QTL for seed protein and amino acids in the Benning × Danbaekkong soybean population.

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. 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.

Soybean lines lacking the 120,000-dalton seed lectin.

Seeds of 102 lines of Glycine max (L.) Merr., the soybean, were screened quantitatively for the presence of the 120,000-dalton soybean lectin. Wide variation in the content of this lectin was noted, and five lines of soybean whose seed totally lacked the lectin were identified. Roots of all five lines were effectively nodulated by several strains of Rhizobium japonicum, thus indicating that the 120,000-dalton soybean seed lectin is probably not required for the initiation of soybean-Rhizobium symbiosis.

The Bradyrhizobium japonicum noeD gene: a negatively acting, genotype-specific nodulation gene for soybean.

Bradyrhizobium japonicum strain USDA 110 is restricted for nodulation by soybean genotype PI 417566. We previously reported the identification of a USDA 110 Tn5 mutant, strain D4.2-5, that had the ability to overcome nodulation restriction conditioned by PI 417566 (S. M. Lohrke, J. H. Orf, E. Martínez-Romero, and M. J. Sadowsky, Appl. Environ. Microbiol. 61:2378-2383, 1995). In this study, we report the cloning and characterization of the negatively acting DNA region mutated in strain D4.2-5 that is involved in the genotype-specific nodulation of soybean. The Tn5 integration site was localized to a 5.2-kb EcoRI fragment isolated from wild-type USDA 110 genomic DNA. Saturation Tn5 mutagenesis of this 5.2-kb region and DNA homogenitization studies indicated that a 0.9-kb DNA region was involved in the genotype-specific nodulation of PI 417566. A single open reading frame (ORF) of 474 nucleotides, encoding a predicted protein of 158 amino acids, was identified within this region by DNA sequencing. This ORF was named noeD. Computer comparisons with available data bases revealed no significant similarities between the noeD DNA or predicted amino acid sequence and any known genes or their products. However, comparisons done with the region upstream of noeD revealed a high degree of similarity (about 76% similarity and 62% identity) to the N-terminal regions of the Rhizobium leguminosarum bv. viciae and R. meliloti nodM genes, which have been postulated to encode a glucosamine synthase. Southern hybridization analysis indicated that noeD is not closely linked to the main or auxiliary nodulation gene clusters in B. japonicum and that both nodulation-restricted and -unrestricted B. japonicum serogroup 110 strains contain a noeD homolog. High-performance liquid chromatography and fast atom bombardment-mass spectrometry analyses of the lipo-chitin oligosaccharide (LCO) nodulation signals produced by an noeD mutant showed a higher level of acetylation than that found with wild-type USDA 110. These results suggest that specific LCO signal molecules may be one of the factors influencing nodulation specificity in this symbiotic system.

Soybean Cyst Nematode Population Development and Associated Soybean Yields of Resistant and Susceptible Cultivars in Minnesota.

The soybean cyst nematode (SCN), Heterodera glycines, is a major soybean yield-limiting factor, and the use of resistant cultivars is one of the most effective means to manage the nematode. During the past decade, a number of resistant cultivars in maturity groups I and II have been developed and made available to growers. A total of 47 resistant cultivars and nine susceptible cultivars were evaluated at 15 SCN-infested field sites and two noninfested sites during 1996 to 1998 in Minnesota. As expected, more nematodes developed on susceptible cultivars than on resistant cultivars. Egg density on susceptible cultivars increased by 1.9- to 10.6-fold during the growing season at 12 sites and did not change at the other three sites. Average egg density decreased over time for resistant cultivars at all sites, except where the initial egg density was low (≤455 eggs per 100 cm3 soil). Nematode reproduction factors (Rf = egg density at harvest/egg density at planting) for individual resistant and susceptible cultivars were highly consistent across the eight sites where initial SCN density was more than 1,000 eggs per 100 cm3 soil. Resistance, however, varied among the cultivars, with the average Rf of individual resistant cultivars across the sites ranging from 0.3 to 1.7. Resistant cultivars produced an average yield of 3,082 kg/ha compared with 2,497 kg/ha by susceptible cultivars at eight of 10 sites where egg density at planting was greater than 700 eggs per 100 cm3 soil. In contrast, no difference in yield was observed between resistant and susceptible cultivars at sites where egg density at planting was lower than 500 eggs per 100 cm3 soil. Yield differences between resistant and susceptible cultivars increased with increasing initial SCN egg density. In six fields infested with initial densities of more than 5,000 eggs per 100 cm3 soil, resistant cultivars produced 28.4% (676 kg/ha) more yield on average than susceptible cultivars. Soybean yield increased when cultivars with increasing resistance to the SCN (lower Rf or females formed on roots) were grown in fields infested with SCN. Average relative yield (yield of a cultivar/average yield of all resistant cultivars at a site) of individual resistant cultivars across all SCN-infested sites ranged from 0.76 to 1.10. Yield consistency of soybean cultivars was low among the different sites, indicating that many other factors affected yield. Our results suggest growing resistant cultivars is an effective method to manage SCN in Minnesota while minimizing yield loss due to SCN.

