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. 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. 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.

中文翻译：

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关联作图确定稻草消化率的数量性状位点 (QTL)

将农业废弃物中的木质纤维素生物质转化为生物燃料和化学品被认为是在不损害粮食安全的情况下提供可持续低碳产品的一种有前途的方法。然而，木质纤维素生物质在生物燃料和化学生产中的使用受到生产过程的成本效益的限制，因为它对酶水解和可发酵的糖释放（即糖化）具有抗拒性。稻草是一种特别有吸引力的原料，因为目前每年有数百万吨在田间燃烧处理。本研究的目的是探索影响水稻（Oryza sativa）秸秆对酶促糖化的抗拒性的潜在自然遗传变异。最终，我们想调查我们是否可以识别出可用于水稻育种的遗传标记，以改进该性状的商业品种。在这里，我们描述了越南水稻全基因组关联面板的开发和表征、稻草糖化和木质素含量的高通量分析，以及组合数据集的初步全基因组关联研究 (GWAS) 的结果。我们确定了可能对稻草糖化产生影响的 QTL 和可能的候选基因。我们组装了一个多样性小组，其中包括来自越南种植的商业、历史优良品种和传统地方品种的 151 种水稻基因型（籼稻和粳稻类型）。多样性面板使用基因分型测序 (GBS) 方法进行基因分型，总共产生 328 个，915 个单核苷酸多态性 (SNP)。我们从这 151 个基因型的茎中收集了生物质糖化和木质素含量的表型数据。在 2 年内对籼稻基因型使用 GWAS，我们确定了 10 个重要的糖化（消化率）QTL 和 7 个重要的木质素 QTL。11 号染色体上的一个 QTL 出现在 GWAS 中，用于消化率和木质素。在研究的两年中观察到了关于 CH2、CH6、CH7、CH8 和 CH11 的 7 个消化率 QTL。用于糖化的 QTL 区域包括三个可能影响消化率的候选基因：OsAT10；奥斯IRX9；和 OsMYB58/63-L。尽管新种质中复杂性状的多阶段分析存在困难，中等分辨率 GWAS 成功地鉴定了遗传关联，包括参与确定稻草的糖化潜力和木质素含量的已知和/或新基因。QTL 区域内可能的候选者，特别是那些在细胞壁生物合成中起作用的候选者，已被确定，但需要验证以确认它们在水稻育种中的应用价值。