Large scale deletion and rebalancing within the k1C kafirin family in sorghum

Tyler W. Ferris¹Preston J. Hurst¹Abou Yobi²Bara Alartouri¹Aixia Li³Ruthie Angelovici²Tom Clemente¹David Richard Holding^1*

• ¹University of Nebraska-Lincoln, Lincoln, United States
• ²University of Missouri, Columbia, United States
• ³Shandon Agricultural University, Shandon, China

Sorghum bicolor (L.) Monech (sorghum) is cultivated as food for humans and livestock and is valued for its low input requirements. However, sorghum grain protein is deficient in the essential amino acid lysine and has poor protein digestibility. This is because of the highly abundant proline-rich kafirins that constitute >70% of proteins and form low-digestibility protein bodies. To reduce kafirin expression in the endosperm and elicit wholesale proteome rebalancing to increase non-kafirin proteins, a single-guide RNA (sgRNA) Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9) construct was previously used to target members of the highly-repetitive alpha-kafirin family, k1C in RTx430 sorghum. The current study was conceived to evaluate nutritional and biophysical characteristics of two sorghum lines with k1C family deletions compared to unedited RTx430. Despite confirming a ~400 kb deletion in the k1C family of both edited lines encompassing seven active genes, we observed no significant decrease in k1C expression or compensatory increase in non-kafirin proteins. We observed a significant increase in protein-bound amino acids in both k1C-deleted lines and in both edited lines relative to unedited RTx430 which increased total seed protein in one line. Protein bodies were observed to be more irregularly shaped with seeds retaining wild-type levels of vitreous endosperm. RNA IsoSeq was performed to measure k1C family gene expression and capture differentially-expressed non-kafirin genes. We observed that five k1C members had biologically significant expression with only two of the residual, non-deleted k1C genes having elevated expression in lines with the deletion. The results of this study demonstrate the ability of CRISPR/Cas9 editing of kafirins to elicit changes to the amino acid profile of sorghum and increase protein. Moreover, the results demonstrate an extreme example of the ability of highly repetitive genome regions such as the k1C subfamily to compensate the effects of CRISPR-induced multigene deletions.