Genomic changes underlying disease resistance and high protein QTL

Underlying genomic changes to disease resistance QTL cqSCN-006 and cqSCN-007 Soybean Cyst Nematode (SCN) is the most devastating pest of Glycine max (soybean). Currently control of SCN is through planting of non-host crops and the use of disease-resistant soybean germplasm containing resistance genes Rhg1 and Rhg4. Over-reliance on these sources necessitates identifying and characterizing new sources of resistance to SCN. CqSCN-006 and cqSCN-007 are both novel SCN resistance QTL that have been fine-mapped to a relatively narrow candidate gene region in the nearest ancestral relative, Glycine soja. In this study genomic changes were identified in candidate genes for the G. soja resistant line PI 468916 through examining whole genome sequence scaffolds and cloned fosmids. Compelling genomic changes in a gamma-SNAP in cqSCN-006 and CAF1 (chromosomal assembly factor 1) in cqSCN-007 are examined for their potential to be causative for SCN resistance in cqSCN-006 and cqSCN-007. Structural variation causes high protein phenotype in cqProt-003 In addition to the G. soja genotype PI 468916 having resistance to SCN, it also contains genes for increased protein production. Three genes have been annotated in the genetically defined interval cqProt-003 from PI 468916, which conveys a high protein phenotype. In two of these genes, Glyma.20G085200 and Glyma.20G85100, large structural variants were found. Markers were developed for these structural variants and a panel of accessions tested to determine correlation of the presence of the high-protein QTL and the genotype of the structural variants. The structural variant at Glyma.20G85100 followed the pattern of the high-protein QTL and was further investigated using linkage disequilibrium (LD) analysis, haplotype analysis, and stable transgenics expressing an RNAi hairpin construct. Seed protein in the stable transgenic plants was significantly higher in three of five segregating T3 populations studied when the transgene was detected. The structural variant between G. soja and G. max at Glyma.20G85100 was found to be an insertion into G. max (Williams 82) relative to G. soja (PI 468916), and was not found to be in LD with any of the surrounding SNPs. Haplotype analysis indicated that the PI 468916 genotype at this site (missing the insertion) was present in accessions which had Williams 82-like SNPs surrounding the variant. Additionally, examination for the sequence of the insertion showed evidence of transposon relatedness. Thus, the insertion at Glyma.20G85100 in G. max (Williams 82) caused a low protein phenotype in Williams 82, and at some frequency the sequence reverts to the ancestral PI468916 form, potentially through the excision of a mobile element, producing seed with higher protein levels.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Crop Sciences

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2020

Author dc:creator

• Fliege, Christina Elizabeth

Contributors dc:contributor

• Hudson, Matthew E.
• Vodkin, Lila
• Clough, Steve
• Diers, Brian

• soybean, genomics, protein, SCN,

Statement dc:rights

• Copyright 2019 Christina Fliege

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/106255

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/106255