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The crystal proteins coded by transgenes from Bacillus thuringiensis (Bt) have shown considerable value in providing effective insect resistance in a number of crop species, including soybean, Glycine max (L.) Merr. Additional sources of soybean insect resistance would be desirable to manage the development of tolerance/resistance to crystal proteins by defoliating insects and to sustain the deployment of Bt crops. The objective of this study was to evaluate the effects and interactions of three insect resistance quantitative trait loci (QTLs; QTL-M, QTL-H, and QTL-G) originating from Japanese soybean PI 229358 and a cry1Ac gene in a “Benning” genetic background. A set of 16 BC6F2-derived near isogenic lines (NILs) was developed using marker-assisted backcrosses and evaluated for resistance to soybean looper [SBL, Pseudoplusia includens (Walker)] and corn earworm [CEW, Helicoverpa zea (Boddie)] in field cage, greenhouse, and detached leaf assays. Both Bt and QTL-M had significantly reduced defoliation by both SBL and CEW and reduced larval weight of CEW. The antibiosis QTL-G had a significant effect on reducing CEW larval weight and also a significant effect on reducing defoliation by SBL and CEW in some assays. The antixenosis QTL-H had no main effect, but it appeared to function through interaction with QTL-M and QTL-G. Adding QTL-H and QTL-G further enhanced the resistance of the Bt and QTL-M combination to CEW in the field cage assay. These results should help guide the development of strategies for effective management of insect pests and for sustainable deployment of Bt genes. [ABSTRACT FROM AUTHOR]

In soybean [Glycine max (L.) Merr.], there is limited and inconsistent information on the confirmation of previously reported QTL. The objectives of this study were to: (i) confirm previously reported QTL for seed protein, seed oil, and seed weight in an independent population of P197100 × 'Coker 237' with the same RFLP markers and (ii) verify previously reported QTL in an independent population of 'Young' × PI416937 for the same seed traits using SSR markers mapped in the same region as the original RFLP markers. Each population consisted of 176 F2:4 lines and was grown in randomized complete block trials in two or three different environments. Singlefactor analysis of variance was used to verify the QTL that had significant (F ≤ 0.01) associations. In the P197100 × Coker 237 population, two (cqProt-001 and cqProt-002) of four previously described QTL for seed protein, two (cqOil-001 and cqOil-002) of three QTL for oil content, and none of three QTL for seed weight were confirmed in the independent population. In the Young X PI416937 population, none of the three previously reported QTL for protein was confirmed. One (cqOil-003) of three QTL for oil content and two (cqSd wt-001 and cqSd wt-002) of three QTL for seed weight were verified. The unconfirmed QTL may have been false positive or they may have been specific for the sample of lines used in the original populations. These results confirm the necessity of validating QTL in parallel populations before utilizing them in a plant improvement program. [ABSTRACT FROM AUTHOR]

Soybean (Glycine max [L.] Merr.) meal is the largest source of protein meal with essential amino acids. Soybean seed protein is negatively correlated with both yield and oil, complicating the simultaneous improvement of seed protein and yield. A major protein quantitative trait locus (QTL) on chromosome (Chr) 20 was identified in genome‐wide association and bi‐parental population mapping studies. The Chr 20 high‐protein allele from 'Danbaekkong' was introgressed into an elite maturity group (MG) VII cultivar, Benning. Two groups of near‐isogenic lines (NILs) of Benning, with or without the Danbaekkong Chr 20 allele, were developed and yield‐tested in two years. The Danbaekkong allele was associated with a significant 33.6 g kg–1 increase in protein and 14.3 g kg–1 decrease in oil (P < 0.05). Average yield of NILs with the Danbaekkong allele were lower than those of NILs without the allele and recurrent parent Benning in both years, but were only significantly lower in 2005 (P < 0.05). Due to its high yield performance, one NIL was yield tested against Benning for two additional years. Combined results from 14 environments over four years revealed yield parity between Benning and Benning high protein (HP), and Benning HP possessed 40.0 g kg–1 more seed protein and 17.3 g kg–1 less oil than Benning. Despite overall yield drag by the Danbaekkong Chr 20 high‐protein allele, we demonstrate that a significant increase in seed protein without associated reduction in yield is possible with breeding and careful progeny selection using this allele. [ABSTRACT FROM AUTHOR]

Soybean [Glycine max (L.) Merr.] is an important source of protein and vegetable oil. Genetic improvement of soybean seed yield and composition are ultimate breeding goals. During the past 80 yr, breeders have selected for high yield and other desired traits to make genetic improvements. To quantify the genetic changes to seed yield, yield stability, and other important agronomic and end‐use quality traits, we evaluated 93 soybean cultivars in Maturity Groups (MG) V, VI, and VII that were released from 1928 to 2008. Replicated yield trials specific for each MG set of cultivars were conducted during 2010 to 2011 in a total of 27 southeastern US year‐location environments. A mixed linear model was used to calculate best linear unbiased predictors (BLUPs) for each cultivar for each measured trait within each MG. Regressed cultivar effect BLUPs of each trait by year of cultivar release revealed positive linear trends for annualized genetic yield gains of 17.6, 13.5, and 10.3 kg ha−1 yr−1 for MG V, VI, and VII, respectively. Averaged across MGs, the annualized rate of genetic gain was estimated to be 13.7 kg ha−1 yr−1. Yield stability analyses revealed significant differences in regression coefficients (b), which were >1.0 for newer cultivars but <1.0 for older cultivars. Overall, the average annualized rate of genetic gains for seed yield reported herein are equivalent to those previously reported, indicating that a yield plateau has not been reached for MG V, VI or VII soybean cultivars. [ABSTRACT FROM AUTHOR]

Phakopsora pachyrhizi is a fungal pathogen and the cause of Asian soybean rust. P. pachyrhizi was first detected in the continental USA in 2004 and has since been a threat to the soybean industry. There are six described loci that harbor resistance to P. pachyrhizi ( Rpp) genes. The resistance of PI 423972 was previously shown to be within 5 cM of the Rpp4 locus of PI 459025B, yet had differential reactions when challenged with P. pachyrhizi isolates India 1973 and Taiwan 1972. In this study, the resistance of PI 423972 was mapped to a 187.5 kb interval between the SNP markers GSM0543 and GSM0387 on chromosome 18 (51,397,064 to 51,584,617 bp, Glyma.Wm82.a2) that overlaps the interval for Rpp4 and is designated as Rpp4-b. A unique haplotype is described for PI 423972 that separates it from PI 459025B, 32 North American soybean ancestors, and all described sources of Rpp gene resistance. [ABSTRACT FROM AUTHOR]

