Shrestha Swati, Michael Vincent Njung'e, Fu Yuqing, Meru Geoffrey
Horticultural Sciences Department, Tropical Research and Education Center, University of Florida, Homestead, FL 33031, USA.
Plants (Basel). 2021 Sep 17;10(9):1935. doi: 10.3390/plants10091935.
Zucchini Yellow Mosaic Virus (ZYMV) is an aphid-transmitted potyvirus that causes severe yield losses in squash () production worldwide. Development of resistant cultivars using traditional breeding approaches relies on rigorous and resource-intensive phenotypic assays. QTL-seq, a whole genome re-sequencing based bulked segregant analysis, is a powerful tool for mapping quantitative trait loci (QTL) in crop plants. In the current study, the QTL-seq approach was used to identify genetic loci associated with ZYMV resistance in an F population (n = 174) derived from a cross between Nigerian Local (resistant) and Butterbush (susceptible). Whole genome re-sequencing of the parents and bulks of resistant and susceptible F progeny revealed a mapping rate between 94.04% and 98.76%, and a final effective mapping depth ranging from 81.77 to 101.73 across samples. QTL-seq analysis identified four QTLs significantly ( < 0.05) associated with ZYMV resistance on chromosome 2 (), 4 (), 8 () and 20 (). Seven markers within the QTL intervals were tested for association with ZYMV resistance in the entire F population. For , one single nucleotide polymorphism (SNP) marker (KASP-6) was found to be significantly ( < 0.05) associated with ZYMV resistance, while two SNPs (KASP-1 and KASP-3) and an indel (Indel-2) marker were linked to resistance within . KASP-3 and KASP-6 are non-synonymous SNPs leading to amino acid substitutions in candidate disease resistant gene homologs on chromosomes 20 () and 8 (), respectively. Identification of QTL and SNP markers associated with ZYMV resistance will facilitate marker-assisted selection for ZYMV resistance in squash.
西葫芦黄花叶病毒（ZYMV）是一种由蚜虫传播的马铃薯Y病毒，在全球南瓜生产中会导致严重的产量损失。利用传统育种方法培育抗性品种依赖于严格且资源密集型的表型分析。QTL-seq是一种基于全基因组重测序的混合分组分析法，是在作物中定位数量性状基因座（QTL）的强大工具。在本研究中，采用QTL-seq方法在一个由尼日利亚本地品种（抗性）与巴特布什（感病）杂交产生的F群体（n = 174）中鉴定与ZYMV抗性相关的基因座。对亲本以及抗性和感病F子代的混合样本进行全基因组重测序，样本的映射率在94.04%至98.76%之间，最终有效映射深度在81.77至101.73之间。QTL-seq分析在第2号（）、4号（）、8号（）和20号（）染色体上鉴定出四个与ZYMV抗性显著相关（< 0.05）的QTL。在整个F群体中，对QTL区间内的7个标记进行了与ZYMV抗性的关联测试。对于，发现一个单核苷酸多态性（SNP）标记（KASP - 6）与ZYMV抗性显著相关（< 0.05），而两个SNP（KASP - 1和KASP - 3）和一个插入缺失（Indel - 2）标记与内的抗性相关。KASP - 3和KASP - 6是非同义SNP，分别导致20号（）和8号（）染色体上候选抗病基因同源物中的氨基酸替换。鉴定与ZYMV抗性相关的QTL和SNP标记将有助于在南瓜中进行ZYMV抗性的标记辅助选择。
