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Editing of the of the gene model underlying the major protein quantitative trait loci (QTL), cqSeed protein-003, and its paralog in soybean

ABSTRACT: A major seed protein quantitative trait locus (QTL) in soybean resides on chromosome 20, cqSeed protein-003, which was recently mapped to gene model Glyma.20G085100 (Gm20P), with its paralog present on chromosome 10, Glyma.10G134400 (Gm10P). To gain insight into how Gm20P and GM10P influence seed reserve content in the crop, genome editing reagents were designed to create null mutations in both Gm20P and Gm10P. Two soybean lines were identified and characterized, possessing INDELs in Gm10P and Gm20P, and lacking editing reagents. One is a gm20p mutant, and the other is a gm10p gm20p double mutant. Seed protein content of the gm10p gm20p double mutant was significantly lower relative to the gm20p mutant and wildtype, with a concomitant increase in oil and starch content. A delayed maturity phenotype was observed in the single and dual edited lines under field settings across multiple environments. The delay in maturity phenotype was influenced by day length, wherein under a short-day environment, the delay mirrored what was observed under field conditions, while under a long-day environment, no delay in maturity was observed, but changes in growth were detected in the double mutant line. Transcriptomic analysis revealed repression of genes involved in light signaling and enhanced expression of JAZs alleles that repress JA signaling, suppression of ABA-responsive genes and senescence-related genes, and elevation of genes that inhibit IAA signaling in the gm10p gm20p double mutant. The status of a wide range of downstream transporter genes for transport of hormones, metabolites, heavy metals, and essential nutrients, nitrogen (N) and phosphorus (P), was significantly reformed as a result of altered interactions of light-phytohormone signaling in the double mutant. Furthermore, the double null mutant displayed higher sensitivity to salt and ABA during germination. These results suggest that both Gm10P and Gm20P alleles modulate light signaling, which in turn impacts soybean development, maturity, and seed reserve content.

ORGANISM(S): Glycine max

PROVIDER: GSE300521 | GEO | 2026/04/15

REPOSITORIES: GEO

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Project description:Molecular characterization of leaf development has not been well studied in soybean. Studies have shown that genomic regions controlling multifoliate leaf morphology in Glycine max also regulates important agronomic characters including yield, seed weight, seed number, shattering, plant growth, and flowering. Two soybean isolines that differed in leaf phenotype were profiled by high throughput RNA and small RNA (sRNA) sequencing. A Clark isoline, homozygous for a dominant mutant allele, Lf1, that specifies a five-foliate compound leaf was compared to wild type Clark that is homozygous for the standard allele that produces trifoliate leaves. Although Lf1 is dominant, it presents variable expressivity as the young plantlets with the Lf1Lf1 genotype initially have trifoliate leaves in the first few weeks, after which they transition to five-foliate leaves. At later developmental stages, they begin to produce four-foliate or trifoliate leaves. In RNA-Seq experiments, a total of 91 and 95 million reads were generated in each lane of Illumina sequencing for the shoot tip of wild type Clark standard (CS) and mutant Clark five-foliate (CF) libraries, respectively. Of these, ~70% million reads aligned to the 78,743 target Glyma models from the reference soybean genome (cv. Williams 82) with maximum of 3 mismatches and up to 25 alignments. Where as in vegetative bud, 56 (CS) to 59 (CF) million reads were produced and of these ~80% aligned to the soybean reference genome. The comparative studies of the transcript profiles of the wild-type versus mutant line revealed a number of differentially expressed genes. A total of 1,296 and 2,083 genes were up-regulated in the shoot tip of CS and CF, respectively that showed ≥2-fold expression difference. On the contrary in the vegetative bud, much smaller number of genes 14 (CS) and 94 (CF) showed increased transcript abundance. In sRNA analysis, a collection of 200,447 and 268,508 unique sRNA sequences isolated from shoot tip tissue of CS and CF were aligned to the soybean reference genome and their target glyma models were predicted using bioinformatics. This sRNA analysis at genome level reveals differences in size distribution of classes in the CS and CF. This study provides insight into the initial understanding of leaf development in soybean by revealing a number of genes and sRNAs differentially expressed between the CS and CF.

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Editing of the of the gene model underlying the major protein quantitative trait loci (QTL), cqSeed protein-003, and its paralog in soybean

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