13 ERA-CAPS BARLEY NAM - Locating exotic genes that control agronomic traits under stress in a wild barley nested association mapping (NAM) population

13 ERA-CAPS BARLEY NAM - 定位野生大麦嵌套关联作图 (NAM) 群体中胁迫下控制农艺性状的外来基因

• 批准号: BB/M004856/1
• 负责人: Andrew Flavell
• 金额: $ 59.08万
• 依托单位: University of Dundee
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM004856%2F1
• 关键词: 13; ERA; CAPS; BARLEY; NAM

Delivering sustainable food production in the face of climate change with reduced fertilizer and pesticide input requires a revolution in crop improvement. Meanwhile, modern crops are becoming increasingly depleted in gene biodiversity. Extending crop biodiversity and supporting future crop improvements can be achieved by 'mining' allelic variants of genes from ancestral wild germplasm. Novel strategies to utilize multi-parental breeding populations and apply the genomics revolution offer a promising route towards exploitation of exotic germplasm for breeding. We will test both approaches using wild barley (Hordeum vulgare ssp. spontaneum) as a model to improve agronomic performance of cultivated barley under abiotic and biotic stress conditions. For this, we will explore a nested association mapping (NAM) approach using the first cereal NAM population HEB-25 ('Halle Exotic Barley') to simultaneously test 25 wild barley accessions for beneficial gene effects. HEB-25 consists of 1,420 BC1S3 lines, each of which carrying ca. 25% of wild barley genome from one of 25 exotic donors on a 75% genetic background of the recipient spring barley cultivar Barke. First, the HEB-25 lines will be assessed for allele content, employing state-of-the-art Exome Capture with Next Generation Sequencing (EC-Seq) to discover single nucleotide polymorphisms (SNP) for 21,643 genes in each of the 1,420 HEB-25 lines. We expect to map roughly 400,000 SNPs, giving several SNPs per gene with the goal to distinguish any wild barley allele from the recipient Barke allele. Second, the HEB-25 lines will be cultivated in field trials in Germany, Scotland and Israel, to assess phenotypic stress performance under either nitrogen deficiency, drought or pathogen attack. Morphologic, agronomic, and nutrient content traits will be scored, as well as resistances against the important barley diseases leaf rust, yellow rust and net blotch. In addition, agronomic performance will be modeled in Israel by up-to-date remote sensing technology, to establish non-invasive phenotype prediction models. Third, the collected data sets will be archived and further processed in a central data warehouse at Halle, built around a custom web-accessible relational database, enabling universal access to the project outputs.Fourth, the resulting genotypic and phenotypic data sets will be combined in a Genome-Wide Association Scan (GWAS) to identify wild barley alleles that improve plant performance under stress. Because the gene resolution is extremely high this study will yield individual high confidence candidate alleles that putatively regulate the studied traits.Fifth, to validate the identified trait-improving exotic alleles in follow up studies, high-resolution offspring populations derived from the originally studied HEB-25 lines will be developed in Halle by backcrossing.The expected outcome of the BARLEY-NAM project will be beneficial in two directions. On one hand, the molecular regulation of new HEB properties will be studied in detail using the developed backcross lines. On the other hand, trait improving exotic alleles will be used in future breeding programs. This will ultimately lead to new elite barley cultivars with improved properties and, simultaneously, extend the biodiversity of our modern elite barley gene pool due to the incorporation of wild barley germplasm.

面对气候变化，通过减少化肥和农药的投入来实现可持续粮食生产，需要对作物改良进行一场革命。与此同时，现代作物的基因多样性正日益枯竭。通过从祖先野生种质中“挖掘”基因的等位变体，可以扩大作物的生物多样性并支持未来的作物改良。利用多亲本育种群体和应用基因组学革命的新策略为利用外来种质进行育种提供了一条有前途的途径。我们将使用野生大麦（Hordeum vulgare ssp. spontaneum）作为模型来测试这两种方法，以提高栽培大麦在非生物和生物胁迫条件下的农艺性能。为此，我们将探索嵌套关联作图 (NAM) 方法，使用第一个谷物 NAM 群体 HEB-25（“Halle Exotic Barley”）同时测试 25 个野生大麦种质的有益基因效应。 HEB-25 由 1,420 个 BC1S3 系组成，每个系携带约 1,420 个 BC1S3 系。 25% 的野生大麦基因组来自 25 个外来捐赠者之一，其 75% 的遗传背景为受体春大麦品种 Barke。首先，将评估 HEB-25 系的等位基因含量，采用最先进的外显子组捕获和下一代测序 (EC-Seq) 来发现 1,420 个 HEB-25 系中每个系的 21,643 个基因的单核苷酸多态性 (SNP)。我们期望绘制大约 400,000 个 SNP，为每个基因提供多个 SNP，目的是区分任何野生大麦等位基因与受体 Barke 等位基因。其次，HEB-25 品系将在德国、苏格兰和以色列进行田间试验，以评估缺氮、干旱或病原体攻击下的表型胁迫表现。将对形态、农艺和营养成分特征以及对重要大麦病害叶锈病、黄锈病和网斑病的抗性进行评分。此外，以色列将利用最新的遥感技术对农艺表现进行建模，以建立非侵入性表型预测模型。第三，收集到的数据集将在哈勒的中央数据仓库中存档并进一步处理，该数据仓库围绕定制的可通过网络访问的关系数据库构建，从而实现项目输出的普遍访问。第四，所得的基因型和表型数据集将在全基因组关联扫描（GWAS）中进行组合，以识别可提高植物在压力下表现的野生大麦等位基因。由于基因分辨率极高，这项研究将产生个体高置信度候选等位基因，这些等位基因可能调节所研究的性状。第五，为了在后续研究中验证已鉴定的性状改善外来等位基因，将通过回交在 Halle 中开发源自最初研究的 HEB-25 品系的高分辨率后代群体。BARLEY-NAM 项目的预期结果将在两个方向上受益。一方面，将使用开发的回交系详细研究新 HEB 特性的分子调控。另一方面，性状改良的外来等位基因将用于未来的育种计划。这最终将产生具有改进特性的新优良大麦品种，同时由于野生大麦种质的纳入，扩大了我们现代优良大麦基因库的生物多样性。

项目成果

Genome-wide association of yield traits in a nested association mapping population of barley reveals new gene diversity for future breeding.

• DOI: 10.1093/jxb/ery178
• 发表时间: 2018-07-18
• 期刊: Journal of experimental botany
• 影响因子: 6.9
• 作者: Sharma R;Draicchio F;Bull H;Herzig P;Maurer A;Pillen K;Thomas WTB;Flavell AJ
• 通讯作者: Flavell AJ

Contrasting genetic regulation of plant development in wild barley grown in two European environments revealed by nested association mapping.

• DOI: 10.1093/jxb/ery002
• 发表时间: 2018-03-24
• 期刊: Journal of experimental botany
• 影响因子: 6.9
• 作者: Herzig P;Maurer A;Draba V;Sharma R;Draicchio F;Bull H;Milne L;Thomas WTB;Flavell AJ;Pillen K
• 通讯作者: Pillen K

An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome.

• DOI: 10.1186/s12859-015-0801-z
• 发表时间: 2015-11-11
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Ribeiro A;Golicz A;Hackett CA;Milne I;Stephen G;Marshall D;Flavell AJ;Bayer M
• 通讯作者: Bayer M