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Ramstein GP, Evans J, Nandety A, Saha MC, Brummer EC, Kaeppler SM, Buell CR, Casler MD. Candidate Variants for Additive and Interactive Effects on Bioenergy Traits in Switchgrass ( Panicum virgatum L.) Identified by Genome-Wide Association Analyses. Plant Genome 2018; 11:180002. [PMID: 30512032 DOI: 10.3835/plantgenome2018.01.0002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Switchgrass ( L.) is a promising herbaceous energy crop, but further gains in biomass yield and quality must be achieved to enable a viable bioenergy industry. Developing DNA markers can contribute to such progress, but depiction of genetic bases should be reliable, involving simple additive marker effects and also interactions with genetic backgrounds (e.g., ecotypes) or synergies with other markers. We analyzed plant height, C content, N content, and mineral concentration in a diverse panel consisting of 512 genotypes of upland and lowland ecotypes. We performed association analyses based on exome capture sequencing and tested 439,170 markers for marginal effects, 83,290 markers for marker × ecotype interactions, and up to 311,445 marker pairs for pairwise interactions. Analyses of pairwise interactions focused on subsets of marker pairs preselected on the basis of marginal marker effects, gene ontology annotation, and pairwise marker associations. Our tests identified 12 significant effects. Homology and gene expression information corroborated seven effects and indicated plausible causal pathways: flowering time and lignin synthesis for plant height; plant growth and senescence for C content and mineral concentration. Four pairwise interactions were detected, including three interactions preselected on the basis of pairwise marker correlations. Furthermore, a marker × ecotype interaction and a pairwise interaction were confirmed in an independent switchgrass panel. Our analyses identified reliable candidate variants for important bioenergy traits. Moreover, they exemplified the importance of interactive effects for depicting genetic bases and illustrated the usefulness of preselecting marker pairs for identifying pairwise marker interactions in association studies.
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Evans J, Crisovan E, Barry K, Daum C, Jenkins J, Kunde-Ramamoorthy G, Nandety A, Ngan CY, Vaillancourt B, Wei CL, Schmutz J, Kaeppler SM, Casler MD, Buell CR. Diversity and population structure of northern switchgrass as revealed through exome capture sequencing. Plant J 2015; 84:800-15. [PMID: 26426343 DOI: 10.1111/tpj.13041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/31/2015] [Accepted: 09/03/2015] [Indexed: 05/11/2023]
Abstract
Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype, composed of tetraploid and octoploid accessions, and a southern lowland ecotype, composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single-nucleotide polymorphisms (SNPs), of which 1 590 653 high-confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype-restricted, non-synonymous SNPs that are predicted to affect the protein function of CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering, which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up-CNVs), 112 630 genes present in fewer copies than in the reference genome (down-CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland-specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.
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Affiliation(s)
- Joseph Evans
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Emily Crisovan
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Kerrie Barry
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Chris Daum
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - Aruna Nandety
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Chew Yee Ngan
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Brieanne Vaillancourt
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Chia-Lin Wei
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Shawn M Kaeppler
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Michael D Casler
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- USDA-ARS, U.S. Dairy Forage Research Center, 1925 Linden Dr., Madison, WI, 53706-1108, USA
| | - Carol Robin Buell
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
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Evans J, Kim J, Childs KL, Vaillancourt B, Crisovan E, Nandety A, Gerhardt DJ, Richmond TA, Jeddeloh JA, Kaeppler SM, Casler MD, Buell CR. Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum. Plant J 2014; 79:993-1008. [PMID: 24947485 PMCID: PMC4309430 DOI: 10.1111/tpj.12601] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/31/2014] [Accepted: 06/09/2014] [Indexed: 05/23/2023]
Abstract
Switchgrass (Panicum virgatum) is a polyploid, outcrossing grass species native to North America and has recently been recognized as a potential biofuel feedstock crop. Significant phenotypic variation including ploidy is present across the two primary ecotypes of switchgrass, referred to as upland and lowland switchgrass. The tetraploid switchgrass genome is approximately 1400 Mbp, split between two subgenomes, with significant repetitive sequence content limiting the efficiency of re-sequencing approaches for determining genome diversity. To characterize genetic diversity in upland and lowland switchgrass as a first step in linking genotype to phenotype, we designed an exome capture probe set based on transcript assemblies that represent approximately 50 Mb of annotated switchgrass exome sequences. We then evaluated and optimized the probe set using solid phase comparative genome hybridization and liquid phase exome capture followed by next-generation sequencing. Using the optimized probe set, we assessed variation in the exomes of eight switchgrass genotypes representing tetraploid lowland and octoploid upland cultivars to benchmark our exome capture probe set design. We identified ample variation in the switchgrass genome including 1,395,501 single nucleotide polymorphisms (SNPs), 8173 putative copy number variants and 3336 presence/absence variants. While the majority of the SNPs (84%) detected was bi-allelic, a substantial number was tri-allelic with limited occurrence of tetra-allelic polymorphisms consistent with the heterozygous and polyploid nature of the switchgrass genome. Collectively, these data demonstrate the efficacy of exome capture for discovery of genome variation in a polyploid species with a large, repetitive and heterozygous genome.
