Schoonmaker Ashley N, Hulse-Kemp Amanda M, Youngblood Ramey C, Rahmat Zainab, Atif Iqbal Muhammad, Rahman Mehboob-Ur, Kochan Kelli J, Scheffler Brian E, Scheffler Jodi A
Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695, USA.
Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA.
Plants (Basel). 2023 Mar 3;12(5):1153. doi: 10.3390/plants12051153.
Cotton leaf curl virus (CLCuV) causes devastating losses to fiber production in Central Asia. Viral spread across Asia in the last decade is causing concern that the virus will spread further before resistant varieties can be bred. Current development depends on screening each generation under disease pressure in a country where the disease is endemic. We utilized quantitative trait loci (QTL) mapping in four crosses with different sources of resistance to identify single nucleotide polymorphism (SNP) markers associated with the resistance trait to allow development of varieties without the need for field screening every generation. To assist in the analysis of multiple populations, a new publicly available R/Shiny App was developed to streamline genetic mapping using SNP arrays and to also provide an easy method to convert and deposit genetic data into the CottonGen database. Results identified several QTL from each cross, indicating possible multiple modes of resistance. Multiple sources of resistance would provide several genetic routes to combat the virus as it evolves over time. Kompetitive allele specific PCR (KASP) markers were developed and validated for a subset of QTL, which can be used in further development of CLCuV-resistant cotton lines.
棉花曲叶病毒（CLCuV）给中亚的棉花纤维生产造成了毁灭性损失。在过去十年中，该病毒在亚洲各地传播，这引发了人们的担忧，即在培育出抗性品种之前，该病毒会进一步扩散。目前的进展依赖于在疾病流行的国家，在病害压力下对每一代进行筛选。我们利用在四个具有不同抗性来源的杂交组合中进行数量性状位点（QTL）定位，来鉴定与抗性性状相关的单核苷酸多态性（SNP）标记，从而能够培育出无需每代都进行田间筛选的品种。为了协助对多个群体进行分析，开发了一个新的公开可用的R/Shiny应用程序，以简化使用SNP阵列的遗传图谱绘制，并提供一种将遗传数据转换并存入CottonGen数据库的简便方法。结果在每个杂交组合中都鉴定出了几个QTL，表明可能存在多种抗性模式。随着病毒随时间演变，多种抗性来源将提供多条对抗该病毒的遗传途径。针对一部分QTL开发并验证了竞争性等位基因特异性PCR（KASP）标记，这些标记可用于进一步培育抗CLCuV的棉花品系。
