Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes

INTRODUCTION: Sorghum (Sorghum bicolor (L.) Moench) is an agriculturally and economically important staple crop that has immense potential as a bioenergy feedstock due to its relatively high productivity on marginal lands. To capitalize on and further improve sorghum as a potential source of sustainable biofuel, it is essential to understand the genomic mechanisms underlying complex traits related to yield, composition, and environmental adaptations. METHODS: Expanding on a recently developed mapping population, we generated de novo genome assemblies for 10 parental genotypes from this population and identified a comprehensive set of over 24 thousand large structural variants (SVs) and over 10.5 million single nucleotide polymorphisms (SNPs). RESULTS: We show that SVs and nonsynonymous SNPs are enriched in different gene categories, emphasizing the need for long read sequencing in crop species to identify novel variation. Furthermore, we highlight SVs and SNPs occurring in genes and pathways with known associations to critical bioenergy-related phenotypes and characterize the landscape of genetic differences between sweet and cellulosic genotypes. DISCUSSION: These resources can be integrated into both ongoing and future mapping and trait discovery for sorghum and its myriad uses including food, feed, bioenergy, and increasingly as a carbon dioxide removal mechanism

BREEDING SWITCHGRASS FOR RESISTANCE TO BIPOLARIS DISEASES

Switchgrass (Panicum virgatum L.), a perennial C4 biomass crop native to North America, suffers from a reduction in germination due to Bipolaris seed rot (BSR) and yield reduction from Bipolaris leaf spot (BLS), both caused by a necrotrophic ascomycete fungus named Bipolaris oryzae (Breda de Haan) Shoemaker. To manage the diseases under economically competitive conditions, breeding switchgrass for resistance and silicon amendment were two potential approaches. Screening methods in a greenhouse were established for BSR in seeds and BLS in 4-week-old seedlings. Half-sib progenies were used to estimate narrow-sense heritability of resistance to the two diseases. Moderate heritability estimates of resistance to BSR suggested successful gain from selection, whereas non-significant heritability of resistance to BLS suggested no progress from selection. Such heritabilities accurately predicted the result from two cycles of recurrent phenotypic selection in ‘Cave-in-Rock’ and ‘Shelter’. The progress of resistance to BSR was more than 50% cycle-1 in both cultivars whereas the progress of resistance to BLS was not significant. Such difference between resistances to BSR and BLS resulted in no correlation between the disease resistances. To dissect the resistance to BLS, genome-wide association was conducted in the Northern Association Panel. The BLS evaluation was conducted in 479 mature switchgrass plants via field evaluation, detached leaf assay, and leaf disk assay. Multi-trait Genome-wide association studies (GWAS) from different phenotype combinations in four subgroups revealed potential resistance genes associated with 18 markers on chromosomes 1b, 2a, 2b, 3a, 3b, 5a, 5b, 6a, 7a, 8a, 9a, and 9b explaining phenotypic variances of 6.32 to 26.72%. Within linkage disequilibrium of 20 kb, there are some potential resistance genes including genes encoding Myb, cytochrome P450, isocitrate lyase, E3 ubiquitin-protein, etc. These markers can be used in genomics-assisted breeding in the future. Besides breeding, silicon amendment has also explored the potential based on the effectiveness against BLS in rice. However, for switchgrass in a greenhouse, silicon amendment (either incorporated into the potting mix or foliar drenches) showed no significant effect BSR and BLS, suggesting more studies are needed on field application and long-term effects of silicon

Raw genotyped total called structural variant (SV)

Genomic structural mutations especially deletion are an important source of variation in many species and can play key roles in phenotypic diversification and evolution. Previous work in many plant species, including some crops, has identified multiple instances of structural variations (SVs) occurring in or near genes related to stress response and disease resistance, suggesting a possible role for SVs in local adaptation. Sorghum (Sorghum bicolor (L.) Moench) is one of the most widely grown cereal crops in the world, and over the course of its history it has been adapted to an array of different climates as well as bred for multiple purposes, resulting in a striking phenotypic diversity within the existing germplasm. In this study, we identified genome-wide deletions in the Biomass Association Panel (BAP), a collection of 347 diverse sorghum genotypes collected from multiple countries and continents. Using Illumina-based, short-read whole genome resequencing data from every genotype, we found a total of 22,359 deletions after filtering. The size of deletions ranged from 51 to 89,716 bp with a median size of 956 bp. The global site frequency spectrum of the deletions fit a model of neutral evolution, suggesting that the majority of deletions were not under any types of selection. Clustering results based on SNPs separated the deletions of the genotypes into eight clusters which largely corresponded with geographic origins. Even though most deletions appeared to be neutral, a handful of cluster-specific deletions were found in genes related to biotic (plant defense and bacterial resistance) and abiotic stress (drought and temperature) responses, supporting the possibility that at least some deletions contribute to local adaptation in sorghum.,The VCF file was the product of LUMPY pipeline integrating with genotyping and CNV detecting step to generate a merge SV,The pipeline for calling SVs in the BAP was adopted from the svtools pipeline (Larson et al. 2019). Briefly, de-multiplexed sequences reads in FASTQ format for each individual were aligned to version 3.0.1 of the BTx623 reference genome (as downloaded from Phytozome v12.1.6: https://phytozome.jgi.doe.gov/pz/portal.html) using the program speedseq (Chiang et al. 2015). Structural variations were identified in each individual aligned BAM file using LUMPY (Layer et al. 2014) with default parameters. The resulting 347 structural variation files were then sorted and merged with svtools (Larson et al. 2019). A full tutorial of this process has been delineated by the authors of svtools, and can be found at https://github.com/hall-lab/svtools/blob/master/Tutorial.md. The merged vcf was then used to calculate a genotype for each individual at the variant positions resulting in a fully genotyped vcf file of each individual. CNVnator(Abyzov et al. 2011) was run within svtools in order to annotate the called variants based on copy number. Subsequently, svtools merged the genotyped and CNV-annotated vcf files to remove any redundant variants that were called by both programs

