Single Nucleotide Polymorphism (SNP) Marker-Assisted Breeding and Stability Analysis of Low Phytate Soybean.

Lowering phytate concentration in soybean [Glycine max (L.) Merr] has become a growing concern to breeders in the United States. This phytate or myo-inositol-1,2,3,4,5,6-hexakisphosphate is a stored form of phosphorus in the soybean seed that cannot be digested by livestock with monogastric digestive systems. The inability of complete phytate digestion has contributed to phosphorus contamination and eutrophication of fresh water due to leeching and run-off. Additionally, phytate chelates with several other minerals essential to livestock health, creating deficiencies despite the presence of these minerals in livestock diets. The Satt237 and Satt561 simple sequence repeat markers (SSRs) were discovered to be linked to confirmed quantitative trait loci cqPha-001 and cqPha-002 for phytate levels in soybean seed. Recently perfect single nucleotide polymorphisms (SNPs), derived from DNA sequence, have been developed for those loci.

The objective of this study was to use SSRs and SNPs to introgress the low phytate, high inorganic phosphorous (Pi) loci to a high yielding genetic background and to test the stability of seed phytate content over a broad range of environments. We developed the low phytate high Pi line TN09-239 through four generations of molecular backcrossing to the high yielding recurrent parent cultivar 5601T. The line CX1834-1-2 served as the donor of the two recessive alleles for low phytate high Pi. TN09-239 was evaluated compared to its recurrent parent 5601T at 11 locations in the USDA Southern Regional Test. In a companion study at three Tennessee locations (the East Tennessee Research and Education Center at Knoxville, TN, the Highland Rim Research and Education Center at Springfield, TN, and the Research and Education Center at Milan, TN), lines TN09-239, TN07-602, TN07-604, and 5601T, representing BC4, BC3, BC2, and recurrent parent were evaluated. In the USDA test, TN09-239 was equivalent to 5601T for seed protein and oil concentration. The low phytate line TN09-239 has significantly higher Pi (1,959 ng P µL^-1) than 5601T (170 ng P µL^-1). The Pi for TN09-239 ranged from a low of 1,380 ng P µL^-1 at Rohwer, AR to a high of 2,555 ng P µL^-1 at Jackson, TN. In the study at three Tennessee locations, lines TN09-239, TN07-602, TN07-604, and 5601T had Pi concentrations of 1,967, 330, 742, and 176 ng P µL^-1, respectively. Molecular backcrossing using the SNP markers was effective in introgressing the low phytate high Pi trait to an elite genetic background.