Assessing myBaits Target Capture Sequencing Methodology Using Short-Read Sequencing for Variant Detection in Oat Genomics and Breeding.

The integration of target capture systems with next-generation sequencing has emerged as an efficient tool for exploring specific genetic regions with a high resolution and facilitating the rapid discovery of novel alleles. Despite these advancements, the application of targeted sequencing methodologies, such as the myBaits technology, in polyploid oat species remains relatively unexplored. In this study, we utilized the myBaits target capture method offered by Daicel Arbor Biosciences to detect variants and assess their reliability for variant detection in oat genomics and breeding. Ten oat genotypes were carefully chosen for targeted sequencing, focusing on specific regions on chromosome 2A to detect variants. The selected region harbors 98 genes. Precisely designed baits targeting the genes within these regions were employed for the target capture sequencing. We employed various mappers and variant callers to identify variants. After the identification of variants, we focused on the variants identified via all variants callers to assess the applicability of the myBaits sequencing methodology in oat breeding. In our efforts to validate the identified variants, we focused on two SNPs, one deletion and one insertion identified via all variant callers in the genotypes KF-318 and NOS 819111-70 but absent in the remaining eight genotypes. The Sanger sequencing of targeted SNPs failed to reproduce target capture data obtained through the myBaits technology. Similarly, the validation of deletion and insertion variants via high-resolution melting (HRM) curve analysis also failed to reproduce target capture data, again suggesting limitations in the reliability of the myBaits target capture sequencing using short-read sequencing for variant detection in the oat genome. This study shed light on the importance of exercising caution when employing the myBaits target capture strategy for variant detection in oats. This study provides valuable insights for breeders seeking to advance oat breeding efforts and marker development using myBaits target capture sequencing, emphasizing the significance of methodological sequencing considerations in oat genomics research.

The addition of magnesium sulfate and borax to urea reduced soil NH3 emissions but increased N2O emissions from soil with grass.

Nitrogen (N) use efficiency can be increased by the addition of substances to urea. Magnesium sulfate (MgSO4) and boron were considered as plant nutrients, while zeolite was used as soil conditioner. The addition of these substances may affect soil NH3 and N2O emissions, by increasing N use efficiency. We conducted an 30 days incubation experiment with ryegrass using fertilizer treatments (12 g N m-2) as follows: urea (U); urea + MgSO4 (UM); urea + MgSO4 + borax (UMB); zeolite + urea + MgSO4 (Z-UM); and zeolite + urea + MgSO4 + borax (Z-UMB). We measured NH3 and N2O emissions and the aboveground N uptake of ryegrass. Cumulative NH3 emissions of UM, UMB, Z-UM and Z-UMB were 10%, 53%, 21% and 58% lower than U, respectively, while their N2O emissions were 32%, 133%, 43% and 72% higher than U, respectively. Aboveground N uptake of UM, UMB, Z-UM and Z-UMB were 9%, 6%, 12% and 13% higher than U, respectively. Overall, we suggest that the addition of MgSO4 and borax were effective in reducing NH3 emissions and potentially increase plant N uptake. However, the risk of higher denitrification and N2O emissions also needs to be considered. This study reveals the considerable effect of MgSO4 and borax in soil N cycles. Future research should evaluate how the application of urea + MgSO4 + borax effects gaseous emissions and crop yield of dicotyledons and in drier soil conditions.