Association mapping identifies quantitative trait loci (QTL) for digestibility in rice straw
Abstract Background The conversion of lignocellulosic biomass from agricultural waste into biofuels and chemicals is considered a promising way to provide sustainable low carbon products without compromising food security. However, the use of lignocellulosic biomass for biofuel and chemical producti...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-10-01
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| Series: | Biotechnology for Biofuels |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13068-020-01807-8 |
| _version_ | 1828328861393223680 |
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| author | Duong T. Nguyen Leonardo D. Gomez Andrea Harper Claire Halpin Robbie Waugh Rachael Simister Caragh Whitehead Helena Oakey Huong T. Nguyen Tuat V. Nguyen Tu X. Duong Simon J. McQueen-Mason |
| author_facet | Duong T. Nguyen Leonardo D. Gomez Andrea Harper Claire Halpin Robbie Waugh Rachael Simister Caragh Whitehead Helena Oakey Huong T. Nguyen Tuat V. Nguyen Tu X. Duong Simon J. McQueen-Mason |
| author_sort | Duong T. Nguyen |
| collection | DOAJ |
| description | Abstract Background The conversion of lignocellulosic biomass from agricultural waste into biofuels and chemicals is considered a promising way to provide sustainable low carbon products without compromising food security. However, the use of lignocellulosic biomass for biofuel and chemical production is limited by the cost-effectiveness of the production process due to its recalcitrance to enzymatic hydrolysis and fermentable sugar release (i.e., saccharification). Rice straw is a particularly attractive feedstock because millions of tons are currently burned in the field each year for disposal. The aim of this study was to explore the underlying natural genetic variation that impacts the recalcitrance of rice (Oryza sativa) straw to enzymatic saccharification. Ultimately, we wanted to investigate whether we could identify genetic markers that could be used in rice breeding to improve commercial cultivars for this trait. Here, we describe the development and characterization of a Vietnamese rice genome-wide association panel, high-throughput analysis of rice straw saccharification and lignin content, and the results from preliminary genome-wide association studies (GWAS) of the combined data sets. We identify both QTL and plausible candidate genes that may have an impact on the saccharification of rice straw. Results We assembled a diversity panel comprising 151 rice genotypes (Indica and Japonica types) from commercial, historical elite cultivars, and traditional landraces grown in Vietnam. The diversity panel was genotyped using genotype by sequencing (GBS) methods yielding a total of 328,915 single nucleotide polymorphisms (SNPs). We collected phenotypic data from stems of these 151 genotypes for biomass saccharification and lignin content. Using GWAS on the indica genotypes over 2 years we identified ten significant QTL for saccharification (digestibility) and seven significant QTL for lignin. One QTL on chromosome 11 occurred in both GWAS for digestibility and for lignin. Seven QTL for digestibility, on CH2, CH6, CH7, CH8, and CH11, were observed in both years of the study. The QTL regions for saccharification include three potential candidate genes that have been previously reported to influence digestibility: OsAT10; OsIRX9; and OsMYB58/63-L. Conclusions Despite the difficulties associated with multi-phasic analysis of complex traits in novel germplasm, a moderate resolution GWAS successfully identified genetic associations encompassing both known and/or novel genes involved in determining the saccharification potential and lignin content of rice straw. Plausible candidates within QTL regions, in particular those with roles in cell wall biosynthesis, were identified but will require validation to confirm their value for application in rice breeding. |
| first_indexed | 2024-04-13T20:15:51Z |
| format | Article |
| id | doaj.art-d198d2ab34db4fe2aea4b459ea8710b6 |
| institution | Directory Open Access Journal |
| issn | 1754-6834 |
| language | English |
| last_indexed | 2024-04-13T20:15:51Z |
| publishDate | 2020-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Biotechnology for Biofuels |
