Identification of several small main-effect QTLs and a large number of epistatic QTLs for drought tolerance related traits in groundnut (Arachishypogaea L.)

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Abstract

Cultivated groundnut or peanut ( Arachis hypogaea L.), an allotetraploid (2 n = 4 x = 40), is a self pollinated and widely grown crop in the semi-arid regions of the world. Improvement of drought tolerance is an important area of research for groundnut breeding programmes. Therefore, for the identification of candidate QTLs for drought tolerance, a comprehensive and refined genetic map containing 191 SSR loci based on a single mapping population (TAG 24 × ICGV 86031), segregating for drought and surrogate traits was developed. Genotyping data and phenotyping data collected for more than ten drought related traits in 2–3 seasons were analyzed in detail for identification of main effect QTLs (M-QTLs) and epistatic QTLs (E-QTLs) using QTL Cartographer, QTLNetwork and Genotype Matrix Mapping (GMM) programmes. A total of 105 M-QTLs with 3.48–33.36% phenotypic variation explained (PVE) were identified using QTL Cartographer, while only 65 M-QTLs with 1.3–15.01% PVE were identified using QTLNetwork. A total of 53 M-QTLs were such which were identified using both programmes. On the other hand, GMM identified 186 (8.54–44.72% PVE) and 63 (7.11–21.13% PVE), three and two loci interactions, whereas only 8 E-QTL interactions with 1.7–8.34% PVE were identified through QTLNetwork. Interestingly a number of co-localized QTLs controlling 2–9 traits were also identified. The identification of few major, many minor M-QTLs and QTL × QTL interactions during the present study confirmed the complex and quantitative nature of drought tolerance in groundnut. This study suggests deployment of modern approaches like marker-assisted recurrent selection or genomic selection instead of marker-assisted backcrossing approach for breeding for drought tolerance in groundnut.

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Z. -B. Zeng (1994)

Adequate separation of effects of possible multiple linked quantitative trait loci (QTLs) on mapping QTLs is the key to increasing the precision of QTL mapping. A new method of QTL mapping is proposed and analyzed in this paper by combining interval mapping with multiple regression. The basis of the proposed method is an interval test in which the test statistic on a marker interval is made to be unaffected by QTLs located outside a defined interval. This is achieved by fitting other genetic markers in the statistical model as a control when performing interval mapping. Compared with the current QTL mapping method (i.e., the interval mapping method which uses a pair or two pairs of markers for mapping QTLs), this method has several advantages. (1) By confining the test to one region at a time, it reduces a multiple dimensional search problem (for multiple QTLs) to a one dimensional search problem. (2) By conditioning linked markers in the test, the sensitivity of the test statistic to the position of individual QTLs is increased, and the precision of QTL mapping can be improved. (3) By selectively and simultaneously using other markers in the analysis, the efficiency of QTL mapping can be also improved. The behavior of the test statistic under the null hypothesis and appropriate critical value of the test statistic for an overall test in a genome are discussed and analyzed. A simulation study of QTL mapping is also presented which illustrates the utility, properties, advantages and disadvantages of the method.

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Expressed sequence tag (EST) projects have generated a vast amount of publicly available sequence data from plant species; these data can be mined for simple sequence repeats (SSRs). These SSRs are useful as molecular markers because their development is inexpensive, they represent transcribed genes and a putative function can often be deduced by a homology search. Because they are derived from transcripts, they are useful for assaying the functional diversity in natural populations or germplasm collections. These markers are valuable because of their higher level of transferability to related species, and they can often be used as anchor markers for comparative mapping and evolutionary studies. They have been developed and mapped in several crop species and could prove useful for marker-assisted selection, especially when the markers reside in the genes responsible for a phenotypic trait. Applications and potential uses of EST-SSRs in plant genetics and breeding are discussed.

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It is now possible to use complete genetic linkage maps to locate major quantitative trait loci (QTLs) on chromosome regions. The current methods of QTL mapping (e.g., interval mapping, which uses a pair or two pairs of flanking markers at a time for mapping) can be subject to the effects of other linked QTLs on a chromosome because the genetic background is not controlled. As a result, mapping of QTLs can be biased, and the resolution of mapping is not very high. Ideally when we test a marker interval for a QTL, we would like our test statistic to be independent of the effects of possible QTLs at other regions of the chromosome so that the effects of QTLs can be separated. This test statistic can be constructed by using a pair of markers to locate the testing position and at the same time using other markers to control the genetic background through a multiple regression analysis. Theory is developed in this paper to explore the idea of a conditional test via multiple regression analysis. Various properties of multiple regression analysis in relation to QTL mapping are examined. Theoretical analysis indicates that it is advantageous to construct such a testing procedure for mapping QTLs and that such a test can potentially increase the precision of QTL mapping substantially.

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Author and article information

Contributors

: +91-40-30713305 , +91-40-30713074 , r.k.varshney@cgiar.org

Journal

Journal ID (nlm-ta): Theor Appl Genet

Title: TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik

Publisher: Springer-Verlag (Berlin/Heidelberg )

ISSN (Print): 0040-5752

ISSN (Electronic): 1432-2242

Publication date (Electronic): 30 December 2010

Publication date PMC-release: 30 December 2010

Publication date (Print): April 2011

Volume: 122

Issue: 6

Pages: 1119-1132

Affiliations

[1 ]International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India

[2 ]Kazusa DNA Research Institute (KDRI), Chiba, 292-0818 Japan

[3 ]Institute of Plant Breeding, Genetics, and Genomics, The University of Georgia, Athens, GA 30602 USA

[4 ]University of Agricultural Sciences, Dharwad, 580005 India

[5 ]Directorate of Groundnut Research (DGR), Junagadh, 362001 India

[6 ]Universidade Católica de Brasília (UCB), Brasília, DF, CEP 70.790-160 Brazil

[7 ]Universidade de Brasília, Brasilia, DF, CEP 70.910-900 Brazil

[8 ]Generation Challenge Programme (GCP), c/o CIMMYT, 06600 Mexico DF, Mexico

Author notes

Communicated by H. T. Nguyen.

Article

Publisher ID: 1517

DOI: 10.1007/s00122-010-1517-0

PMC ID: 3057011

PubMed ID: 21191568

SO-VID: 50ac29ff-5621-432b-b1ea-b661efbf5ea4

History

Date received : 7 August 2010

Date accepted : 8 December 2010

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: peanut,molecular markers,main-effect qtls,drought tolerance,genetic map,epistatic qtls,molecular breeding

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ScienceOpen disciplines: Genetics

Keywords: peanut, molecular markers, main-effect qtls, drought tolerance, genetic map, epistatic qtls, molecular breeding

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Identification of several small main-effect QTLs and a large number of epistatic QTLs for drought tolerance related traits in groundnut ( Arachis hypogaea L.)

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Most cited references 40

Precision mapping of quantitative trait loci.

Genic microsatellite markers in plants: features and applications.

Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci.

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Cited by 81

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