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Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass.

ABSTRACT: Long-term climate change and periodic environmental extremes threaten food and fuel security¹ and global crop productivity^2-4. 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.

SUBMITTER: Lovell JT

PROVIDER: S-EPMC7886653 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass.

Lovell John T JT MacQueen Alice H AH Mamidi Sujan S Bonnette Jason J Jenkins Jerry J Napier Joseph D JD Sreedasyam Avinash A Healey Adam A Session Adam A Shu Shengqiang S Barry Kerrie K Bonos Stacy S Boston LoriBeth L Daum Christopher C Deshpande Shweta S Ewing Aren A Grabowski Paul P PP Haque Taslima T Harrison Melanie M Jiang Jiming J Kudrna Dave D Lipzen Anna A Pendergast Thomas H TH Plott Chris C Qi Peng P Saski Christopher A CA Shakirov Eugene V EV Sims David D Sharma Manoj M Sharma Rita R Stewart Ada A Singan Vasanth R VR Tang Yuhong Y Thibivillier Sandra S Webber Jenell J Weng Xiaoyu X Williams Melissa M Wu Guohong Albert GA Yoshinaga Yuko Y Zane Matthew M Zhang Li L Zhang Jiyi J Behrman Kathrine D KD Boe Arvid R AR Fay Philip A PA Fritschi Felix B FB Jastrow Julie D JD Lloyd-Reilley John J Martínez-Reyna Juan Manuel JM Matamala Roser R Mitchell Robert B RB Rouquette Francis M FM Ronald Pamela P Saha Malay M Tobias Christian M CM Udvardi Michael M Wing Rod A RA Wu Yanqi Y Bartley Laura E LE Casler Michael M Devos Katrien M KM Lowry David B DB Rokhsar Daniel S DS Grimwood Jane J Juenger Thomas E TE Schmutz Jeremy J

Nature 20210127 7846

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 as ...[more]

PMID: 33505029

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Project description:BackgroundSwitchgrass, a C4 species and a warm-season grass native to the prairies of North America, has been targeted for development into an herbaceous biomass fuel crop. Genetic improvement of switchgrass feedstock traits through marker-assisted breeding and biotechnology approaches calls for genomic tools development. Establishment of integrated physical and genetic maps for switchgrass will accelerate mapping of value added traits useful to breeding programs and to isolate important target genes using map based cloning. The reported polyploidy series in switchgrass ranges from diploid (2X = 18) to duodecaploid (12X = 108). Like in other large, repeat-rich plant genomes, this genomic complexity will hinder whole genome sequencing efforts. An extensive physical map providing enough information to resolve the homoeologous genomes would provide the necessary framework for accurate assembly of the switchgrass genome.ResultsA switchgrass BAC library constructed by partial digestion of nuclear DNA with EcoRI contains 147,456 clones covering the effective genome approximately 10 times based on a genome size of 3.2 Gigabases (~1.6 Gb effective). Restriction digestion and PFGE analysis of 234 randomly chosen BACs indicated that 95% of the clones contained inserts, ranging from 60 to 180 kb with an average of 120 kb. Comparative sequence analysis of two homoeologous genomic regions harboring orthologs of the rice OsBRI1 locus, a low-copy gene encoding a putative protein kinase and associated with biomass, revealed that orthologous clones from homoeologous chromosomes can be unambiguously distinguished from each other and correctly assembled to respective fingerprint contigs. Thus, the data obtained not only provide genomic resources for further analysis of switchgrass genome, but also improve efforts for an accurate genome sequencing strategy.ConclusionsThe construction of the first switchgrass BAC library and comparative analysis of homoeologous harboring OsBRI1 orthologs present a glimpse into the switchgrass genome structure and complexity. Data obtained demonstrate the feasibility of using HICF fingerprinting to resolve the homoeologous chromosomes of the two distinct genomes in switchgrass, providing a robust and accurate BAC-based physical platform for this species. The genomic resources and sequence data generated will lay the foundation for deciphering the switchgrass genome and lead the way for an accurate genome sequencing strategy.

Project description:Learning more about the biodiversity and composition of arbuscular mycorrhizal fungi (AMF) under alternative agricultural management scenarios may be important to the sustainable intensification of switchgrass grown as a bioenergy crop. Using PacBio single-molecule sequencing and taxonomic resolution to the level of amplicon sequence variant (ASV), we assessed the effects of nitrogen amendment on AMF associating with switchgrass and explored relationships between AMF and switchgrass yield across three sites of various productivities in Wisconsin. Nitrogen amendment had little effect on AMF diversity metrics or community composition. While AMF ASV diversity was not correlated with switchgrass yield, AMF family richness and switchgrass yield had a strong, positive relationship at one of our three sites. Each of our sites was dominated by unique ASVs of the species Paraglomus brasilianum, indicating regional segregation of AMF at the intraspecific level. Our molecular biodiversity survey identified putative core members of the switchgrass microbiome, as well as novel clades of AMF, especially in the order Paraglomerales and the genus Nanoglomus Furthermore, our phylogenies unite the cosmopolitan, soil-inhabiting clade deemed GS24 with Pervetustaceae, an enigmatic family prevalent in stressful environments. Future studies should isolate and characterize the novel genetic diversity found in switchgrass agroecosystems and explore the potential yield benefits of AMF richness.IMPORTANCE We assessed the different species of beneficial fungi living in agricultural fields of switchgrass, a large grass grown for biofuels, using high-resolution DNA sequencing. Contrary to our expectations, the fungi were not greatly affected by fertilization. However, we found a positive relationship between plant productivity and the number of families of beneficial fungi at one site. Furthermore, we sequenced many species that could not be identified with existing reference databases. One group of fungi was highlighted in an earlier study for being widely distributed but of unknown taxonomy. We discovered that this group belonged to a family called Pervetustaceae, which may benefit switchgrass in stressful environments. To produce higher-yielding switchgrass in a more sustainable manner, it could help to study these undescribed fungi and the ways in which they may contribute to greater switchgrass yield in the absence of fertilization.

Dataset Information

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass.

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Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass.

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