Key message: We identified QTL associated with protein and amino acids in a soybean mapping population that was grown in five environments. These QTL could be used in MAS to improve these traits. Abstract: Soybean, rather than nitrogen-containing forages, is the primary source of quality protein in feed formulations for domestic swine, poultry, and dairy industries. As a sole dietary source of protein, soybean is deficient in the amino acids lysine (Lys), threonine (Thr), methionine (Met), and cysteine (Cys). Increasing these amino acids would benefit the feed industry. The objective of the present study was to identify quantitative trait loci (QTL) associated with crude protein (cp) and amino acids in the 'Benning' × 'Danbaekkong' population. The population was grown in five southern USA environments. Amino acid concentrations as a fraction of cp (Lys/cp, Thr/cp, Met/cp, Cys/cp, and Met + Cys/cp) were determined by near-infrared reflectance spectroscopy. Four QTL associated with the variation in crude protein were detected on chromosomes (Chr) 14, 15, 17, and 20, of which, a QTL on Chr 20 explained 55 % of the phenotypic variation. In the same chromosomal region, QTL for Lys/cp, Thr/cp, Met/cp, Cys/cp and Met + Cys/cp were detected. At these QTL, the Danbaekkong allele resulted in reduced levels of these amino acids and increased protein concentration. Two additional QTL for Lys/cp were detected on Chr 08 and 20, and three QTL for Thr/cp on Chr 01, 09, and 17. Three QTL were identified on Chr 06, 09 and 10 for Met/cp, and one QTL was found for Cys/cp on Chr 10. The study provides information concerning the relationship between crude protein and levels of essential amino acids and may allow for the improvement of these traits in soybean using marker-assisted selection. [ABSTRACT FROM AUTHOR]

Soybean is one of the most important oil crops worldwide, and reducing the linolenic acid content of soybean oil will provide increased stability of the oil to consumers and limit the amount of trans fat in processed foods. The linolenic content in soybean seed is controlled by three fatty acid desaturase (FAD) three enzymes, FAD3A, B, and C. The soybean lines with 1 % linolenic acid content which are widely used in breeding for reduced linolenic acid in the USA have mutations in each of the three FAD genes derived from lines A5 (deletion of FAD3A), A26, and A23 (missense mutations in FAD3B and C, respectively). Although soybean line A5 has been released for 30 years, the extent and definition of the deletion of the FAD3A gene has not been characterized, which has prevented researchers from designing robust molecular markers for effective marker-assisted selection (MAS). Using a PCR-based genomic strategy, we have identified a 6.4-kbp deletion of the FAD3A gene in A5 and developed a TaqMan detection assay by targeting the deletion junction in A5, which could be used to distinguish the homozygotes and heterozygotes of the gene. In addition, based on mutant single nucleotide polymorphisms in FAD3B and FAD3C identified in A26 and A23, respectively, we have also developed TaqMan assays for high-throughput MAS. The TaqMan assays have proven to be a very effective platform for detecting the mutant FAD3 alleles and thus will greatly facilitate high-throughput MAS for development of soybean lines with reduced linolenic acid content. [ABSTRACT FROM AUTHOR]

Aluminum (Al) toxicity is an important abiotic stress that affects soybean production in acidic soils throughout the world. Development of Al-tolerant cultivars is an efficient and environmentally friendly solution to the problem. A previous report identified quantitative trait loci (QTL) for Al tolerance inherited from PI 416937, using restriction fragment length polymorphism markers, in a population of Young × PI 416937. The population was genotyped with 162 simple sequence repeats to enhance the power of QTL detection and enable the selection of candidate genes for functional marker development. Two QTL that explained 54 % of the phenotypic variation in root extension under Al stress conditions (HIAL) were refined on chromosomes (chr) Gm08 and Gm16. Three QTL located on chr Gm08, Gm16 and Gm19 explained 59 % of the phenotypic variation in root extension as a percent of control (PC). Two major QTL, designated qAL_HIAL_08 and qAL_PC_08, controlling HIAL and PC, respectively, were mapped to the same genomic region on chr Gm08 and inherited their favorable allele from PI 416937. These QTL explained 45 and 41 % of phenotypic variation in HIAL and PC, respectively. Six homologues for citrate synthase (CS) genes were found in the soybean genome sequence at chr Gm02, Gm08, Gm14, Gm15, and Gm18. Sixteen single nucleotide polymorphisms (SNPs) were identified in the CS homologue on chr Gm08. A SimpleProbe assay of Glyma08g42400- SNP was developed for the major QTL on chr Gm08. The SNPs identified from this region could be used for marker-assisted selection of Al tolerance. [ABSTRACT FROM AUTHOR]

Meloidogyne incognita (Kofoid and White) Chitwood (Mi) is the most economically damaging species of the root-knot nematode to soybean and other crops in the southern USA. PI 96354 was identified to carry a high level of resistance to galling and Mi egg production. Two Quantitative Trait Locus (QTLs) were found to condition the resistance in PI 96354 including a major QTL and a minor QTL on chromosome 10 and chromosome 18, respectively. To fine map the major QTL on chromosome 10, F recombinant inbred lines from the cross between PI 96354 and susceptible genotype Bossier were genotyped with Simple Sequence Repeats (SSR) markers to identify recombinational events. Analysis of lines carrying key recombination events placed the Mi-resistant allele on chromosome 10 to a 235-kb region of the 'Williams 82' genome sequence with 30 annotated genes. Candidate gene analysis identified four genes with cell wall modification function that have several mutations in promoter, exon, 5′, and 3′UTR regions. qPCR analysis showed significant difference in expression levels of these four genes in Bossier compared to PI 96354 in the presence of Mi. Thirty Mi-resistant soybean lines were found to have same SNPs in these 4 candidate genes as PI 96354 while 12 Mi-susceptible lines possess the 'Bossier' genotype. The mutant SNPs were used to develop KASP assays to detect the resistant allele on chromosome 10. The four candidate genes identified in this study can be used in further studies to investigate the role of cell wall modification genes in conferring Mi resistance in PI 96354. [ABSTRACT FROM AUTHOR]

