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Yang Y, La TC, Gillman JD, Lyu Z, Joshi T, Usovsky M, Song Q, Scaboo A. Linkage analysis and residual heterozygotes derived near isogenic lines reveals a novel protein quantitative trait loci from a Glycine soja accession. Front Plant Sci 2022; 13:938100. [PMID: 35968122 PMCID: PMC9372550 DOI: 10.3389/fpls.2022.938100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
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.
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Affiliation(s)
- Yia Yang
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Thang C. La
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Jason D. Gillman
- Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Columbia, MO, United States
| | - Zhen Lyu
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, United States
| | - Trupti Joshi
- Department of Health Management and Informatics, MU Institute of Data Science and Informatics and Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO, United States
| | - Mariola Usovsky
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Andrew Scaboo
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
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