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Recent advances in molecular marker techniques: Insight into QTL mapping, GWAS and genomic selection in plants

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Abstract

Recent advances in sequencing technology have brought several novel platforms for marker development and subsequent genotyping. The high-throughput and cost effective marker techniques have changed the entire scenario of marker applications. The huge genotypic data obtained with next generation sequencing (NGS) also demands analytical tools, statistical advances, and comprehensive understanding to cope with breeding applications. In the present review, we discussed different available marker techniques, their strengths, and limitations. Emphasis was given on software tools, analytical pipelines, workbenches, and online resources available for marker development. Comparison of SNP genotyping involving complexity reduction techniques like GBS, RRL, RAD, and array-based platforms were presented in a view to describe suitability for specific purposes. We found that genotyping by whole genome re-sequencing has great potential, and could be a routine application in the near future with continuously decreasing cost of sequencing. Microsatellites, still a valuable option for breeders, have also advanced with NGS. Here a catalogue of tools for microsatellite evaluation in short sequence reads was provided. The most common applications of molecular marker like QTL mapping, genome-wide association mapping (GWAS), and genomic selection were highlighted. The present review will be helpful for the effective utilization of available resources and for the planning of crop improvement programs employing molecular marker techniques.

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Abbreviations

AFLP:

amplified fragment length polymorphism

CRoPS:

complexity reduction of polymorphic sequences

DArT:

diversity array technology

EST:

expressed sequence tag

GBS:

genotyping by sequencing

GS:

genomic selection

GWAS:

genomewide association studies

MAS:

marker-assisted selection

NGS:

next generation sequencing

PCR:

polymerase chain reaction

QTL:

quantitative trait loci

RAD:

restriction site-associated DNA

RFLP:

restriction fragment length polymorphism

RRLs:

reduced-representation libraries

RRS:

reduced representation sequencing

SCAR:

sequence characterized amplified region

SGS:

second generation sequencing

STS:

sequence tagged site

TILLING:

targeting induced local lesions in genomes

WGS:

whole genome sequencing

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Authors and Affiliations

  1. Centre for Plant Biotechnology, Division of Biotechnology, S K University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, 190025, India

    Sajad Majeed Zargar

  2. International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia

    Bodo Raatz

  3. Département de phytologie-FSAA, Université Laval, Québec, Qc, G1V 0A6, Canada

    Humira Sonah

  4. Department of Botany, Faculty of Science, Jamia Hamdard University, New Delhi, 110062, India

    MuslimaNazir

  5. Division of Plant Breeding & Genetics, S K University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu, Jammu & Kashmir, 180009, India

    Javid A. Bhat

  6. Division of Plant Breeding & Genetics, S K University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, 190025, India

    Zahoor Ahmad Dar

  7. IndiaResearch Laboratory for Biotechnology and Biochemistry (RLABB), P.O. Box 13265, Kathmandu, Nepal

    Ganesh Kumar Agrawal & Randeep Rakwal

  8. Organization for Educational Initiatives, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, 305-8577, Ibaraki, Japan

    Randeep Rakwal

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  1. Sajad Majeed Zargar
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Zargar, S.M., Raatz, B., Sonah, H. et al. Recent advances in molecular marker techniques: Insight into QTL mapping, GWAS and genomic selection in plants. J. Crop Sci. Biotechnol. 18, 293–308 (2015). https://doi.org/10.1007/s12892-015-0037-5

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  • DOI: https://doi.org/10.1007/s12892-015-0037-5

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