Use of microsatellite markers for the assessment of bambara groundnut breeding system and varietal purity before genome sequencing.
Use of microsatellite markers for the assessment of bambara groundnut breeding system and varietal purity before genome sequencing.
复制标题
在基因组测序之前使用微卫星标记评估班巴拉花生育种系统和品种纯度。
作者：
W. K. Ho;A. Muchugi;Samuel Muthemba;R. Kariba;Busiso Olga Mavenkeni;Prasad S. Hendre;Bo Song;A. Van Deynze;F. Massawe;S. Mayes
对于次要和利用不足的作物来说，如何从有限的投资中获得最大的研究成果往往是一项重大挑战。然而，这些作物可能对生物和非生物胁迫具有耐受性，并适应当地、边缘和低投入环境。在气候变化和需要实现粮食安全的背景下，通过育种发展这些作物将为未来农业系统的复原力和多样化提供重要资源。非洲孤生作物联合会认识到基因组资源在促进改良这类作物方面的价值。在开始基因组测序之前，需要评估品系品种纯度并估计任何残余杂合性。本文介绍了一个以黄毛豇豆（Vignasubaruea（L.）Verdc.），一种未充分利用的耐旱非洲豆科植物。利用20个种特异性SSR标记对2个津巴布韦品种进行了基因分型。结果表明，这些品种实际上是相关近交基因型的混合，并且分析允许使用单株选择策略来产生用于WGS的非异质DNA。这些标记也证实了个体植物内非常低水平的杂合性。预筛选使用共显性微卫星标记的应用程序，预计将大大提高基因组组装，相比，可以通过品种膨化的方法。
Maximizing the research output from a limited investment is often the major challenge for minor and underutilized crops. However, such crops may be tolerant to biotic and abiotic stresses and are adapted to local, marginal, and low-input environments. Their development through breeding will provide an important resource for future agricultural system resilience and diversification in the context of changing climates and the need to achieve food security. The African Orphan Crops Consortium recognizes the values of genomic resources in facilitating the improvement of such crops. Prior to beginning genome sequencing there is a need for an assessment of line varietal purity and to estimate any residual heterozygosity. Here we present an example from bambara groundnut (Vigna subterranea (L.) Verdc.), an underutilized drought tolerant African legume. Two released varieties from Zimbabwe, identified as potential genotypes for whole genome sequencing (WGS), were genotyped with 20 species-specific SSR markers. The results indicate that the cultivars are actually a mix of related inbred genotypes, and the analysis allowed a strategy of single plant selection to be used to generate non-heterogeneous DNA for WGS. The markers also confirmed very low levels of heterozygosity within individual plants. The application of a pre-screen using co-dominant microsatellite markers is expected to substantially improve the genome assembly, compared to a cultivar bulking approach that could have been adopted.