Linkage analysis and residual heterozygotes derived near isogenic lines reveals a novel protein quantitative trait loci from a Glycine soja accession

Authors: YANG, YIA - University Of Missouri; LA, THANG - University Of Missouri; Gillman, Jason; LYU, ZHEN - University Of Missouri; JOSHI, TRUPTI - University Of Missouri; USOVSKY, MARIOLA - University Of Missouri; Song, Qijian; SCABOO, ANDREW - University Of Missouri

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/7/2022
Publication Date: 7/29/2022
Citation: Yang, Y., La, T., Gillman, J.D., Lyu, Z., Joshi, T., Usovsky, M., Song, Q., Scaboo, A. 2022. Linkage analysis and residual heterozygotes derived near isogenic lines reveals a novel protein quantitative trait loci from a Glycine soja accession. Frontiers in Plant Science. 13. Article 938100. https://doi.org/10.3389/fpls.2022.938100.
DOI: https://doi.org/10.3389/fpls.2022.938100

Interpretive Summary: The soybean crop is an economic powerhouse due to its high seed yield, its ability to fix nitrogen and oil and protein rich seeds valuable for human and animal nutrition. Despite these boons, soybean suffers from very low genetic diversity compared to many crop species, in large part due to its self-pollinating floral biology. This lack of genetic diversity has been made worse by events that occurred during domestication, the introduction of soybean to the United States and early soybean breeding. To ensure long-term genetic gain potential for seed yield and nutritional potential, we developed wild soybean derived populations and performed genetic analysis. We identified several novel genomic regions correlated with changes in seed protein and oil content. One genomic region was identified that increased seed protein levels (+0.7%) but had no significant impact on seed oil content. This finding was in stark contrast to many other sources of elevated seed protein which have significant costs in terms of seed oil and/or seed yield. We validated our finding by further population development, which allowed us to narrow down to allow candidate genes to be identified. We also developed new molecular biology selection tools to streamline breeding for this new protein gene. Our results will enable higher protein content soybean germplasm/cultivars, and a wealth of new genetic information may enable us to clone the direct molecular genetic cause behind this trait in the near future.

Technical Abstract: Modern soybean [Glycine max (L.) Merr] cultivars have low overall genetic variation due to repeated bottleneck events that arose during domestication and from selection strategies typical of many soybean breeding programs. In both public and private soybean breeding programs, the introgression of wild soybean (Glycine soja Siebold and Zucc.) alleles is a viable option to increase genetic diversity and identify new sources for traits of value. The objectives of our study were to examine the genetic architecture responsible for seed protein and oil using a recombinant inbred line (RIL) population derived from hybridizing a G. max line (‘Osage’) with a G. soja accession (PI 593983). Linkage mapping identified a total of seven significant quantitative trait loci on chromosomes 14 and 20 for seed protein and on chromosome 8 for seed oil with LOD scores ranging from 5.3 to 31.7 for seed protein content and from 9.8 to 25.9 for seed oil content. We analyzed 3,015 single F4:9 soybean plants to develop two residual heterozygotes derived near isogenic lines (RHD-NIL) populations by targeting nine SNP markers from genotype-by-sequencing, which corresponded to two novel quantitative trait loci (QTL) derived from G. soja: one for a novel seed oil QTL on chromosome 8 and another for a novel protein QTL on chromosome 14. Single marker analysis and linkage analysis using 50 RHD-NILs validated the chromosome 14 protein QTL, and whole genome sequencing of RHD-NILs allowed us to reduce the QTL interval from ~16.5 to ~4.6 Mbp. We identified two genomic regions based on recombination events which had significant increases of 0.65 and 0.72% in seed protein content without a significant decrease in seed oil content. A new Kompetitive allele-specific polymerase chain reaction (KASP) assay, which will be useful for introgression of this trait into modern elite G. max cultivars, was developed in one region. Within the significantly associated genomic regions, a total of eight genes are considered as candidate genes, based on the presence of gene annotations associated with the protein or amino acid metabolism/movement. Our results provide better insights into utilizing wild soybean as a source of genetic diversity for soybean cultivar improvement utilizing native traits.