warmer greenhouse (27 °C day/23 °C night) temperature. In a 1‐year field experiment in Knoxville, TN, there was no significant difference in seed yield between the transgenic and nontransgenic soybean under conditions with negligible SCN infection. We hypothesize that GmSAMT1 expression affects salicylic acid biosynthesis, which, in turn, attenuates SCN development, without negative consequences to soybean yield or other morphological traits. Thus, we conclude that GmSAMT1 overexpression confers broad resistance to multiple SCN races, which would be potentially applicable to commercial production.     

Seed yield of near-isogenic soybean lines with introgressed quantitative trait loci conditioning resistance to corn earworm (Lepidoptera: Noctuidae) and soybean looper (Lepidoptera: Noctuidae) from PI 229358

The development of superior soybean, Glycine max (L.) Merr., cultivars exhibiting resistance to insects has been hindered due to linkage drag, a common phenomenon when introgressing alleles from exotic germplasm. Simple-sequence repeat (SSR) markers were used previously to map soybean insect resistance (SIR) quantitative trait loci (QTLs) in a'Cobb' X PI 229358 population, and subsequently used to create near-isogenic lines (NILs) with SIR QTL i n a 'Benning' genetic background. SIR QTLs were mapped on linkage groups (LGs) M (SIRQTL-M), G (SIRQTL-G), and H (SIRQTL-H). The objectives of this study were to 1) evaluate linkage drag for seed yield by using Benning-derived NILs selected for SIRQTL-M, SIRQTL-H, and SIRQTL-G; 2) assess the amount of PI 229358 genome surrounding the SIR QTL in each Benning NIL; and 3) evaluate the individual effects these three QTLs on antibiosis and antixenosis to corn earworm, Helicoverpa zea (Boddie), and soybean looper, Pseudoplusia includens (Walker). Yield data collected in five environments indicated that a significant yield reduction is associated with SIRQTL-G compared with NILs without SIR QTL. Overall, there was no yield reduction associated with SIRQTL-M or SIRQTL-H. A significant antixenosis and antibiosis effect was detected for SIRQTL-M in insect feeding assays, with no effect detected in antixenosis or antibiosis assays for SIRQTL-G or SIRQTL-H without the presence of PI 229358 alleles at SIRQTL-M. These results support recent findings concerning these loci.     

Effect of Soil Temperature and pH on Resistance of Soybean to Heterodera glycines

Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is a major pest of soybean, Glycine max L. Merr. Soybean cultivars resistant to SCN are commonly grown in nematode-infested fields. The objective of this study was to examine the stability of SCN resistance in soybean genotypes at different soil temperatures and pH levels. Reactions of five SCN-resistant genotypes, Peking, Plant Introduction (PI) 88788, Custer, Bedford, and Forrest, to SCN races 3, 5, and 14 were studied at 20, 26, and 32 C, and at soil pH''s 5.5, 6.5, and 7.5. Soybean cultivar Essex was included as a susceptible check. Temperature, SCN race, soybean genotype, and their interactions significantly affected SCN reproduction. The effect of temperature on reproduction was quadratic with the three races producing significantly greater numbers of cysts at 26 C; however, reproduction on resistant genotypes remained at a low level. Higher numbers of females matured at the soil pH levels of 6.5 and 7.5 than at pH 5.5. Across the ranges of temperature and soil pH studied, resistance to SCN in the soybean genotypes remained stable.     

Identification of QTL in soybean underlying resistance to herbivory by Japanese beetles (Popillia japonica, Newman)

Soybean [Glycine max (L.) Merr.] was one of the most important legume crops in the world in 2010. Japanese beetles (JB; Popillia japonica, Newman) in the US were an introduced and potentially damaging insect pest for soybean. JBs are likely to spread across the US if global warming occurs. Resistance to JB in soybean was previously reported only in plant introductions. The aims here were to identify loci underlying resistance to JB herbivory in recombinant inbred lines (RILs) derived from the cross of Essex × Forrest cultivars (EF94) and to correlate those with loci with factors that confer insect resistance in soybean cultivars. The RIL population was used to map 413 markers, 238 satellite markers and 177 other DNA markers. Field data were from two environments over 2 years. Pest severity (PS) measured defoliation on a 0–9 scale. Pest incidence (PI) was the percentage of plants within each RIL with beetles on them. Antibiosis and antixenosis data were from feeding assays with detached leaves in petri plates. Five QTL were detected for the mean PS field trait (16% < R ² < 27%). The loci were within the intervals Satt632–A2D8 on linkage group (LG) A2 (chromosome 8); Satt583–Satt415 on LG B1 (11); Satt009–Satt530 on LG N (3); and close to two markers OB02_140 (LG E; 20 cM from Satt572) and OZ15_150 LG (19 cM from Satt291 C2). Two QTL were detected for the mean PI field trait (16% < R ² < 18%) close to Satt385 on LG A1 and Satt440 on LG I. The no choice feeding studies detected three QTL that were significant; two for antixenosis (22% < R ² < 24%) between Satt632–A2D8 on LG A2 (8) and Sat_039–Satt160 on LG F (13); and a major locus effect (R ² = 54%) for antibiosis on LG D2 (17) between Satt464–Satt488. Therefore, loci underlying resistance to JB herbivory were a mixture of major and minor gene effects. Some loci were within regions underlying resistance to soybean cyst nematode (LGs A2 and I) and root knot nematode (LG F) but not other major loci underlying resistance to nematode or insect pests (LGs G, H and M).     

