Microsatellite or simple sequence repeat (SSR) markers have been successfully used for genomic mapping, DNA fingerprinting, and marker-assisted selection in many plant species. Here we report the first successful assignment of 15 SSR markers to the Phaseolus vulgaris molecular linkage map. A total of 37 SSR primer pairs were developed and tested for amplification and product-length polymorphism with BAT93 and Jalo EEP558, the parental lines of an F7 recombinant inbred (RI) population previously used for the construction of a common bean molecular linkage map. Sixteen of the SSRs polymorphic to the parental lines were analyzed for segregation and 15 of them were assigned to seven different linkage groups, indicating a widespread distribution throughout the bean genome. Map positions for genes coding for DNAJ-like protein, pathogenesis-related protein 3, plastid-located glutamine synthetase, endochitinase, sn-glycerol-3 phosphate acyltransferase, NADP-dependent malic enzyme, and protein kinase were determined for the first time. Addition of three SSR loci to linkage group B4 brought two separated smaller linkage groups together to form a larger linkage group. Analysis of allele segregation in the F7 RI population revealed that all 16 SSRs segregated in the expected 1:1 ratio. These SSR markers were stable and easy to assay by polymerase chain reaction (PCR). They should be useful markers for genetic mapping, genotype identification, and marker-assisted selection of common beans.

Soybean improvement via plant breeding has been critical for the success of the crop. The objective of this study was to quantify genetic change in yield and other traits that occurred during the past 80 yr of North American soybean breeding in Maturity Groups (MGs) II, III, and IV. Historic sets of 60 MG II, 59 MG III, and 49 MG IV soybean cultivars, released from 1923 to 2008, were evaluated in field trials conducted in 17 U.S. states and one Canadian province during 2010 to 2011. Averaged over 27 MG II and MG IV and 26 MG III site-years of data, the estimated rates of yield improvement during the 80 yr were 23 kg ha -1 yr -1 for MGs II and III, and 20 kg ha -1 yr -1 for MG IV cultivars. However, a two-segment linear regression model provided a better fit to the data and indicated that the average current rate of genetic yield gain across MGs is 29 kg ha -1 yr -1 . Modern cultivars yielded more than old cultivars in all environments, but particularly in high-yielding environments. New cultivars in the historic sets used in this study are shorter in height, mature later, lodge less, and have seeds with less protein and greater oil concentration. Given that on-farm soybean yields in the United States are also increasing at a rate of 29 kg ha -1 yr -1 , it can be inferred that continual release of greater-yielding cultivars has been a substantive driver of the U.S. onfarm realized yield increases.

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The simple sequence repeat (SSR) or microsatellite marker is currently the preferred molecular marker due to its highly desirable properties. The aim of this study was to develop and characterize more SSR markers because the number of SSR markers currently available in tomato is very limited. Five hundred DNA sequences of tomato were searched for SSRs and analyzed for the design of PCR primers. Of the 158 pairs of SSR primers screened against a set of 19 diverse tomato cultivars, 129 pairs produced the expected DNA fragments in their PCR products, and 65 of them were polymorphic with the polymorphism information content (PIC) ranging from 0.09 to 0.67. Among the polymorphic loci, 2-6 SSR alleles were detected for each locus with an average of 2.7 alleles per locus; 49.2% of these loci had two alleles and 33.8% had three alleles. The vast majority (93.8%) of the microsatellite loci contained di- or tri-nucleotide repeats and only 6.2% had tetra- and penta-nucleotide repeats. It was also found that TA/AT was the most frequent type of repeat, and the polymorphism information content (PIC) was positively correlated with the number of repeats. The set of 19 tomato cultivars were clustered based on the banding patterns generated by the 65 polymorphic SSR loci. Since the markers developed in this study are primarily from expressed sequences, they can be used not only for molecular mapping, cultivar identification and marker-assisted selection, but for identifying gene-trait relations in tomato.

