Progress 08/01/01 to 07/31/05
Outputs
Our objective in this project has been to understand the mechanism whereby interactions between QTLs serve to adapt inbred plants to their environment. The model system uses 3 large, related, recombinant inbred (RI) segregant soybean populations. All three populations had been characterized by more than 600 RFLP and SSR genetic markers as well as for values of agricultural traits in different environments. Recently we completed mapping an additional 500 SNP markers in the Minsoy x Noir RI population, filling gaps in the map and adding more markers to regions containing only a few. Additional markers also were added in the Minsoy x Archer and Noir x Archer RI populations. In the summer of 2001 we had measured trait values for all three populations in the third common environment, completing our goal of three different common environments. With the recently updated genetic map of the RI populations we can proceed to compare agronomic QTLs in the three environments. A
striking observation in this third environment was the variation between RI segregants for MF (leaflet number > 3) plants/row. More than ten QTLs were responsible for this trait, many of which interacted with each other. Expression of these was environment specific. The leaflet model system promises to be valuable in demonstrating the interactions of QTLs with the genome on the one hand and the environment on the other. The results suggest that the LF phenotype may be a useful indicator of interaction between the soybean genome and particular environments. (see abstract below). Principal component analysis of environments was undertaken using the different traits that were measured in the different environments. This type of analysis clearly separated environments into clusters differentiated by location, year or specific growth parameters (irrigation or drought etc.).
Impacts
Marker assisted selection of desired traits has been proposed as a major tool for improvement of agronomic crops including soybean. However, this tool is only useful insofar as the marker is linked to a trait gene whose value is independent of the genome background into which it is placed. Our research is demonstrating that the usefulness of this tool for selecting certain agronomic traits is limited in soybean. Thus, different breeding strategies may be required.
Publications
- Publications: Tischner, T., Allphin, L., Chase, K., Orf, J.H. and K.G. Lark (2003) Genetics of seed abortion and reproductive traits in soybean. Crop Sci. 43: 464-473.
- Song, Q. J., Marek, L.F., Shoemaker, R.C., Lark, K.G., Concibido, V.C., Delannay, X., Specht, J.E. and P.B. Cregan (2004) A New Integrated Genetic Linkage Map of the Soybean . Theor. App. Genet. 109:122-128.
- Orf, J.H., Chase, K., Specht, J.E., Cregan, P.B. and K.G. Lark (2005) Abnormal leaf formation in Soybean: Genetic and environmental effects. Theor. App. Genet. (Submitted).
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Progress 10/01/03 to 09/30/04
Outputs
Soybean [Glycine max (L.) Merrill] is trifoliolate, but 4, 5, or 6 foliolate leaves have been reported and expression of such multi-foliolate leaf forms (MF) has been shown to be heritable. Here we analyze the genetic complexity of the MF phenotype and the dependence of its expression on the environment. Recombinant inbred (RI) segregants of soybean were grown in different environments. The frequency of plants that expressed the MF phenotype as well as the frequency of nodes exhibiting MF leaves varied with both the environment and the RI segregant genotype. Growth chamber experiments supported field observations suggesting that the environment (day length, temperature etc.) at emergence influenced expression of MF during subsequent growth. Marker facilitated analyses of three RI segregant populations identified QTLs in 17 regions of the soybean genome. These either directly regulated MF phenotype expression, or were involved in interactions with such loci. Loci,
identified in one RI population were also identifiable in another, different, RI population. Most of the loci affected both the frequency of plants expressing MF, and the number of nodes on MF plants that expressed the phenotype. However, a few loci differentiated between these two effects. Many loci affected plants in both field experiments, however, a few differentiated between the two environments. Similar patterns were observed for interactions between loci. QTLs regulating the MF phenotype were located in genome regions that also contained QTLs regulating major agronomic traits, e.g. yield, lodging, seed number, maturity and disease or pest resistance. This suggests that the loci involved regulate plant growth at some over-arching level, controlling multiple phenotypes or traits.
