Flowering is indicative of the transition from vegetative to reproductive phase, a critical event in the life cycle of plants. In soybean (Glycine max), a flowering quantitative trait locus, FT2, corresponding to the maturity locus E2, was detected in recombinant inbred lines (RILs) derived from the varieties “Misuzudaizu” (ft2/ft2; JP28856) and “Moshidou Gong 503” (FT2/FT2; JP27603). A map-based cloning strategy using the progeny of a residual heterozygous line (RHL) from the RIL was employed to isolate the gene responsible for this quantitative trait locus. A GIGANTEA ortholog, GmGIa (Glyma10g36600), was identified as a candidate gene. A common premature stop codon at the 10th exon was present in the Misuzudaizu allele and in other near isogenic lines (NILs) originating from Harosoy (e2/e2; PI548573). Furthermore, a mutant line harboring another premature stop codon showed an earlier flowering phenotype than the original variety, Bay (E2/E2; PI553043). The e2/e2 genotype exhibited elevated expression of GmFT2a, one of the florigen genes that leads to early flowering. The effects of the E2 allele on flowering time were similar among NILs and constant under high (43°N) and middle (36°N) latitudinal regions in Japan. These results indicate that GmGIa is the gene responsible for the E2 locus and that a null mutation in GmGIa may contribute to the geographic adaptation of soybean.

Photosensitivity plays an essential role in the response of plants to their changing environments throughout their life cycle. In soybean [Glycine max (L.) Merrill], several associations between photosensitivity and maturity loci are known, but only limited information at the molecular level is available. The FT3 locus is one of the quantitative trait loci (QTL) for flowering time that corresponds to the maturity locus E3. To identify the gene responsible for this QTL, a map-based cloning strategy was undertaken. One phytochrome A gene (GmPhyA3) was considered a strong candidate for the FT3 locus. Allelism tests and gene sequence comparisons showed that alleles of Misuzudaizu (FT3/FT3; JP28856) and Harosoy (E3/E3; PI548573) were identical. The GmPhyA3 alleles of Moshidou Gong 503 (ft3/ft3; JP27603) and L62-667 (e3/e3; PI547716) showed weak or complete loss of function, respectively. High red/far-red (R/FR) long-day conditions enhanced the effects of the E3/FT3 alleles in various genetic backgrounds. Moreover, a mutant line harboring the nonfunctional GmPhyA3 flowered earlier than the original Bay (E3/E3; PI553043) under similar conditions. These results suggest that the variation in phytochrome A may contribute to the complex systems of soybean flowering response and geographic adaptation.

A genetic linkage map covering a large region of the genome with informative markers is essential for plant genome analysis, including identification of quantitative trait loci (QTLs), map-based cloning, and construction of a physical map. We constructed a soybean genetic linkage map using 190 F2 plants derived from a single cross between the soybean varieties Misuzudaizu and Moshidou Gong 503, based on restriction-fragment-length polymorphisms (RFLPs) and simple-sequence-repeat polymorphisms (SSRPs). This linkage map has 503 markers, including 189 RFLP markers derived from expressed sequence tag (EST) clones, and consists of 20 major linkage groups that may correspond to the 20 pairs of soybean chromosomes, covering 2908.7 cM of the soybean genome in the Kosambi function. Using this linkage map, we identified 4 QTLs--FT1, FT2, FT3, and FT4--for flowering time, the QTLs for the 5 largest principal components determining leaflet shape, 6 QTLs for single leaflet area, and 18 regions of segregation distortion. All 503 analyzed markers identified were located on the map, and almost all phenotypic variations in flowering time were explained by the detected QTLs. These results indicate that this map covers a large region of the soybean genome.

