Common bean (Phaseolus vulgaris L.) is an important staple crop for smallholder farmers, particularly in Eastern and Southern Africa. To support common bean breeding and seed dissemination, a high throughput SNP genotyping platform with 1500 established SNP assays has been developed at a genotyping service provider which allows breeders without their own genotyping infrastructure to outsource such service. A set of 708 genotypes mainly composed of germplasm from African breeders and CIAT breeding program were assembled and genotyped with over 800 SNPs. Diversity analysis revealed that both Mesoamerican and Andean gene pools are in use, with an emphasis on large seeded Andean genotypes, which represents the known regional preferences. The analysis of genetic similarities among germplasm entries revealed duplicated lines with different names as well as distinct SNP patterns in identically named samples. Overall, a worrying number of inconsistencies was identified in this data set of very diverse origins. This exemplifies the necessity to develop and use a cost-effective fingerprinting platform to ensure germplasm purity for research, sharing and seed dissemination. The genetic data also allows to visualize introgressions, to identify heterozygous regions to evaluate hybridization success and to employ marker-assisted selection. This study presents a new resource for the common bean community, a SNP genotyping platform, a large SNP data set and a number of applications on how to utilize this information to improve the efficiency and quality of seed handling activities, breeding, and seed dissemination through molecular tools.

中文翻译：

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使用 SNP 指纹平台分析非洲菜豆 (Phaseolus vulgaris L.) 种质：多样性、质量控制和分子育种。

菜豆（Phaseolus vulgaris L.）是小农的重要主粮作物，特别是在东部和南部非洲。为了支持菜豆育种和种子传播，基因分型服务提供商开发了一个高通量 SNP 基因分型平台，其中包含 1500 个已建立的 SNP 检测，允许没有自己的基因分型基础设施的育种者外包此类服务。主要由来自非洲育种者和CIAT育种计划的种质组成的一组708个基因型被组装并与800多个SNP进行基因分型。多样性分析显示，中美洲和安第斯基因库都在使用，重点是大种子安第斯基因型，这代表了已知的区域偏好。对种质条目之间遗传相似性的分析揭示了不同名称的重复品系以及相同名称样本中不同的 SNP 模式。总体而言，在这个来源非常不同的数据集中发现了令人担忧的大量不一致之处。这说明有必要开发和使用具有成本效益的指纹识别平台，以确保研究、共享和种子传播的种质纯度。遗传数据还允许可视化基因渗入、识别杂合区域以评估杂交成功并采用标记辅助选择。这项研究为普通菜豆社区提供了一种新资源、一个 SNP 基因分型平台、一个大型 SNP 数据集以及一些关于如何利用这些信息来提高种子处理活动、育种和种子传播的效率和质量的应用程序。分子工具。