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Trait Mapping Approaches Through Linkage Mapping in Plants

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Plant Genetics and Molecular Biology

Part of the book series: Advances in Biochemical Engineering/Biotechnology ((ABE,volume 164))

Abstract

Quantitative trait loci (QTL) mapping in crop plants has now become a common practice due to the advances made in the area of molecular markers as well as that of statistical genomics. Consequently, large numbers of QTLs have been identified in different crops for a variety of traits. Several computational tools are now available that suit the type of mapping population and the trait(s) to be studied for QTL analyses as well as the objective of the program. These methods are comprised of simpler approaches like single marker analysis and simple interval mapping to relatively exhaustive inclusive composite interval mapping and Bayesian interval mapping. The relative significance of each of these methods varies considerably. The progress made in the area of computational analysis involving the identification of QTLs either through interval mapping or association mapping is unprecedented, and it is expected that it will continue to evolve over the coming years. An overview of the different methods of linkage-based QTL analysis is provided in this chapter.

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Abbreviations

AB-QTL:

Advanced backcross QTL

AM:

Association mapping

BSA:

Bulk segregant analysis

CIM:

Composite interval mapping

DH:

Doubled haploid

EM algorithm:

Expectation maximization algorithm

eQTL:

Expression QTL

GLM:

General linear model

GS:

Genomic selection

GWAS:

Genome wide association studies

ICIM:

Inclusive composite interval mapping

IM:

Interval mapping

JLAM:

Joint linkage-association mapping

LD:

Linkage disequilibrium

MAGIC:

Multi-parent advanced generation intercross

MAS:

Marker-assisted selection

MCILs:

Multiline cross-inbred lines

MIM:

Multiple interval mapping

M-QTL:

Main effect QTL

mQTL:

Metabolite QTL

MTA:

Marker-trait association

MTMIM:

Multiple-trait multiple interval mapping

NAM:

Nested association mapping

pQTL:

Protein QTL

QDR:

Quantitative disease resistance

QE:

QTL × environment interactions

QQ:

QTL × QTL interactions

QQE:

QTL × QTL × environment interactions

QRL:

Quantitative resistance loci

QTL:

Quantitative trait loci

RIAILs:

Recombinant inbred advanced intercross lines

SIM:

Simple interval mapping

SMA:

Single marker analysis

TFM:

Time-fixed mapping

TRM:

Time-related mapping

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  1. State Level Biotechnology Centre, Mahatma Phule Agricultural University, Rahuri, Maharashtra, India

    Pawan L. Kulwal

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  1. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India

    Rajeev K. Varshney

  2. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India

    Manish K. Pandey

  3. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India

    Annapurna Chitikineni

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Kulwal, P.L. (2018). Trait Mapping Approaches Through Linkage Mapping in Plants. In: Varshney, R., Pandey, M., Chitikineni, A. (eds) Plant Genetics and Molecular Biology. Advances in Biochemical Engineering/Biotechnology, vol 164. Springer, Cham. https://doi.org/10.1007/10_2017_49

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