Drought stress adversely affects [ Glycine max (L.) Merr] soybean at most developmental stages, which collectively results in yield reduction. Little information is available on relative contribution and chromosomal locations of quantitative trait loci (QTL) conditioning drought tolerance in soybean. A Japanese germplasm accession, PI 416937, was found to possess drought resistance. Under moisture-deficit conditions, PI 416937 wilted more slowly in the field than elite cultivars and has been used as a parent in breeding programs to improve soybean productivity. A recombinant inbred line (RIL) population was derived from a cross between PI 416937 and Benning, and the population was phenotyped for canopy wilting under rain-fed field conditions in five distinct environments to identify the QTL associated with the canopy-wilting trait. In a combined analysis over environments, seven QTL that explained 75 % of the variation in canopy-wilting trait were identified on different chromosomes, implying the complexity of this trait. Five QTL inherited their positive alleles from PI 416937. Surprisingly, the other two QTL inherited their positive alleles from Benning. These putative QTL were co-localized with other QTL previously identified as related to plant abiotic stresses in soybean, suggesting that canopy-wilting QTL may be associated with additional morpho-physiological traits in soybean. A locus on chromosome 12 (Gm12) from PI 416937 was detected in the combined analysis as well as in each individual environment, and explained 27 % of the variation in canopy-wilting. QTL identified in PI 416937 could provide an efficient means to augment field-oriented development of drought-tolerant soybean cultivars. [ABSTRACT FROM AUTHOR]

Soybean ( Glycine max (L.) Merr.) genotype PI 416937 has been identified as expressing a 'slow-wilting' phenotype in the field and this has been traced to a low hydraulic conductance in its leaves. The transpiration rate of de-rooted shoots of this genotype has been found to be insensitive to the aquaporin inhibitor silver nitrate compared to elite cultivars which are silver nitrate sensitive. These results indicated that PI 416937 might have a unique aquaporin population. The objective of this study was to determine if QTLs could be identified that are associated with the lack of sensitivity in PI 416937 to silver. To identify the genomic locations and genetic bases of this trait, a recombinant inbred line population was derived from a mating between PI 416937 and the cultivar 'Benning'. The RILs were all phenotyped for their response to the silver inhibitor and the results were subjected to a QTL analysis. Four QTL were identified as putatively associated with the silver response (qSV). These QTL explained from 17.7 to 24.7% of the phenotypic variation with qSV_Gm12 explaining the greatest amount of phenotypic variation. The qSV_Gm03 and qSV_Gm10 QTL inherited their positive alleles from PI 416937, while qSV_Gm05 and qSV_Gm12 inherited their favorable alleles from Benning. Co-localized silver nitrate response QTL with other morpho-physiological traits could help to explain soybean plant's ability to tolerate water-deficit stress. [ABSTRACT FROM AUTHOR]

ian soybean rust (ASR), caused by Phakopsora pachyrhizi Syd., has the potential to become a serious threat to soybean, Glycine max L. Merr., production in the USA. A novel rust resistance gene, Rpp?(Hyuuga), from the Japanese soybean cultivar Hyuuga has been identified and mapped to soybean chromosome 6 ( Gm06). Our objectives were to fine-map the Rpp?(Hyuuga) gene and develop a high-throughput single nucleotide polymorphism (SNP) assay to detect this ASR resistance gene. The integration of recombination events from two different soybean populations and the ASR reaction data indicates that the Rpp?(Hyuuga) locus is located in a region of approximately 371 kb between STS70887 and STS70923 on chromosome Gm06. A set of 32 ancestral genotypes which is predicted to contain 95% of the alleles present in current elite North American breeding populations and the sources of the previously reported ASR resistance genes ( Rpp1, Rpp2, Rpp3, Rpp4, Rpp5, and rpp5) were genotyped with five SNP markers. We developed a SimpleProbe assay based on melting curve analysis for SNP06-44058 which is tighly linked to the Rpp?(Hyuuga) gene. This SNP assay can differentiate plants/lines that are homozygous/homogeneous or heterozygous/heterogeneous for the resistant and susceptible alleles at the Rpp?(Hyuuga) locus. [ABSTRACT FROM AUTHOR]

Peanut root-knot nematode [Meloidogyne arenaria (Neal) Chitwood or Ma] is an increasingly common pest in the southern United States where crops such as peanut (Arachis hypogaea L.) and soybean [Glycine max (L.) Merr.] are grown. Four soybean plant introductions (Pls) are highly resistant to the peanut root-knot nematode. To determine if Pl 594403, Pl 594427C, and Pl 594651 B contain useful resistance genes from those previously characterized in Pl 200538, populations developed from the PIs crossed to Pl 200538 were tested for Ma response. Highly galled and highly resistant F2 plants were observed in each population. In two of the three populations, the highly galled F2 plants produced progeny that sustained significantly greater galling (P < 0.001) than those derived from highly resistant F2 plants. While the F2-derived progeny from the third population had more variability than was observed in the other crosses, progeny means of the lines were significantly different (P < 0.05). Individual F2-derived lines from highly galled or resistant F2 plants within all of the populations were significantly different from each other or from the parents. Thus, it is evident that these Pls likely contain unique resistance genes that, when combined with Pl 200538-derived Ma resistance, could improve the level of Ma resistance in soybean cultivars. [ABSTRACT FROM AUTHOR]