Correlation of Female Indices From Virulence Assays on Inbred Lines and Field Populations of Heterodera glycines

A lack of diversity and durability of resistant soybean varieties complicates management of the soybean cyst nematode (SCN), Heterodera glycines, exemplified by the current overdependence on the PI 88788 source of resistance. Of interest is the effect of adaptation of a SCN population to a source of resistance on its subsequent ability to develop on others. Female indices (FI) from virulence assays (race, HG Type and SCN Type tests) for SCN field populations and inbred lines were analyzed. Female indices on PI 88788, PI 209332 and PI 548316 were highly correlated, as were those of PI 548402, PI 90763, PI 89772 and PI 438489B. Previous studies on resistant SCN-infected soybean roots indicated that the cellular resistance response was similar within these two groups of soybean genotypes. In field populations, highly significant correlations were also found between FI on PI 88788 and PI 548402 and those on PI 89772 and PI 437654. In inbred lines, FI on PI 437654 were correlated with PI 90763 and PI 438489B. To avoid further adaptation, rotation of cultivars with resistance from these groups should be carefully monitored, including those from the most promising source of resistance, PI 437654, such as CystX. In a separate test, 10 soybean varieties developed from CystX were tested against HG Type 0, HG Type 2.5.7 and HG Type 1–7. Female development occurred in all tests but one. Although identification and deployment of unique resistance is needed, management strategies to prevent and detect adaptation should be emphasized.     

Seed and agronomic QTL in low linolenic acid, lipoxygenase-free soybean (Glycine max (L.) Merrill) germplasm.

Linolenic acid and seed lipoxygenases are associated with off flavours in soybean products. F5 recombinant inbred lines (RILs) from a cross between a low linolenic acid line (RG10) and a seed lipoxygenase-free line (OX948) were genotyped for simple sequence repeats (SSR), random amplified polymorphic DNA (RAPD), sequence-tagged sites (STS), and cleaved amplified polymorphic sequence (CAPS) markers and evaluated for seed and agronomic traits at 3 Ontario locations in 2 years. One hundred twenty markers covering 1247.5 cM were mapped to 18 linkage groups (LGs) in the soybean composite genetic map. Seed lipoxygenases L-1 and L-2 mapped as single major genes to the same location on LG G13-F. L-3 mapped to LG G11-E. This is the first report of a map position for L-3. A major quantitative trait locus (QTL) associated with reduced linolenic acid content was identified on LG G3-B2. QTLs for 12 additional seed and agronomic traits were detected. Linolenic acid content, linoleic acid content, yield, seed mass, protein content, and plant height QTL were present in at least 4 of 6 environments. Three to 8 QTLs per trait were detected that accounted for up to 78% of total variation. Linolenic acid and lipoxygenase loci did not overlap yield QTL, suggesting that it should be possible to develop high-yielding lines resistant to oxidative degradation by marker-assisted selection (MAS).     

Genome-wide association study for soybean cyst nematode resistance in Chinese elite soybean cultivars

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is a highly recalcitrant endoparasite of soybean roots, causing more yield loss than any other pest. To identify quantitative trait loci (QTL) controlling resistance to SCN (HG type 2.5.7, race 1), a genome-wide association study (GWAS) was performed. The association panel, consisting of 120 Chinese soybean cultivars, was genotyped with 7189 single nucleotide polymorphism (SNPs). A total of 6204 SNPs with minor allele frequency >0.05 were used to estimate linkage disequilibrium (LD) and population structure. The mean level of LD measured by r ² declined very rapidly to half its maximum value (0.51) at 220 kb. The overall population structure was approximately coincident with geographic origin. The GWAS results identified 13 SNPs in 7 different genomic regions significantly associated with SCN resistance. Of these, three SNPs were localized in previously mapped QTL intervals, including rhg1 and Rhg4. The GWAS results also detected 10 SNPs in 5 different genomic regions associated with SCN resistance. The identified loci explained an average of 95.5% of the phenotypic variance. The proportion of phenotypic variance was due to additive genetic variance of the validated SNPs. The present study identified multiple new loci and refined chromosomal regions of known loci associated with SCN resistance. The loci and trait-associated SNPs identified in this study can be used for developing soybean cultivars with durable resistance against SCN.     

