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A major QTL simultaneously increases the number of spikelets per spike and thousand-kernel weight in a wheat line

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Abstract

Key message

A novel and stably expressed QTL QSNS.sicau-SSY-7A for spikelet number per spike in wheat without negative effects on thousand-kernel weight was identified and validated in different genetic backgrounds.

Abstract

Spikelet number per spike (SNS) is an important determinant of yield in wheat. In the present study, we combined bulked segregant analysis (BSA) and the wheat 660 K single-nucleotide polymorphism (SNP) array to rapidly identify genomic regions associated with SNS from a recombinant inbred line (RIL) population derived from a cross between the wheat lines S849-8 and SY95-71. A genetic map was constructed using Kompetitive Allele Specific PCR markers in the SNP-enriched region on the long arm of chromosome 7A. A major and stably expressed QTL, QSNS.sicau-SSY-7A, was detected in multiple environments. It was located in a 1.6 cM interval on chromosome arm 7AL flanked by the markers AX-109983514 and AX-109820548. This QTL explained 6.86–15.72% of the phenotypic variance, with LOD values ranging from 3.66 to 8.66. Several genes associated with plant growth and development were identified in the interval where QSNS.sicau-SSY-7A was located on the ‘Chinese Spring’ wheat and wild emmer reference genomes. Furthermore, the effects of QSNS.sicau-SSY-7A and WHEAT ORTHOLOG OFAPO1(WAPO1) on SNS were analyzed. Interestingly, QSNS.sicau-SSY-7A significantly increased SNS without negative effects on thousand-kernel weight, anthesis date and plant height, demonstrating its great potential for breeding aimed at improving grain yield. Taken together, these results indicate that QSNS.sicau-SSY-7A is a promising locus for yield improvement, and its linkage markers are helpful for fine mapping and molecular breeding.

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Data availability

All data generated or analyzed during this study are included in this published article and its supplementary information files or from the corresponding authors upon reasonable request.

Abbreviations

SNS:

Spikelet number per spike

BSA:

Bulked segregant analysis

SNP:

Single-nucleotide polymorphism

RIL:

Recombinant inbred line

KNS:

Kernel number per spike

TKW:

Thousand-kernel weight

QTL:

Quantitative trait loci

KASP:

Kompetitive allele-specific PCR

BLUP:

Best linear unbiased prediction

AD:

Anthesis date

PTN:

Productive tiller number

PH:

Plant height

SL:

Spike length

KL:

Kernel length

SSY:

S849-8/SY95-71 (216 F6 lines including two parents)

SCN:

S849-8/CN16 (217 F6 lines including two parents)

S83:

S849-8/3642 (227 F6 lines including two parents)

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Acknowledgements

We thank the anonymous referees for critical reading and revising this manuscript.

Funding

This work is supported by the National Natural Science Foundation of China (31971937 and 31970243), Natural Science Foundation of Sichuan Province (2022NSFSC1729 and 2023NSFSC0223), the Key Research and Development Program of Sichuan Province (2022ZDZX0014 and 2021YFYZ0002), Sichuan Science and Technology Program (2021YFH0083), and Sichuan Province Science Foundation for Distinguished Young Scholars (2022JDJQ0006). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Author notes

  1. Conghao Zhao and Jieguang Zhou contributed equally to this paper.

Authors and Affiliations

  1. State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China

    Conghao Zhao, Jieguang Zhou, Cong Li, Yanling Liu, Huaping Tang, Mei Deng, Qiang Xu, Yazhou Zhang, Qiantao Jiang, Guoyue Chen, Pengfei Qi, Yunfeng Jiang, Jirui Wang, Youliang Zheng, Yuming Wei & Jian Ma

  2. Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China

    Conghao Zhao, Jieguang Zhou, Cong Li, Yanling Liu, Huaping Tang, Mei Deng, Qiang Xu, Yazhou Zhang, Qiantao Jiang, Guoyue Chen, Pengfei Qi, Yunfeng Jiang, Jirui Wang, Youliang Zheng, Yuming Wei & Jian Ma

  3. College of Agronomy, Sichuan Agricultural University, Chengdu, China

    Wei Li & Zhien Pu

  4. College of Resources, Sichuan Agricultural University, Chengdu, China

    Guangdeng Chen

  5. Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy ofAgricultural Sciences, Chengdu, China

    Yun Jiang

  6. CSIRO Agriculture and Food, 306 Carmody Road, Saint Lucia, QLD, 4067, Australia

    Zhi Zheng & Chunji Liu

  7. Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China

    Jianing You

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  1. Conghao Zhao
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Contributions

CHZ finished the study and wrote this manuscript. JGZ participated in field work and analyzed data. CL, JNY and YLL helped with the phenotype measurement and data analysis. HPT, MD, QX, YZZ and QTJ did field work and data analysis. GYC, PFQ, YFJ and JRW collected and analyzed data. WL, ZEP, GDC and YJ helped with data analysis. ZZ, CJL and YLZ revised the manuscript. YMW discussed results and revised the manuscript. JM designed the experiments, guided the entire study, participated in data analysis, wrote and extensively revised this manuscript. All authors participated in the research and approved the final manuscript.

Corresponding authors

Correspondence to Yuming Wei or Jian Ma.

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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 Diane E. Mather.

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Supplementary Information

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Fig. S1 Schematic diagram of construction mixed pools

Supplementary file1 (TIF 624 KB)

Fig. S2 Reintegration of genetic map for SSY population with the inclusion of KASP-WAPO1

Supplementary file2 (TIF 3814 KB)

122_2023_4459_MOESM3_ESM.tif

Fig. S3 Analysis of the effect of QSNS.sicau-SSY-7A on agronomic traits. kernel length (KL); thousand-kernel weight (TKW); spike length (SL); plant height (PH); anthesis date (AD); productive tiller number (PTN). ‘+’ and ‘−’ represent homozygous lines carrying ‘S849-8’ and ‘SY95-71’ alleles, respectively. **Significance at the 0.01 probability level. *Significant difference at the 0.05 probability level

Supplementary file3 (TIF 1755 KB)

122_2023_4459_MOESM4_ESM.tif

Fig. S4 Pyramid analysis of the effects of QSNS.sicau-SSY-7A and WAPO1 on other agronomic traits. Kernel length (KL); Spike length (SL); Plant height (PH); Anthesis date (AD); Productive tiller number (PTN). ‘+’ and ‘−’ represent homozygous lines carrying ‘S849-8’ and ‘SY95-71’ alleles, respectively. Differences between the two groups were labeled above the significant levels **Significance at the 0.01 probability level. *Significance at the 0.05 probability level

Supplementary file4 (TIF 2060 KB)

Fig. S5 Analysis of spatiotemporal expression patterns of some genes within the interval

Supplementary file5 (TIF 8028 KB)

Supplementary file6 (DOCX 17 KB)

Supplementary file7 (DOCX 19 KB)

Supplementary file8 (DOCX 16 KB)

Supplementary file9 (DOCX 16 KB)

Supplementary file10 (DOCX 17 KB)

Supplementary file11 (DOCX 19 KB)

Supplementary file12 (DOCX 18 KB)

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Zhao, C., Zhou, J., Li, C. et al. A major QTL simultaneously increases the number of spikelets per spike and thousand-kernel weight in a wheat line. Theor Appl Genet 136, 213 (2023). https://doi.org/10.1007/s00122-023-04459-y

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