Researchers Uncover Genetic Basis of Wheat Spike Morphology Evolution Using High-Throughput Phenotyping Platform

A collaborative research team led by LU Fei from the Institute of Genetics and Developmental Biology and GUO Zifeng from Institute of Botany, Chinese Academy of Sciences (CAS), together with their colleagues, has pinpointed key genetic factors shaping wheat spike morphology—a critical trait for yield—using a high-throughput phenotyping platform. Their findings, published in Cell Reports, offer molecular targets to boost wheat yields via precision breeding.

 

The morphology of wheat spikes directly influences key yield components such as grain number per spike and thousand grain weight, but traditional manual measurements fail to precisely quantify local phenotypic variations in different spike regions (base, center, apex, etc.). This limitation not only hinders the fine-scale dissection of the genetic regulatory mechanisms underlying spike morphology but also results in insufficient mining of key genes controlling partial "source-sink" allocation in spikes, preventing optimal regulation of "source-sink" allocation efficiency. To address this, the research team developed an image-based high-throughput phenotyping platform, employing 3D segmentation technology to accurately measure spike parameters such as length, width, thickness, area, and volume. For the first time, the team systematically quantified 54 spike morphological traits (Figure 1), laying a crucial data foundation for in-depth genetic analysis of spike architecture.

 

Using genome-wide association studies (GWAS), the team identified 288 significantly associated genomic regions in a global panel of 306 wheat accessions and pinpointed 303 key regions in 1,053 Chinese-bred cultivars. The study revealed that geographical differentiation and breeding selection trends in spike morphology (e.g., intercontinental differences in spike volume) are primarily regulated by haplotype combinations. Notably, different haplotypes in the 2D chromosomal region (containing TaDA1 and Rht8 genes) significantly modulate spike length and width. Importantly, the negative correlation between spike length and width/thickness, commonly observed in global landraces, was overcome through modern breeding by selecting synergistic haplotypes (e.g., C-trait3-2D.1, C-trait9-1A.4, and C-trait15-5B.2).

 

Analysis of China's century-long breeding history showed that while spike length remained stable, continuous increases in spike width and thickness led to a significant boost in spike volume. Of particular interest, haplotypes controlling spike volume in different spatial partitions (P1-P5) exhibited directional enrichment during modern breeding. For instance, the frequency of the advantageous haplotype C-trait51-5B.2 surged from 12.6% to 61.14%. Molecular validation demonstrated that the favorable haplotype of TraesCS1D02G068300 could increase spike volume by 53.23%.

 

This critical finding not only confirms that haplotype stacking is an effective strategy for yield enhancement, but also provides key theoretical foundations and valuable genetic resources for molecular design of high-yield wheat varieties.

 

This study, a collaboration across multiple Chinese institutions, was supported by the CAS Strategic Priority Research Program, National Natural Science Foundation of China, and National Key Research and Development Program of China.

 

 

Article link: https://doi.org/10.1016/j.celrep.2025.116120

 

Contact:

Dr. LU Fei from the

Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

Email: flu@genetics.ac.cn

Dr. GUO Zifeng

Institute of Botany, Chinese Academy of Sciences

Email: guozifeng@ibcas.ac.cn