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Dissection and validation of a promising QTL controlling spikelet number on 5B in bread wheat

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Abstract

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Five environmentally stable QTLs for spikelet number per spike and days to heading were identified using a high-genetic map containing 95,444 SNPs, among which QSns.ucas-5B was validated using residual heterozygous line at multiple environments.

Abstract

Spikelet number per spike (SNS) and days to heading (DTH) play pivotal roles in the improvement of wheat yield. In this study, a high-density genetic map for a recombinant inbred lines (RILs) population derived from Zhengnong 17 (ZN17) and Yangbaimai (YBM) was constructed using 95,444 single-nucleotide polymorphism (SNP) markers from the Wheat660K SNP array. Our study identified a total of five environmentally stable QTLs for SNS and DTH, one of which was named QSns.ucas-5B, with a physical interval of approximately 545.4–552.1 Mb on the 5BL chromosome arm. Importantly, the elite haplotype within QSns.ucas-5B showed a consistent and positive effect on SNS, grain number and weight per spike, without extending the days to heading. These findings provide a foundation for future efforts to map and clone the gene(s) responsible for QSns.ucas-5B and further indicate the potential application of the developed and validated InDel marker of QSns.ucas-5B for molecular breeding purposes, aimed at improving wheat grain yield.

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Availability of data and material

All data generated or analyzed during this study are included in the main text article and its supplementary files. The raw sequencing data of ZN17 and YBM have been deposited in National Genomics Data Center (NGDC, https://ngdc.cncb.ac.cn/) under accession numbers CRR290233 and CRR290167, respectively.

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Funding

This work was supported by grants from the Strategic Priority Research Program of Chinese Academy of Sciences (Grant No. XDA24010104-1) and China Postdoctoral Science Foundation (2022M710163).

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Author notes

  1. Yaoqi Si, Shuiquan Tian and Jianqing Niu have equally contributed to this work.

Authors and Affiliations

  1. State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Bei**g, 100101, China

    Yaoqi Si, Shuiquan Tian, Jianqing Niu, Shengwei Ma, Huilan Wu, Hong-Qing Ling & Shusong Zheng

  2. College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Bei**g, 100049, China

    Shuiquan Tian, Qiao Lu, Huilan Wu, Hong-Qing Ling & Shusong Zheng

  3. National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China

    Zhongqing Yu

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  1. Yaoqi Si
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Contributions

H-Q L and SZ conceived the project and revised the manuscript; SZ developed the map** population; YS, ST, JN, ZY, SM, QL and HW carried out the experiments; YS analyzed data and wrote the manuscript; all authors assisted in revising the manuscript.

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Correspondence to Hong-Qing Ling or Shusong Zheng.

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Fig. S1

Based on the physical locations of these mapped markers on the IWGSC RefSeq v2.1 genome, the marker order was relatively consistent with that in the wheat genome assembly on most of the chromosomes, except for part of chromosome 1A and 6B. The ordinate and abscissa represent the physical position and the genetic position of markers, respectively. (PPT 172KB)

Fig. S2

Frequency distribution and Shapiro-Wilk test indicated that spikelet number per spike exhibited normal distribution with the BLUP value of nine environments (P > 0.05). (PPT 45KB)

Fig. S3

The stable QTL on 1B may be located on the 1BS/1RS translocation chromosome. (a) and (b) represent the results of map** spikelet number per spike using partial 1BL and 1B full-length genetic map, respectively. Colored lines represent environments (E1–9). (PPT 123KB)

Fig. S4

Days to heading of QSns.ucas-5B in different environments. Significant differences were detected between lines RHL-55YBM and RHL-55ZN17 derived from a residual heterogeneous line at the QSns.ucas-5B region. Statistical analysis was carried out using Student's t-test and significance was denoted by ** for P < 0.01. (PPT 42KB)

Fig. S5

The expression pattern of two candidate genes in different tissues.

The relevant data and analysis was download from the WheatOmics database (http://wheatomics.sdau.edu.cn/) constructed by Ma et al. (2021). (PPT 483KB)

Fig. S6

The sequence alignment of candidate gene TraesCS5B03G0915200 between the two parents. Highlight homology level: black, 100%; pink, ≥ 75%; blue, ≥ 50%. (PPT 137KB)

Table S1

Detailed information of the nine planting environments. Table S2 The detail information of the high-density map constructed in the study. Table S3 The deleted SNPs located on 7B chromosome due to distorted segregation. Table S4 Correlation coefficients analysis among the mean values of spikelet number per spike and days to heading. Table S5 The reconstructed full-length 1B chromosome genetic map. Table S6 Effects of putative QTLs for spikelet number per spike in individual environments. Table S7 Putative function genes in the intervals of stable QTL. Table S8 Variant comparison in the interval of QSns.ucas-5B. Table S9 Analysis of amino acid polymorphism of parents within QSns.ucas-5B interval. Table S10 Comparative analysis of QSns.ucas-5B locus with previously study. (XLSX 3,387KB)

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Si, Y., Tian, S., Niu, J. et al. Dissection and validation of a promising QTL controlling spikelet number on 5B in bread wheat. Theor Appl Genet 136, 240 (2023). https://doi.org/10.1007/s00122-023-04488-7

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