Liu Shengjie, Xiang Mingjie, Wang Xiaoting, Li Jiaqi, Cheng Xiangrui, Li Huaizhou, Singh Ravi P, Bhavani Sridhar, Huang Shuo, Zheng Weijun, Li Chunlian, Yuan Fengping, Wu Jianhui, Han Dejun, Kang Zhensheng, Zeng Qingdong
State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
Plant Commun. 2025 Jan 13;6(1):101138. doi: 10.1016/j.xplc.2024.101138. Epub 2024 Sep 24.
Single-nucleotide polymorphisms (SNPs) are widely used as molecular markers for constructing genetic linkage maps in wheat. Compared with available SNP-based genotyping platforms, a genotyping by target sequencing (GBTS) system with capture-in-solution (liquid chip) technology has become the favored genotyping technology because it is less demanding and more cost effective, flexible, and user-friendly. In this study, a new GenoBaits WheatSNP16K (GBW16K) GBTS array was designed using datasets generated by the wheat 660K SNP array and resequencing platforms in our previous studies. The GBW16K array contains 14 868 target SNP regions that are evenly distributed across the wheat genome, and 37 669 SNPs in these regions can be identified in a diversity panel consisting of 239 wheat accessions from around the world. Principal component and neighbor-joining analyses using the called SNPs are consistent with the pedigree information and geographic distributions or ecological environments of the accessions. For the GBW16K marker panel, the average genetic diversity among the 239 accessions is 0.270, which is sufficient for linkage map construction and preliminary mapping of targeted genes or quantitative trait loci (QTLs). A genetic linkage map, constructed using the GBW16K array-based genotyping of a recombinant inbred line population derived from a cross of the CIMMYT wheat line Yaco"S" and the Chinese landrace Mingxian169, enables the identification of Yr27, Yr30, and QYr.nwafu-2BL.4 for adult-plant resistance to stripe rust from Yaco"S" and of Yr18 from Mingxian169. QYr.nwafu-2BL.4 is different from any previously reported gene/QTL. Three haplotypes and six candidate genes have been identified for QYr.nwafu-2BL.4 on the basis of haplotype analysis, micro-collinearity, gene annotation, RNA sequencing, and SNP data. This array provides a new tool for wheat genetic analysis and breeding studies and for achieving durable control of wheat stripe rust.
单核苷酸多态性（SNPs）被广泛用作构建小麦遗传连锁图谱的分子标记。与现有的基于SNP的基因分型平台相比，采用溶液捕获（液相芯片）技术的靶向测序基因分型（GBTS）系统已成为备受青睐的基因分型技术，因为它要求较低、成本效益更高、更灵活且用户友好。在本研究中，利用我们之前研究中通过小麦660K SNP芯片和重测序平台生成的数据集，设计了一种新的GenoBaits WheatSNP16K（GBW16K）GBTS芯片。GBW16K芯片包含14868个目标SNP区域，这些区域均匀分布在小麦基因组中，在一个由来自世界各地的239份小麦种质组成的多样性群体中，可以鉴定出这些区域中的37669个SNP。使用所调用的SNP进行的主成分分析和邻接法分析与种质的系谱信息以及地理分布或生态环境一致。对于GBW16K标记组，239份种质之间的平均遗传多样性为(0.270)，这足以用于构建连锁图谱以及对目标基因或数量性状位点（QTL）进行初步定位。利用基于GBW16K芯片对由国际玉米小麦改良中心（CIMMYT）小麦品系Yaco“S”与中国地方品种铭贤169杂交产生的重组自交系群体进行基因分型构建的遗传连锁图谱，能够鉴定出来自Yaco“S”的成株期抗条锈病基因Yr27、Yr30和QYr.nwafu - 2BL.4，以及来自铭贤169的Yr18。QYr.nwafu - 2BL.4与之前报道过的任何基因/QTL都不同。基于单倍型分析、微共线性、基因注释、RNA测序和SNP数据，已鉴定出QYr.nwafu - 2BL.4的三种单倍型和六个候选基因。该芯片为小麦遗传分析和育种研究以及实现对小麦条锈病的持久控制提供了一种新工具。
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