Linolenic acid and seed lipoxygenases are associated with off flavours in soybean products. F5 recombinant inbred lines (RILs) from a cross between a low linolenic acid line (RG10) and a seed lipoxygenase-free line (OX948) were genotyped for simple sequence repeats (SSR), random amplified polymorphic DNA (RAPD), sequence-tagged sites (STS), and cleaved amplified polymorphic sequence (CAPS) markers and evaluated for seed and agronomic traits at 3 Ontario locations in 2 years. One hundred twenty markers covering 1247.5 cM were mapped to 18 linkage groups (LGs) in the soybean composite genetic map. Seed lipoxygenases L-1 and L-2 mapped as single major genes to the same location on LG G13-F. L-3 mapped to LG G11-E. This is the first report of a map position for L-3. A major quantitative trait locus (QTL) associated with reduced linolenic acid content was identified on LG G3-B2. QTLs for 12 additional seed and agronomic traits were detected. Linolenic acid content, linoleic acid content, yield, seed mass, protein content, and plant height QTL were present in at least 4 of 6 environments. Three to 8 QTLs per trait were detected that accounted for up to 78% of total variation. Linolenic acid and lipoxygenase loci did not overlap yield QTL, suggesting that it should be possible to develop high-yielding lines resistant to oxidative degradation by marker-assisted selection (MAS).

The possibility of using random amplified polymorphic DNA (RAPD) markers previously mapped in the common bean PC50/XANI59 population to select for resistance to common bacterial blight (CBB) in different populations was examined. Two out of 02 selected RAPD markers were polymorphic in HR56 and W0633d, the parental lines used in this experiment. Cosegregation analysis of the two polymorphic markers and disease reaction in a recombinant inbred (RI) population derived from HR67/W1744d confirmed that one of the two RAPD markers, BC420900, was significantly associated with a major quantitative trait locus‐conditioning resistance to CBB in HR67. This locus accounted for approximately 51) of the phenotypic variation. The RAPD marker was transformed into a sequence characterized amplified region (SCAR) marker and used for selection in a different population derived from ‘Envoy’/HR67. Prediction for resistance to CBB with the BC420.990 SCAR marker was 94.2% accurate in this population. A comparison between marker‐assisted selection (MAS) and conventional greenhouse screening showed that the cost of MAS is about one‐third less than that of the greenhouse test.

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formulas (Setchell et al., 1997;Fitzpatrick, 1998;Yellayi et al., 2002). Therefore, breeding soybean with increased Dietary intake of isoflavones has been shown to reduce the risk or decreased isoflavone content in the seed would be of several major diseases in humans. Therefore, breeding soybean desirable for the health and food industries.[Glycine max (L.) Merrill] seeds with desirable isoflavone content would be beneficial to the food and health industries, but the environ-Breeding soybean for high or low isoflavone content mental sensitivity of the trait complicates phenotypic selection. The in the seed is challenging since isoflavone content is objective of this study was to identify quantitative trait loci (QTL) and heavily influenced by environment (Eldridge and Kwoepistatic interactions associated with isoflavone contents in soybean lek, 1983;Wang and Murphy, 1994; Carrao-Panizzi and seeds. A population of 207 F 4:6 recombinant inbred lines (RILs) was Kitamura, 1995;Hoeck et al., 2000; Lee et al., 2002). produced from the cross 'AC756' ϫ 'RCAT Angora'. The population Since molecular markers are not affected by environwas phenotyped at two locations in Ontario, Canada, and genotyped ment, the genetic dissection and characterization of by means of 99 polymorphic SSR markers. A significant genotype ϫ many quantitatively inherited agronomic and seed qualenvironment interaction was found. Seventeen QTLs were detected ity traits in soybean is possible. A limited number of re-(P Ͻ 0.01) by single-factor ANOVA. Individual loci explained up to searchers have attempted to map quantitative trait loci 10.5% (P Ͻ 0.0001) of the phenotypic variation. Interval mapping and composite interval mapping identified nine genomic regions (LGs (QTL) associated with isoflavone content in soybean A1, C2, D1a, F, G, H, J, K, and M) associated with isoflavone contents. seeds. Currently, QTL associated with this trait have Some QTL associated with agronomic or seed quality traits mapped been reported on LGs A1, B1, B2, D1aϩQ, H, K, and to the same regions as those for individual isoflavone contents on N in the mapping population Essex ϫ Forrest (Njiti et LGs A1, C2, F, J, K, M, and N. Twenty-three epistatic interactions al. , 1999; Meksem et al., 2001; Kassem et al., 2004). were detected for isoflavones. Multiple locus models explained up to Our mapping population was derived from germplasm 25.0% (P Ͻ 0.0001) of the phenotypic variation without epistasis and adapted to southern Ontario environments, which could up to 35.8% (P Ͻ 0.0001) with it. The QTL identified in this study could assist in identifying additional QTL and perhaps confirm be useful for developing soybean varieties with desirable isoflavone some of the previously identified QTL. The use of these content in the seed through marker-assisted selection (MAS).QTL through MAS could be advantageous in the design of an efficient and cost-effective breeding strategy for developing high or low isoflavone soybean varieties.