Chowdhury Rawnaq N, Nandety Raja Sekhar, Yimer Belayneh Admassu, Fiedler Jason, Sapkota Suraj, Klos Kathy Esvelt
Oak Ridge Institute for Science and Education (ORISE) Research Participant, Small Grains and Potato Germplasm Research Unit, Aberdeen, Idaho, United States of America.
USDA-ARS, Edward T. Schafer Agricultural Research Centre, Fargo, North Dakota, United States of America.
PLoS One. 2025 Jun 23;20(6):e0324826. doi: 10.1371/journal.pone.0324826. eCollection 2025.
Crown rust caused by Puccinia coronata Cda. f. sp. avenae P. Syd. (Pca) is considered the most destructive disease of oat, causing yield and grain quality losses. Over a hundred crown rust race-specific resistance genes have been identified, but the history of cultivar development has left the identity of Pc resistance genes elusive. Closely linked molecular markers may be used to identify the carrier status of a particular Pc resistance allele in any given oat line. However, elevated false positive rates could lead to misidentifying carriers, potentially excluding valuable genetic material from breeding programs. There are very few studies that examine the reliability of gene molecular markers in a diverse genetic background. In this study, molecular markers with genotype data from the T3/Oat database and map data from GrainGenes, which indicated linkage to Pc genes, were evaluated for their predictive potential. A panel of non-carrier lines for Pc genes was identified using phenotype data downloaded from T3/Oat database and pedigree records from Pedigrees of Oat Lines database. The false positive rate of the markers was calculated as the percentage of non-carriers possessing the allele associated with the Pc gene. Using the available map information, thirty SNPs associated with 15 Pc genes were selected and assessed for their predictive capabilities. Eight out of the thirty markers, linked to seven Pc genes, showed potential in predicting carrier status with a false positive rate of ≤25% in non-carrier lines. Particularly, markers for Pc38 and Pc68 perfectly corresponded to carrier status across all lines. Furthermore, validation of published predictive markers for four Pc genes in this non-carrier panel demonstrated consistency with published data, with only a 6-17% genotyping error observed for three markers. Such markers have potential to identify Pc genes present in germplasm with resistance of unknown derivation, thereby enhancing the marker assisted selection process for oat breeding.
由燕麦冠锈菌（Puccinia coronata Cda. f. sp. avenae P. Syd.，简称Pca）引起的冠锈病被认为是燕麦最具毁灭性的病害，会导致产量和谷物品质下降。已经鉴定出了一百多个冠锈病小种特异性抗性基因，但品种培育的历史使得Pc抗性基因的身份难以确定。紧密连锁的分子标记可用于鉴定任何给定燕麦品系中特定Pc抗性等位基因的携带状态。然而，较高的假阳性率可能导致携带者被误判，从而可能将有价值的遗传材料排除在育种计划之外。很少有研究在不同的遗传背景下检验基因分子标记的可靠性。在本研究中，对来自T3/燕麦数据库的基因型数据和来自谷物基因数据库的图谱数据表明与Pc基因连锁的分子标记进行了预测潜力评估。利用从T3/燕麦数据库下载的表型数据和燕麦品系谱系数据库的系谱记录，鉴定出一组Pc基因的非携带者品系。标记的假阳性率计算为拥有与Pc基因相关等位基因的非携带者的百分比。利用现有的图谱信息，选择了与15个Pc基因相关的30个单核苷酸多态性（SNP）并评估其预测能力。这30个标记中有8个与7个Pc基因连锁，在预测携带者状态方面显示出潜力，在非携带者品系中的假阳性率≤25%。特别是，Pc38和Pc68的标记在所有品系中都与携带者状态完全对应。此外，在这个非携带者群体中对四个Pc基因的已发表预测标记进行验证，结果与已发表数据一致，三个标记的基因分型错误率仅为6 - 17%。这类标记有潜力鉴定出存在于来源不明抗性种质中的Pc基因，从而加强燕麦育种的标记辅助选择过程。
