Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
Institute of Plant Breeding, Genetics and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
Theor Appl Genet. 2021 Jul;134(7):1957-1975. doi: 10.1007/s00122-021-03798-y. Epub 2021 Mar 24.
Mapping combined with expression and variant analyses in switchgrass, a crop with complex genetics, identified a cluster of candidate genes for leaf wax in a fast-evolving region of chromosome 7K. Switchgrass (Panicum virgatum L.) is a promising warm-season candidate energy crop. It occurs in two ecotypes, upland and lowland, which vary in a number of phenotypic traits, including leaf glaucousness. To initiate trait mapping, two F mapping populations were developed by crossing two different F sibs derived from a cross between the tetraploid lowland genotype AP13 and the tetraploid upland genotype VS16, and high-density linkage maps were generated. Quantitative trait locus (QTL) analyses of visually scored leaf glaucousness and of hydrophobicity of the abaxial leaf surface measured using a drop shape analyzer identified highly significant colocalizing QTL on chromosome 7K (Chr07K). Using a multipronged approach, we identified a cluster of genes including Pavir.7KG077009, which encodes a Type III polyketide synthase-like protein, and Pavir.7KG013754 and Pavir.7KG030500, two highly similar genes that encode putative acyl-acyl carrier protein (ACP) thioesterases, as strong candidates underlying the QTL. The lack of homoeologs for any of the three genes on Chr07N, the relatively low level of identity with other switchgrass KCS proteins and thioesterases, as well as the organization of the surrounding region suggest that Pavir.7KG077009 and Pavir.7KG013754/Pavir.7KG030500 were duplicated into a fast-evolving chromosome region, which led to their neofunctionalization. Furthermore, sequence analyses showed all three genes to be absent in the two upland compared to the two lowland accessions analyzed. This study provides an example of and practical guide for trait mapping and candidate gene identification in a complex genetic system by combining QTL mapping, transcriptomics and variant analysis.
利用连锁作图结合表达和变异分析，在遗传结构复杂的柳枝稷中鉴定出 7K 染色体上一个快速进化区域中与叶蜡相关的候选基因簇。柳枝稷（Panicum virgatum L.）是一种很有前途的暖季能源作物。它有两种生态型，即高地型和低地型，在许多表型特征上存在差异，包括叶片的白化程度。为了启动性状作图，通过杂交两个不同的 F 系（来自四倍体低地基因型 AP13 和四倍体高地基因型 VS16 之间的杂交），建立了两个 F 作图群体，并生成了高密度连锁图谱。对视觉评分的叶片白化程度和使用液滴形状分析仪测量的下表皮疏水性的数量性状位点（QTL）分析，鉴定出在 7K 染色体（Chr07K）上高度显著的共定位 QTL。利用多管齐下的方法，我们鉴定出包括 Pavir.7KG077009 在内的基因簇，它编码一种 III 型聚酮合酶样蛋白，以及 Pavir.7KG013754 和 Pavir.7KG030500 两个高度相似的基因，它们编码假定的酰基辅酶 A（ACP）硫酯酶，作为 QTL 的强候选基因。在 Chr07N 上，这三个基因没有同源基因，与其他柳枝稷 KCS 蛋白和硫酯酶的同源性较低，以及周围区域的组织，表明 Pavir.7KG077009 和 Pavir.7KG013754/Pavir.7KG030500 被复制到一个快速进化的染色体区域，导致它们的新功能化。此外，序列分析表明，与分析的两个低地基因型相比，这三个基因在两个高地基因型中均缺失。本研究为在复杂遗传系统中通过 QTL 作图、转录组学和变异分析相结合进行性状作图和候选基因鉴定提供了一个实例和实用指南。