Soybean (Glycine max (L.) Merrill) is the most important leguminous crop in the world due to the high contents of protein and oil, and accumulation of various physiologically active substances. However, most of the genomic and economic traits in soybean are quantitative, controlled by multiple genes and easily affected by environmental conditions. Based on recombinant inbred lines (F 8 ), a genetic linkage map with 177 RFLP, 150 SSR, 28 AFLP markers and 5 phenotypic markers was constructed. The map covered a distance of 2663.6 cM of the soybean genome comprising 20 linkage groups. The average distance between two adjacent marker loci was 7.89 cM. In this population, we detected thirty-nine QTLs for all the reproductive development and seed quality traits investigated, that is, three for flowering time (FT1-3), four for maturity (HAV1-4), three for reproductive period (RP1-3), three for seed hardness (RAS1-3), five for viability of seed (VIS1-5), four for germination rate of seed (GRS1-4), five for water absorbability of seed (WAS1-5) and twelve QTLs for seed weight (SWE1-6 and SWH1-6). Out of these QTLs, twenty-eight were detected in nearly the same regions of the linkage map by both IM (interval mapping) and CIM (composite interval mapping) analysis. The proportion of variance explained of these QTLs ranged from 3.4 % to 67.1 %. Epistatic interactions were detected among various QTLs. Especially there was a strong interaction among the effects of FT1 and FT2, and FT1 and FT3. Multiple correlation coefficients between FT1 and FT2, and FT1 and FT3 accounted for 79.6 % and 74.1 % of the phenotypic variation of flowering time, respectively.

In recent years soybean rust, caused by Phakopsora pachyrhizi has become one of the most serious threats to soybean production in Brazil. Breeding lines and varieties have been selected for resistance to soybean rust in Asia. However, differences in virulence between Asian and Brazilian rust populations should be considered in order to select and use resistant resources from Asia. Here, we suggest criteria for distinguishing resistant from susceptible types by the analysis of four resistance characters: frequency of lesions having uredinia, number of uredinia per lesion, frequency of open uredinia, and sporulation level, determined by the utilization of 63 genotypes. Under growth chamber conditions, a set of 13 soybean varieties were exposed to three rust populations-one from Japan and two from Braziland evaluated for the resistance characters mentioned above. The Japanese and Brazilian populations clearly differed in virulence, as did the two Brazilian populations. Only two resistance genes, Rpp4 from PI459025 and Rpp5 from Shiranui, commonly conferred resistance on all three rust populations. The number of resistant varieties or resistance genes useful in both countries appears limited. Therefore, a resistant cultivar that is universally effective against soybean rust should be developed by pyramiding some major resistance genes and by introducing horizontal resistance. Keywords: Phakopsora pachyrhizi, lesion type, pathogenicity, resistant variety. RESUMO Desenvolvimento de critério de classificação da resistência à ferrugem asiática da soja e diferenças de virulência entre populações do Japão e do BrasilNos últimos anos a ferrugem asiática, causada pelo fungo Phakopsora pachyrhizi tornou-se uma das mais sérias ameaças a produção de soja Brasileira. Linhagens melhoradas e variedades têm sido selecionadas para a resistência à ferrugem da soja na Ásia, entretanto para a seleção e utilização dessas fontes de resistência, diferenças de virulência entre populações Asiáticas e Brasileiras desse fungo devem ser consideradas. Neste trabalho sugerimos um critério para se distinguir resistência de susceptibilidade pela análise de quatro caracteres de resistência: freqüência de lesões contendo urédias, número de urédias por lesão, freqüência de urédias abertas e nível de esporulação determinados pela utilização de 63 genótipos. Sob condições controladas em câmaras de crescimento, treze variedades de soja foram expostas a três populações de fungos -uma população proveniente do Japão e duas populações provenientes do Brasil-e avaliadas quanto aos caracteres de resistência mencionados acima. As populações Brasileiras diferiram entre si claramente quanto a virulência e em relação à população de isolados do Japão. Apenas dois genes de resistência, Rpp4 presente na variedade PI459025 e Rpp5 presente na variedade Shiranui conferiram resistência as três populações da ferrugem. O número de variedades ou genes resistentes úteis em ambos os países parece ser limitado. Assim, um cultivar universalmente efetivo contra a ferru...

