Genomic and genetic resource for soybean disease resistance improvement

Glycine latifolia (Benth.) Newell & Hymowitz (2n=40), one of the 27 wild perennial relatives of soybean, possesses genetic diversity and agronomically favorable traits that are lacking in soybean. The first chapter describes 939-Mb draft genome assembly of G. latifolia (PI 559298) using exclusively linked-reads sequenced from a single Chromium library. We organized scaffolds into 20 chromosome-scale pseudomolecules utilizing two genetic maps and the Glycine max (L.) Merr. genome sequence. High copy numbers of putative 91-bp centromere-specific tandem repeats were observed in consecutive blocks within predicted pericentromeric regions on several pseudomolecules. No evidence of 92-bp centromeric repeats, which are abundant in G. max, were detected in G. latifolia or G. tomentella. Annotation of the assembled genome yielded 64,692 protein-coding loci. A total of 304 putative nucleotide-binding site (NBS)-leucine-rich-repeat (LRR) genes were identified in this genome assembly. Different from other legume species, we observed a scarcity of TIR-NBS-LRR genes in G. latifolia. The whole genome sequence and annotation of G. latifolia provides a valuable source of alternative alleles and novel genes to facilitate soybean improvement. This study also highlights the efficacy and cost-effectiveness of the application of Chromium linked-reads in diploid plant genome de novo assembly. With the growing knowledge of the vital regulatory role of miRNAs in gene expression over the past two decades, there has been great interest to identify both conserved and novel miRNAs in response to environmental signals and biotic stresses in plants. To date, no study has been carried out describing the composition of miRNAs in any wild perennial relatives of soybean. In this study, we provided the first profile of miRNAs in G. latifolia by sequencing a small RNA library constructed using multiple tissues. A total of 40 conserved miRNA families representing 169 MIR genes were identified, including a number of previously identified stress-responsive miRNAs. In addition, 16 novel miRNAs that could not be assigned to a previously established family ID were detected. Comparison analysis against G. max, Medicago truncatula, and Arabidopsis thaliana, revealed nine Glycine-specific miRNA families. Gene targets of pre-identified miRNAs were also predicted using degradome sequencing reads as the direct evidence of decayed mRNAs. Two prediction tools yielded two distinct nonoverlapping sets of targets. Our findings on miRNAs in G. latifolia add to our knowledge of small regulatory RNAs in legumes and may provide insights into the development of a novel approach to improve soybean biotic and abiotic stress resistance. Soybean mosaic virus (SMV) causes significant reductions in soybean yield and seed quality. In North America, seedborne infections are the primary sources of inoculum for SMV infections. Therefore, host-plant resistance to SMV seed transmission provides a means to limit the impacts of SMV on soybean production. In this study, two diverse population panels composed of 409 and 199 plant introductions from the United States Department of Agriculture Soybean Germplasm Collection were evaluated for seed transmission rates, seed coat mottling, and seed number impacted by SMV infection using two different SMV strains. To identify loci associated with the traits, the phenotypic data and single nucleotide polymorphism (SNP) data from the SoySNP50K dataset were analyzed using R packages, GAPIT and rrBLUP. A single significant locus for SMV seed transmission was identified on chromosome (chr) 9 in the first population. The high LD region on chr 9 contained a predicted nonsense-mediated RNA decay gene and multiple pectin methylesterase inhibitor (PMEI) genes, which are involved in restricting virus movement in plants. Two loci were significantly associated with degree of SMV-induced seed coat mottling, one on chr 3 and one on chr 9. The high LD regions on chr 3 and 9 contained predicted PMEI genes and the chalcone synthase 6 (CHS6) gene, respectively. CHS6 is involved in stress-induced anthocyanin biosynthesis, which could be involved in seed-coat mottling. Additionally, two loci associated with seed number index were identified in the second population. One of these two loci confirmed one quantitative trait locus (QTL) associated with seed number in a previous linkage mapping study, suggesting high efficacy of GWAS at identifying novel loci and confirming linkage mapping results. Marker-assisted selection and genomic selection (GS) were compared for prediction accuracy of SMV seed transmission rate. This study provides the most comprehensive analysis of loci associated with seed transmission of an economically important plant virus