Southern root-knot nematode [RKI; Meloidogyne incognita (Kofoid and White) Chitwood] is an important soybean [Glycine max (L.) Merr.] pest. When RKI resistance was introgressed from the highly resistant, gray pubescent breeding line G93-9009 into moderately resistant, tawny pubescent cultivars BoggsRR and BenningRR, higher than expected proportions of two advanced backcross populations had gray pubescence. Introgressing genes from unadapted breeding lines into cultivars may reduce seed yield or quality of the resulting lines. This study's objectives were to determine if (i) an RKI resistance quantitative trait locus (QTL) is linked to the T-locus conditioning pubescence color in G93-9009, and (ii) a yield or seed quality loss is associated with introgressing G93-9009 RKI resistance QTL into BenningRR and BoggsRR. Tawny and gray pubescent F2:4 lines of BoggsRR(6) × G93-9009 and BenningRR(5) × G93-9009 were evaluated in greenhouse experiments for RKI resistance and in field experiments grown in four environments for seed yield and quality. Gray lines of both populations averaged 75% fewer RKI eggs per plant than tawny lines. There were no significant differences in seed yield. Differences in agronomic traits such as plant height, seed size, and oil and protein content were observed. These results suggest an RKI resistance QTL exists near the T-locus and the potential to introgress resistance from G93-9009 into other genetic backgrounds without a loss in yield or major impact on other agronomic traits. [ABSTRACT FROM AUTHOR]

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi Syd., is a widespread disease of soybean [Glycine max (L.) Merrj with the potential to cause serious economic losses. The objective of this study was to genetically map red-brown lesion type resistance from the cultivar Hyuuga. A population of 117 recombinant inbred lines (RILs) from the cross of Dillon (tan lesion) × Hyuuga (red-brown [RB] lesion) was rated for ASR lesion type in the field and inoculated with P. pachyrhizi in the greenhouse. The RB resistance gene mapped between Satt460 and Satt307 on linkage group (LG)-C2. When field severity and lesion density in the greenhouse were mapped, the Rpp?(Hyuuga) locus explained 22 and 15% of the variation, respectively (P < 0.0001). The RB lesion type was associated with lower severity, fewer lesions, and reduced sporulation when compared to the tan lesion type. A population from the cross of Benning × Hyuuga was screened with simple sequence repeat (SSR) markers in the region on LG-C2 flanked by Satt134 and Satt460. Genotype at these markers was used to predict lesion type when the plants were exposed to P. pachyrhizi. All the lines selected for the Hyuuga markers in this interval had the RB lesion type and they averaged approximately 50% fewer lesions compared to lines with tan lesions. Sporulation was only detected in 6% of the RB lines compared with 100% of the tan lines. Markerassisted selection can be used to develop soybean cultivars with the Rpp?(Hyuuga) gene for resistance to ASR. [ABSTRACT FROM AUTHOR]

Glyphosate application to glyphosate-tolerant soybean [Glycine max (L.) Merr.] cultivars expressing a CP4 EPSPS transgene has become the most common method of soybean weed control in the USA. The objectives of this research were (i) to determine whether atypical segregation ratios for glyphosate tolerance and glyphosate sensitivity in the progeny of hemizygous plants resulted from gametic selection caused by glyphosate applications, (ii) to investigate the effects of different glyphosate application rates and timing of application on segregation ratios, and (iii) to determine whether male gametes, female gametes, or both were sensitive to the levels of glyphosate used. Segregation for glyphosate tolerance in a no-glyphosate control treatment fit the expected 3:1 segregation ratio, indicating segregation of a single transgene. Glyphosate applications at three stages of plant development (V3, V3 + 2 to 3 wk, V3 + 3 to 4 wk) eliminated the glyphosate-sensitive phenotypic class irrespective of plant maturation stage in a field experiment. Variations observed in the relative proportions of lines with either all-tolerant or segregating phenotypic classes depended on glyphosate dosage and stage of plant development at the time of application. Overall, the data suggest that glyphosate application to hemizygous plants shortly before the onset of flowering was lethal to male gametes that do not carry the glyphosate tolerance transgene. [ABSTRACT FROM AUTHOR]

Bud blight, caused by Tobacco ringspot virus (TRSV; Genus: Nepovirus; Family: Comoviridae), can significantly reduce the seed yield and seed quality of soybean [Glycine max (L.) Merr.]. The identification of resistance genes and the development of resistant cultivars constitute an effective strategy for preventing yield loss. The objectives of this study were to identify and map quantitative trait loci (QTLs) conditioning resistance to bud blight and validate their genomic location with two populations derived from the cross of 'Young' (resistant) × PI 416937 (susceptible). One population consisted of 116 F[sub 4:7] lines and was used to map restriction fragment length polymorphism (RFLP) markers associated with resistance to bud blight. The lines were grown in one-row plots in a randomized complete block design with two replications. The plots were naturally infected with TRSV. At maturity, soybean plots were visually scored according to the number of plants that exhibited terminal bud death. A major QTL was identified and mapped on linkage group (LG) F by the RFLP marker K644_1. It accounted for 82% of the variation in bud blight score. To verify the genomic location of the major bud blight QTL, a second population of Young × PI 416937 that consisted of 180 F[sub 2:3] lines was evaluated. In this population, simple sequence repeat (SSR) markers on LG F near the putative genomic location of the bud blight QTL were utilized. The major QTL conditioning bud blight resistance was confirmed and found to be closely linked to the Satt510 marker. [ABSTRACT FROM AUTHOR]

Drought is the primary abiotic stress that limits yield of soybean (Glycine max (L.) Merr.). The study aimed to identify yield-related quantitative trait loci (QTLs) in soybeans using a population of 160 F4-derived lines from 'Hutcheson' × PI 471938 crosses, which were cultivated under rain-fed and irrigated conditions. Seed yield was determined based on a total of nine irrigated and five rain-fed environments over two years. Twenty and twenty-seven SSR markers associated with yield (p ≤ 0.05) were identified in the irrigated and rain-fed environments, respectively. Four markers accounted for 22% of the yield variation in the irrigated environments (IR-YLD) and five markers explained 34% of the yield variation in the rain-fed environments (RF-YLD). Two independent IR-YLD and RF-YLD QTLs on chromosome (Chr) 13 (LG-F) were mapped to the Satt395-Sat_074 interval (4.2 cM) and near Sat_375 (3.0 cM), which explained 8% (LOD = 2.6) and 17% (LOD = 5.5) of the yield variation, respectively. The lines homozygous for the Hutcheson allele at the IR-YLD QTL linked to Sat_074 averaged 100 kg ha−1 higher yield than the lines homozygous for the PI 471938 allele. At two independent RF-YLD QTLs on Chr 13 and Chr 17, the lines homozygous for the PI 471938 alleles were 74 to 101 kg ha−1 higher in yield than the lines homozygous for the Hutcheson alleles. Three of the five significant SSR markers associated with RF-YLD were located in a genomic region known for canopy-wilting QTLs, in which the favorable alleles were inherited from PI 471938. The identification of yield-QTLs under the respective rain-fed and irrigated environments provides knowledge regarding differential responses of yield under different irrigation conditions, which will be helpful in developing high-yielding soybean cultivars. [ABSTRACT FROM AUTHOR]

