Salt is a severe abiotic stress that reduces soybean [Glycine max (L.) Merr.] yield by >20% in saline soils and irrigated fields. Marker‐assisted selection (MAS) is an efficient method to identify salt‐tolerant soybean lines. ‘Osage’ is a salt‐tolerant and high‐yielding cultivar in the Mid‐South of the United States and is a distant progeny tracing five generations back to ‘S‐100’. The objective of this study was to determine the inheritance of salt tolerance in Osage soybean by identifying the quantitative trait loci (QTL) controlling the trait. A chloride (Cl−) includer, ‘RA‐452’, was crossed with Cl− excluder, Osage, to develop an F4:6 mapping population. The F4:6 lines were genotyped by 5403 single nucleotide polymorphism (SNP) markers spanning 20 chromosomes (Chr.), of which, 1269 were polymorphic. The salt stress response of F4:6 lines, along with parental genotypes, was evaluated in the greenhouse in April and June 2013. Three different treatments (120 mM NaCl, 120 mM KCl, and water) were initiated at V1 stage and continued for ∼18 to 21 d. The leaf Cl− contents were quantified by inductively coupled plasma optical emission spectroscopy. Composite interval mapping analysis indicated that a major Cl−–tolerant QTL was confirmed and narrowed down on Chr. 3 in both NaCl and KCl treatments, a novel Cl−–tolerant QTL on Chr. 15 was identified in NaCl treatment, and a novel Cl−–tolerant QTL on Chr. 13 was identified in the KCl treatment. Two annotated genes, Glyma.13G161800 and Glyma.15G091600, were proposed to be the candidate gene conferring the Cl− tolerance within QTL region on Chr. 13 and 15, respectively. A total of 27 SNP markers were significantly associated with Cl− tolerance, which could be used for MAS in breeding salt‐tolerant soybean lines.

ABSTRACT. In this study, we identified simple sequence repeat, amplified fragment length polymorphism, and sequence-related amplified polymorphism markers linked to quantitative trait loci (QTLs) for resistance to white mold disease in common bean progenies derived from a cross between lines CNFC 9506 and RP-2, evaluated using the oxalic acid test and using Bayesian analysis. DNA was extracted from 186 F 2 plants and their parental lines for molecular analysis. Fifteen experiments were carried out for phenotypic analysis, which included 186 F 2:4 progenies, the F 1 generation, the F 2 generation, and the lines CNFC 9506, RP-2, and G122 as common treatments. A completely randomized experimental design with 3 replications was used in controlled environments. The adjusted means for the F 2:4 generation were to identify QTLs by Bayesian shrinkage analysis. Significant differences were observed among the progenies for the reaction to white mold. The moving away method under the Bayes- Identification of QTLs for resistance to white mold ian approach was effective for identifying QTLs when it was not possible to obtain a genetic map because of low marker density. Using the Wald test, 25 markers identified QTLs for resistance to white mold, as well as 16 simple sequence repeats, 7 amplified fragment length polymorphisms, and 2 sequence-related amplified polymorphisms. The markers BM184, BM211, and PV-gaat001 showed low distances from QTLs related white mold resistance. In addition, these markers showed, signal effects with increasing resistance to white mold and high heritability in the analysis with oxalic acid, and thus, are promising for marker-assisted selection.

The aims of this study were to evaluate the reaction of common bean lines to white mold, the aggressiveness of different Sclerotinia sclerotiorum isolates from various common bean production areas in Brazil, and comparison of the diallel and GGE (genotype main effect plus genotype-by-environment interaction) biplot analysis procedures via study of the line-by-isolate interaction. Eleven common bean (Phaseolus vulgaris) lines derived from 3 backcross populations were used. Field experiments were performed in the experimental area of the Departamento de Biologia of the Universidade Federal de Lavras, Lavras, MG, Brazil, in the 2011 and 2012 dry crop season and 2011 winter crop season through a randomized block design with 3 replications. This study was also set up in a greenhouse. Inoculations were performed 28 days after sowing by means of the straw test method. The reaction of the bean lines to white mold was assessed according to a diagrammatic scale from 1 (plant without symptoms) to 9 (dead plant). Estimations of general reaction capacity (lines) and general aggressiveness capacity (isolates) indicated different horizontal levels of resistance in the lines and levels of aggressiveness in the isolates. Therefore, it was possible to select more resistant lines and foresee those crosses that are the most promising for increasing the level of resistance. It was also possible to identify the most aggressive isolates that were more efficient in distinguishing the lines. Both diallel and GGE biplot analyses were useful in identifying the genotypic values of lines and isolates.

Edamame is a vegetable‐typesoybean [Glycine max (L.) Merr.] with large seed size, typically twice that of commodity soybean. Understanding the genetic diversity among large‐seeded germplasm as well as the genetic variation for seed size in the germplasm pool is important for edamame breeding. The objectives of this study were to analyze the genetic diversity of 343 edamame soybean accessions and 36 breeding lines, and to identify quantitative trait loci (QTLs) associated with seed weight (SW), seed volume (VOL), seed length (SL), seed breadth (SB), and seed height (SH) through genome‐wide association studies. We observed two main genetic groups among the 343 accessions and found that the breeding lines were genetically dissimilar to germplasm accessions. Through single‐ and multi‐locus models, a total of two, two, seven, one, and four SNPs were reported to be associated with SW, VOL, SL, SB, and SH located across two, two, five, one, and four chromosomes, respectively. There were three SNPs associated with SL, SB, and/or SH that were not found to be within a previously reported SL, SB, or SH QTL. The SNP ss715587475, positioned at the 24.9‐Mb position on chromosome 4, was located within the gene Glyma04g21680 which was associated with SW in Arabidopsis and may be a candidate gene for SW in edamame soybean. There were four additional SNPs positioned within genes that encode proteins that may relate to plant growth and development in soybean. Identifying and pyramiding favorable alleles for seed size and weight will enhance edamame breeding efforts.

ABSTRACT. In many species, low levels of polymorphism prevent the assembly of linkage maps that are used to identify genetic markers related to the expression of quantitative trait loci (QTLs). This study compared two methods of locating QTLs in association studies that do not require a previous estimation of linkage maps. Method I (MI) was a Bayesian multiple marker regression and Method II (MII) combined multiple QTL mapping and "moving away from markers". In this method, markers are not directly regressed to the phenotype, but are used as pivots to search for QTLs along the genome. To compare methods, we simulated 300 individuals from an F 2 progeny with two levels of marker loss (20 and 80%). A total of 165 markers and seven QTLs were spread along 11 chromosomes (roughly emulating the genetic structure of the common bean, Phaseolus vulgaris). A real data example with 186 progenies of a F 2:4 generation of the species was analyzed using 59 markers (17 simple sequence repeats, 31 amplified fragment length polymorphisms, and 11 sequence-related amplified polymorphisms). MII was more precise than MI for both levels of marker loss. For real data, MII detected 17 candidate positions for QTLs, whereas MI did not detect any. MII is a powerful method that requires further studies with actual data and other designs such as crossover, and genome-wide studies.