Impacts
Marker assisted selection of desired traits has been proposed as a major tool for improvement of agronomic crops including soybean. However, this tool is only useful insofar as the marker is linked to a trait gene whose value is independent of the genome background into which it is placed. Our research is demonstrating that the usefulness of this tool for selecting certain agronomic traits is limited in soybean. Thus, different breeding strategies may be required.
Publications
- James H. Orf, Kevin Chase, James Specht, Ik-Young Choi, Perry B. Cregan, and Karl G. Lark (2005) Abnormal leaf formation in Soybean: Genetic and environmental effects. Submitted: Crop Science.
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Progress 10/01/02 to 09/30/03
Outputs
This progress report covers the period 08/01/2001 through 09/30/2003. Our objective is to understand the mechanism whereby interactions between QTLs serve to adapt inbred plants to their environment. The model system uses 3 large, related, recombinant inbred segregant soybean populations. All three populations have been characterized by more than 600 RFLP and SSR genetic markers as well as for values of agricultural traits in different environments. In the summer of 2001 we measured trait values for all three populations in the third common environment, completing our goal of three different common environments. A striking observation in this third environment was the variation between RI segregants for MF (leaflet number > 3) plants/row. At least ten QTLs were responsible for this trait, many of which interacted with each other. Expression of these was environment specific. The leaflet model system promises to be valuable in demonstrating the interactions of QTLs
with the genome on the one hand and the environment on the other. Principal component analysis of environments was undertaken using the different traits that had been measured. This type of analysis clearly separated environments into clusters differentiated by location, year or specific growth factors (irrigation or drought etc.). Due to a lack of available personnel during FY2003, expenditure was minimal and the project was extended for one year without additional funds. Completion of research during the third year is anticipated. Publication Summary: Tischner (2003) QTLs that regulate different parameters of seed set were identified. The numbers of ovules/pod and seeds/ovule (abortions) were measured in RI segregants of soybean, as were positions and developmental stages of abortions within pods. Abortions occurred most frequently in the basal position of the pod and embryo development either failed to or ceased growth just after cotyledon differentiation. QTLs in U11 were linked
to QTLs for flowering date, reproductive period and maturity. QTLs on U13 were linked to genes for sterility (Ms1, Ms6, or St5) and for disease resistance. One QTL on U22 was associated with a QTL for water use efficiency. A QTL on U3 linked to Lf1 that determined the number of ovules/pod, suggesting a common regulation of leaf and flower primordia. Song (2004) SSRs derived from genomic libraries are a superior source of polymorphic markers. The 420 newly developed SSRs were mapped in one or more of five soybean mapping populations. JoinMap was used to combine the five maps into an integrated genetic map spanning 2523.6 cM across 20 linkage groups that contained1849 markers, including 1015 SSRs, 709 RFLPs, 73 RAPDs, 24 classical traits, six AFLPs, ten isozymes, and 12 others. In the integrated map, SSR marker/map distance did not differ among 18 of the linkage groups, however, the SSRs were not uniformly spaced over a linkage group. clusters of SSRs with very limited recombination
were frequently present. These clusters of SSRs may be indicative of gene-rich regions of soybean. SSR markers from map-referenced BAC clones are an effective means of targeting markers to marker-scarce positions in the genome.
Impacts
Marker assisted selection of desired traits has been proposed as a major tool for improvement of agronomic crops including soybean. However, this tool is only useful insofar as the marker is linked to a trait gene whose value is independent of the genome background into which it is placed. Our research is demonstrating that the usefulness of this tool for selecting certain agronomic traits is limited in soybean. Thus, different breeding strategies may be required.
Publications
- Tischner, T., Allphin, L., Chase, K., Orf, J.H. and K.G. Lark (2003) Genetics of seed abortion and reproductive traits in soybean. Crop Sci. 43:464-473.
- Song, Q. J., L.F. Marek, R.C. Shoemaker, K.G. Lark, V.C. Concibido, X. Delannay, J.E. Specht and P.B. Cregan. 2004. A New Integrated Genetic Linkage Map of the Soybean . Theor. App. Genet. In press.
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