Asian soybean rust (ASR) is caused by the fungal pathogen Phakopsora pachyrhizi Sydow & Sydow. It was first identified in Brazil in 2001 and quickly infected soybean areas in several countries in South America. Primary efforts to combat this disease must involve the development of resistant cultivars. Four distinct genes that confer resistance against ASR have been reported: Rpp1, Rpp2, Rpp3, and Rpp4. However, no cultivar carrying any of those resistance loci has been released. The main objective of this study was to genetically map Rpp2 and Rpp4 resistance genes. Two F(2:3) populations, derived from the crosses between the resistant lines PI 230970 (Rpp2), PI 459025 (Rpp4) and the susceptible cultivar BRS 184, were used in this study. The mapping populations and parental lines were inoculated with a field isolate of P. pachyrhizi and evaluated for lesion type as resistant (RB lesions) or susceptible (TAN lesions). The mapping populations were screened with SSR markers, using the bulk segregant analysis (BSA) to expedite the identification of linked markers. Both resistance genes showed an expected segregation ratio for a dominant trait. This study allowed mapping Rpp2 and Rpp4 loci on the linkage groups J and G, respectively. The associated markers will be of great value on marker assisted selection for this trait.

Fine-mapping of loci related to complex quantitative traits is essential for map-based cloning. A residual heterozygous line (RHL) of soybean (Glycine max) derived from a recombinant inbred line (RIL) was used for fine-mapping FT1, which is a major quantitative trait locus (QTL) responsible for soybean flowering time. The residual heterozygous line RHL1-156 was selected from the RILs that were derived from two distantly related varieties, Misuzudaizu and Moshidou Gong 503. The genome of RHL1-156 contains a heterozygous segment (approximately 17 cM) surrounding the FT1 locus but is homozygous in other regions, including three other loci affecting flowering time. A large segregating population of 1,006 individuals derived by selfing of RHL1-156 included two homozygous genotypes for the nearest marker of FT1 whose flowering time differed by 26 days. No continuous range of phenotypes was observed, in contrast to the F2 population, suggesting that a single FT1 locus affected the flowering time in the RHL1-156 line. Linkage analysis revealed that the FT1 locus mapped as a single Mendelian factor between two tightly linked DNA markers, Satt365 and GM169, at distances of approximately 0.1 cM and 0.4 cM, respectively. Our results show that a RHL derived from RILs can be used to fine-map a QTL and that RHLs can be an efficient tool for a systematic fine-mapping of QTLs.

Phakopsora pachyrhizi, the cause of soybean rust, is an economically important pathogen of soybean in South America. Understanding the pathogenicity of indigenous fungal populations is useful for identifying resistant plant genotypes and targeting effective cultivars against certain populations. Fifty-nine rust populations from Argentina, Brazil, and Paraguay were evaluated for pathogenicity in three cropping seasons, 2007/2008-2009/ 2010, using 16 soybean differentials. Only two pairs of P. pachyrhizi populations displayed identical pathogenicity profiles, indicating substantial pathogenic variation in the rust populations. Comparative analysis of 59 South American and five Japanese samples revealed that pathogenic differences were not only detected within South America but also distinct between the P. pachyrhizi populations from South America and Japan. In addition, seasonal changes in rust pathogenicity were detected during the sampling period. The differentials containing resistance genes (Rpp: resistance to P. pachyrhizi) Rpp1, Rpp2, Rpp3, and Rpp4, except for Plant Introduction (PI) 587880A, displayed a resistant reaction to only 1.8-14, 24-28, 22, and 36 % of South American P. pachyrhizi populations, respectively. In contrast, PI 587880A (Rpp1), Shiranui (Rpp5), and 3 Rpp-unknown differentials (PI 587855, PI 587905, and PI 594767A) showed a resistant reaction to 78-96 % of all populations. This study demonstrated that P. pachyrhizi populations from South America vary geographically and temporally in pathogenicity and that the known Rpp genes other than Rpp1 in PI 587880A and Rpp5 have been less effective against recent pathogen populations in the countries studied.