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Southern stem canker (SSC) in soybean [Glycine max (L.) Merrill], caused by the fungal pathogen Diaporthe aspalathi, is a major disease in the southern United States. It can cause up to 80% yield loss in severely infected fields. Plant introduction (PI) 398469, a Maturity Group VI soybean accession from South Korea, is one of six known sources of resistance to SSC. To determine the genetics of the resistance provided by PI 398469, F2:3 and F5‐derived recombinant inbred line (RIL) populations were developed from a cross with the susceptible breeding line G81‐2057. Both populations were phenotyped in the greenhouse using a modified toothpick method. The SSC‐resistant and susceptible DNA bulks consisting of 20 resistant and 18 susceptible families were created from the F2:3 population and genotyped using the Infinium SoySNP50K BeadChips for a bulked segregant analysis (BSA). Based on BSA results, 22 Kompetitive allele specific polymerase chain reaction (KASP) markers were designed to genotype the RIL population. Quantitative trait locus (QTL) analysis identified qRdm_14, on chromosome (Chr) 14 with an R2 of 62%. Linkage mapping in the F2:3 population confirmed the presence of a QTL on Chr 14. F5‐derived RILs derived from G81‐2057 × Crockett were phenotyped for SSC resistance and genotyped with the KASP markers to examine the relationship between Rdm3 from Crockett and qRdm_14 from PI 398469. Both PI 398469 and Crockett carried realleles at the Rdm3 locus for resistance to SSC. The QTL and KASP marker information could be used to screen breeding lines for resistance to SSC. Core Ideas: Resistance to soybean southern stem canker is provided by a major QTL on chromosome 14 from PI 398469.Both PI 398469 and Crockett carry resistance alleles at the Rdm3 locus on chromosome 14 for SSC resistance.KASP markers developed for the Rdm3 locus can be used by breeders to perform marker‐assisted selection. [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 (PIs) are highly resistant to the peanut root-knot nematode. To determine if PI 594403, PI 594427C, and PI 594651B contain useful resistance genes from those previously characterized in PI 200538, populations developed from the PIs crossed to PI 200538 were tested for Ma response. Highly galled and highly resistant [F.sub.2] plants were observed in each population. In two of the three populations, the highly galled [F.sub.2] plants produced progeny that sustained significantly greater galling (P < 0.001) than those derived from highly resistant [F.sub.2] plants. While the [F.sub.2]--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 [F.sub.2]--derived lines from highly galled or resistant [F.sub.2] plants within all of the populations were significantly different from each other or from the parents. Thus, it is evident that these PIs likely contain unique resistance genes that, when combined with PI 200538--derived Ma resistance, could improve the level of Ma resistance in soybean cultivars. doi: 10.2135/cropsci2009.02.0059

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 [F.sub.2:4] lines of BoggsRR(6) x G93-9009 and BenningRR(5) x 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.

The fatty acid composition of soybean [Glycine max (L.) Merr.] seed affects the flavor, nutritional value, and stability of the oil. Increasing oleic acid content in soybean oil would reduce the need for hydrogenation, a process that creates unhealthy trans fatty acids. The objective of this study was to map and confirm the areas of the soybean genome associated with oleic acid content from the soybean line N00-3350 (~583 g [kg.sup.-1] oleic acid) using simple sequence repeat (SSR) markers. An [F.sub.2:3] population of 259 lines from the cross of G99-G725 x N00-3350 was used as a mapping population, and an [F.sub.2:3] population of 231 lines from the cross of G99-G3438 x N00-3350 was used for confirmation. Using single-factor analysis of variance, interval mapping, and composite interval mapping, six quantitative trait loci (QTLs) for oleic acid content were found on linkage groups LG-A1 (Satt211, [R.sup.2] = 4%), LG-D2 (Satt389, [R.sup.2] = 6%), LG-G (Satt394, [R.sup.2] = 13%), LG-G (Satt191, [R.sup.2] = 7%), LG-L (Satt418, [R.sup.2] = 9%), and LG-L (Satt561, [R.sup.2] = 25%) in the G99-G725 x N00-3350 population. All six QTLs for oleic acid were confirmed in the G99-3438 x N00-3350 population. The designations cqOle-001, cqOle-002, cqOle-003, cqOle-004, cqOle-005, and cqOle-006 have been assigned to these confirmed QTLs by the Soybean Genetics Committee. The identification of SSR markers linked to the oleic acid QTLs will facilitate the use of marker-assisted selection (MAS) in soybean breeding programs to increase the oleic acid content in soybean seed.

