The U.S. apple industry, annually worth $15 billion, experiences millions of dollars in annual losses due to various biotic and abiotic stresses, ongoing stress management, and multi-year impacts from the loss of fruit-bearing trees. Over the growing season, apple orchards are under constant threat from a large number of insects, as well as fungal, bacterial, and viral pathogens, particularly in the northeastern United States (Fig. 1). Depending on the incidence and severity of infection by diseases and insects, impacts range from unappealing cosmetic appearance, low marketability, and poor quality of fruit, to decreased yield or complete loss of fruit or trees, causing huge economic losses (Sutton et al., 2014). Early pest and disease detection are critical for appropriate and timely deployment of disease and pest management programs (Bessin et al., 1998). Disease and pest risk prediction models and management programs are developed based on incidence, severity, and timing of infection, taking into account current and forecasted weather data (

Single nucleotide polymorphisms (SNPs) are highly abundant, amendable to high-throughput genotyping, and useful for a number of breeding and genetics applications in crops. SNP frequencies vary depending on the species and populations under study, and therefore target SNPs need to be carefully selected to be informative for each application. While multiple SNP genotyping systems are available for rice (Oryza sativa L. and its relatives), they vary in their informativeness, cost, marker density, speed, flexibility, and data quality. In this study, we report the development and performance of the Cornell-IR LD Rice Array (C7AIR), a second-generation SNP array containing 7,098 markers that improves upon the previously released C6AIR. The C7AIR is designed to detect genome-wide polymorphisms within and between subpopulations of O. sativa, as well as O. glaberrima, O. rufipogon and O. nivara. The C7AIR combines top-performing SNPs from several previous rice arrays, including 4,007 SNPs from the C6AIR, 2,056 SNPs from the High Density Rice Array (HDRA), 910 SNPs from the 384-SNP GoldenGate sets, 189 SNPs from the 44K array selected to add information content for elite U.S. tropical japonica rice varieties, and 8 traitspecific SNPs. To demonstrate its utility, we carried out a genome-wide association analysis for plant height, employing the C7AIR across a diversity panel of 189 rice accessions and identified 20 QTLs contributing to plant height. The C7AIR SNP chip has so far been used for genotyping >10,000 rice samples. It successfully differentiates the five subpopulations of Oryza sativa, identifies introgressions from wild and exotic relatives, and is useful for quantitative trait loci (QTL) and association mapping in diverse materials. Moreover, data from the

Amaranthus L. is genus of C4 dicotyledonous herbaceous plants comprising approximately 70 species, with three subgenera, which contains both cultivated and wild types, where cultivated ones are used for food grains, leafy vegetables, potential forages and ornamentals. Grain amaranth are pseudocereals from three species domesticated in North and South America and are notable for containing high amount of protein and minerals and balanced amino acid in their small seeds. Genetic diversity analysis of amaranths is important for development of core set of germplasm with widely diverse population and effective utilization of plant genetic resources. In this study, we evaluated a germplasm collection of 260 amaranth accessions from United State Department of Agriculture (USDA) and 33 accessions from Seed Savers' Exchange (SSE). We evaluated morphological traits like blade pigmentation, blade shape, petiole pigmentation, branching index, flower color, stem color, inflorescence density, inflorescence shape, terminal inflorescence attitude, plant height and yield characteristics across all 293 accessions. We compared clustering within the USDA and SSE collection and across both collections. Data analysis of morphological data showed significant difference of petiole pigmentation, stem color, blade pigmentation, blade shape and flower color across different clusters of accessions of USDA unlike among different clusters of SSE where we found significant difference of only blade pigmentation, blade shape and flower color. The relationship depicted by neighbor-joining dendogram using the morphological markers was consistent with some but not all of the differences observed between species. Some divisions were found between cultivated and weedy amaranths that was substantiated by morphological characteristics but no separation of South and Central American species was observed. Substantial phenotypic plasticity limits the use of morphological analysis for phylogenetic analysis but does show that important morphological traits such as inflorescence type and plant architecture can cross species boundaries. Similarly, color variants for leaves, flowers and seeds are not exclusive to one cluster in our study nor to one species and can be used widely for breeding any of the cultigens, but not to species identification. Our findings will help in germplasm conservation of grain amaranths and facilitate in this crop's improvement. It will also help on developing effective breeding programs involving different plant characteristics and morphological traits of Amaranths.