Monolithically integrated polarization beam splitters (PBSs) are needed to reduce the form-factor and assembly cost of optical coherent receivers. A highly efficient passive polarization rotator and splitter based on mode-evolution is demonstrated. The device is fabricated on InP substrate with a single etch-step and uses an adiabatic mode-converter and an asymmetric Y-coupler. Despite its simple fabrication process, the device shows a polarization extinction ratio (PER) better than 19 dB over 1520 nm to 1620 nm, thus covering both C- and L-band. The peak value of 24 dB is obtained for TE and TM polarizations. Its fabrication tolerance is large, so that even under a width variation of +/- 200 nm the PER remains above 17 dB over the entire C- and L-band.

One potential issue with the invited essay's (Zwarenstein 2015) proposed evaluation approach is the Darwinian evolution of a system versus the evaluation/testing of a series of pinpoint solutions. There are many examples of bad research based on the influence of a single factor on a specific outcome. But in reality we need to look at larger systems and their interdependence. Quick testing is great as long as it can be tied to a larger ecosystem of causes and effects.

In applied soybean (Glycine max L.) breeding programs, marker-assisted selection has become a necessity to select value-added quantitative trait loci. The goal of this work was to improve marker-assisted selection workflow by developing a reliable, inexpensive, high-throughput DNA extraction protocol for soybean seed and leaf samples that does not generate hazardous waste. The DNA extraction protocol developed allows for the leverage of robust SNP genotyping platforms such as the Simple Probe Assay and KASPar v4.0 SNP Genotyping System to genotype thousands of seeds or leaves non-destructively in a single day with a 95 % success rate. This methodology makes it possible to run up to 150 SNP markers on the DNA extracted from a single seed chip or leaf sample.

Genetic variation within homogeneous gene pools in various crops is assumed to be very limited. One objective of this study was to use 144 simple sequence repeat (SSR) markers to determine if the single-plant lines selected at ultra-low plant density in honeycomb designs within the soybean cultivars Benning, Haskell, and Cook had unique SSR genetic fingerprints. Another objective was to investigate if the variation found was the result of residual genetic heterozygosity that could be detected in the original gene pool where selection initiated. Our results showed that the phenotypic variation for seed protein content and seed weight has a genotypic component identified by the SSR band variation. The 7 lines from Haskell had a total of 63 variant alleles, the 5 lines from Benning had 34 variant alleles, and the 7 lines from Cook had 34 variant alleles, therefore, possessing unique genetic fingerprints. Most of the intracultivar SSR band variation discovered was the result of residual heterozygosity in the initial plant selected to become the cultivar. More specifically, 82% of the SSR variant alleles were traced in the Benning Foundation seed source, 93% in the Haskell seed source, and 82% in the Cook seed source. The remaining variant bands (18% for Benning, 7% for Haskell, and 18% for Cook) could not be detected in the Foundation seed source and were likely the result of mutation or some other mechanism generating de novo variation. These results provide evidence that genetic variation among individual plants is present even in homogeneous gene pools and can be further utilized in breeding programs.

Insect resistance in soybean has been an objective in numerous breeding programs, but efforts to develop high yielding cultivars with insect resistance have been unsuccessful. Three Japanese plant introductions, PIs 171451, 227687 and 229358, have been the primary sources of insect resistance alleles, but a combination of quantitative inheritance of resistance and poor agronomic performance has hindered progress. Linkage drag caused by co-introgression of undesirable agronomic trait alleles linked to the resistance quantitative trait loci (QTLs) is a persistent problem. Molecular marker studies have helped to elucidate the numbers, effects and interactions of insect resistance QTLs in the Japanese PIs, and markers are now being used in breeding programs to facilitate transfer of resistance alleles while minimizing linkage drag. Molecular markers also make it possible to evaluate QTLs independently and together in different genetic backgrounds, and in combination with transgenes from Bacillus thuringiensis.

Deployment of salt tolerant cultivars is an effective approach to minimize yield loss in a saline soil. In soybean, Glycine max (L.) Merr., substantial genetic variation exists for salt response. However, breeding for salt tolerance is hampered because no economically viable screening method has been developed for practical breeding. To facilitate the development of an effective screening method for salt tolerance in soybean, the present study was conducted to determine the heritability of salt tolerance and to identify associated quantitative trait loci (QTL). F2:5 lines from the cross of 'S-100' (salt tolerant) x 'Tokyo' (salt sensitive) were evaluated in a saline field in Hyde County, N.C., USA, in 1999 and in a greenhouse located in Raleigh, N.C., USA, in 2001. S-100 and Tokyo are ancestors of popular soybean cultivars released for the southern USA. The visual salt tolerance ratings of the F2:5 lines ranged from 0 (complete death) to 5 (normal healthy appearance). The entry-mean heritability for salt tolerance was 0.85, 0.48, and 0.57 in the field (four replications), greenhouse (two replications), and combined environments, respectively. The genotypic correlation between field and greenhouse ratings was 0.55, indicating reasonably good agreement between the two screening environments. To identify QTL associated with salt tolerance, each line was characterized with RFLP markers and an initial QTL single-factor analysis was completed. These results were used to identify genomic regions associated with the trait and to saturate the selected genomic regions with SSR markers to improve mapping precision. Subsequently, a major QTL for salt tolerance was discovered near the Sat&#95;091 SSR marker on linkage group (LG) N, accounting for 41, 60, and 79% of the total genetic variation for salt tolerance in the field, greenhouse, and combined environments, respectively. The QTL allele associated with tolerance was derived from S-100. Pedigree tracking was used to examine the association between the salt tolerance QTL and flanking SSR marker alleles in U.S. cultivars descended from S-100 or Tokyo through 60 years of breeding. The presence of alleles from S-100 at the Sat&#95;091 and Satt237 marker loci was always associated with salt tolerance in descendants. Alleles from Tokyo for these same markers were generally associated with salt sensitivity in descendent cultivars. The strong relationship between the SSR marker alleles and salt tolerance suggests that these markers could be used for marker-assisted selection in commercial breeding.