Separate loci underlie resistance to root infection and leaf scorch during soybean sudden death syndrome

Soybean [Glycine max (L.) Merr.] cultivars show differences in their resistance to both the leaf scorch and root rot of sudden death syndrome (SDS). The syndrome is caused by root colonization by Fusarium virguliforme (ex. F. solani f. sp. glycines). Root susceptibility combined with reduced leaf scorch resistance has been associated with resistance to Heterodera glycines HG Type 1.3.6.7 (race 14) of the soybean cyst nematode (SCN). In contrast, the rhg1 locus underlying resistance to Hg Type 0 was found clustered with three loci for resistance to SDS leaf scorch and one for root infection. The aims of this study were to compare the inheritance of resistance to leaf scorch and root infection in a population that segregated for resistance to SCN and to identify the underlying quantitative trait loci (QTL). “Hartwig”, a cultivar partially resistant to SDS leaf scorch, F. virguliforme root infection and SCN HG Type 1.3.6.7 was crossed with the partially susceptible cultivar “Flyer”. Ninety-two F5-derived recombinant inbred lines and 144 markers were used for map development. Four QTL found in earlier studies were confirmed. One contributed resistance to leaf scorch on linkage group (LG) C2 (Satt277; P = 0.004, R ² = 15%). Two on LG G underlay root infection at R8 (Satt038; P = 0.0001 R ² = 28.1%; Satt115; P = 0.003, R ² = 12.9%). The marker Satt038 was linked to rhg1 underlying resistance to SCN Hg Type 0. The fourth QTL was on LG D2 underlying resistance to root infection at R6 (Satt574; P = 0.001, R ² = 10%). That QTL was in an interval previously associated with resistance to both SDS leaf scorch and SCN Hg Type 1.3.6.7. The QTL showed repulsion linkage with resistance to SCN that may explain the relative susceptibility to SDS of some SCN resistant cultivars. One additional QTL was discovered on LG G underlying resistance to SDS leaf scorch measured by disease index (Satt130; P = 0.003, R ² = 13%). The loci and markers will provide tagged alleles with which to improve the breeding of cultivars combining resistances to SDS leaf scorch, root infection and SCN HG Type 1.3.6.7. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic mapping of QTLs conditioning soybean sprout yield and quality

Soybean sprouts have been used as a food in the Orient since ancient times. In this study, 92 restriction fragment length polymorphism (RFLP) loci and two morphological markers (W1 and T) were used to identify quantitative trait loci (QTLs) associated with soybean sprout-related traits in 100 F₂-derived lines from the cross of ’Pureunkong’×’Jinpumkong 2’. The genetic map consisted of 76 loci which covered about 756 cM and converged into 20 linkage groups. Eighteen markers remained unlinked. Phenotypic data were collected in 1996 and 1997 for hypocotyl length, percentage of abnormal seedlings, and sprout yield 6 days after germination at 20°C. Hypocotyl length was determined as the average length from the point of initiation of the first secondary root to the point of attachment of the cotyledons. The number of decayed seeds and seedlings, plus the number of stunted seedlings (less than 2-cm growth), was recorded a s abnormal seedlings. Seed weight was determined based on the 50-seed sample. Sprout yield was recorded as the total fresh weight of soybean sprouts produced from the 50-seed sample divided by the dry weight of the 50-seed sample. Four QTLs were associated with sprout yield in the combined analysis across 2 years. For the QTL linked to L154 on the Linkage Group (LG) G the positive allele was derived from Pureunkong (R ² = 0.19), whereas at the other three QTLs (A089 on LG B1, A668n on LG K and B046 on LG L) the positive alleles were from Jinpumkong 2. QTLs conditioning seed weight were linked to markers A802n (LG B1), A069 (LG E), Cr321 (LG F) and A235 (LG G). At these four markers, the Jinpumkong allele increased seed weight. Markers K011n on LG B1, W1 on LG F and A757 on LG L were linked to QTLs conditioning hypocotyl length; and Bng119, K455n and K418n to QTLs conditioning the abnormal seedlings. The QTLs conditioning sprout yield were in the same genomic locations as the QTLs for seed weight identified in this population or from previously published research, indicating that QTLs for sprout yield are genetically linked to seed-weight QTLs or else that seed-weight QTLs pleiotropically condition sprout yield. These data demonstrate that effective marker-assisted selection may be feasible for enhancing sprout yield in a soybean. The transgressive segregation of sprout yield, as well as the existence of two QTLs conditioning greater than 10% of the phenotypic variation in sprout yields provides an opportunity to select for progeny lines with a greater sprout yield than currently preferred cultivars such as Pureunkong. Received: 23 August 2000 / Accepted: 23 January 2001     

