Environmental and genetic regulation of plant height in soybean.

BACKGROUND: Shoot architecture is fundamentally crucial to crop growth and productivity. As a key component of shoot architecture, plant height is known to be controlled by both genetic and environmental factors, though specific details remain scarce. RESULTS: In this study, 308 representative soybean lines from a core collection and 168 F9 soybean progeny were planted at distinct field sites. The results demonstrated the presence of significant genotype × environment interaction (G × E) effects on traits associated with plant height in a natural soybean population. In total, 19 loci containing 51 QTLs (quantitative trait locus) for plant height were identified across four environments, with 23, 13 and 15 being QTLs for SH (shoot height), SNN (stem node number) and AIL (average internode length), respectively. Significant LOD ranging from 2.50 to 16.46 explained 2.80-26.10% of phenotypic variation. Intriguingly, only two loci, Loc11 and Loc19-1, containing 20 QTLs, were simultaneously detected across all environments. Results from Pearson correlation analysis and PCA (principal component analysis) revealed that each of the five agro-meteorological factors and four soil properties significantly affected soybean plant height traits, and that the corresponding QTLs had additive effects. Among significant environmental factors, AD (average day-length), AMaT (average maximum temperature), pH, and AN (available nitrogen) had the largest impacts on soybean plant height. Therefore, in spite of uncontrollable agro-meteorological factors, soybean shoot architecture might be remolded through combined efforts to produce superior soybean genetic materials while also optimizing soil properties. CONCLUSIONS: Overall, the comprehensive set of relationships outlined herein among environment factors, soybean genotypes and QTLs in effects on plant height opens new avenues to explore in work aiming to increase soybean yield through improvements in shoot architecture.

Identification and mapping of two independent recessive loci for the root hairless mutant phenotype in soybean.

KEY MESSAGE: Two functional complementation QTLs were identified for root hairless formation in soybean. Root hairs play critical roles not only in nutrient/water uptake from soils, but also in plant-microorganism interactions. However, genetic information about root hair development remains fragmented. We previously identified a soybean natural mutant (RBC-HL) with the root hairless (HL) phenotype. In order to reveal the genetic basis for this phenotype, a polymorphic population was constructed using RBC-HL and a genotype (RBC-NH) with normal root hairs (NH). Three representative phenotypes of root hair formation were observed in the progeny, including NH, medium (MH) and HL. All F1 plants were of the NH type, and the respective segregation ratios in F2, F2:3 and RIL (F5:7) plants fit the theoretical ratio of 15:1, 7:8:1 and 3:1, indicating that the HL mutation is controlled by two independent recessive loci. In order to map HL-associated loci, a high-density genetic map was constructed using 8784 bin markers covering a total genetic distance of 3108.2 cM, and an average distance between adjacent markers of 0.4 cM. Two major QTLs, qRHLa and qRHLb, were identified and mapped on chromosome 01 and 11, and further delimited to interval regions of ~ 289 kb and ~ 1120 kb, respectively. Phylogenetic analysis suggested that the two candidate regions originated from soybean duplication events, where seven pairs of homologous genes shared 86-97% sequence identify. In conclusion, we partially uncovered the genetic mechanism underlying root hair formation in soybean. Namely, two independent recessive loci, qRHLa and qRHLb, containing several candidate genes were predicted to control the root hairless mutant RBC-HL.

Genetic analysis and fine mapping of phosphorus efficiency locus 1 (PE1) in soybean.

KEY MESSAGE: PE1 is a valuable locus synergistically regulating both P acquisition and utilization efficiency. Phosphorus (P) is required for crop production, particularly for soybean, due to its high protein and oil contents, and large demands for P in biological nitrogen fixation. Therefore, enhancing P efficiency is a practical and important target for soybean-breeding programs; however, the genetic mechanisms are still unclear. Previously, we identified a phosphorus efficiency locus 1 (PE1) in soybean through field evaluation. Here, fine mapping of PE1 was conducted in field using an expanded RIL population containing 168 F9:11 families derived from the same parents, BX10 and BD2. A high-resolution genetic map covering a 67.39 cM genetic region in a ~ 20.1 M physical region was constructed using 117 bin markers from chromosome 11, and scaffolds-21 and -32. The results revealed that PE1 was comprised of 15 QTLs for 11 of 18 tested traits, all of which could be detected under both P-deficient and P-sufficient conditions. Through map-based cloning, PE1 was further delimited to a 200-kb region located on scaffold-32, where 16 candidate genes were predicted for the PE1 locus. A set of NILs were also evaluated in P-deficient field conditions, with the results that P content and grain yield were 27.9% and 74.8% higher, respectively, and 25.4% more P was allocated to reproductive tissues in #pe1 than in #PE1 plants. The results herein suggest that PE1 is a valuable locus underlying both P absorption and utilization efficiency, which may be directly applicable in breeding programs seeking to develop elite P-efficient soybean varieties.

Genetic Analysis and Mapping of QTLs for Soybean Biological Nitrogen Fixation Traits Under Varied Field Conditions.

Soybean is an important economic and green manure crop that is widely used in intercropping and rotation systems due to its high biological nitrogen fixation (BNF) capacity and the resulting reduction in N fertilization. However, the genetic mechanisms underlying soybean BNF are largely unknown. Here, two soybean parent genotypes contrasting in BNF traits and 168 F9:11 recombinant inbred lines (RILs) were evaluated under four conditions in the field. The parent FC1 always produced more big nodules, yet fewer nodules in total than the parent FC2 in the field. Furthermore, nodulation in FC1 was more responsive to environmental changes than that in FC2. Broad-sense heritability (h2 b ) for all BNF traits varied from 0.48 to 0.87, which suggests that variation in the observed BNF traits was primarily determined by genotype. Moreover, two new QTLs for BNF traits, qBNF-16 and qBNF-17, were identified in this study. The qBNF-16 locus was detected under all of the four tested conditions, where it explained 15.9-59.0% of phenotypic variation with LOD values of 6.31-32.5. Meanwhile qBNF-17 explained 12.6-18.6% of observed variation with LOD values of 4.93-7.51. Genotype group analysis indicated that the FC1 genotype of qBNF-16 primarily affected nodule size (NS), while the FC2 genotype of qBNF-16 promoted nodule number (NN). On the other hand, the FC1 genotype of qBNF-17 influenced NN and the FC2 genotype of qBNF-17 impacted NS. The results on the whole suggest that these two QTLs might be valuable markers for breeding elite soybean varieties with high BNF capacities.