The identification of single nucleotide polymorphism (SNP) markers tightly linked to soybean [Glycine max (L.) Merr.] quantitative trait loci (QTL) conditioning resistance to southern root-knot nematode (Meloidogyne incognita) (Mi) would enhance the efficiency and cost effectiveness of marker-assisted selection (MAS) for this trait. Bacterial artificial chromosome (BAC) ends and simple sequence repeat (SSR)-containing genomic DNA clones were used to develop SNP markers linked to two soybean Mi resistance QTL on Linkage Group 0 (LG-O) and LG-G. A total of 14 BAC-end sequences and seven SSR flanking regions were used to design primers to amplify genomic frogments of PI 96354 (Mi resistant) and 'Bossier' (Mi susceptible). We discovered three SNPs in Satt358 source-sequences located near a major Mi-resistant QTL on LG-O and three SNPs in Sott199 source-sequences located near a minor Mi-resistant QTL on LG-G. Using a direct hybridization SNP assay detected on a Luminex 100 flow cytometer, the SNP358 genotypes of 94 [F.sub.2:3] lines from a cross of PI 96354 x Bossier were congruent with the genotypes of the SSR marker Sart358. The genotypes of SNP199 marker which targets a SNP in Satt199 source-sequence also showed 100% congruence with the genotypes of the SSR marker Satt199. SNP genotyping of 24 known Mi-resistant or Mi-susceptible cultivars showed that SNP358 and SNP199 markers should be highly effective in MAS for the Mi-resistance QTL on LG-O and LG-G.

Recently, reniform nematode (Rotylenchulus reniformis Linford and Oliveira) has been recognized to be a major problem on soybean [Glycine max (L.) Merr.] in the southern USA. Planting reniform nematode-resistant soybean cultivars is the most cost effective control method. With restriction fragment length polymorphism (RFLP) markers, Pioneer Hi-Bred International, Inc. had previously identified quantitative trait loci (QTL) on linkage group B1 (LG-B1) and another on LG-L associated with reniform nematode resistance in a cross between 'BSR101' and PI 437654. In this study, we refined the QTL locations and identified additional QTL conditioning resistance to reniform nematode in a population of 228 recombinant inbred lines (RILs) from a cross of BSR101 x PI 437654. A QTL ([R.sup.2] = 21%) conditioning reniform reproductive index (RI) was found on LG-L and was flanked by Sat 184 and Satt513. Two other QTL were identified, one on LG-B1 ([R.sup.2] = 16%) and the other on LG-G ([R.sup.2] = 8%). These two QTL acted in an epistatic manner with lines homozygous for PI 437654 alleles at both QTL providing the lowest reniform RI. The 31 RILs from BSR101 x PI 437654 that were homozygous for the PI 437654 alleles at Satt513, Satt359, and Sat_168 averaged 1077 reniform eggs and juveniles (RI = 0.63), while the 33 RILs homozygous for the BSR101 alleles averaged 10606 (RI = 6.24). By screening the RILs population of 'Prichard' x 'Anand' we confirmed that the QTL on LG-G and-B1 conditioned reniform RI.

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi Syd., is a widespread disease of soybean [Glycine max (L.) Merr.] 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) x 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 x 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. Marker-assisted selection can be used to develop soybean cultivars with the Rpp?(Hyuuga) gene for resistance to ASR.

Despite its importance, exploitation of intra-cultivar variation has been very limited due to the belief that elite cultivars are highly homogeneous. The main objective of this study was to investigate the presence of exploitable intra-cultivar variation for seed weight, maturity, and other agronomic traits within elite soybean cultivars released for their superior productivity and resistance to various diseases. Single-plant progeny lines, selected at very low plant density from within these cultivars, were evaluated for seed weight, maturity, plant height, lodging, and seed yield in row-plot replicated randomized complete block designs across years. For seed weight, the magnitude of intra-caltivar variation across years between the largest- and the smallest-seeded lines averaged 36 mg [seed.sup.-1] for Banning, 22 mg [seed.sup.-1] for Cook, and 45 mg [seed.sup.-1] for Haskell. For maturity, the magnitude of intra-caltivar variation was 5 d in Banning, 4 d in Cook, and 7 d in Haskell. Furthermore, we discovered intra-cultivar variation for plant height within Cook and Haskell, and for lodging within Haskell. This study is the first one to report evidence of significant intra-cultivar variation for seed weight, maturity, plant height, and lodging within soybean cultivars. The results suggest that cultivars may not be permanent records with nonexistent variation but genetic material that can be upgraded to maintain uniformity in the long term and further improve desirable agronomic or seed-trait characteristics.

