Jerome H. Cherney

Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol.

Switchgrass (Panicum virgatum L.) is a perennial grass that has been designated as an herbaceous model biofuel crop for the United States of America. To facilitate accelerated breeding programs of switchgrass, we developed both an association panel and linkage populations for genome-wide association study (GWAS) and genomic selection (GS). All of the 840 individuals were then genotyped using genotyping by sequencing (GBS), generating 350 GB of sequence in total. As a highly heterozygous polyploid (tetraploid and octoploid) species lacking a reference genome, switchgrass is highly intractable with earlier methodologies of single nucleotide polymorphism (SNP) discovery. To access the genetic diversity of species like switchgrass, we developed a SNP discovery pipeline based on a network approach called the Universal Network-Enabled Analysis Kit (UNEAK). Complexities that hinder single nucleotide polymorphism discovery, such as repeats, paralogs, and sequencing errors, are easily resolved with UNEAK. Here, 1.2 million putative SNPs were discovered in a diverse collection of primarily upland, northern-adapted switchgrass populations. Further analysis of this data set revealed the fundamentally diploid nature of tetraploid switchgrass. Taking advantage of the high conservation of genome structure between switchgrass and foxtail millet (Setaria italica (L.) P. Beauv.), two parent-specific, synteny-based, ultra high-density linkage maps containing a total of 88,217 SNPs were constructed. Also, our results showed clear patterns of isolation-by-distance and isolation-by-ploidy in natural populations of switchgrass. Phylogenetic analysis supported a general south-to-north migration path of switchgrass. In addition, this analysis suggested that upland tetraploid arose from upland octoploid. All together, this study provides unparalleled insights into the diversity, genomic complexity, population structure, phylogeny, phylogeography, ploidy, and evolutionary dynamics of switchgrass.

Biomass Yield of Naturalized Populations and Cultivars of Reed Canary Grass

Reed canary grass is a widely adapted temperate grass with a circumglobal distribution in the northern hemisphere. Because it has relatively high biomass yields under relatively infrequent harvest systems, this species is receiving increasing attention as a bioenergy feedstock. The objective of this study was to conduct a comparative biomass yield evaluation of reed canary grass accessions from a wide range of habitats in the north central and northeastern USA. Eight cultivars and 72 accessions were evaluated for biomass yield over 2xa0years at five locations in Iowa, New York, and Wisconsin. Accessions produced, on average, 6.7% higher biomass yield than the cultivars. Cultivars ranked from 50th to 77th in biomass yield out of a total of 80 cultivars and accessions. Genetic expression for biomass yield was highly consistent across locations and years. Accessions from southern and western collection sites tended to have the highest biomass yield. Reed canary grass populations in rural landscapes of the central and northeastern USA have value for increasing biomass yield potential of this bioenergy feedstock candidate species. The high biomass yield of many of these populations, combined with the large amount of genetic variability among these populations, offers potential for both short-term gains by selecting superior accessions and long-term gains by selection and breeding.

Split Application of Nitrogen on Temperate Perennial Grasses in the Northeast USA

Timing of N applications on grasses can impact agronomic forage traits as well as the environment. We studied the impact of split N applications on yield, quality, and N recovery in orchardgrass, reed canarygrass, and tall fescue. Nitrogen fertilizer was applied at 200 lb N per acre at spring greenup, or 100 lb N fertilizer per acre at spring greenup followed by 100 lb N per acre after first cut, or 100 lb N fertilizer/acre at spring greenup followed by 50 lb N per acre after first cut and 50 lb N per acre after second cut. Plots were harvested three times per season for three years at two locations in central New York. There was about a 12% yield increase associated with split application of N in the spring and after first cut, but no yield advantage to using a three-way split of N over the season. Nitrogen yield and apparent N recovery were not influenced by timing of N application. Highest N fertilizer rates prior to the first and second cuts resulted in increased crude protein and reduced neutral detergent fiber, but fertilization after second cut had no impact on third cut quality. Fertilization with a split application of N will maximize yield, most of which is suitable forage for lactating dairy cows.

Genome-Wide Association Study Based on Multiple Imputation with Low-Depth Sequencing Data: Application to Biofuel Traits in Reed Canarygrass

