Michael B. Kantar

A Roadmap for Functional Structural Variants in the Soybean Genome

Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared with genes that have not retained paralogs. Increases in gene copy number, similar to that described at the Rhg1 resistance locus, account for approximately one-fourth of the genic SV events. This assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits.

Ecogeography and utility to plant breeding of the crop wild relatives of sunflower (Helianthus annuus L.)

Crop wild relatives (CWR) are a rich source of genetic diversity for crop improvement. Combining ecogeographic and phylogenetic techniques can inform both conservation and breeding. Geographic occurrence, bioclimatic, and biophysical data were used to predict species distributions, range overlap and niche occupancy in 36 taxa closely related to sunflower (Helianthus annuus L.). Taxa lacking comprehensive ex situ conservation were identified. The predicted distributions for 36 Helianthus taxa identified substantial range overlap, range asymmetry and niche conservatism. Specific taxa (e.g., Helianthus deblis Nutt., Helianthus anomalus Blake, and Helianthus divaricatus L.) were identified as targets for traits of interest, particularly for abiotic stress tolerance, and adaptation to extreme soil properties. The combination of techniques demonstrates the potential for publicly available ecogeographic and phylogenetic data to facilitate the identification of possible sources of abiotic stress traits for plant breeding programs. Much of the primary genepool (wild H. annuus) occurs in extreme environments indicating that introgression of targeted traits may be relatively straightforward. Sister taxa in Helianthus have greater range overlap than more distantly related taxa within the genus. This adds to a growing body of literature suggesting that in plants (unlike some animal groups), geographic isolation may not be necessary for speciation.

Vitamin variation in capsicum spp. Provides opportunities to improve nutritional value of human diets

Chile peppers, native to the Americas, have spread around the world and have been integrated into the diets of many cultures. Much like their heat content, nutritional content can vary dramatically between different pepper types. In this study, a diverse set of chile pepper types were examined for nutrient content. Some pepper types were found to have high levels of vitamin A, vitamin C, or folate. Correlations between nutrient content, species, cultivation status, or geographic region were limited. Varietal selection or plant breeding offer tools to augment nutrient content in peppers. Integration of nutrient rich pepper types into diets that already include peppers could help combat nutrient deficiencies by providing a significant portion of recommended daily nutrients.

Co-expression of soybean Dicer-like genes in response to stress and development

Regulation of gene transcription and post-transcriptional processes is critical for proper development, genome integrity, and stress responses in plants. Many genes involved in the key processes of transcriptional and post-transcriptional regulation have been well studied in model diploid organisms. However, gene and genome duplication may alter the function of the genes involved in these processes. To address this question, we assayed the stress-induced transcription patterns of duplicated gene pairs involved in RNAi and DNA methylation processes in the paleopolyploid soybean. Real-time quantitative PCR and Sequenom MassARRAY expression assays were used to profile the relative expression ratios of eight gene pairs across eight different biotic and abiotic stress conditions. The transcriptional responses to stress for genes involved in DNA methylation, RNAi processing, and miRNA processing were compared. The strongest evidence for pairwise co-expression in response to stresses was exhibited by non-paralogous Dicer-like (DCL) genes GmDCL2a-GmDCL3a and GmDCL1b-GmDCL2b, most profoundly in root tissues. Among homoeologous or paralogous DCL genes, the Dicer-like 2 (DCL2) gene pair exhibited the strongest response to stress and most conserved co-expression pattern. This was surprising because the DCL2 duplication event is more ancient than the other DCL duplications. Possible mechanisms that may be driving the DCL2 co-expression are discussed.

MicroRNA Maturation and MicroRNA Target Gene Expression Regulation Are Severely Disrupted in Soybean dicer-like1 Double Mutants.

Small nonprotein-coding microRNAs (miRNAs) are present in most eukaryotes and are central effectors of RNA silencing-mediated mechanisms for gene expression regulation. In plants, DICER-LIKE1 (DCL1) is the founding member of a highly conserved family of RNase III-like endonucleases that function as core machinery proteins to process hairpin-like precursor transcripts into mature miRNAs, small regulatory RNAs, 21–22 nucleotides in length. Zinc finger nucleases (ZFNs) were used to generate single and double-mutants of putative soybean DCL1 homologs, DCL1a and DCL1b, to confirm their functional role(s) in the soybean miRNA pathway. Neither DCL1 single mutant, dcl1a or dcl1b plants, exhibited a pronounced morphological or molecular phenotype. However, the dcl1a/dcl1b double mutant expressed a strong morphological phenotype, characterized by reduced seed size and aborted seedling development, in addition to defective miRNA precursor transcript processing efficiency and deregulated miRNA target gene expression. Together, these findings indicate that the two soybean DCL1 paralogs, DCL1a and DCL1b, largely play functionally redundant roles in the miRNA pathway and are essential for normal plant development.

Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja, the Wild Progenitor of Cultivated Soybeans

Natural populations across a species range demonstrate population structure owing to neutral processes such as localized origins of mutations and migration limitations. Selection also acts on a subset of loci, contributing to local adaptation. An understanding of the genetic basis of adaptation to local environmental conditions is a fundamental goal in basic biological research. When applied to crop wild relatives, this same research provides the opportunity to identify adaptive genetic variation that may be used to breed for crops better adapted to novel or changing environments. The present study explores an ex situ conservation collection, the USDA germplasm collection, genotyped at 32,416 SNPs to identify population structure and test for associations with bioclimatic and biophysical variables in Glycine soja, the wild progenitor of Glycine max (soybean). Candidate loci were detected that putatively contribute to adaptation to abiotic stresses. The identification of potentially adaptive variants in this ex situ collection may permit a more targeted use of germplasm collections.

