Using genome-wide association studies, 39 SNP markers likely tagging 21 different loci for carbon isotope ratio (δ (13) C) were identified in soybean. Water deficit stress is a major factor limiting soybean [Glycine max (L.) Merr.] yield. Soybean genotypes with improved water use efficiency (WUE) may be used to develop cultivars with increased yield under drought. A collection of 373 diverse soybean genotypes was grown in four environments (2 years and two locations) and characterized for carbon isotope ratio (δ(13)C) as a surrogate measure of WUE. Population structure was assessed based on 12,347 single nucleotide polymorphisms (SNPs), and genome-wide association studies (GWAS) were conducted to identify SNPs associated with δ(13)C. Across all four environments, δ(13)C ranged from a minimum of -30.55‰ to a maximum of -27.74‰. Although δ(13)C values were significantly different between the two locations in both years, results were consistent among genotypes across years and locations. Diversity analysis indicated that eight subpopulations could contain all individuals and revealed that within-subpopulation diversity, rather than among-subpopulation diversity, explained most (80%) of the diversity among the 373 genotypes. A total of 39 SNPs that showed a significant association with δ(13)C in at least two environments or for the average across all environments were identified by GWAS. Fifteen of these SNPs were located within a gene. The 39 SNPs likely tagged 21 different loci and demonstrated that markers for δ(13)C can be identified in soybean using GWAS. Further research is necessary to confirm the marker associations identified and to evaluate their usefulness for selecting genotypes with increased WUE.

Water deficit stress is a major factor limiting soybean [Glycine max (L.) Merr.] yield. High water use efficiency (WUE) offers a means to potentially ameliorate drought impact, but increased WUE is often associated with a reduction in transpiration (T) and an accompanied reduction in photosynthesis. This interdependence of T and photosynthesis is a major constraint in selection for high WUE by breeding programs. Measurement of genetic variability in WUE and T through carbon isotope ratio (δ13C) and oxygen isotope ratio (δ18O), respectively, could be important in identifying genotypes with high WUE that also have relatively high T, and thus higher rates of biomass production. This study's objective was to identify genomic regions associated with δ13C and δ18O. A diverse collection of 373 soybean genotypes was grown in four field environments, and whole‐plant samples collected at early reproductive growth were characterized for δ13C and δ18O. After quality assessment, 31,260 polymorphic single‐nucleotide polymorphism (SNP) markers with a minor allele frequency ≥5% were used for association analysis. Genome‐wide association analysis identified 54 environment‐specific SNPs associated with δ13C and 47 SNPs associated with δ18O. These SNP markers tagged 46 putative loci for δ13C and 21 putative loci for δ18O and may represent an important resource for pyramiding favorable alleles for drought tolerance and identifying genotypes with high WUE.

BackgroundThe Protein Disulfide Isomerase (PDI) gene family encodes several PDI and PDI-like proteins containing thioredoxin domains and controlling diversified metabolic functions, including disulfide bond formation and isomerisation during protein folding. Genomic, cDNA and promoter sequences of the three homoeologous wheat genes encoding the "typical" PDI had been cloned and characterized in a previous work. The purpose of present research was the cloning and characterization of the complete set of genes encoding PDI and PDI like proteins in bread wheat (Triticum aestivum cv Chinese Spring) and the comparison of their sequence, structure and expression with homologous genes from other plant species.ResultsEight new non-homoeologous wheat genes were cloned and characterized. The nine PDI and PDI-like sequences of wheat were located in chromosome regions syntenic to those in rice and assigned to eight plant phylogenetic groups. The nine wheat genes differed in their sequences, genomic organization as well as in the domain composition and architecture of their deduced proteins; conversely each of them showed high structural conservation with genes from other plant species in the same phylogenetic group. The extensive quantitative RT-PCR analysis of the nine genes in a set of 23 wheat samples, including tissues and developmental stages, showed their constitutive, even though highly variable expression.ConclusionsThe nine wheat genes showed high diversity, while the members of each phylogenetic group were highly conserved even between taxonomically distant plant species like the moss Physcomitrella patens. Although constitutively expressed the nine wheat genes were characterized by different expression profiles reflecting their different genomic organization, protein domain architecture and probably promoter sequences; the high conservation among species indicated the ancient origin and diversification of the still evolving gene family. The comprehensive structural and expression characterization of the complete set of PDI and PDI-like wheat genes represents a basis for the functional characterization of this gene family in the hexaploid context of bread wheat.

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