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A 4.43-Kb deletion of chromosomal segment containing an ovate family protein confers long capsule in sesame (Sesamum indicum L.)

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Abstract

Key message

A 4.43-Kb structural variation in the sesame genome results in the deletion of the Siofp1 gene and induces the long capsule length trait.

Abstract

Capsule length (CL) has a positive effect on seed weight and yield in various agronomically important species; however, the molecular mechanism underlying long capsule trait regulation in sesame remains unknown. The inheritance analysis showed that long capsule traits (CL > 4.0 cm) were dominant over normal length (average CL = 3.0 cm) and were controlled by a single gene pair. Association mapping with a RIL population and 259 natural sesame germplasm accessions indicated that the target interval was 52,830–730,961 bp of SiChr.10 in sesame. Meanwhile, the structural variation (SV) of the association mapping revealed that only SV_414325 on chromosome 10 was significantly associated with the CL trait, with a P value of 1.1135E−19. SV_414325 represents a 4430-bp deletion from 414,325 to 418,756 bp on SiChr.10, covering Sindi_2155000 (named SiOFP1). In the normal length type, Siofp1 encodes 411 amino acids of the ovate family proteins and is highly expressed in the leaf, stem, bud, and capsule tissues of sesame. In accordance with the transcriptional repressor character, Siofp1 overexpression in transgenic Arabidopsis (T0 and T1 generations) induced a 25–39% greater shortening of silique length than the wild type (P < 0.05), as well as round cauline leaves and short carpels. These results confirm that SiOFP1 plays a key role in regulating CL trait in sesame and other flowering plants. These findings provide a theoretical and material basis for sesame capsule development and high-yield breeding research.

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Data availability

The cDNA sequence of Siofp1 gene has been submitted to NCBI dataset (NCBI accession no. MT394498). All data supporting the conclusions of this article are provided within the article (and its Supplementary Information).

Abbreviations

CL:

Capsule length

DELs:

Deletions

DUPs:

Duplications

EMS:

Ethylmethane sulfonate

GLM:

General linear model

GN:

Grain number per capsule

GWAS:

Genome-wide association studies

INSs:

Insertions

INVs:

Inversions

InDel:

Insertion–deletion

KEGG:

Kyoto Encyclopedia of Genes and Genomes

LD:

Linkage disequilibrium

LG:

Linkage group

NR:

Non-redundant

PCA:

Principal component analysis

OFP:

Ovate family protein

QTL:

Quantitative trait loci

qRT-PCR:

Quantitative real-time PCR

RIL:

Recombinant inbred line

SV:

Structural variation

SNP:

Single nucleotide polymorphism

TRAs:

Translocations

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Acknowledgements

This work was supported by the earmarked fund of China Agriculture Research System of MOF and MARA (CARS-14-1-04), the Key Project of Science and Technology in Henan Province (201300110600), the Shennong Laboratory First Class Program (SN01-2022-04), the National Natural Science Foundation of China (No. 32172094), the Henan Province Specific Professor Position Program (SPPP2022), the Innovation Scientists and Technicians Troop Construction Projects of Henan Province (2023TD04), Key Research and Development Project of Henan Province (221111520400) and Science and Technology Foundation for The Excellent Youth Scholars of Henan Academy of Agricultural Sciences (2022YQ14).

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Authors and Affiliations

  1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China

    Cuiying Wang, Jiaojiao Niu & Haiyang Zhang

  2. Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People’s Republic of China

    Cuiying Wang, Libin Wei, Chun Li, Guiting Li, Qiuzhen Tian, Ming Ju, Qin Ma, Hengchun Cao, Yinghui Duan, Hui Guo, Haiyang Zhang & Hongmei Miao

  3. The Shennong Laboratory, Zhengzhou, 450002, Henan, China

    Chun Li, Yinghui Duan & Haiyang Zhang

  4. Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China

    Cuiying Wang, Libin Wei, Chun Li, Guiting Li, Qiuzhen Tian, Ming Ju, Qin Ma, Hengchun Cao, Yinghui Duan, Hui Guo, Haiyang Zhang & Hongmei Miao

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Contributions

ZH conceived the technical route and guided the manuscript for publishing. MH, WL and WC guided the experiments, performed the data analysis and drafted the manuscript. LC, LG, CH, NJ and GH conducted the main data analysis and experiments. TQ, JM and MQ performed the genetic experiments and participated in result validation. All authors read and approved the final manuscript.

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Wang, C., Niu, J., Wei, L. et al. A 4.43-Kb deletion of chromosomal segment containing an ovate family protein confers long capsule in sesame (Sesamum indicum L.). Theor Appl Genet 136, 221 (2023). https://doi.org/10.1007/s00122-023-04465-0

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