Growth Stage at Harvest of a Winter Rye Cover Crop Influences Soil Moisture and Nitrogen

Producers may offset the cost associated with winter rye (Secale cereale L.) cover cropping by harvesting the rye as forage, but care must be taken to avoid yield suppression of a primary crop induced by soil water and nitrogen depletion by the rye. The objective was to determine the effect of rye growth stage in the spring on the soil moisture and soil nitrogen under a fall-sown cereal rye cover crop. Field studies were conducted in Morris and St. Paul, MN, from September 2007 through June 2008. Soil moisture and soil NO -N were monitored for eight rye harvest dates in the spring and summer of 2008. Soil moisture in late April and early May was similar for rye and fallow treatments. At boot stage, rye had depleted soil moisture by 10% and soil NO -N by 83% when averaged across locations. Rye reduced soil NO -N compared to the fallow at all growth stages. Harvest timing may be an important management tool to conserve soil moisture for the primary crop. Spring N fertilization is likely necessary when a non-legume such as corn (Zea mays L.) follows rye. Introduction Corn and soybean (Glycine max L.) are the most widely grown crops in the Upper Midwest. These annual crops have relatively short growing seasons with active plant growth and significant ground cover for as little as three or four months per year. The result is a landscape that is prone to off-site nutrient transport, increased soil erosion, and loss of soil organic matter. Planting cover crops after corn or soybean is one approach to addressing these concerns. In the Midwest, winter rye cover cropping has been shown to scavenge excess soil NO -N (11) and reduce NO -N leaching (14,26). Increased surface cover may also reduce soil erosion (16), while the cover crop biomass may help mitigate loss of soil organic matter (15,22). Rye is particularly well suited for use in the Upper Midwest because it grows well after harvest of the main crop in the fall, is winter hardy, and begins regrowth early in the spring (25). In addition, rye tends to reach optimum forage harvest stage sooner than other small grains, which makes it the preferred small grain species for early-season forage production (18). Producers are often reluctant to plant winter rye because of costs associated with rye management. If the environmental benefits associated with rye production are to be realized, there must be some immediate economic incentive for producers. Including rye as part of a double-crop forage production system may justify its cost. On farm research in the Upper Midwest has emphasized that rye can be an integral component of soil conservation and nutrient management, as well as provide producers a high-quality forage (10). Dairy farmers have reported high rye forage yields and increased milk 3

The Genetics and Genomics of Plant Domestication

Food plants are a fundamental aspect of how people relate to their environment and how they experience culture. A primary goal cutting across the fields of plant genetics, evolutionary biology, and anthropology is to understand where, when, and how contemporary food plants were domesticated from their wild ancestors and modified for modern agriculture. In pursuing these goals, investigators are not only learning how traits that improve nutrition, yield, and ease of cultivation have changed, but they are also revealing important context about the origins of cultural traditions while yielding clues to the natural human lifestyle in prehistory. Recent advances in high throughput sequencing and computational techniques have fostered new approaches in studying the genetic and genomic changes that have accompanied plant domestication. In this article, we consider what these studies have taught us about the process of domestication, focusing on comparisons of crop plants and their wild progenitors. We first explore how domestication proceeds and the types of traits most often subject to change. Then, we consider how this process has pervasive impacts on the genes and genomic diversity of crop plants. We conclude with a discussion of promising future research areas enabled by technological and analytical advances in plant genomics, including large-scale germplasm resequencing and ancient DNA analyses.

Optimization of screening of native and naturalized plants from Minnesota for antimicrobial activity

1 Department of Agronomy and Plant Genetics, 411 Borlaug Hall, 1991 Buford Circle, University of Minnesota St. Paul MN 55108, USA. 2 Department of Plant Biological Sciences, 250 Biological Science Center, University of Minnesota, St. Paul MN 55108, USA. 3 Department of Food Science and Nutrition, University of Minnesota, 1334 Eckles Avenue, St. Paul, MN 55108, USA. 4 White Earth Tribal and Community College, 202 South Main Street, Mahnomen, MN 56557, USA. 5 Department of Plant Pathology, 495 Borlaug Hall 1991, Upper Buford Circle, University of Minnesota, St. Paul, MN 55108-6030, USA.

Relationship between Planting Date, Growing Degree Days and the Winter Rye ( Secale cereale L.) Variety “Rymin” in Minnesota

This study evaluated the influence of fall planting date on winter rye (Secale cereale L.) anthesis at three Minnesota locations for five dates from late August through October. This represents the time when fall-planted cover crops would likely be seeded in Minnesota. Earliness to anthesis is important in organic production systems where timing of rye management is affected by rye growth stage. The relationships among growing degree days (GDD), growth stage, and aboveground biomass were evaluated to predict how these factors influence anthesis date and how late in the fall rye could be planted without delaying anthesis. The study occurred in 2006 and 2007, which happened to have abnormally warm and cool growing seasons, with the earliest anthesis dates in 2007 being 25 May, 28 May, and 5 June at St. Paul, Lamberton, and Roseau, respectively, and dates in 2008 of 10 June, 11 June, and 17 June. Our results indicate that there was no fall biomass requirement but also that it was critical to accumulate at least 309 GDD in the fall so as not to delay spring anthesis. This information enables growers to choose appropriate planting dates for rye that will not delay anthesis. The optimal planting date corresponded to planting by late September (~20) in southern and early September (~8) in northern Minnesota.