Effective strategies are needed to manage insect resistance to Bacillus thuringiensis (Bt) proteins expressed in transgenic crops. To evaluate a multiple resistance gene pyramiding strategy, eight soybean (Glycine max) lines possessing factorial combinations of two quantitative trait loci (QTLs) from plant introduction (PI) 229358 and a synthetic Bt cry1Ac gene were developed using marker-assisted selection with simple sequence repeat markers. Field studies were conducted in 2000 and 2001 to evaluate resistance to corn earworm (Helicoverpa zea) and soybean looper (Pseudoplusia includens), and detached leaf bioassays were used to test antibiosis resistance to Bt-resistant and Bt-susceptible strains of tobacco budworm (TBW; Heliothis virescens). Based on defoliation in the field and larval weight gain on detached leaves, lines carrying a combination of cry1Ac and the PI 229358 allele at a QTL on linkage group M were significantly more resistant to the lepidopteran pests, including the Bt-resistant TBW strain, than were the other lines. This is the first report of a complementary additive effect between a Bt transgene and a plant insect resistance QTL with an uncharacterized mode of action that was introgressed using marker-assisted selection.

The Rxp locus in soybean [Glycine max (L.) Merr.] that conditions reaction to bacterial pustule was mapped by simple sequence repeat (SSR) marker analysis. A population of 116 F4-derived lines from a cross between the resistant parent Young and the susceptible parent PI 416937 was used for mapping. The Rxp locus was mapped 3.9 cM from Satt372 and 12.4 cM from Satt014 on linkage group D2. Linkage associations were confirmed by identifying a close association between the SSR genotype at each locus identified as flanking Rxp and the bacterial pustule reaction of individual lines derived from a population different from the one used for mapping. A molecular pedigree analysis showed that bacterial pustule-resistant cultivars inherited the resistance gene rxp from the ancestral cultivar CNS based on their consistent genotypic pattern at flanking marker loci. Based on the results of the study, marker-assisted selection for rxp would be very effective.

Seed weight (SW) is a component of soybean, Glycine max (L.) Merr., seed yield, as well as an important trait for food-type soybeans. Two soybean populations, 120 F4-derived lines of 'Young'xPI416937 (Pop1) and 111 F2-derived lines of PI97100x'Coker 237' (Pop2), were mapped with RFLP makers to identify quantitative trait loci (QTLs) conditioning SW across environments and populations. The genetic map of Pop1 consisted of 155 loci covering 973 cM, whereas Pop2 involved 153 loci and covered 1600 cM of map distance. For Pop1, the phenotypic data were collected from Plains, GA., Windblow, N.C., and Plymouth, N.C., in 1994. For Pop2, data were collected from Athens, GA., in 1994 and 1995, and Blackville, S.C., in 1995. Based on single-factor analysis of variance (ANOVA), seven and nine independent loci were associated with SW in Pop1 and Pop2, respectively. Together the loci explained 73% of the variability in SW in Pop1 and 74% in Pop2. Transgressive segregation occurred among the progeny in both populations. The marker loci associated with SW were highly consistent across environments and years. Two QTLs on linkage group (LG) F and K were located at similar genomic regions in both populations. The high consistency of QTLs across environments indicates that effective marker-assisted selection is feasible for soybean SW.

Penetration, post-infectional development, reproduction, and fecundity of Meloidogyne arenaria races 1 and 2 were studied on susceptible (CNS), partially resistant (Jackson), and highly resistant (PI 200538 and PI 230977) soybean genotypes in the greenhouse. The ability to locate and invade roots was similar between races, but more juveniles penetrated roots of susceptible CNS than the resistant genotypes. At 10 days after inoculation, 56% and 99% to 100% of race 1 second-stage juveniles were vermiform or sexually undifferentiated in CNS and the resistant genotypes, respectively. In contrast, only 2%, 42%, 44%, and 62% of race 2 juveniles had not initiated development in CNS, Jackson, PI 200538, and PI 230977, respectively. By 20 days after inoculation, 88% to 100% of race 2 nematodes in roots of all genotypes were females, whereas only 25% and 1% of race 1 were females in CNS and the resistant genotypes, respectively. For all four genotypes, race 1 produce 85% to 96% fewer eggs per root system 45 days after inoculation than race 2. At 45 days after inoculation race 2 produced more eggs on CNS than the other genotypes.

The cellular responses induced by Meloidogyne arenaria races 1 and 2 in three soybean genotypes, susceptible CNS, resistant Jackson, and resistant PI 200538, were examined by light microscopy 20 days after inoculation. Differences in giant-cell development were greater between races than among the soybean genotypes. M. arenaria race 1 stimulated small, poorly formed giant-cells in contrast with M. arenaria race 2, which induced well-developed, thick-walled, multinucleate giant-cells. The number of nuclei per giant-celt was variable, but fewer nuclei were usually present in giant-cells induced by race 1 (mean 16 nuclei) than in giant-cells induced by race 2 (mean 41 nuclei). Differences observed in giant-cell development were related to differences in growth and maturation of M. arenaria races 1 and 2 and host suitability of the soybean genotypes.

