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Identification and validation of two major QTL for grain number per spike on chromosomes 2B and 2D in bread wheat (Triticum aestivum L.)

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Major QTL for grain number per spike were identified on chromosomes 2B and 2D. Haplotypes and candidate genes of QGns.cib-2B.1 were analyzed.


Grain number per spike (GNS) is one of the main components of wheat yield. Genetic dissection of their regulatory factors is essential to improve the yield potential. In present study, a recombinant inbred line population comprising 180 lines developed from the cross between a high GNS line W7268 and a cultivar Chuanyu12 was employed to identify quantitative trait loci (QTL) associated with GNS across six environments. Two major QTL, QGns.cib-2B.1 and QGns.cib-2D.1, were detected in at least four environments with the phenotypic variations of 12.99–27.07% and 8.50–13.79%, respectively. And significant interactions were observed between the two major QTL. In addition, QGns.cib-2B.1 is a QTL cluster for GNS, grain number per spikelet and fertile tiller number, and they were validated in different genetic backgrounds using Kompetitive Allele Specific PCR (KASP) markers. QGns.cib-2B.1 showed pleotropic effects on other yield-related traits including plant height, spike length, and spikelet number per spike, but did not significantly affect thousand grain weight which suggested that it might be potentially applicable in breeding program. Comparison analysis suggested that QGns.cib-2B.1 might be a novel QTL. Furthermore, haplotype analysis of QGns.cib-2B.1 indicated that it is a hot spot of artificial selection during wheat improvement. Based on the expression patterns, gene annotation, orthologs analysis and sequence variations, the candidate genes of QGns.cib-2B.1 were predicted. Collectively, the major QTL and KASP markers reported here provided a wealth of information for the genetic basis of GNS and grain yield improvement.

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Data availability statement

All data and materials described in this paper are available from the corresponding author upon request. The datasets retrieved and analyzed during the current study are available in the Triticeae Multi-omics Center (


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We express our gratitude to the Triticeae Multi-omics Center ( for providing us with an integrated platform of tools and genomic data, which greatly facilitated our research. We also acknowledge the Wheat-SnpHub-Portal ( for providing the genomic variation datasets of wheat, and Bioacme Biotechnology Co., Ltd. (Wuhan, China, for their assistance with the BSR-Seq analysis.


This work is supported by the Sichuan Science and Technology Program, China (2022ZDZX0016), the West Light Foundation of the Chinese Academy of Sciences (2022XBZG_XBQNXZ_A_001), and the Major Science and Technology Achievement Transformation of Central Universities and Institutes in Sichuan Projects (2022ZHCG0131).

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Authors and Affiliations



SML conducted the field trials, analyzed the data, and drafted the manuscript. ZBX constructed the mapping population. XLF and QZ assisted with the field trails. SML, JC, XFL, FM and YLW participated in phenotyping. TW provided guidance throughout the study and contributed to result discussions. BF designed the experiments, participated in data analysis, discussed the results, and revised the manuscript. All authors have read and approved the final manuscript.

Corresponding author

Correspondence to Bo Feng.

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All authors declare that there is no conflict of interest.

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All experiments and data analyses were conducted in Sichuan. All authors contributed to the study and approved the final version for submission. The manuscript has not been submitted to any other journal.

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Communicated by Philomin Juliana.

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Liao, S., Xu, Z., Fan, X. et al. Identification and validation of two major QTL for grain number per spike on chromosomes 2B and 2D in bread wheat (Triticum aestivum L.). Theor Appl Genet 137, 147 (2024).

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