Response of young chicks to raw, defatted, Kunitz trypsin inhibitor variant soybeans as sources of dietary protein.

Two trials, using 264 8-day-old male crossbred chicks, were conducted to evaluate the nutritional value of two trypsin-inhibitor (Kunitz) variant soybeans. These two variants, designated PI 157440 (PI) and number 661, have lower trypsin-inhibitor activities than do US commercially grown soybean cultivars such as Amsoy 71. Raw PI, 661, and Amsoy 71 soybeans were defatted and then compared to a commercially processed solvent extracted soybean meal (SBM) using purified diets with soybeans or SBM as the sole source of protein. Trials 1 and 2, respectively, were of 6 and 7 days duration. SBM was superior to each of the raw meals. In Trial 1, gain/feed was higher from PI than from Amsoy 71. In Trial 2, gain and gain/feed were higher (P < .05) from PI and 661 than from Amsoy 71. Pancreas weight as a percent of body weight reflected the trypsin-inhibitor intake. The addition of .3% DL-methionine to each diet improved (P < .05) gain and gain/feed. In Trial 2 gain and gain/feed from PI plus methionine was greater (P < .05) than from 661 plus methionine. In both trials, raw PI plus 3% methionine produced gain and gain/feed comparable to SBM without added methionine.

A Revised Classification Scheme for Genetically Diverse Populations of Heterodera glycines.

Heterodera glycines, the soybean cyst nematode, is a major yield-limiting pathogen in most soybean production areas worldwide. Field populations of H. glycines exhibit diversity in their ability to develop on resistant soybean cultivars. Since 1970, this diversity has been characterized by a bioassay used to assign a race classification to a population. The value of the race scheme is reflected in the number and quality of resistant soybean cultivars that have been developed and released by soybean breeders and nematologists working in concert. However, the race scheme also has been misapplied as a means of studying H. glycines genotypes, in part due to the use of the term "race." For fungal and bacterial pathogen species, "race" can theoretically be applied to individuals of a population, thus allowing inference of individual genotypes. Application of a race designation to an individual egg or second-stage juvenile (J2) of H. glycines is not possible because a single J2 cannot be tested on multiple hosts. For other nematode species, "race" is defined by host ranges involving different plant species, whereas the H. glycines race test involves a set of lines of the same plant species. Nonetheless, because H. glycines populations vary in genetic diversity, and this variation has implications for management strategies, a mechanism is needed for documenting and discussing population differences. The HG Type scheme described herein avoids the implication of genetic uniformity or predictability in contrast to the way the race scheme has been used.

Quantitative trait loci controlling sulfur containing amino acids, methionine and cysteine, in soybean seeds.

Soybean [Glycine max (L.) Merr.] is the single largest source of protein in animal feed. However, a major limitation of soy proteins is their deficiency in sulfur-containing amino acids, methionine (Met) and cysteine (Cys). The objective of this study was to identify quantitative trait loci (QTL) associated with Met and Cys concentration in soybean seed. To achieve this objective, 101 F(6)-derived recombinant inbred lines (RIL) from a population developed from a cross of N87-984-16 x TN93-99 were used. Ground soybean seed samples were analyzed for Met and Cys concentration using a near infrared spectroscopy instrument. Data were analyzed using SAS software and QTL Cartographer. RIL differed (P<0.01) in Met and Cys concentrations, with a range of 5.1-7.3 (g kg(-1) seed dry weight) for Cys and 4.4-8.8 (g kg(-1) seed dry weight) for Met. Heritability estimates on an entry mean basis were 0.14 and 0.57 for Cys and Met, respectively. A total of 94 polymorphic simple sequence repeat molecular genetic markers were screened in the RIL. Single factor ANOVA was used to identify candidate QTL, which were confirmed by composite interval mapping using QTL Cartographer. Four QTL linked to molecular markers Satt235, Satt252, Satt427 and Satt436 distributed on three molecular linkage groups (MLG) D1a, F and G were associated with Cys and three QTL linked to molecular markers Satt252, Satt564 and Satt590 distributed on MLG F, G and M were associated with Met concentration in soybean seed. QTL associated with Met and Cys in soybean seed will provide important information to breeders targeting improvements in the nutritional quality of soybean.

Interactions between quantitative trait loci in soybean in which trait variation at one locus is conditional upon a specific allele at another.

