Long-term climate change and periodic environmental extremes threaten food and fuel security1 and global crop productivity2–4. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience5, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation6—knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate–gene–biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene–trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.

Local adaptation is the process by which natural selection drives adaptive phenotypic divergence across environmental gradients. Theory suggests that local adaptation results from genetic trade-offs at individual genetic loci, where adaptation to one set of environmental conditions results in a cost to fitness in alternative environments. However, the degree to which there are costs associated with local adaptation is poorly understood because most of these experiments rely on two-site reciprocal transplant experiments. Here, we quantify the benefits and costs of locally adaptive loci across 17° of latitude in a four-grandparent outbred mapping population in outcrossing switchgrass (Panicum virgatumL.), an emerging biofuel crop and dominant tallgrass species. We conducted quantitative trait locus (QTL) mapping across 10 sites, ranging from Texas to South Dakota. This analysis revealed that beneficial biomass (fitness) QTL generally incur minimal costs when transplanted to other field sites distributed over a large climatic gradient over the 2 y of our study. Therefore, locally advantageous alleles could potentially be combined across multiple loci through breeding to create high-yielding regionally adapted cultivars.

The objective of this study was to characterize residual feed intake (RFI) and to estimate phenotypic and genetic correlations with performance and ultrasound carcass traits in growing heifers. Four postweaning feed efficiency trials were conducted using 468 Brangus heifers. The complete Brangus pedigree file from Camp Cooley Ranch (Franklin, TX), which included 31,215 animals, was used to generate genetic parameter estimates. The heifer progeny from 223 dams were sired by 36 bulls, whereas the complete pedigree file contained 1,710 sires and 8,191 dams. Heifers were individually fed a roughage-based diet (ME = 1.98 Mcal/kg of DM) using Calan gate feeders for 70 d. Heifer BW was recorded weekly and ultrasound measures of 12th- to 13th-rib fat thickness (BF) and LM area (LMA) obtained at d 0 and 70. Residual feed intake (RFIp) was computed as actual minus predicted DMI, with predicted DMI determined by linear regression of DMI on mid-test BW(0.75) (MBW) and ADG with trial, trial x MBW, and trial x ADG as random effects. Overall means for ADG, DMI, and RFI were 1.01 (SD = 0.15), 9.51 (SD = 1.02), and 0.00 (SD = 0.71) kg/d, respectively. Stepwise regression analysis revealed that inclusion of gain in BF and final LMA into the base model increased the R(2) (0.578 vs. 0.534) and accounted for 9% of the variation in DMI not explained by MBW and ADG (RFIp). Residual feed intake and carcass-adjusted RFI (RFIc) were strongly correlated phenotypically and genetically with DMI and FCR, but not with ADG or MBW. Gain in BF was phenotypically correlated (P < 0.05) with RFIp (0.22), but not with FCR or RFIc; however, final BF was genetically correlated (P < 0.05) with RFIp (0.36) and RFIc (0.39). Gain in LMA was weakly phenotypically correlated with FCR, but not with RFIp or RFIc; however, gain in LMA was strongly genetically correlated with RFIp (0.55) and RFIc (0.77). The Spearman rank correlation between RFIp and RFIc was high (0.96). These results suggest that adjusting RFI for ultrasound carcass composition traits will facilitate selection phenotypically independent of growth, body size, and carcass composition; however, genetic relationships may still exist between RFI and carcass composition.

Residual feed intake (RFI) testing has increased selection pressure on biological efficiency in cattle. The objective of this study was to assess the association of the rumen microbiome in inefficient, positive RFI (p-RFI) and efficient, negative RFI (n-RFI) Brahman bulls grazing ‘Coastal’ bermudagrass [Cynodondactylon (L.) Pers.]under two levels of forage allowance (high and low stocking intensity). Sixteen Brahman bulls were previously fed in confinement for 70 d to determine the RFI phenotype. Bulls were then allotted 60 d stocking on bermudagrass pastures to estimate RFI using the n-alkane technique. At the conclusion of the grazing period, rumen liquid samples were collected from each bull by stomach tube to evaluate the rumen microbiome. Extraction of DNA, amplification of the V4-V6 region of the 16S rRNA gene, and 454 pyrosequencing were performed on each sample. After denoising the sequences, chimera checking, and quality trimming, 4,573 ± 1,287 sequences were generated per sample. Sequences were then assigned taxonomy from the Greengenes database using the RDP classifier. Overall, 67.5 and 22.9% of sequences were classified as Bacteroidetes and Firmicutes, respectively. Within the phylum Bacteroidetes, Prevotella was the most predominant genus and was observed in greater relative abundance in p-RFI bulls compared with n-RFI bulls (P = 0.01). In contrast, an unidentified Bacteroidales family was greater in relative abundance for n-RFI bulls than p-RFI (26.7 vs. 19.1%; P = 0.03). Ruminococcaceae was the third most abundant family in our samples, but it was not affected by RFI phenotype. No effect of stocking intensity was observed for bacterial taxa, but there was a tendency for alpha diversity and operational taxonomic unit richness to increase with lower stocking intensity. Results suggested the rumen microbiome of p-RFI Brahman bulls has greater levels of Prevotella, but the bacterial community composition was unaffected by stocking intensity.

In the Gulf Costal Plain adapted summer annual forages such as pearl millet [Pennisetum typhoides (Burm.) Stapf and C. E. Hubb] are generally higher in energy content than perennial grasses and are capable of producing higher rates of gain. However, practically no data are available which define animal performance at different levels of forage utilization. The lack of definitive data on which to base a grazing program with pearl millet prompted this study which determined liveweight gains of weanling cattle grazing ]pearl millet and evaluated the relationships between gain, forage yield, forage quality, grazing pressure, and profitability. A hybrid pearl millet ‘Millex 23’ was seeded at the rate of 15 kg/ha on Thenas (Fluvaquentic Eutrochrept; coarse, loamy, mixed, thermic) soil and fertilized with 112 kg/ha each of N, P2O5, and K2O in each of 2 years. Weanling crossbred beef calves were used as tester animals and grazed at stocking rates ranging from 3.73 to 11.35 animals/ha. Liveweight average daily gains (ADG) from 0.27 to 1.01 kg were shown to be a non‐linear function of forage availability and a positive linear function of percent in vitro dry matter disappearance (IVDMD) available forage. Percent IVDMD of available forage varied from 36.29 to 63.57% and was inversely related to length of trial. Neutral detergent fiber values for available forage were negatively correlated with ADG (r= −0.84). Maximum profitability, expressed as return per ha, was found at intermediate grazing pressure and was dependent upon the magnitude of positive or negative margin between the time of purchase and the time of selling. Maximum profit occurred at greater grazing pressures as the positive margin between selling and purchase price increased. The most important factor affecting the profitability of grazing pearl millet was the differential between buying and selling price of the cattle. Aside from this factor, which the farmer seldom controls, grazing pressure is the most important determinant of profit. It was concluded that the greatest profit or least loss occurs at medium grazing pressures which, in this study, was approximately 2 kg of available forage per kg of animal liveweight.