Three physiological traits that may affect performance of soybean [Glycine max (L.) Merr.] when soil water availability is limiting are (i) water use efficiency (WUE), (ii) regulation of whole plant water use in response to soil water content, and (iii) leaf epidermal conductance ([g.sub.e]) when stomata are closed. Six soybean plant introductions (PIs), eight breeding lines derived from them, and nine cultivars were compared for variability in these three traits during vegetative growth in two greenhouse studies. In the first experiment, whole plant water use, normalized both to plant size and evaporative demand (the normalized transpiration ratio, NTR), was monitored during a 10-d cycle of gradually increasing drought stress and then for an additional 2 d following rewatering. The critical soil water content at which each plant began to reduce its water use (FFS[W.sub.c]), was determined. The WUE was estimated as the ratio of total plant dry weight to total water used. In the second experiment, [g.sub.e] was determined for these same 23 genotypes by measuring leaf water vapor exchange after a 36-h dark adaptation. Substantial variation was found among genotypes for WUE, FFS[W.sub.c], [g.sub.e], and also the extent to which NTR recovered on rewatering. Generally, adapted cultivars had greater WUE and lower [g.sub.e] than did PIs. However, PI 471938 and its progeny N98-7264 were clear exceptions to this trend. An unexpected finding was that WUE was significantly negatively correlated with [g.sub.e] across genotypes.

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) tn 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., A GLYPHOSATE-TOLERANT (GT) soybean line, 40-3-2, was developed by the Monsanto Company (Padgette et al., 1995). Glyphosate [N-(phosponomethyl)-glycine] inhibits the activity of 5-enol-pyruvylshikimate-3-phosphate synthase (EPSPS), an enzyme crucial to biosynthesis [...]

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 PI97100 x 'Coker 237' with the same RFLP markers and (ii) verify previously reported QTL in an independent population of 'Young' x PI416937 for the same seed trails using SSR markers mapped in the same region as the original RFLP markers. Each population consisted of 176 [F.sub.2:4] lines and was grown in randomized complete block trials in two or three different environments. Single-factor analysis of variance was used to verify the QTL that had significant (P ≤ 0.01) associations. In the PI97100 x 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., THE ABILITY to utilize DNA markers to identify the genomic location of plant genes has played an important role in revolutionizing the science of plant breeding and genetics. In soybean, [...]

The southern root-knot nematode [Meloidogyne incognita (Kofoid and White) Chitwood] (Mi) is a serious pest of soybean [Glycine max (L.) Merr.] in the southern USA. Many soybean cultivars with Mi resistance and high productivity have been developed in the USA during the past few decades. DNA markers have been used to identify a major quantitative trait locus (QTL) near the top of Linkage Group O (LG-O) conferring resistance to Mi. The objectives of this study were to determine the frequency of elite Mi-resistant cultivars that inherited the major Mi resistance QTL on LG-O and determine the ancestral source of the Mi-resistance allele at this QTL. Forty-eight soybean lines, including ancestral, Mi-susceptible, and Mi-resistant genotypes were analyzed at six simple sequence repeat (SSR) loci that flank the major Mi QTL on LG-O. Codescent analysis of markers and phenotypes across six cycles of breeding showed that Mi-resistant cultivars inherited a 200-bp band at Satt358 and a 238-bp band at Sat_132 from 'Palmetto'. The tight linkage of both San358 and Sat_132 to the Mi QTL on LG-O indicates that selection for the Mi-resistant parent's allele at either of these markers should be highly effective in identifying Mi-resistant plants of lines., ROOT-KNOT NEMATODES (Meloidogyne spp.) are economically important plant pathogens that cause extensive crop losses all over the world (Sasser, 1977). They have extensive host ranges, their distribution is worldwide, and [...]