Raatz Bodo, Mukankusi Clare, Lobaton Juan David, Male Alan, Chisale Virginia, Amsalu Berhanu, Fourie Deidré, Mukamuhirwa Floride, Muimui Kennedy, Mutari Bruce, Nchimbi-Msolla Susan, Nkalubo Stanley, Tumsa Kidane, Chirwa Rowland, Maredia Mywish K, He Chunlin
1Present Address: Bean Program, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia.
International Centre for Tropical Agriculture (CIAT), 15 km Bombo Road, Kawanda, Box 6247, Kampala, Uganda.
Genet Resour Crop Evol. 2019;66(3):707-722. doi: 10.1007/s10722-019-00746-0. Epub 2019 Feb 19.
Common bean ( 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.
普通菜豆（Phaseolus vulgaris L.）是小农的重要主食作物，在东非和南部非洲尤为如此。为了支持普通菜豆育种和种子传播，一家基因分型服务提供商开发了一个拥有1500个既定SNP检测的高通量SNP基因分型平台，这使得没有自己基因分型基础设施的育种者能够将此类服务外包。收集了一组主要由非洲育种者的种质和国际热带农业中心（CIAT）育种项目组成的708个基因型，并用800多个SNP进行基因分型。多样性分析表明，中美洲和安第斯基因库都在使用，重点是大粒安第斯基因型，这代表了已知的区域偏好。种质条目之间的遗传相似性分析揭示了具有不同名称的重复品系以及同名样品中不同的SNP模式。总体而言，在这个来源非常多样的数据集中发现了数量令人担忧的不一致情况。这例证了开发和使用具有成本效益的指纹识别平台以确保种质纯度用于研究、共享和种子传播的必要性。遗传数据还可以可视化基因渐渗，识别杂合区域以评估杂交成功率，并采用标记辅助选择。本研究为普通菜豆群体提供了一种新资源，即一个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通过分子工具提高种子处理活动、育种和种子传播的效率和质量的应用。