Resistant plant introductions, PI 230977 and PI 200538, and partially resistant Jackson and susceptible CNS were evaluated for seed yield in response to races 1 and 2 of Meloidogyne arenaria. Initial soil population densities (Pi) of the nematode were 0, 31, 125, and 500 eggs/100 cm(3) soil. At the highest Pi, yield suppressions of CNS, Jackson, PI 230977, and PI 200538 were 55, 28, 31, and 29%, and 99, 86, 66, and 58% for races 1 and 2 compared with uninfested controls. Numbers of second-stage juveniles (J2) present in roots 14 days after planting increased as Pi increased, but did not differ between the two races. At the highest Pi, fewer race 1 (40-57%) and race 2 (53-68%) J2 were present in roots of the plant introductions than in roots of Jackson. Soil population densities of race 1 J2 at 135 days after planting were 83-89% lower on the resistant genotypes than on CNS. These numbers did not differ for race 2. Reproductive factors were considerably higher for race 2 compared to race 1 for all genotype by Pi combinations, except for CNS at the highest Pi.

Plant breeders and nematologists have developed improved cultivars of important crop species with resistance to plant-parasitic nematodes. The effectiveness of these breeding efforts has depended on the availability of efficient screening procedures, identification of adequate sources of durable resistance, nature of the nematode feeding habit, and knowledge of the inheritance of resistance. These factors determine to a large degree the breeding method and potential success of the research. Systematic searches for nematode resistance have identified resistant germplasm lines within crop species or from related species. When the resistance gene(s) is from related species, incongruity barriers or sterility of the resulting hybrids often must be overcome. In these situations, backcrossing is usually necessary to incorporate the resistance gene(s) and recover the desirable commercial traits of the crop species. If the resistance gene(s) is present within the crop species, the choice of breeding method depends on the inheritance of the resistance, type of screening procedure, and other important breeding objectives for the species. In the future, plant molecular biologists and geneticists will make available novel sources of nematode resistance through incorporation of transgenes from other genera. These efforts will likely require conventional breeding strategies before commercial utilization of an improved resistant cultivar.

One hundred thirty-nine cultivars of soybean (Glycine max) in Maturity Groups V, VI, VII, and VIII were evaluated in a greenhouse for resistance to Heterodera glycines races 3 and 14 and Meloidogyne incognita, M. arenaria, and M. javanica. Of the cultivars tested, 37% had resistance to H. glycines race 3 alone, 12% had resistance to both races 3 and 14, and 69% exhibited a moderate or high level of resistance to one or more of the Meloidogyne spp. However, 24% were susceptible to each race of H. glycines and to all Meloidogyne spp. Whereas 40% of the cultivars were moderately resistant to M. javanica, only 23% were moderately resistant to M. incognita and 24% to M. arenaria. Although 28% of the cultivars had a high level of resistance to M. incognita, only 6 and 3% had this level of resistance to M. javanica and M. arenaria, respectively. Seventeen percent of the cultivars possessed a moderate or high level of resistance to all three Meloidogyne spp., and 37 % had resistance to H. glycines race 3 and M. incognita. With the exception of resistance to H. glycines race 14, resistance in soybean to these nematodes was fairly uniformly distributed across maturity groups.

Meloidogyne incognita penetration and development were studied in roots of highly resistant (PI 96354, PI 417444), resistant (Forrest), and susceptible (Bossier) soybean genotypes. Although more second-stage juveniles (J2) had penetrated roots of PI 96354 and PI 417444 than roots of Forrest and Bossier by 2 days after inoculation, fewer J2 were present in roots of PI 96354 at 4 days after inoculation. Juvenile development in all genotypes was evident by 6 days after inoculation, with the highest number of swollen J2 present in roots of Bossier. At 16 days after inoculation, roots of PI 96354 had 87%, 74%, and 53% fewer J2 than were present in roots of Bossier, Forrest, and PI 417444, respectively. Differential emigration of J2, not fewer invasion sites, was responsible for the low number of nematodes in roots of the highly resistant PI 96354. Some 72% of the J2 penetrating the roots of this genotype emerged within 5 days after inoculation, whereas 4%, 54%, and 83% emerged from roots of Bossier, Forrest, and PI 417444, respectively. Penetration of roots of PI 96354 decreased the ability of J2 emerging from these roots to infect other soybean roots.

The response of two soybean plant introductions, PI 96354 and PI 417444, highly resistant to Meloidogyne incognita, to increasing initial soil population densities (Pi) (0, 31, 125, and 500 eggs/100 cm(3) soil) of M. incognita was studied in field microplots for 2 years. The plant introductions were compared to the cultivars Forrest, moderately resistant, and Bossier, susceptible to M. incognita. Averaged across years, the yield suppressions of Bossier, Forrest, PI 417444, and PI 96354 were 97, 12, 18, and < 1%, respectively, at the highest Pi when compared with uninfested control plots. Penetration of roots by second-stage juveniles (J2) increased linearly with increasing Pi at 14 days after planting. At the highest Pi, 62% fewer J2 were present in roots of PI 96354 than in roots of the other resistant genotypes. Soil population densities of M. incognita were lower on both plant introductions than on Forrest. At 75 and 140 days after planting, PI 96354 had the lowest number of J2 in the soil, with 49% and 56% fewer than Forrest at the highest Pi. The resistance genes in PI 96354 should be useful in a breeding program to improve the level of resistance to M. incognita in soybean cultivars.

Fifty-four susceptible soybean, Glycine max, cultivars or plant introductions were evaluated for tolerance to H. glycines, the soybean cyst nematode (SCN). Seed yields of genotypes were compared in nematicide-treated (1,2-dibromo-3-chloropropane, 58 kg a.i./ha) and nontreated plots at two SCN-infested locations over 3 years. Distinct and consistent levels of tolerance to SCN were observed among soybean genotypes. PI 97100, an introduction from Korea, exhibited the highest level of tolerance with an average tolerance index ([yield in nontreated plot / yield in nematicide-treated plot] x 100) of 96 over 2 years. Coker 156 and Wright had moderate levels of tolerance (range in index values 68 to 95) compared to the intolerant cuhivars Bragg and Coker 237 (range in index values 33 to 68). Most of the soybean genotypes evaluated were intolerant to SCN. The rankings of five genotypes for tolerance to SCN and Hoplolaimus columbus were similar. Tolerance for seed yield was more consistently correlated with tolerance for plant height (r = 0.55 to 0.64) than for seed weight (r = 0.23 to 0.65) among genotypes.

