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High-density genetic linkage map based on arbitrary and microsatellite markers using inter-specific recombinant inbred lines in eggplant (Solanum melongena L.)

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Abstract

Eggplant is an important Solanaceous vegetable crop with distinct morphological forms, colours, and shape of the fruits. Limited genomic coverage of the crop is a major constraint to unfold the cause of morphological variations underlying the contrasting traits. Therefore, with the aim to initiate targeted breeding efforts and to render ready-to-use markers for application in map** quantitative trait loci (QTLs)/genes and to facilitate MAS, arbitrary and microsatellite molecular markers were used to map an inter-specific map** population of 114 F8-recombinant inbred lines (RILs) developed using two contrasting lines, Ramnagar Giant (Solanum melongena L.) and W-4 (S. incanum L.). The arbitrary and microsatellite markers were screened for polymorphism with aim to cover the whole genome of eggplant. Of the total 1443 number of markers investigated, 6.07% RAPDs, 25% ISSR, 46.25% SCoT, and 22.46% SSRs revealed polymorphism between the parental lines, and were used for genoty** the RILs population. The results exhibit robust and sturdy nature of SCoT and microsatellite markers in unwrap** variations between both genotypes. Further, a high-density genetic linkage map was constructed with LOD threshold ≥ 4 clustered into 12 tentative linkage groups and spanning 1165 cM of the eggplant genome with an average marker density of 4.13 cM. The results shall further be used in map** QTLs of agri-horticultural traits in eggplant.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

APS:

Ammonium persulphate

BC:

Back cross

CGA:

Chlorogenic acid

cM:

Centimorgan

CTAB:

Cetyl trimethyl ammonium bromide

GBS:

Genoty** by sequencing

ISSR:

Inter simple sequence repeats

LG:

Linkage groups

LOD:

Logarithm of odds

MAS:

Marker assisted selection

NCBI:

National Centre for Biotechnology Information

NGS:

Next generation sequencing

PAGE:

Polyacrylamide gel electrophoresis

PCR:

Polymerase chain reaction

QTL:

Quantitative trait loci

RAD:

Restriction-site associated DNA

RAPD:

Random amplified polymorphic DNA

RFLP:

Restriction fragment length polymorphism

RIL:

Recombinant inbred line

SCoT:

Start codon targeted

SNV:

Single nucleotide variants

SSR:

Simple sequence repeat

STMS:

Sequence tagged microsatellite site

SBG:

Sequence-based genoty**

TEMED:

Tetramethylethylenediamine

TSA:

Transcriptome shotgun assembly

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Acknowledgements

Authors thankfully acknowledge the support of the Director, ICAR-Indian Institute of Vegetable Research, Varanasi for providing field and laboratory facilities necessary to carry out the present study.

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Author notes

  1. Major Singh

    Present address: ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, Maharashtra, 410505, India

Authors and Affiliations

  1. Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, 221305, India

    Pallavi Mishra, Shailesh K. Tiwari, Sarvesh P. Kashyap & Major Singh

  2. Department of Botany, MMV, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India

    Pallavi Mishra & Kavindra N. Tiwari

  3. Uttar Pradesh Council of Agriculture Research, Lucknow, Uttar Pradesh, India

    Bijendra Singh

Authors
  1. Pallavi Mishra
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  2. Shailesh K. Tiwari
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  3. Sarvesh P. Kashyap
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  4. Kavindra N. Tiwari
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  5. Major Singh
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  6. Bijendra Singh
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Correspondence to Shailesh K. Tiwari.

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Supplementary Table S1

Nucleotide sequence and obtained allele size in polymorphic arbitrary markers. (XLSX 15 kb)

Supplementary Table S2

Nucleotide sequence and obtained allele size in polymorphic microsatellite markers. (XLSX 38 kb)

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Mishra, P., Tiwari, S.K., Kashyap, S.P. et al. High-density genetic linkage map based on arbitrary and microsatellite markers using inter-specific recombinant inbred lines in eggplant (Solanum melongena L.). J. Plant Biochem. Biotechnol. 29, 427–438 (2020). https://doi.org/10.1007/s13562-020-00549-w

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