A large recombinant inbred population of soybean has been characterized for 220 restriction fragment-length polymorphism (RFLP) markers. Values for agronomic traits also have been measured. Quantitative trait loci (QTL) for height, yield, and maturity were located by their linkage to RFLP markers. QTL controlling large amounts of trait variation were analyzed for the dependence of trait variation on particular alleles at a second locus by comparing cumulative distributions of the trait for each genotype (four genotypes per pair of loci). Interesting pairs of loci were analyzed statistically with maximum likelihood and Monte Carlo comparison of additive and epistatic models. For each locus affecting height, variation was conditional upon the presence of a particular allele at a second unlinked locus that itself explained little or no trait variation. The results show that interactions between QTL are frequent and control large effects. Interactions distinguished between different QTL in a single linkage group and between QTL that affect different traits closely linked to one RFLP marker--i.e., distinguished between pleiotropy and closely linked genes. The implications for the evolution of inbreeding plants and for the construction of agronomic breeding strategies are discussed.

Host-Controlled Restriction of Nodulation by Bradyrhizobium japonicum Strains in Serogroup 110.

We previously reported the identification of a soybean plant introduction (PI) genotype, PI 417566, which restricts nodulation by Bradyrhizobium japonicum MN1-1c (USDA 430), strains in serogroup 129, and USDA 110 (P. B. Cregan, H. H. Keyser, and M. J. Sadowsky, Appl. Environ. Microbiol. 55:2532-2536, 1989, and Crop Sci. 29:307-312, 1989). In this study, we further characterized nodulation restriction by PI 417566. Twenty-four serogroup 110 isolates were tested for restricted nodulation on PI 417566. Of the 24 strains examined, 62.5% were restricted in nodulation by the PI genotype. The remainder of the serogroup 110 strains tested (37.5%), however, formed significant numbers of nodules on PI 417566, suggesting that host-controlled restriction of nodulation by members of serogroup 110 is strain dependent. Analysis of allelic variation at seven enzyme-encoding loci by multilocus enzyme electrophoresis indicated that the serogroup 110 isolates can be divided into two major groups. The majority of serogroup 110 isolates which nodulated PI 417566 belonged to the same multilocus enzyme electrophoresis group. B. japonicum USDA 110 and USDA 123 were used as coinoculants in competition-for-nodulation studies using PI 417566. Over 98% of the nodules formed on PI 417566 contained USDA 123, whereas less than 2% contained USDA 110. We also report the isolation of a Tn5 mutant of USDA 110 which has overcome nodulation restriction conditioned by PI 417566. This mutant, D4.2-5, contained a single Tn5 insertion and nodulated PI 417566 to an extent equal to that seen with the unrestricted strain USDA 123. The host range of D4.2-5 on soybean plants and other legumes was unchanged relative to that of USDA 110, except that the mutant nodulated Glycine max cv. Hill more efficiently. While strain USDA 110 has the ability to block nodulation by D4.2-5 on PI 417566, the nodulation-blocking phenomenon was not seen unless strain USDA 110 was inoculated at a 100-fold greater concentration than the mutant strain.

Targeted comparative genome analysis and qualitative mapping of a major partial-resistance gene to the soybean cyst nematode.

A major partial-resistance locus to the soybean cyst nematode (Heterodera glycines Ichinohe; SCN) was identified on linkage group 'G' of soybean [Glycine max (L.) Merr.] using restriction fragment length polymorphisms (RFLPs). This locus explained 51.4% (LOD=10.35) of the total phenotypic variation in disease response in soybean Plant Introduction (PI) 209332, 52.7% (LOD=15.58) in PI 90763, 40.0% (LOD=10.50) in PI 88788, and 28.1% (LOD=6.94) in 'Peking'. Initially, the region around this major resistance locus was poorly populated with DNA markers. To increase marker density in this genomic region, first random, and later targeted, comparative mapping with RFLPs from mungbean [Vigna radiata (L.) R. Wilcz.] and common bean (Phaseolus vulgaris L.) was performed, eventually leading to one RFLP marker every 2.6 centimorgans (cM). Even with this marker density, the inability to resolve SCN disease response into discrete Mendelian categories posed a major limitation to mapping. Thus, qualitative scoring of SCN disease response was carried out in an F5∶6 recombinant inbred population derived from 'Evans'xPI 209332 using a 30% disease index cut-off for resistance. Using the computer program JoinMap, an integrated map of the region of interest was created, placing the SCN resistance locus 4.6 cM from RFLP marker B53 and 2.8 cM from Bng30. This study demonstrates how a combination of molecularmapping strategies, including comparative genome analysis, join mapping, and qualitative scoring of a quantitative trait, potentially provide the necessary tools for high-resolution mapping around a quantitative-trait locus.