| spelling | doaj.art-d198d2ab34db4fe2aea4b459ea8710b62022-12-22T02:31:42ZengBMCBiotechnology for Biofuels1754-68342020-10-0113111610.1186/s13068-020-01807-8Association mapping identifies quantitative trait loci (QTL) for digestibility in rice strawDuong T. Nguyen0Leonardo D. Gomez1Andrea Harper2Claire Halpin3Robbie Waugh4Rachael Simister5Caragh Whitehead6Helena Oakey7Huong T. Nguyen8Tuat V. Nguyen9Tu X. Duong10Simon J. McQueen-Mason11Plant Biotechnology Division,, Field Crops Research Institute (FCRI)Centre for Novel Agricultural Products (CNAP), University of York (UoY)Centre for Novel Agricultural Products (CNAP), University of York (UoY)Division of Plant Sciences, School of Life Sciences, University of Dundee (UoD)Division of Plant Sciences, School of Life Sciences, University of Dundee (UoD)Centre for Novel Agricultural Products (CNAP), University of York (UoY)Centre for Novel Agricultural Products (CNAP), University of York (UoY)Division of Plant Sciences, School of Life Sciences, University of Dundee (UoD)Plant Biotechnology Division,, Field Crops Research Institute (FCRI)Vietnam Academy of Agricultural SciencesPlant Biotechnology Division,, Field Crops Research Institute (FCRI)Centre for Novel Agricultural Products (CNAP), University of York (UoY)Abstract Background The conversion of lignocellulosic biomass from agricultural waste into biofuels and chemicals is considered a promising way to provide sustainable low carbon products without compromising food security. However, the use of lignocellulosic biomass for biofuel and chemical production is limited by the cost-effectiveness of the production process due to its recalcitrance to enzymatic hydrolysis and fermentable sugar release (i.e., saccharification). Rice straw is a particularly attractive feedstock because millions of tons are currently burned in the field each year for disposal. The aim of this study was to explore the underlying natural genetic variation that impacts the recalcitrance of rice (Oryza sativa) straw to enzymatic saccharification. Ultimately, we wanted to investigate whether we could identify genetic markers that could be used in rice breeding to improve commercial cultivars for this trait. Here, we describe the development and characterization of a Vietnamese rice genome-wide association panel, high-throughput analysis of rice straw saccharification and lignin content, and the results from preliminary genome-wide association studies (GWAS) of the combined data sets. We identify both QTL and plausible candidate genes that may have an impact on the saccharification of rice straw. Results We assembled a diversity panel comprising 151 rice genotypes (Indica and Japonica types) from commercial, historical elite cultivars, and traditional landraces grown in Vietnam. The diversity panel was genotyped using genotype by sequencing (GBS) methods yielding a total of 328,915 single nucleotide polymorphisms (SNPs). We collected phenotypic data from stems of these 151 genotypes for biomass saccharification and lignin content. Using GWAS on the indica genotypes over 2 years we identified ten significant QTL for saccharification (digestibility) and seven significant QTL for lignin. One QTL on chromosome 11 occurred in both GWAS for digestibility and for lignin. Seven QTL for digestibility, on CH2, CH6, CH7, CH8, and CH11, were observed in both years of the study. The QTL regions for saccharification include three potential candidate genes that have been previously reported to influence digestibility: OsAT10; OsIRX9; and OsMYB58/63-L. Conclusions Despite the difficulties associated with multi-phasic analysis of complex traits in novel germplasm, a moderate resolution GWAS successfully identified genetic associations encompassing both known and/or novel genes involved in determining the saccharification potential and lignin content of rice straw. Plausible candidates within QTL regions, in particular those with roles in cell wall biosynthesis, were identified but will require validation to confirm their value for application in rice breeding.http://link.springer.com/article/10.1186/s13068-020-01807-8Rice (oryza sativa)LignocelluloseBiomassSaccharificationDigestibilityGWAS |
| spellingShingle | Duong T. Nguyen Leonardo D. Gomez Andrea Harper Claire Halpin Robbie Waugh Rachael Simister Caragh Whitehead Helena Oakey Huong T. Nguyen Tuat V. Nguyen Tu X. Duong Simon J. McQueen-Mason Association mapping identifies quantitative trait loci (QTL) for digestibility in rice straw Biotechnology for Biofuels Rice (oryza sativa) Lignocellulose Biomass Saccharification Digestibility GWAS |
| title | Association mapping identifies quantitative trait loci (QTL) for digestibility in rice straw |
| title_full | Association mapping identifies quantitative trait loci (QTL) for digestibility in rice straw |
| title_fullStr | Association mapping identifies quantitative trait loci (QTL) for digestibility in rice straw |
| title_full_unstemmed | Association mapping identifies quantitative trait loci (QTL) for digestibility in rice straw |
| title_short | Association mapping identifies quantitative trait loci (QTL) for digestibility in rice straw |
| title_sort | association mapping identifies quantitative trait loci qtl for digestibility in rice straw |
| topic | Rice (oryza sativa) Lignocellulose Biomass Saccharification Digestibility GWAS |
| url | http://link.springer.com/article/10.1186/s13068-020-01807-8 |
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