Association mapping for water use efficiency in soybean identifies previously reported and novel loci and permits genomic prediction.

Soybean is a major legume crop cultivated globally due to the high quality and quantity of its seed protein and oil. However, drought stress is the most significant factor that decreases soybean yield, and more than 90% of US soybean acreage is dependent on rainfall. Water use efficiency (WUE) is positively correlated with the carbon isotopic ratio C/C (C13 ratio) and selecting soybean varieties for high C13 ratio may enhance WUE and help improve tolerance to drought.

Identification of genomic regions associated with the plasticity of carbon 13 ratio in soybean.

Improving water use efficiency (WUE) for soybean [Glycine max (L.) Merr.] through selection for high carbon isotope (C13) ratio may increase drought tolerance, but increased WUE may limit growth in productive environments.

Genomic prediction models for traits differing in heritability for soybean, rice, and maize.

Background: Genomic selection is a powerful tool in plant breeding. By building a prediction model using a training set with markers and phenotypes, genomic estimated breeding values (GEBVs) can be used as predictions of breeding values in a target set with only genotype data. There is, however, limited information on how prediction accuracy of genomic prediction can be optimized.

Identification and Confirmation of Loci Associated With Canopy Wilting in Soybean Using Genome-Wide Association Mapping.

Drought causes significant soybean [ (L.) Merr.] yield losses each year in rain-fed production systems of many regions.

Identification of quantitative trait loci for carbon isotope ratio (δC) in a recombinant inbred population of soybean.

QTL analysis identified 16 QTLs, grouped in eight loci on seven soybean chromosomes that were associated with carbon isotope ratio (δC) in a biparental recombinant inbred population. Drought is a major limitation to soybean yield, and the frequency of drought stress is likely to increase under future climatic scenarios. Water use efficiency (WUE) is associated with drought tolerance, and carbon isotope ratio (δC) is positively correlated with WUE.

Genome-Wide Association Mapping of Dark Green Color Index using a Diverse Panel of Soybean Accessions.

Nitrogen (N) plays a key role in plants because it is a major component of RuBisCO and chlorophyll. Hence, N is central to both the dark and light reactions of photosynthesis. Genotypic variation in canopy greenness provides insights into the variation of N and chlorophyll concentration, photosynthesis rates, and N fixation in legumes.

Comparing Different Statistical Models and Multiple Testing Corrections for Association Mapping in Soybean and Maize.

Association mapping (AM) is a powerful tool for fine mapping complex trait variation down to nucleotide sequences by exploiting historical recombination events. A major problem in AM is controlling false positives that can arise from population structure and family relatedness. False positives are often controlled by incorporating covariates for structure and kinship in mixed linear models (MLM).

Estimation of a significance threshold for genome-wide association studies.

Background: Selection of an appropriate statistical significance threshold in genome-wide association studies is critical to differentiate true positives from false positives and false negatives. Different multiple testing comparison methods have been developed to determine the significance threshold; however, these methods may be overly conservative and may lead to an increase in false negatives. Here, we developed an empirical formula to determine the statistical significance threshold that is based on the marker-based heritability of the trait.

Genome-wide association mapping of canopy wilting in diverse soybean genotypes.

Genome-wide association analysis identified 61 SNP markers for canopy wilting, which likely tagged 51 different loci. Based on the allelic effects of the significant SNPs, the slowest and fastest wilting genotypes were identified. Drought stress is a major global constraint for crop production, and slow canopy wilting is a promising trait for improving drought tolerance.