Key message

More than 40 QTLs associated with 14 stress-related, quality and agro-morphological traits were identified. A catalogue of favourable SNP markers for MAS and a list of candidate genes are provided.

Abstract

Cassava (Manihot esculenta) is one of the most important starchy root crops in the tropics due to its adaptation to marginal environments. Genetic progress in this clonally propagated crop can be accelerated through the discovery of markers and candidate genes that could be used in cassava breeding programs. We carried out a genome-wide association study (GWAS) using a panel of 5130 clones developed at the International Institute of Tropical Agriculture—Nigeria. The population was genotyped at more than 100,000 SNP markers via genotyping-by-sequencing (GBS). Genomic regions underlying genetic variation for 14 traits classified broadly into four categories: biotic stress (cassava mosaic disease and cassava green mite severity); quality (dry matter content and carotenoid content) and plant agronomy (harvest index and plant type) were investigated. We also included several agro-morphological traits related to leaves, stems and roots with high heritability. In total, 41 significant associations were uncovered. While some of the identified loci matched with those previously reported, we present additional association signals for the traits. We provide a catalogue of favourable alleles at the most significant SNP for each trait-locus combination and candidate genes occurring within the GWAS hits. These resources provide a foundation for the development of markers that could be used in cassava breeding programs and candidate genes for functional validation.

中文翻译：

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全基因组关联分析揭示了对木薯防御性、农业形态和质量相关性状的遗传结构的新见解。

关键信息

鉴定了 40 多个与 14 个胁迫相关性状、品质性状和农业形态性状相关的 QTL。提供了 MAS 的有利 SNP 标记目录和候选基因列表。

抽象的

木薯 ( Manihot esculenta) 是热带地区最重要的淀粉类块根作物之一，因为它适应边​​缘环境。通过发现可用于木薯育种计划的标记和候选基因，可以加速这种无性繁殖作物的遗传进展。我们使用在尼日利亚国际热带农业研究所开发的一组 5130 个克隆进行了全基因组关联研究 (GWAS)。通过基因分型测序 (GBS) 对群体进行了超过 100,000 个 SNP 标记的基因分型。14 种性状遗传变异的基因组区域大致分为四类：生物胁迫（木薯花叶病和木薯绿螨严重程度）；质量（干物质含量和类胡萝卜素含量）和植物农学（收获指数和植物类型）进行了调查。我们还包括了一些与具有高遗传力的叶子、茎和根相关的农业形态特征。总共发现了 41 个重要关联。虽然一些已识别的基因座与先前报道的基因座相匹配，但我们为这些性状提供了额外的关联信号。我们为每个性状基因座组合和 GWAS 命中中出现的候选基因提供了最重要 SNP 处的有利等位基因目录。这些资源为开发可用于木薯育种计划的标记和用于功能验证的候选基因提供了基础。我们为这些特征提供了额外的关联信号。我们为每个性状基因座组合和 GWAS 命中中出现的候选基因提供了最重要 SNP 处的有利等位基因目录。这些资源为开发可用于木薯育种计划的标记和用于功能验证的候选基因提供了基础。我们为这些特征提供了额外的关联信号。我们为每个性状基因座组合和 GWAS 命中中出现的候选基因提供了最重要 SNP 处的有利等位基因目录。这些资源为开发可用于木薯育种计划的标记和用于功能验证的候选基因提供了基础。