Loci underlying resistance to Race 3 of soybean cyst nematode in Glycine soja plant introduction 468916

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is an important soybean [Glycine max (L.) Merr.] pest in the U.S. and throughout the world. Genetic resistance is the primary method for controlling SCN and there is a need to identify new resistance genes. Glycine soja Sieb. and Zucc. is the wild ancestor of domesticated soybean and is a potential source of new SCN resistance genes. The goal of this research was to map quantitative trait loci (QTLs) that provide resistance to SCN Race 3 from the G. soja plant introduction (PI) 468916. Fifty seven F₂-derived lines from a cross between the G. soja PI 468916 and the G. max experimental line A81-356022 were tested for resistance to an SCN population with a Race-3 phenotype. These lines were also genotyped with 1,004 genetic markers and resistance genes were mapped by composite interval mapping with the computer program QTL-Cartographer. In the F₂ population, three significant (LOD > 3.0) QTLs were detected that explained from 5% to 27% of the variation for Race-3 resistance. The two most significant QTLs identified in the F₂ population were tested in a population of 100 BC1F₂ plants developed by crossing A81-356022 to a line from the F₂ population that carried the two resistance QTLs from G. soja. In the backcross population, both Race-3 resistance QTLs were significant, which confirms the existence of these QTLs. The QTLs identified in this experiment map to positions where SCN resistance genes have not been previously identified, suggesting that these are novel genes that could be useful for diversifying the resistance genes currently used in cultivar development. Received: 7 August 2000 / Accepted: 4 December 2000     

SNP identification and marker assay development for high-throughput selection of soybean cyst nematode resistance

Background

Soybean cyst nematode (SCN) is the most economically devastating pathogen of soybean. Two resistance loci, Rhg1 and Rhg4 primarily contribute resistance to SCN race 3 in soybean. Peking and PI 88788 are the two major sources of SCN resistance with Peking requiring both Rhg1 and Rhg4 alleles and PI 88788 only the Rhg1 allele. Although simple sequence repeat (SSR) markers have been reported for both loci, they are linked markers and limited to be applied in breeding programs due to accuracy, throughput and cost of detection methods. The objectives of this study were to develop robust functional marker assays for high-throughput selection of SCN resistance and to differentiate the sources of resistance.

Results

Based on the genomic DNA sequences of 27 soybean lines with known SCN phenotypes, we have developed Kompetitive Allele Specific PCR (KASP) assays for two Single nucleotide polymorphisms (SNPs) from Glyma08g11490 for the selection of the Rhg4 resistance allele. Moreover, the genomic DNA of Glyma18g02590 at the Rhg1 locus from 11 soybean lines and cDNA of Forrest, Essex, Williams 82 and PI 88788 were fully sequenced. Pairwise sequence alignment revealed seven SNPs/insertion/deletions (InDels), five in the 6th exon and two in the last exon. Using the same 27 soybean lines, we identified one SNP that can be used to select the Rhg1 resistance allele and another SNP that can be employed to differentiate Peking and PI 88788-type resistance. These SNP markers have been validated and a strong correlation was observed between the SNP genotypes and reactions to SCN race 3 using a panel of 153 soybean lines, as well as a bi-parental population, F₅–derived recombinant inbred lines (RILs) from G00-3213 x LG04-6000.

Conclusions

Three functional SNP markers (two for Rhg1 locus and one for Rhg4 locus) were identified that could provide genotype information for the selection of SCN resistance and differentiate Peking from PI 88788 source for most germplasm lines. The robust KASP SNP marker assays were developed. In most contexts, use of one or two of these markers is sufficient for high-throughput marker-assisted selection of plants that will exhibit SCN resistance.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1531-3) contains supplementary material, which is available to authorized users.