Abstract
BackgroundTo elucidate features of seed development, we investigated the transcriptome of a soybean isoline from the germplasm collection that contained an introgressed allele known as minute hilum (mi) which confers a smaller hilum region where the seed attaches to the pod and also results in seed coat cracking surrounding the hilum region.ResultsRNAs were extracted from immature seed from an extended hilum region (i.e., the hilum and a small ring of tissue surrounding the hilum in which the cracks form) at three different developmental stages:10–25, 25–50 and 50–100 mg seed fresh weight in two independent replicates for each stage. The transcriptomes of these samples from both the Clark isoline containing the mi allele (PI 547628, UC413, iiR t mi G), and its recurrent Clark 63 parent isoline (PI 548532, UC7, iiR T Mi g), which was used for six generations of backcrossing, were compared for differential expression of 88,648 Glyma models of the soybean genome Wm82.a2. The RNA sequence data obtained from the 12 cDNA libraries were subjected to padj value < 0.05 and at least two-fold expression differences to select with confidence genes differentially expressed in the hilum-containing tissue of the seed coat between the two lines. Glyma.09G008400 annotated as encoding an ethylene forming enzyme, ACC oxidase (ACO), was found to be highly overexpressed in the mi hilum region at 165 RPKMs (reads per kilobase per million mapped reads) compared to the standard line at just 0.03 RPKMs. Evidence of changes in expression of genes downstream of the ethylene pathway included those involved in auxin and gibberellin hormone action and extensive differences in expression of cell wall protein genes. These changes are postulated to determine the restricted hilum size and cracking phenotypes.ConclusionsWe present transcriptome and phenotypic evidence that substantially higher expression of an ethylene-forming ACO gene likely shifts hormone balance and sets in motion downstream changes resulting in a smaller hilum phenotype and the cracks observed in the minute hilum (mi) isoline as compared to its recurrent parent.
Highlights
To elucidate features of seed development, we investigated the transcriptome of a soybean isoline from the germplasm collection that contained an introgressed allele known as minute hilum which confers a smaller hilum region where the seed attaches to the pod and results in seed coat cracking surrounding the hilum region
The present study focuses on the global expression changes occurring in a morphological seed coat variant, the minute hilum allele, found in UC413 (ii R t mi G), an isoline that results in a smaller hilum, the area of the seed coat immediately adjacent to the scar left by the funiculus that attaches the seed to its pod
Genetic background and phenotypic manifestation in the seed of minute hilum gene in the UC413 Clark isoline Figure 1 illustrates the phenotypes of the two Clark isolines, UC413 (ii R t mi G) and it’s recurrent parent line UC7 (Clark 63, ii R T Mi g) and Additional file 1 shows the Plant Introduction numbers, and relevant genotypes and phenotypes of the lines used in this study
Summary
To elucidate features of seed development, we investigated the transcriptome of a soybean isoline from the germplasm collection that contained an introgressed allele known as minute hilum (mi) which confers a smaller hilum region where the seed attaches to the pod and results in seed coat cracking surrounding the hilum region. The endosperm begins to degenerate and the cotyledons and embryo continue to grow for another 45 days and up to a maximum fresh weight of approximately 400–500 mg for the green seed. After that time dessication and yellowing proceeds until approximately 70 DAP, depending on the variety and maturity group with mature seeds of fresh weight of approximately 200 mg and 10% moisture content. During this process the seed coat (testa), which envelopes the cotyledons, develops from the ovule after fertilization and is essential in transferring assimilates and nutrients that allow the cotyledons to accumulate large amounts of storage proteins and oils in the soybean seed. Mutations affecting seed coat composition, structure, or morphology would likely affect its function
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