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Identification of novel QTL for plant height and internode length in wheat based on a 120K liquid-phase chip

Guan Pan-Feng1,Ge Shuai1,Wan Zi-Dong1,Li Meng-Xin1,Wang Xin-Yan1,Lu Jia-Ling1,Zhu Yu-Pan1,Li Bing1,Xu Hang-Bo1,Ma Ruo-Nan1,Jiao Zhen1,Wei Wen-Hui2,*,Cui Dong-Jie1,*   

  1. 1 School of Agriculture and Biomanufacturing, Zhengzhou University / Henan Key Laboratory of Ion-beam Green Agriculture Bioengineering, Zhengzhou 450001, Henan, China; 2 College of Agronomy and Life Sciences, Zhaotong University, Zhaotong 657000, Yunnan, China
  • Received:2026-04-30 Revised:2026-08-21 Accepted:2026-08-21 Published:2026-09-01
  • Supported by:
    This study was supported by the Scientific and Technological Research Project of Henan Province of China (242102111135), the Natural Science Foundation of Henan Province of China (242300421543), and the China Postdoctoral Science Foundation (2024M752946).

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Abstract: Plant height (PH) is a crucial agronomic trait that influences plant architecture and yield potential in wheat. An appropriate combination of PH and internode length (IL) not only enhances lodging resistance but also contributes to a higher harvest index, helping ensure high and stable yields. To further identify novel quantitative trait loci (QTL) controlling wheat PH and its components, a recombinant inbred line (RIL) population (AK58/ZYM2-RIL) comprising 183 lines was developed using the Chinese elite wheat variety Bainong Aikang 58 (AK58) as the maternal parent and the introduced variety Zhengyinmai 2 (ZYM2) as the paternal parent. A high-density genetic linkage map was constructed using the wheat 120K liquid-phase chip (120K-4HWA) genotyping data. Using phenotypic values from six field environments over three consecutive years, a genome-wide QTL analysis was conducted for PH and the five ILs in the AK58/ZYM2-RIL population. A total of 33 stable major QTL controlling PH and IL were detected on chromosomes 2D, 4B, 4D, 5A, 6A, 6B, and 7A, explaining 2.8% to 50.4% of the phenotypic variation. Among these, 24 allelic variations that reduced PH and IL originated from AK58. Additive effect analysis indicated that pyramiding favorable dwarfing alleles significantly reduced PH and each IL. The interactive functional gene discovery platform based on the wheat integrative regulatory network (wGRN) was used to predict candidate genes within stable major QTL intervals. A total of 25 potential candidate genes were identified, including the “Green Revolution” genes Rht1 and Rht2. Functional molecular markers were used to genotype Rht1, Rht2, and Rht8 within the intervals of QPh.zzu.4B.2, QPh.zzu.4D.1, and QPh.zzu.2D.2, respectively. The genetic effects of the Rht1 gene were verified using its near-isogenic lines, which were derived from a residual heterozygous line (RHL). Moreover, a competitive allele-specific PCR (KASP) marker was developed for the novel stable QTL QPh.zzu.5A.4/QIl2.zzu.5A.2 on chromosome 5AL controlling PH and IL for use in marker-assisted breeding. Overall, this study provides novel QTL and candidate genes for elucidating the genetic basis of wheat PH and its components, as well as functional molecular markers for breeding applications.

Key words: wheat, plant height, internode length, 120K liquid-phase chip, QTL, candidate gene, KASP marker

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