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Identification of a major QTL and genome-wide epistatic interactions for single vs. paired spikelets in a maize-teosinte F2 population

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Abstract

Maize ear carries paired spikelets, whereas the ear of its wild ancestor, teosinte, bears single spikelets. However, little is known about the genetic basis of the processes of transformation of single spikelets in teosinte ear to paired spikelets in maize ear. In this study, a two-ranked, paired-spikelets primitive maize and a two-ranked, single-spikelet teosinte were utilized to develop an F2 population, and quantitative trait locus (loci) (QTL) mapping for single vs. paired spikelets (PEDS) was performed. One major QTL (qPEDS3.1) for PEDS located on chromosome 3S was identified in the 162 F2 plants using the inclusive composite interval mapping of additive (ICIM-ADD) module, explaining 23.79% of the phenotypic variance. Out of the 409 F2 plants, 43 plants with PEDS = 0% and 43 plants with PEDS > 20% were selected for selective genotyping, and the QTL (qPEDS3.1) was detected again. Moreover, the QTL (qPEDS3.1) was validated in three environments, which explained 31.05%, 38.94%, and 23.16% of the phenotypic variance, respectively. In addition, 50 epistatic QTLs were detected in the 162 F2 plants using the two-locus epistatic QTL (ICIM-EPI) module; they were distributed on all 10 chromosomes and explained 94.40% of the total phenotypic variance. The results contribute to a better understanding of the genetic basis of domestication of paired spikelets and provide a genetic resource for future map-based cloning; in addition, the systematic dissection of epistatic interactions underlies a theoretical framework for overcoming epistatic effects on QTL fine mapping.

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The data are provided in the Supplementary information and the materials available on request from the authors.

Abbreviations

DISA:

Tendency of ear to shatter

FM:

Floral meristems

GLUM:

Hardness and angle of outer glume

InDel:

Insertion-deletion

LIBN:

Number of branches in primary lateral inflorescence

NILs:

Near-isogenic lines

RANK:

Number of rows of cupules

SDRs:

Segregation distortion regions

SM:

Spikelet meristems

SPM:

Spikelet pair meristems

OPA:

Oligonucleotides pool assay

PEDS:

Percentage of cupules lacking the pedicellate spikelet

QTL:

Quantitative trait locus (loci

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Funding

This research was provided by the National Basic Research Program of China (the “973” project, 2014CB138203), the State Key Laboratory of Grassland Agro-ecosystems (SKLGAE201509), and the National Natural Science Foundation of China (31101161).

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Author notes

  1. Zhengjie Chen and Kun Hu contributed equally to this work.

Authors and Affiliations

  1. Maize Research Institute, Sichuan Agricultural University, No.211 Huiming Road, Wenjiang District, Chengdu, 611130, Sichuan, China

    Zhengjie Chen, Kun Hu, Yong Yin, Dengguo Tang, Jixing Ni, Peng Li, Le Wang, Tingzhao Rong & Jian Liu

  2. Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avenue, Qingbaijiang District, Chengdu, 610300, Sichuan, China

    Zhengjie Chen

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  1. Zhengjie Chen
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  2. Kun Hu
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Contributions

J.L and T.R conceived and designed the experiments. ZC, KH, YY, DT, JN, PL, and LW conducted phenotyping measurement in the field trial and performed the experiments. ZC analyzed the data. ZC and JL wrote and revised the manuscript.

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Correspondence to Jian Liu.

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Chen, Z., Hu, K., Yin, Y. et al. Identification of a major QTL and genome-wide epistatic interactions for single vs. paired spikelets in a maize-teosinte F2 population. Mol Breeding 42, 9 (2022). https://doi.org/10.1007/s11032-022-01276-x

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