Interactions among Meloidogyne incognita, Pratylenchus brachyurus, and soybean genotype on plant growth and nematode reproduction were studied in a greenhouse. Coker 317 (susceptible to both nematodes) and Gordon (resistant to M. incognita, susceptible to P. brachyurus) were inoculated with increasing initial population densities (Pi) of both nematodes individually and combined. M. incognita and P. brachyurus individually usually suppressed shoot growth of both cultivars, but only root growth on Coker 317 was influenced by a M. incognita x P. brachyurus interaction. Reproduction of both nematodes, although dependent on Pi, was mutually suppressed on Coker 317. P. brachyurus reproduced better on Gordon than on Coker 317 but did not affect resistance to M. incognita. Root systems of Coker 317 were split and inoculated with M. incognita or P. brachyurus or both to determine the nature of the interaction. M. incognita suppressed reproduction of P. brachyurus either when coinhabiting a half-root system or infecting opposing half-root systems; however, P. brachyurus affected M. incognita only if both nematodes infected the same half-root system.

Five soybean cultivars (Braxton, Gordon, Jeff, Bragg, and Wright) resistant to Meloidogyne incognita (Mi) and three susceptible cultivars (Coker 156, GaSoy 17, and Coker 237) were grown at two locations for four seasons in microplots with increasing initial soil population densities (Pi) of Mi. The resistant cultivars and Coker 156 yielded better than GaSoy 17 and Coker 237 at all Pi. Yield response was dependent on environmental conditions and at one location was stimulated on Braxton, Gordon, Jeff, and Bragg by low Pi. Although Mi reproduced well on all cultivars, the pattern of reproduction differed. Population densities of Mi leveled off after 90 days on GaSoy 17 and Coker 237 but were still increasing after 120 days on the resistant cultivars; population densities were lower on resistant than on the susceptible cultivars. The population density of Mi on Coker 156 after 120 days was intermediate between those on the other susceptible and on the resistant cultivars. Mi population densities followed the same pattern under varying environmental conditions.

Bragg soybeans were planted in nematicide-treated and nontreated plots on 15 May, 15 June, 1 July, and 15 July in 1980 and 1981 to determine the influence of planting date on damage caused by H. glycines. Although earlier studies showed the nematode was sensitive to high soil temperatures (> 34 C), late planting did not reduce damage caused by the nematode. Yields from plots treated with 1, 2-dibromo-3-chloropropane (57.5 kg a.i./ha) were 48, 118, 395, and 403% higher than yields from nontreated plots with planting dates of 15 May, 15 June, 1 July, and 15 July, respectively, when data were averaged over the 2 years. Increase in both seed size and number accounted for the yield increases in treated plots. Soil temperatures were highest during July in 1980, averaging 8.9 and 6.5 hours per day above 34 C at 10- and 20-cm depths, respectively. Larvae populations of H. glycines were reduced by the nematicide but not by late planting. These results indicate that damage caused by H. glycines may actually increase with later planting and that nematicides may be more beneficial when soybeans are planted late in a double-cropped production system.

Greenhouse and field microplot studies were conducted to compare soybean shoot and root growth responses to root penetration by Heterodera glycines (Hg) and Meloidogyne incognita (Mi) individually and in combination. Soybean cultivars Centennial (resistant to Hg and Mi), Braxton (resistant to Mi, susceptible to Hg), and Coker 237 (susceptible to Hg and Mi) were selected for study. In the greenhouse, pot size and number of plants per pot had no effect on Hg or Mi penetration of Coker 237 roots; root weight was higher in the presence of either nematode species compared with the noninoculated controls. In greenhouse studies using a sand or soil medium, and in field microplot studies, each cultivar was grown with increasing initial population densities (Pi) of Hg or Mi. Interactions between Hg and Mi did not affect early plant growth or number of nematodes penetrating roots. Root penetration was the only response related to Pi. Mi penetration was higher in sand than in soil, and higher in the greenhouse than in the field, whereas Hg penetration was similar under all conditions. At 14 days after planting, more second-stage juveniles were present in roots of susceptible than in roots of resistant plants. Roots continued to lengthen in the greenhouse in the presence of either Mi or Hg regardless of host genotype, but only in the presence of Mi in microplots; otherwise, responses in field and greenhouse studies were similar and differed only in magnitude and variability.

The effects of host genotype and initial nematode population densities (Pi) on yield of soybean and soil population densities of Heterodera glycines (Hg) race 3 and Meloidogyne incognita (Mi) race 3 were studied in a greenhouse and field microplots in 1983 and 1984. Centennial (resistant to Hg and Mi), Braxton (resistant to Mi, susceptible to Hg), and Coker 237 (susceptible to Hg and Mi) were planted in soil infested with 0, 31, or 124 eggs of Hg and Mi, individually and in all combinations, per 100 cm(3) soil. Yield responses of the soybean cultivars to individual and combined infestations of Hg and Mi were primarily dependent on soybean resistance or susceptibility to each species separately. Yield of Centennial was stimulated or unaffected by nematode treatments, yield of Braxton was suppressed by Hg only, and yield suppressions caused by Hg and Mi were additive and dependent on Pi for Coker 237. Other plant responses to nematodes were also dependent on host resistance or susceptibility. Population densities of Mi second-stage juveniles (J2) in soil were related to Mi Pi and remained constant in the presence of Hg for all three cultivars. Population densities of Hg J2 on the two Hg-susceptible Cultivars, Braxton and Coker 237, were suppressed in the presence of Mi at low Hg Pi.

Twenty-six susceptible and resistant soybean, Glycine max, cultivars in Maturity Groups V, VI, VII, and VIII were compared with Coker 156, Wright, and PI97100 for tolerance to Heterodera glycines races 3 and 14. Seed yields were compared in nematicide-treated (EDB, fenamiphos) and untreated plots at two H. glycines-infested locations over 3 years. Coker 488, DP 417, and NK S72-60 had the highest average tolerance indices ([yield in untreated plot + yield in nematicide-treated plot] x 100) of the race 3-susceptible cultivars to races 3 and 14. Plant height and seed weight of untreated soybean plants were suppressed in race 3-infested soil, but only plant height was suppressed at the race 14-infested location. Several race 3-resistant and race 14-susceptible cultivars were moderately tolerant to race 14.