Bewick, P. | bioRxiv Science

bioRxiv2024

Long-read sequencing reveals novel structural variation markers for key agronomic and quality traits of soybean

In plant genomic research, long read sequencing has been widely used to detect structure variations that are not captured by short read sequencing. In this letter, we described an analysis of whole genome re-sequencing of 29 soybean varieties using nanopore long-read sequencing. The compiled germplasm reflects diverse applications, including livestock feeding, soy milk and tofu production, as well as consumption of natto, sprouts, and vegetable soybeans (edamame). We have identified 365,497 structural variations in these newly re-sequenced genomes and found that the newly identified structural variations are associated with important agronomic traits. These traits include seed weight, flowering time, plant height, oleic acid content, methionine content, and trypsin inhibitor content, all of which significantly impact soybean production and quality. Experimental validation supports the roles of predicted candidate genes and structural variant in these biological processes. Our research provides a new source for rapid marker discovery in crop genomes using structural variation and whole genome sequencing.

genomics↗

bioRxiv2022

Development of molecular markers of the KTI mutant alleles generated by CRISPR/Cas9-mediated mutagenesis in soybean

The digestibility of soybean meal can be severely impacted by trypsin inhibitor (TI), one of the most abundant anti-nutritional factors present in soybean seeds. TI can restrain the function of trypsin, a critical enzyme that breaks down proteins in the digestive tract. Soybean accessions with low TI content have been identified. However, it is challenging to breed the low TI trait into elite cultivars due to a lack of molecular markers associated with low TI traits. We identified Kunitz trypsin inhibitor 1 (KTI1, Glyma01g095000) and KTI3 (Glyma08g341500) as two seed-specific TI genes. Mutant kti1 and kti3 alleles carrying small deletions or insertions within the gene open reading frames were created in the soybean cultivar Glycine max cv. Williams 82 (WM82) using the CRISPR/Cas9-mediated genome editing approach. The KTI content and TI activity both remarkably reduced in kti1/3 mutants compared to the WM82 seeds. There was no significant difference in terms of plant growth or maturity days of kti1/3 transgenic and WM82 plants in greenhouse condition. We further identified a T1 line, #5-26, that carried double homozygous kti1/3 mutant alleles, but not the Cas9 transgene. Based on the sequences of kti1/3 mutant alleles in #5-26, we developed markers to co-select for these mutant alleles by using a gel-electrophoresis-free method. The kti1/3 mutant soybean line and associated selection markers will assist in accelerating the introduction of low TI trait into elite soybean cultivars in the future.

plant biology↗