Identification and characterization of the soybean IPK1 ortholog of a low phytic acid mutant reveals an exon-excluding splice-site mutation.
Phytic acid (myo-inositol 1, 2, 3, 4, 5, 6 hexakisphosphate) is an important constituent of soybean meal. Since phytic acid and its mineral salts (phytates) are almost indigestible for monogastrics, their abundance in grain food/feed causes nutritional and environmental problems; interest in breeding low phytic acid has therefore increased considerably. Based on gene mapping and the characteristics of inositol polyphosphates profile in the seeds of a soybean mutant line Gm-lpa-ZC-2, the soybean ortholog of inositol 1,3,4,5,6 pentakisphosphate (InsP(5)) 2-kinase (IPK1), which transforms InsP(5) into phytic acid, was first hypothesized as the candidate gene responsible for the low phytic acid alteration in Gm-lpa-ZC-2. One IPK1 ortholog (Glyma14g07880, GmIPK1) was then identified in the mapped region on chromosome 14. Sequencing revealed a G → A point mutation in the genomic DNA sequence and the exclusion of the entire fifth exon in the cDNA sequence of GmIPK1 in Gm-lpa-ZC-2 compared with its wild-type progenitor Zhechun No. 3. The excluded exon encodes 37 amino acids that spread across two conserved IPK1 motifs. Furthermore, complete co-segregation of low phytic acid phenotype with the G → A mutation was observed in the F(2) population of ZC-lpa x Zhexiandou No. 4 (a wild-type cultivar). Put together, the G → A point mutation affected the pre-mRNA splicing and resulted in the exclusion of the fifth exon of GmIPK1 which is expected to disrupt the GmIPK1 functionality, leading to low phytic acid level in Gm-lpa-ZC-2. Gm-lpa-ZC-2, would be a good germplasm source in low phytic acid soybean breeding.
Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
Feng-Jie
FJ
Yuan
Dan-Hua
DH
Zhu
Yuan-Yuan
YY
Tan
De-Kun
DK
Dong
Xu-Jun
XJ
Fu
Shen-Long
SL
Zhu
Bai-Quan
BQ
Li
Qing-Yao
QY
Shu
D001483:Base Sequence; D003433:Crosses, Genetic; D018076:DNA, Complementary / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D005091:Exons / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics; D006720:Homozygote; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics*; D010641:Phenotype; D010710:Phosphates / Q000378:metabolism; D017853:Phosphotransferases (Alcohol Group Acceptor) / Q000235:genetics; D020161:Physical Chromosome Mapping; D010833:Phytic Acid / Q000378:metabolism*; D022821:RNA Splice Sites / Q000235:genetics*; D012639:Seeds / Q000235:genetics / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D013025:Glycine max / Q000196:embryology / Q000201:enzymology* / Q000235:genetics*; D014158:Transcription, Genetic
D018076:DNA, Complementary; D018744:DNA, Plant; D010710:Phosphates; D022821:RNA Splice Sites; D010833:Phytic Acid; D017853:Phosphotransferases (Alcohol Group Acceptor)