D. R. Viands

Soluble saccharides and cyclitols in alfalfa (Medicago sativa L.) somatic embryos, leaflets, and mature seeds

Abstract Soluble carbohydrates were identified and quantified during development, maturation and desiccation of somatic embryos of alfalfa ( Medicago sativa L.) and compared to soluble carbohydrates in leaflets and mature seeds, to relate changes in soluble carbohydrates to maturation events. Somatic embryos have elevated levels of sucrose. However, in contrast to mature seeds, alfalfa somatic embryos do not accumulate d -pinitol or the galactosyl derivatives of d -pinitol such as galactopinitol A, galactopinitol B and ciceritol. Lower levels of stachyose accumulate during maturation of somatic embryos, but stachyose increases to levels in mature seeds during desiccation of somatic embryos. When stachyose accumulation is limited in somatic embryos, galactinol and digalactosyl myo -inositol increase. Reducing sugars decline to low levels during desiccation of somatic embryos and sucrose: oligosaccharide ratio decreases from 2.7 to 0.9, approaching the ratio 0.2 to 0.3 in mature dry seeds. Except for the lack of pinitol and galactosyl pinitols, changes in soluble carbohydrates during the maturation and desiccation of alfalfa somatic embryos are typical of changes occurring in mature seeds that have been reported to be associated with desiccation tolerance and storability.

Association Mapping of Biomass Yield and Stem Composition in a Tetraploid Alfalfa Breeding Population

Alfalfa (Medicago sativa L.), an important forage crop that is also a potential biofuel crop, has advantages of high yield, high lignocellulose concentration in stems, and has low input costs. In this study, we investigated population structure and linkage disequilibrium (LD) patterns in a tetraploid alfalfa breeding population using genome‐wide simple sequence repeat (SSR) markers and identified markers related to yield and cell wall composition by association mapping. No obvious population structure was found in our alfalfa breeding population, which could be due to the relatively narrow genetic base of the founders and/or due to two generations of random mating. We found significant LD (p < 0.001) between 61.5% of SSR marker pairs separated by less than 1 Mbp. The observed large extent of LD could be explained by the effect of bottlenecking and selection or the high mutation rates of SSR markers. Total marker heterozygosity was positively related to biomass yield in each of five environments, but no relationship was noted for stem composition traits. Of a total of 312 nonrare (frequency >10%) alleles across the 71 SSR markers, 15 showed strong association (p < 0.005) with yield in at least one of five environments, and most of the 15 alleles were identified in multiple environments. Only one allele showed strong association with acid detergent fiber (ADF) and one allele with acid detergent lignin (ADL). Alleles associated with traits could be directly applied in a breeding program using marker‐assisted selection. However, based on our estimated LD level, we would need about 1000 markers to explore the whole alfalfa genome for association between markers and traits.

Genomic Prediction of Biomass Yield in Two Selection Cycles of a Tetraploid Alfalfa Breeding Population

Alfalfa (Medicago sativa L.) is a widely planted perennial forage legume grown throughout temperate and dry subtropical regions in the world. Long breeding cycles limit genetic improvement of alfalfa, particularly for complex traits such as biomass yield. Genomic selection (GS), based on predicted breeding values obtained using genome‐wide molecular markers, could enhance breeding efficiency in terms of gain per unit time and cost. In this study, we genotyped tetraploid alfalfa plants that had previously been evaluated for yield during two cycles of phenotypic selection using genotyping‐by‐sequencing (GBS). We then developed prediction equations using yield data from three locations. Approximately 10,000 single nucleotide polymorphism (SNP) markers were used for GS modeling. The genomic prediction accuracy of total biomass yield ranged from 0.34 to 0.51 for the Cycle 0 population and from 0.21 to 0.66 for the Cycle 1 population, depending on the location. The GS model developed using Cycle 0 as the training population in predicting total biomass yield in Cycle 1 resulted in accuracies up to 0.40. Both genotype × environment interaction and the number of harvests and years used to generate yield phenotypes had effects on prediction accuracy across generations and locations, Based on our results, the selection efficiency per unit time for GS is higher than phenotypic selection, although accuracies will likely decline across multiple selection cycles. This study provided evidence that GS can accelerate genetic gain in alfalfa for biomass yield.

Switchgrass nitrogen response and estimated production costs on diverse sites

Switchgrass (Panicum virgatum L.) has been the principal perennial herbaceous crop investigated for bioenergy production in North America given its high production potential, relatively low input requirements, and potential suitability for use on marginal lands. Few large trials have determined switchgrass yields at field scale on marginal lands, including analysis of production costs. Thus, a field‐scale study was conducted to develop realistic yield and cost estimates for diverse regions of the USA. Objectives included measuring switchgrass response to fertility treatments (0, 56, and 112 kg N ha−1) and generating corresponding estimates of production costs for sites with diverse soil and climatic conditions. Trials occurred in Iowa, New York, Oklahoma, South Dakota, and Virginia, USA. Cultivars and management practices were site specific, and field‐scale equipment was used for all management practices. Input costs were estimated using final harvest‐year (2015) prices, and equipment operation costs were estimated with the MachData model (

Biomass production of herbaceous energy crops in the United States: field trial results and yield potential maps from the multiyear regional feedstock partnership