Genotyping by sequencing allows for large-scale genetic analyses in plant species with no reference genome, but sets the challenge of sound inference in presence of uncertain genotypes. We report an imputation-based genome-wide association study (GWAS) in reed canarygrass (Phalaris arundinacea L., Phalaris caesia Nees), a cool-season grass species with potential as a biofuel crop. Our study involved two linkage populations and an association panel of 590 reed canarygrass genotypes. Plants were assayed for up to 5228 single nucleotide polymorphism markers and 35 traits. The genotypic markers were derived from low-depth sequencing with 78% missing data on average. To soundly infer marker-trait associations, multiple imputation (MI) was used: several imputes of the marker data were generated to reflect imputation uncertainty and association tests were performed on marker effects across imputes. A total of nine significant markers were identified, three of which showed significant homology with the Brachypodium dystachion genome. Because no physical map of the reed canarygrass genome was available, imputation was conducted using classification trees. In general, MI showed good consistency with the complete-case analysis and adequate control over imputation uncertainty. A gain in significance of marker effects was achieved through MI, but only for rare cases when missing data were <45%. In addition to providing insight into the genetic basis of important traits in reed canarygrass, this study presents one of the first applications of MI to genome-wide analyses and provides useful guidelines for conducting GWAS based on genotyping-by-sequencing data.

Forage Quality Differences of Corn Hybrids as Influenced by Ensiling

Our objective was to determine the impact of ensiling on forage quality of 54 corn hybrids (Zea mays L.). Four field replicates of each hybrid were planted at each of two locations in NY in 2003 (Groveland Station and Aurora, NY). There were differences among hybrids in pH (P < 0.01) at both sites. The pH of ensiled samples was positively correlated with silage DM (r = 0.82) and increased 0.016 pH units for each 1.0% increase in DM. Crude protein of ensiled samples was highly correlated (r = 0.95) with CP of fresh samples, but CP was 0.41% greater in the ensiled samples. Sugar of fresh samples averaged 9.9% while that of corresponding ensiled samples averaged 3.6%. Ranking of hybrids for sugar changed from fresh to ensiled, but was not consistent between sites. There were hybrid × ensiling/fresh interactions for NDF and IVTD at one site; this interaction was not significant at either site for fiber digestibility (NDFD). There was a significant correlation between fresh and ensiled sample NDFD (r = 0.74, P < 0.01). These data suggest little difference between fresh or ensiled hybrid rankings for NDFD, which implies that differences among hybrids in NDFD could be selected by using fresh samples. Inconsistencies for hybrid × ensiling/fresh interactions indicated that more research is needed to fully assess the relative benefits of ensiling prior to quality comparisons of corn hybrids.

Estimation of spring forage quality for alfalfa in New York State

Equations were developed to estimate alfalfa neutral detergent fiber (NDF) concentration in spring growth in New York State, using easily available variables and a typical cutting height used by growers. Models with two or three explanatory variables had greater predictive accuracy than models containing more variables. Models combining alfalfa height, growing degree days, and Julian date offer the greatest potential to increase predictive accuracy. Stage of maturity did not improve prediction accuracy. Predictions using the predictive equations for alfalfa quality (PEAQ) with alfalfa sampled in New York were biased, possibly due to differences in cutting height between observations used to fit the equation, and typical cutting heights in New York State. An equation previously fit to New York, using only the explanatory variable alfalfa height, was less biased.

Effects of weed control and manure application on nutrient fluxes in the shifting cultivation milpa system of Yucatán

Maize (Zea mays L.) cultivation under the shifting cultivation system of Yucatán, Mexico, is normally limited to 2–3 years due to nutrient depletion and weed pressure. This study was undertaken to evaluate the effect of manure application and weed control on partial nutrient budgets for maize, and assess the effect of grain-only or whole-plant harvest on nutrient removal. Two farms were selected near Mérida, Mexico, each including two cultivation years. Maize grain, stem, and leaf fractions were harvested and analyzed for N, P, and K concentrations, and compared to quantities added through manure, to generate partial nutrient budgets. Multiple years of cultivation did not change soil organic matter content while extractable P was reduced (53–62%) at both farms and extractable K was lower (22%) for farm 1. Plant fractions contained similar amounts of N, while P accumulated in grain, and stem and leaf contained the largest K pools. Applied treatments affected crop nutrient removal predominantly through crop yield. Partial nutrient budgets suggested that with stover removal, the lower rate of manure may be sufficient to maintain P, but not N or K; whereas with the higher rate of manure all partial budgets were positive, suggesting nutrient accumulation over time.

Developing Association Mapping in Polyploid Perennial Biofuel Grasses: Final Technical Report

This project had six objectives, four of which have been completed: 1) Association panels of diverse populations and linkage populations for switchgrass and reed canarygrass (~1,000 clones each) were assembled and planted in two sites (Ithaca, NY and Arlington, WI); 2) Key biofeedstock characteristics were evaluated in these panels for three field seasons; 3) High density SNP markers were developed in switchgrass; and 4) Switchgrass association panels and linkage populations were genotyped. The remaining two original objectives will be met in the next year, as the analyses are completed and papers published: 5) Switchgrass population structure and germplasm diversity will be evaluated; and 6) Association mapping will be established and marker based breeding values estimated in switchgrass. We also completed a study of the chromosome-number variation found in switchgrass.