Development and application of the GenoBaits WheatSNP16K array to accelerate wheat genetic research and breeding

Shengjie Liu; Mingjie Xiang; Xiaoting Wang; Jiaqi Li; Xiangrui Cheng; Huaizhou Li; Ravi P Singh; Sridhar Bhavani; Shuo Huang; Weijun Zheng; Chunlian Li; Fengping Yuan; Jianhui Wu; Dejun Han; Zhensheng Kang; Qingdong Zeng

doi:10.1016/j.xplc.2024.101138

Development and application of the GenoBaits WheatSNP16K array to accelerate wheat genetic research and breeding

Plant Commun. 2025 Jan 13;6(1):101138. doi: 10.1016/j.xplc.2024.101138. Epub 2024 Sep 24.

Authors

Affiliations

¹ State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
² State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
³ International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, Estado de México 56237, Mexico; Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China.
⁴ International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, Estado de México 56237, Mexico.
⁵ Key Laboratory of Plant Design, Chinese Academy of Sciences, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200000, China.
⁶ State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China. Electronic address: handj@nwafu.edu.cn.
⁷ State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China. Electronic address: kangzs@nwsuaf.edu.cn.
⁸ State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China. Electronic address: zengqd@nwafu.edu.cn.

PMID: 39318097
DOI: 10.1016/j.xplc.2024.101138

Abstract

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.

Keywords: genotyping by target sequencing; liquid array; resistance gene; stripe rust; wheat.

MeSH terms

Chromosome Mapping / methods
Genome, Plant
Genotyping Techniques / methods
Plant Breeding* / methods
Plant Diseases / genetics
Plant Diseases / microbiology
Polymorphism, Single Nucleotide*
Triticum* / genetics