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

Switchgrass (Panicum virgatum L.), a northern native perennial grass, suffers from yield reduction from Bipolaris leaf spot caused by Bipolaris oryzae (Breda de Haan) Shoemaker. This study aimed to determine the resistant populations via multiple phenotyping approaches and identify potential resistance genes from genome-wide association studies (GWAS) in the switchgrass northern association panel. The disease resistance was evaluated from both natural (field evaluations in Ithaca, New York and Phillipsburg, Philadelphia) and artificial inoculations (detached leaf and leaf disk assays). The most resistant populations based on a combination of three phenotyping approaches—detached leaf, leaf disk, and mean from two locations—were ‘SW788’, ‘SW806’, ‘SW802’, ‘SW793’, ‘SW781’, ‘SW797’, ‘SW798’, ‘SW803’, ‘SW795’, ‘SW805’. The GWAS from the association panel showed 27 significant SNPs on 12 chromosomes: 1K, 2K, 2N, 3K, 3N, 4N, 5K, 5N, 6N, 7K, 7N, and 9N. These markers accumulatively explained the phenotypic variance of the resistance ranging from 3.28 to 26.52%. Within linkage disequilibrium of 20 kb, these SNP markers linked with the potential resistance genes included the genes encoding for NBS-LRR, PPR, cell-wall related proteins, homeostatic proteins, anti-apoptotic proteins, and ABC transporter

DataSheet_3_Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes.docx

IntroductionSorghum (Sorghum bicolor (L.) Moench) is an agriculturally and economically important staple crop that has immense potential as a bioenergy feedstock due to its relatively high productivity on marginal lands. To capitalize on and further improve sorghum as a potential source of sustainable biofuel, it is essential to understand the genomic mechanisms underlying complex traits related to yield, composition, and environmental adaptations.MethodsExpanding on a recently developed mapping population, we generated de novo genome assemblies for 10 parental genotypes from this population and identified a comprehensive set of over 24 thousand large structural variants (SVs) and over 10.5 million single nucleotide polymorphisms (SNPs).ResultsWe show that SVs and nonsynonymous SNPs are enriched in different gene categories, emphasizing the need for long read sequencing in crop species to identify novel variation. Furthermore, we highlight SVs and SNPs occurring in genes and pathways with known associations to critical bioenergy-related phenotypes and characterize the landscape of genetic differences between sweet and cellulosic genotypes.DiscussionThese resources can be integrated into both ongoing and future mapping and trait discovery for sorghum and its myriad uses including food, feed, bioenergy, and increasingly as a carbon dioxide removal mechanism.</p

DataSheet_6_Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes.docx

IntroductionSorghum (Sorghum bicolor (L.) Moench) is an agriculturally and economically important staple crop that has immense potential as a bioenergy feedstock due to its relatively high productivity on marginal lands. To capitalize on and further improve sorghum as a potential source of sustainable biofuel, it is essential to understand the genomic mechanisms underlying complex traits related to yield, composition, and environmental adaptations.MethodsExpanding on a recently developed mapping population, we generated de novo genome assemblies for 10 parental genotypes from this population and identified a comprehensive set of over 24 thousand large structural variants (SVs) and over 10.5 million single nucleotide polymorphisms (SNPs).ResultsWe show that SVs and nonsynonymous SNPs are enriched in different gene categories, emphasizing the need for long read sequencing in crop species to identify novel variation. Furthermore, we highlight SVs and SNPs occurring in genes and pathways with known associations to critical bioenergy-related phenotypes and characterize the landscape of genetic differences between sweet and cellulosic genotypes.DiscussionThese resources can be integrated into both ongoing and future mapping and trait discovery for sorghum and its myriad uses including food, feed, bioenergy, and increasingly as a carbon dioxide removal mechanism.</p