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Affiliation(s)
- Joseph Evans
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Jeongwoon Kim
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Kevin L Childs
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Brieanne Vaillancourt
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Emily Crisovan
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Aruna Nandety
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, 53706, USA
- US Dairy Forage Research Center, USDA-ARS1925 Linden Dr., Madison, WI, 53706-1108, USA
| | | | | | | | - Shawn M Kaeppler
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, 53706, USA
- Department of Agronomy, University of Wisconsin-Madison1575 Linden Drive, Madison, WI, 53706, USA
| | - Michael D Casler
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, 53706, USA
- US Dairy Forage Research Center, USDA-ARS1925 Linden Dr., Madison, WI, 53706-1108, USA
| | - C Robin Buell
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
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Tao L, Guo XS, Zhou H, Undersander DJ, Nandety A. Short communication: Characteristics of proteolytic activities of endo- and exopeptidases in alfalfa herbage and their implications for proteolysis in silage. J Dairy Sci 2012; 95:4591-5. [PMID: 22818473 DOI: 10.3168/jds.2012-5383] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 04/08/2012] [Indexed: 11/19/2022]
Abstract
The pH optimum and thermostability of both exopeptidases and endopeptidases were investigated in this study to elucidate the possible role of plant proteases in proteolysis during ensiling of alfalfa herbage. Proteolytic activities of 4 classes of endopeptidases (i.e., serine, metallo, aspartic, and cysteine peptidase) and 5 classes of exopeptidases (i.e., aminopeptidase, carboxypeptidase, dipeptidase, dipeptidyl-peptidase, and tripeptidyl-peptidase) were examined within pH values of 3 to 9, and within temperatures from 20 to 90°C. Serine and metalloproteases, the principal endopeptidases that hydrolyzed most of the protein to nonprotein nitrogen in alfalfa silage, had optimum activities at pH 4. Among the major exopeptidases contributing protein degradation in ensiled alfalfa, dipeptidase and tripeptidyl-peptidase had stable activities between pH 4 and 6, and carboxypeptidase activity was optimal at pH 5. The optimum temperature for most peptidase activities was 40°C. Proteolytic activities of both endo- and exopeptidases increased with the elevation of incubating temperature from 20 to 40°C. The pH value in well-preserved alfalfa silage is often above 4.0, and the temperatures in the ensiled mass range from 25 to 40°C. Therefore, high proteolytic activities between pH 4 and 6 and the temperature range of ensiled alfalfa suggest that plant peptidases play a role in hydrolyzing protein during prolonged storage.
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Affiliation(s)
- L Tao
- Institute of Grassland Science, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
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Vadivel V, Nandety A, Biesalski HK. Antioxidant potential and health relevant functionality of traditionally processed Cassia hirsuta L. seeds: an Indian underutilized food legume. Plant Foods Hum Nutr 2011; 66:245-253. [PMID: 21667144 DOI: 10.1007/s11130-011-0237-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The methanolic extract of Cassia hirsuta L. seed materials, an underutilized food legume collected from India, was analyzed for antioxidant activity and health relevant functionality. The methanolic extract of raw seeds contained a total free phenolic content of 15.82 ± 1.69 g catechin equivalent/100 g extract DM. Encouraging levels of ferric reducing/antioxidant power (FRAP, 1,446 mmol Fe[II]/mg extract), inhibition of ß-carotene degradation (48.81%) and scavenging activity against DPPH (64.40%) and superoxide (43.78%) radicals were exhibited by the raw samples. Further, 83.11% of α-amylase and 62.79% of α-glucosidase enzyme inhibition characteristics under in vitro starch digestion bioassay were also recorded. Sprouting + oil-frying caused an apparent increase on the total free phenolic content and a significant improvement in the antioxidant and free radical scavenging capacity of methanolic extract of C. hirsuta seeds, while soaking + cooking as well as open-pan roasting treatments showed diminishing effects. The analysis of the phenolic profile revealed the presence of gallic acid, p-coumaric acid and (+)-catechin in the methanolic extract of these seeds.
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Affiliation(s)
- Vellingiri Vadivel
- Institute for Biological Chemistry and Nutrition, University of Hohenheim, Stuttgart, Germany.
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