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Title:Identification of loci for resistance to Sclerotinia stem rot (white mold) in accessions of perennial relative of soybean (Glycine latifolia)
Author(s):Chang, Sungyul
Director of Research:Domier, Leslie L.
Doctoral Committee Chair(s):Domier, Leslie L.
Doctoral Committee Member(s):Hartman, Glen L.; Lambert, Kris N.; Ming, Ray R.; Brown, Patrick J.
Department / Program:Crop Sciences
Discipline:Crop Sciences
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):Genus Glycine
Glycine latifolia
Sclerotinia Stem Rot
White Mold
Single Nucleotide Polymorphisms (SNPs)
Comparative Genomics
Bioinfomatics
Disease Resistant
Quantitative Trait Locus (QTL)
Next Generation Sequencing
Abstract:Like many widely cultivated crops, soybean (Glycine max) has a relatively narrow genetic base, while its perennial relatives in the subgenus Glycine are more genetically diverse and display desirable traits not present in cultivated soybean. To identify single nucleotide polymorphisms (SNPs) between a pair of G. latifolia accessions that were resistant or susceptible to Sclerotinia sclerotiorum, reduced-representations of DNAs from each accession were sequenced. Sequence reads aligned primarily to gene-rich euchromatic regions on the distal arms of G. max chromosomes. Using the G. max genome sequence as a reference, 9,303 G. latifolia SNPs were identified that aligned to unique positions in the G. max genome. A subset of the SNPs were validated using nine TaqMan and 384 GoldenGate allele-specific assays and analyzed in F2 G. latifolia populations and used to generate genetic linkage maps for G. latifolia, the first genetic maps for any perennial Glycine species. Subsequently, high-density linkage maps were constructed for G. latifolia using SNP markers generated by genotyping by sequencing and evaluated in F2 and F5 populations. In each population, greater than 2,300 SNP markers segregated to form 20 large linkage groups (LGs). Twelve of the 20 G. latifolia linkage groups were nearly collinear with G. max chromosomes. The remaining eight G. latifolia LGs appeared to be products of multiple interchromosomal translocations relative to G. max. Large syntenic blocks also were observed between G. latifolia and Phaseolus vulgaris. These experiments were the first to compare genome organizations among annual and perennial Glycine species and common bean. To identify loci associated with resistance to Sclerotinia stem rot (SSR) in G. latifolia, the F2 and F5 populations were evaluated for their sensitivities to oxalic acid, a pathogenicity determinant for S. sclerotiorum. Major loci for tolerance to oxalic acid were discovered on G. latifolia LGs 14 and 19. The loci on LGs 14 and 19 explained 26% and 27% of the phenotypic variation for the trait, respectively. The locus on G. latifolia LG 19, but not the locus on LG14, overlapped a previously described locus in soybean for resistance to SSR. The sequences of G. latifolia chromosomes corresponding to the genetic intervals on LGs 14 and 19 contained 10 and 68 predicted genes, respectively. These experiments demonstrated that it is possible to identify loci for agronomically important traits in wild perennial relatives of soybean that are not present in the soybean primary gene pool. A draft genome sequence was assembled for G. latifolia form short-insert paired-end libraries and large-insert mate-pair libraries prepared from G. latifolia DNA and sequenced on an Illumina HiSeq2000. The libraries were assembled with ALLPaths-LG and yielded 85% coverage of the estimated 1.05 Gb G. latifolia genome. Whole-genome annotation indicated that G. latifolia shared 33,000 to 41,000 genes with soybean. The G. latifolia genome was predicted to contain 750 resistance gene homologues 93% of which were shared with soybean. A nearly complete pseudomolecule chromosome sequence was assembled for G. latifolia chromosome 6 using soybean chromosome 6 as a guide. The information generated will assist in discovery of genetic diversity for traits that are lacking in soybean germplasm. The development of molecular resources for species closely related to G. max provides information into the evolution of genomes within the genus Glycine and tools to identify genes within perennial wild relatives of cultivated soybean that could be beneficial to soybean production.
Issue Date:2015-01-21
URI:http://hdl.handle.net/2142/72963
Rights Information:Copyright 2013 Chang et al, Creative Commons 2014 Chang et al
Date Available in IDEALS:2015-01-21
Date Deposited:2014-12


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