DataSheet_4_Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes.docx

IntroductionSorghum (Sorghum bicolor (L.) Moench) is an agriculturally and economically important staple crop that has immense potential as a bioenergy feedstock due to its relatively high productivity on marginal lands. To capitalize on and further improve sorghum as a potential source of sustainable biofuel, it is essential to understand the genomic mechanisms underlying complex traits related to yield, composition, and environmental adaptations.MethodsExpanding on a recently developed mapping population, we generated de novo genome assemblies for 10 parental genotypes from this population and identified a comprehensive set of over 24 thousand large structural variants (SVs) and over 10.5 million single nucleotide polymorphisms (SNPs).ResultsWe show that SVs and nonsynonymous SNPs are enriched in different gene categories, emphasizing the need for long read sequencing in crop species to identify novel variation. Furthermore, we highlight SVs and SNPs occurring in genes and pathways with known associations to critical bioenergy-related phenotypes and characterize the landscape of genetic differences between sweet and cellulosic genotypes.DiscussionThese resources can be integrated into both ongoing and future mapping and trait discovery for sorghum and its myriad uses including food, feed, bioenergy, and increasingly as a carbon dioxide removal mechanism.</p

DataSheet_5_Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes.docx

IntroductionSorghum (Sorghum bicolor (L.) Moench) is an agriculturally and economically important staple crop that has immense potential as a bioenergy feedstock due to its relatively high productivity on marginal lands. To capitalize on and further improve sorghum as a potential source of sustainable biofuel, it is essential to understand the genomic mechanisms underlying complex traits related to yield, composition, and environmental adaptations.MethodsExpanding on a recently developed mapping population, we generated de novo genome assemblies for 10 parental genotypes from this population and identified a comprehensive set of over 24 thousand large structural variants (SVs) and over 10.5 million single nucleotide polymorphisms (SNPs).ResultsWe show that SVs and nonsynonymous SNPs are enriched in different gene categories, emphasizing the need for long read sequencing in crop species to identify novel variation. Furthermore, we highlight SVs and SNPs occurring in genes and pathways with known associations to critical bioenergy-related phenotypes and characterize the landscape of genetic differences between sweet and cellulosic genotypes.DiscussionThese resources can be integrated into both ongoing and future mapping and trait discovery for sorghum and its myriad uses including food, feed, bioenergy, and increasingly as a carbon dioxide removal mechanism.</p

Table_2_Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes.docx

IntroductionSorghum (Sorghum bicolor (L.) Moench) is an agriculturally and economically important staple crop that has immense potential as a bioenergy feedstock due to its relatively high productivity on marginal lands. To capitalize on and further improve sorghum as a potential source of sustainable biofuel, it is essential to understand the genomic mechanisms underlying complex traits related to yield, composition, and environmental adaptations.MethodsExpanding on a recently developed mapping population, we generated de novo genome assemblies for 10 parental genotypes from this population and identified a comprehensive set of over 24 thousand large structural variants (SVs) and over 10.5 million single nucleotide polymorphisms (SNPs).ResultsWe show that SVs and nonsynonymous SNPs are enriched in different gene categories, emphasizing the need for long read sequencing in crop species to identify novel variation. Furthermore, we highlight SVs and SNPs occurring in genes and pathways with known associations to critical bioenergy-related phenotypes and characterize the landscape of genetic differences between sweet and cellulosic genotypes.DiscussionThese resources can be integrated into both ongoing and future mapping and trait discovery for sorghum and its myriad uses including food, feed, bioenergy, and increasingly as a carbon dioxide removal mechanism.</p

DataSheet_2_Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes.docx

IntroductionSorghum (Sorghum bicolor (L.) Moench) is an agriculturally and economically important staple crop that has immense potential as a bioenergy feedstock due to its relatively high productivity on marginal lands. To capitalize on and further improve sorghum as a potential source of sustainable biofuel, it is essential to understand the genomic mechanisms underlying complex traits related to yield, composition, and environmental adaptations.MethodsExpanding on a recently developed mapping population, we generated de novo genome assemblies for 10 parental genotypes from this population and identified a comprehensive set of over 24 thousand large structural variants (SVs) and over 10.5 million single nucleotide polymorphisms (SNPs).ResultsWe show that SVs and nonsynonymous SNPs are enriched in different gene categories, emphasizing the need for long read sequencing in crop species to identify novel variation. Furthermore, we highlight SVs and SNPs occurring in genes and pathways with known associations to critical bioenergy-related phenotypes and characterize the landscape of genetic differences between sweet and cellulosic genotypes.DiscussionThese resources can be integrated into both ongoing and future mapping and trait discovery for sorghum and its myriad uses including food, feed, bioenergy, and increasingly as a carbon dioxide removal mechanism.</p