Mbanjo Edwige Gaby Nkouaya, Ogungbesan Adebukola, Agbona Afolabi, Akpotuzor Patrick, Toyinbo Seyi, Iluebbey Peter, Rabbi Ismail Yusuf, Peteti Prasad, Wages Sharon A, Norton Joanna, Zhang Xiaofei, Bohórquez-Chaux Adriana, Mushoriwa Hapson, Egesi Chiedozie, Kulakow Peter, Parkes Elizabeth
International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria.
Texas A&M Agrilife Research & Extension Center, Weslaco, TX 78596, USA.
Plants (Basel). 2024 Aug 21;13(16):2328. doi: 10.3390/plants13162328.
A validated marker system is crucial to running an effective genomics-assisted breeding program. We used 36 Kompetitive Allele-Specific PCR (KASP) markers to genotype 376 clones from the biofortified cassava pipeline, and fingerprinted 93 of these clones with DArTseq markers to characterize breeding materials and evaluate their relationships. The discriminating ability of the 36-quality control (QC) KASP and 6602 DArTseq markers was assessed using 92 clones genotyped in both assays. In addition, trait-specific markers were used to determine the presence or absence of target genomic regions. Hierarchical clustering identified two major groups, and the clusters were consistent with the breeding program origins. There was moderate genetic differentiation and a low degree of variation between the identified groups. The general structure of the population was similar using both assays. Nevertheless, KASP markers had poor resolution when it came to differentiating the genotypes by seed sources and overestimated the prevalence of duplicates. The trait-linked markers did not achieve optimal performance as all markers displayed variable levels of false positive and/or false negative. These findings represent the initial step in the application of genomics-assisted breeding for the biofortified cassava pipeline, and will guide the use of genomic selection in the future.
一个经过验证的标记系统对于开展有效的基因组辅助育种计划至关重要。我们使用36个竞争性等位基因特异性PCR（KASP）标记对来自生物强化木薯管道的376个克隆进行基因分型，并用DArTseq标记对其中93个克隆进行指纹识别，以表征育种材料并评估它们之间的关系。使用在两种检测中都进行了基因分型的92个克隆评估了36个质量控制（QC）KASP标记和6602个DArTseq标记的鉴别能力。此外，使用性状特异性标记来确定目标基因组区域的存在与否。层次聚类识别出两个主要组，这些聚类与育种计划的起源一致。在识别出的组之间存在适度的遗传分化和低程度的变异。两种检测方法得到的群体总体结构相似。然而，KASP标记在按种子来源区分基因型时分辨率较差，并且高估了重复样本的比例。与性状相关的标记未达到最佳性能，因为所有标记都显示出不同程度的假阳性和/或假阴性。这些发现代表了在生物强化木薯管道中应用基因组辅助育种的第一步，并将指导未来基因组选择的使用。