2015). Switchgrass yields generally were below those reported elsewhere, averaging 6.3 Mg ha−1 across sites and treatments. Establishment stand percent ranged from 28% to 76% and was linked to initial year production. No response to N was observed at any site in the first production year. In subsequent seasons, N generally increased yields on well‐drained soils; however, responses to N were nil or negative on less well‐drained soils. Greatest percent increases in response to 112 kg N ha−1 were 57% and 76% on well‐drained South Dakota and Virginia sites, where breakeven prices to justify N applications were over

Divergent phenotypic selection for alfalfa cell wall fractions and indirect response in digestibility

70 and

Genome-Wide Associations with Resistance to Bipolaris Leaf Spot (Bipolaris oryzae (Breda de Haan) Shoemaker) in a Northern Switchgrass Population (Panicum virgatum)

63 Mg−1, respectively. For some sites, typically promoted N application rates may be economically unjustified; it remains unknown whether a bioenergy industry can support the breakeven prices estimated for sites where N inputs had positive effects on switchgrass yield.

Registration of ‘ReGen’ Alfalfa

Current knowledge of yield potential and best agronomic management practices for perennial bioenergy grasses is primarily derived from small‐scale and short‐term studies, yet these studies inform policy at the national scale. In an effort to learn more about how bioenergy grasses perform across multiple locations and years, the U.S. Department of Energy (US DOE)/Sun Grant Initiative Regional Feedstock Partnership was initiated in 2008. The objectives of the Feedstock Partnership were to (1) provide a wide range of information for feedstock selection (species choice) and management practice options for a variety of regions and (2) develop national maps of potential feedstock yield for each of the herbaceous species evaluated. The Feedstock Partnership expands our previous understanding of the bioenergy potential of switchgrass, Miscanthus, sorghum, energycane, and prairie mixtures on Conservation Reserve Program land by conducting long‐term, replicated trials of each species at diverse environments in the U.S. Trials were initiated between 2008 and 2010 and completed between 2012 and 2015 depending on species. Field‐scale plots were utilized for switchgrass and Conservation Reserve Program trials to use traditional agricultural machinery. This is important as we know that the smaller scale studies often overestimated yield potential of some of these species. Insufficient vegetative propagules of energycane and Miscanthus prohibited farm‐scale trials of these species. The Feedstock Partnership studies also confirmed that environmental differences across years and across sites had a large impact on biomass production. Nitrogen application had variable effects across feedstocks, but some nitrogen fertilizer generally had a positive effect. National yield potential maps were developed using PRISM‐ELM for each species in the Feedstock Partnership. This manuscript, with the accompanying supplemental data, will be useful in making decisions about feedstock selection as well as agronomic practices across a wide region of the country.

Genetic Mapping of Biomass Production in Tetraploid Alfalfa

An alfalfa (Medicago sativa L.) breeding strategy to decrease slowly digestible or indigestible fiber and simultaneously increase digestible fiber could improve forage quality without reducing total fiber. The objectives were: (1) to estimate selection responses from divergent and opposite direction selections of (i) hemicellulose (HEM) and acid detergent fiber (ADF), (ii) acid detergent lignin (LIG) and HEM + cellulose (CEL) and (iii) CEL and HEM + LIG, and (2) to determine correlated responses in in vitro true digestibility (IVTD). Selection progress was evaluated in replicated plot trials at two locations, sampled for 2 or 3 yr. Selection for divergent HEM and ADF resulted in change only for ADF [10.9 g kg-1 dry matter (DM)]. Selection for divergent LIG and HEM + CEL, resulted in same direction change in LIG (3.3 g kg-1 DM). Selection for divergent CEL and HEM + LIG resulted in change only in CEL (5.1 g kg-1 DM). Low LIG and high HEM + CEL, and low ADF and high HEM populations had 9.7 and 8.3 g kg-1 DM...

Switchgrass Response to Nitrogen Fertilizer Across Diverse Environments in the USA: a Regional Feedstock Partnership Report

Switchgrass (Panicum virgatum L.), a northern native perennial grass, suffers from yield reduction from Bipolaris leaf spot caused by Bipolaris oryzae (Breda de Haan) Shoe-maker. This study aimed for determining the resistant populations via multiple phenotyping approaches and identifying potential resistance genes to the disease from genome-wide association studies in the switchgrass northern association panel. The disease resistance was evaluated from both natural (field evaluations in NY and PA) and artificial inoculations (detached leaf and leaf disk assays). There are ten out of the 66 populations showed the most resistant based on a combination of detached leaf, leaf disk, and mean from two locations. The GWAS from five subgroups from the association panel to different disease evaluation combinations yielded 27 significant SNPs on 12 chromosomes: 1K, 2K, 2N, 3K, 3N, 4N, 5K, 5N, 6N, 7K, 7N, and 9N accumulatively explaining phenotypic variance of BLUPs of detached leaf percent lesion via image analysis 26.52% at most and BLUPs of leaf disk percent lesion via image analysis 3.28% at least. Within linkage disequilibrium of 20 kb, these SNP markers linked with the potential resistance genes including genes encoding for NBS-LRR, PPR, cell wall related proteins, homeostatic proteins, anti-apoptotic proteins, and ABC transporters.