Genetic analysis of root traits associated with domestication of Phaseolus vulgaris

今天的作物是第一批农业群体对祖先野生种群的遗传变异进行激烈选择的产物。这种活动导致了基因的积累，这些基因控制着一组被称为“驯化综合症”的特征。这些性状包括生长习性、器官大小、种子传播和环境反应的明显变化。然而，除了少数因其可食用根而被驯化的物种外，根性状在驯化研究中一直被忽视。然而，野生和栽培形式的根之间存在形态差异，可以认为是间接选择的产物。这一观察结果引发了关于造成这些差异的基因数量及其身份的问题。该项目的主要目的是鉴定控制与菜豆（Phaseolus vulgaris）驯化相关的根形态变化的基因，菜豆是一种8-1万年前驯化的新世界物种。目标基因及其染色体位置将通过对野生豆和驯化豆杂交后代的根性状（生长速率、分枝等）的统计分析来确定。这种分析需要两条信息：根性状的测量，以及后代中每个个体在先前绘制的覆盖所有染色体的标记基因上的基因组成。根系性状将通过使用根扫描仪进行二维扫描和使用磁共振成像（MRI）进行三维扫描来测量。已经开发了定量评估3D MRI根图像的工具，并将扩展到创建计算机生成的3D根模型。后代的基因组成将通过最新一代的高通量测序和基因分型技术获得。当统计测试表明具有野生型标记基因的后代与具有驯化型标记基因的后代在根性状上表现出显著差异时，控制驯化相关根性状的基因将被识别并定位在染色体上。鉴定与驯化相关的控制根系性状的基因将具有更广泛的科学和教育影响。对这些基因的了解将提高我们对生态系统碳平衡的理解，其中根质量中的碳储量是一个主要问题，也将促进根的遗传操作以改善作物。本项目将生成一个计算机生成的三维根模型，这将是一个强大的教学工具，也是开发基于基因的根模型的起点。对来自佛罗里达大学和佛罗里达农工大学的本科生和研究生的培训将是该项目的主要组成部分之一。佛罗里达农工大学是一个在科学研究界代表性不足的少数民族机构。

Present day crops are the product of the intense selection applied by the first farming communities on the genetic variation of ancestral wild populations. This activity led to the accumulation of genes that control a group of traits known as the "domestication syndrome." These traits comprise visible changes in growth habit, organ size, seed dispersal, and environmental responses. However, with the exception of a few species that were domesticated for their edible roots, root traits have been neglected in domestication studies. Yet, morphological differences between roots of wild and cultivated forms exist and can be considered the product of indirect selection. This observation raises questions about both the number of genes responsible for these differences and their identity. The main objective of this project is the identification of the genes controlling the root morphological changes associated with the domestication of Phaseolus vulgaris, the common bean, a New World species domesticated 8-10,000 years ago. The target genes and their chromosomal position will be identified through a statistical analysis of root traits (growth rates, branching, etc.) in progeny obtained from a cross between a wild and a domesticated bean. This analysis requires two pieces of information: a measurement of the root trait, and the genetic makeup of each individual in the progeny at previously mapped marker-genes covering all chromosomes. Root traits will be measured via 2D scans using a root scanner, and 3D scans using magnetic resonance imaging (MRI). Tools to evaluate 3D MRI root images quantitatively have been developed and will be expanded to create a computer generative 3D root model. The genetic makeup of the progeny will be obtained with the latest generation of high throughput sequencing and genotyping technologies. The genes controlling the domestication-associated root traits will be identified and located on a chromosome when statistical tests show that progeny with the wild version of the marker-gene exhibit significant differences in root traits from those with the domesticated version. Identification of genes controlling root traits associated with domestication will have broader scientific and educational impacts. Knowledge about these genes will improve our understanding of the carbon balance of ecosystems in which the carbon storage in root mass is a major concern, and will also facilitate the genetic manipulation of roots for crop improvement. This project will produce a computer generative 3D root model, which will be a powerful teaching tool, and the starting point in the development of a gene-based root model. The training of undergraduate and graduate students from both the University of Florida and Florida A&M University, an institution with minorities who are under-represented in the scientific research community, will be one of the major components of this project.