Branch angle variation in parent lines
The two parental lines, LD00-3309 and RIL1890 display clear distinction in branch angle (Fig. 1). The average branch angle of the NBA line LD00-3309, is 66.8ᵒ ± 2.2ᵒ, while the average branch angle of the WBA line RIL 1890 is 132.0ᵒ ± 2.4ᵒ. This large phenotypic difference developed over the course of the growing season, with no clear difference observed during the first six weeks after planting. The difference in branch angles between the two parental lines became apparent at 8 and 11 weeks after planting, and the phenotypic difference was most obvious at 20 weeks after planting when the leaves had fallen off and the plants were fully mature.
Mapping of the QTL, qGmBa1, modulating branch angle using a bi-parental F2 population and F3 progeny
The F2 population derived from LD00-3309 and RIL 1890 also showed large variations in branch angle; nevertheless, the majority of the F2 individuals appeared to possess branch angles similar to the two parent lines. Thus, we simply categorized the F2 plants as either WBA or NBA, when they possessed branch angles greater or less than 90ᵒ, respectively. Of 147 F2 plants, 101 were classified as WBA while 46 were classified as NBA (Fig. 2A). This fits a 3:1 phenotypic segregation ratio (χ2 = 3.10, p = 0.08), suggesting that a single major locus is responsible for the branch angle variation observed in this population.
QTL mapping for branch angle was conducted using the phenotypic data of the 147 F2 plants and their genotypes at the 1,132 polymorphic SNP sites across the 20 soybean chromosomes. Consistent to the inheritance pattern, only a single major QTL modulate branch angle was detected (Fig. 2B). This QTL, designated qGmBa1, is located on the short arm of chromosome 19 and could explain 55% of the total phenotypic variation in the mapping population. SNP marker ss715633059 (physical position based on the version 2 assembly: chr19_1163245 (Chr19:1,163,245bp) had the highest LOD value, 30.72, while marker chr19_922646 (Chr19:922,646) and marker chr19_1855442 (Chr19:1,855,442) defined boundaries of this QTL based on the 1.5 LOD drop method (Fig. 2C).
We further compared the average branch angle scores of the F3 families derived from the (LD00-3309 × RIL 1890) F2 plants of the three genotypes at the peak marker chr19_1163245 (Fig. 3). F3 plants with the LD00-3309 genotype (GG) had a score (66.8ᵒ ± 13.0ᵒ) that is very close to that (66.8ᵒ ± 2.2ᵒ) of LD00-3309, while F3 plants with the RIL1890 genotype (AA) had a score (132.0ᵒ ± 15.5ᵒ) that is very close to that (132.0ᵒ ± 2.4ᵒ) of RIL1890. We did not measure the branch angles of (LD00-3309 × RIL 1890) F1 plants as they were grown in the greenhouse, but the F3 plants with the (A/G) genotype had a score (129.3 ᵒ ± 26.5ᵒ) that was close to that of the F3 plants with the (A/A) genotype. These observations further support the single-gene inheritance pattern of branch angle and that WBA is dominant over NBA.
qGmBa1 was also identified by QTL mapping using a bi-parental RIL population
To determine whether the phenotypic variation in branch angle among cultivated soybeans is also modulated by qGmBa1, we performed QTL mapping using 140 RILs derived from a WBA landrace, PI437169B, and an NBA elite cultivar, IA3023, which form one of 40 subpopulations of the SoyNAM population. The same criteria described above were used to phenotype branch angles of the (PI437169B × IA3023) RILs, and this phenotypic data was integrated with the available genotyping data for the 140 RILs and two parent lines (Soybase.org/SoyNAM/). This identified a single major QTL on chromosome 19, which is defined by marker chr19_1286696 (Chr19:1,286,696) at the left boundary. The next marker is Chr19_3291531, but LOD declines well before this, putting the right QTL boundary around 2 megabases. This QTL overlaps with the qGmBa1 region defined by the (LD00-3309 ⋅ RIL1890) population, suggesting they are the same QTL.