Identification of QTLs associated with oil content and mapping FAD2 genes and their relative contribution to oil quality in peanut (Arachis hypogaea L.)

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Abstract

Background

Peanut is one of the major source for human consumption worldwide and its seed contain approximately 50% oil. Improvement of oil content and quality traits (high oleic and low linoleic acid) in peanut could be accelerated by exploiting linked markers through molecular breeding. The objective of this study was to identify QTLs associated with oil content, and estimate relative contribution of FAD2 genes ( ahFAD2A and ahFAD2B) to oil quality traits in two recombinant inbred line (RIL) populations.

Results

Improved genetic linkage maps were developed for S-population (SunOleic 97R × NC94022) with 206 (1780.6 cM) and T-population (Tifrunner × GT-C20) with 378 (2487.4 cM) marker loci. A total of 6 and 9 QTLs controlling oil content were identified in the S- and T-population, respectively. The contribution of each QTL towards oil content variation ranged from 3.07 to 10.23% in the S-population and from 3.93 to 14.07% in the T-population. The mapping positions for ahFAD2A (A sub-genome) and ahFAD2B (B sub-genome) genes were assigned on a09 and b09 linkage groups. The ahFAD2B gene (26.54%, 25.59% and 41.02% PVE) had higher phenotypic effect on oleic acid (C18:1), linoleic acid (C18:2), and oleic/linoleic acid ratio (O/L ratio) than ahFAD2A gene (8.08%, 6.86% and 3.78% PVE). The FAD2 genes had no effect on oil content. This study identified a total of 78 main-effect QTLs (M-QTLs) with up to 42.33% phenotypic variation (PVE) and 10 epistatic QTLs (E-QTLs) up to 3.31% PVE for oil content and quality traits.

Conclusions

A total of 78 main-effect QTLs (M-QTLs) and 10 E-QTLs have been detected for oil content and oil quality traits. One major QTL (more than 10% PVE) was identified in both the populations for oil content with source alleles from NC94022 and GT-C20 parental genotypes. FAD2 genes showed high effect for oleic acid (C18:1), linoleic acid (C18:2), and O/L ratio while no effect on total oil content. The information on phenotypic effect of FAD2 genes for oleic acid, linoleic acid and O/L ratio, and oil content will be applied in breeding selection.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-014-0133-4) contains supplementary material, which is available to authorized users.

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Most cited references 39

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The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.).

D Hoisington, K Seetha, S Knapp … (2009)

Molecular markers and genetic linkage maps are pre-requisites for molecular breeding in any crop species. In case of peanut or groundnut (Arachis hypogaea L.), an amphidiploid (4X) species, not a single genetic map is, however, available based on a mapping population derived from cultivated genotypes. In order to develop a genetic linkage map for tetraploid cultivated groundnut, a total of 1,145 microsatellite or simple sequence repeat (SSR) markers available in public domain as well as unpublished markers from several sources were screened on two genotypes, TAG 24 and ICGV 86031 that are parents of a recombinant inbred line mapping population. As a result, 144 (12.6%) polymorphic markers were identified and these amplified a total of 150 loci. A total of 135 SSR loci could be mapped into 22 linkage groups (LGs). While six LGs had only two SSR loci, the other LGs contained 3 (LG_AhXV) to 15 (LG_AhVIII) loci. As the mapping population used for developing the genetic map segregates for drought tolerance traits, phenotyping data obtained for transpiration, transpiration efficiency, specific leaf area and SPAD chlorophyll meter reading (SCMR) for 2 years were analyzed together with genotyping data. Although, 2-5 QTLs for each trait mentioned above were identified, the phenotypic variation explained by these QTLs was in the range of 3.5-14.1%. In addition, alignment of two linkage groups (LGs) (LG_AhIII and LG_AhVI) of the developed genetic map was shown with available genetic maps of AA diploid genome of groundnut and Lotus and Medicago. The present study reports the construction of the first genetic map for cultivated groundnut and demonstrates its utility for molecular mapping of QTLs controlling drought tolerance related traits as well as establishing relationships with diploid AA genome of groundnut and model legume genome species. Therefore, the map should be useful for the community for a variety of applications.

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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 (Arachishypogaea L.)

T. Ravi, V. Vadez, S. Isobe … (2010)

Cultivated groundnut or peanut (Arachis hypogaea L.), an allotetraploid (2n = 4x = 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. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1517-0) contains supplementary material, which is available to authorized users.

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Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.)

V. Sujay, M. Gowda, M. K. Pandey … (2011)

Late leaf spot (LLS) and rust have the greatest impact on yield losses worldwide in groundnut (Arachis hypogaea L.). With the objective of identifying tightly linked markers to these diseases, a total of 3,097 simple sequence repeats (SSRs) were screened on the parents of two recombinant inbred line (RIL) populations, namely TAG 24 × GPBD 4 (RIL-4) and TG 26 × GPBD 4 (RIL-5), and segregation data were obtained for 209 marker loci for each of the mapping populations. Linkage map analysis of the 209 loci resulted in the mapping of 188 and 181 loci in RIL-4 and RIL-5 respectively. Using 143 markers common to the two maps, a consensus map with 225 SSR loci and total map distance of 1,152.9 cM was developed. Comprehensive quantitative trait locus (QTL) analysis detected a total of 28 QTL for LLS and 15 QTL for rust. A major QTL for LLS, namely QTLLLS01 (GM1573/GM1009-pPGPseq8D09), with 10.27–62.34% phenotypic variance explained (PVE) was detected in all the six environments in the RIL-4 population. In the case of rust resistance, in addition to marker IPAHM103 identified earlier, four new markers (GM2009, GM1536, GM2301 and GM2079) showed significant association with the major QTL (82.96% PVE). Localization of 42 QTL for LLS and rust on the consensus map identified two candidate genomic regions conferring resistance to LLS and rust. One region present on linkage group AhXV contained three QTL each for LLS (up to 67.98% PVE) and rust (up to 82.96% PVE). The second candidate genomic region contained the major QTL with up to 62.34% PVE for LLS. Molecular markers associated with the major QTL for resistance to LLS and rust can be deployed in molecular breeding for developing groundnut varieties with enhanced resistance to foliar diseases. Electronic supplementary material The online version of this article (doi:10.1007/s11032-011-9661-z) contains supplementary material, which is available to authorized users.

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Author and article information

Contributors

Manish K Pandey: m.pandey@cgiar.org

Ming Li Wang: mingli.wang@ars.usda.gov

Lixian Qiao: lxqiao73@163.com

Suping Feng: supingfeng1972@gmail.com

Pawan Khera: pkhera@uga.edu

Hui Wang: huixu@uga.edu

Brandon Tonnis: brandon.tonnis@ars.usda.gov

Noelle A Barkley: elle.barkley@ars.usda.gov

Jianping Wang: wangjp@ufl.edu

C Corley Holbrook: corley.holbrook@ars.usda.gov

Albert K Culbreath: spotwilt@uga.edu

Rajeev K Varshney: r.k.varshney@cgiar.org

Baozhu Guo: baozhu.guo@ars.usda.gov

Journal

Journal ID (nlm-ta): BMC Genet

Journal ID (iso-abbrev): BMC Genet

Title: BMC Genetics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2156

Publication date (Electronic): 10 December 2014

Publication date PMC-release: 10 December 2014

Publication date Collection: 2014

Volume: 15

Issue: 1

Electronic Location Identifier: 133

Affiliations

[ ]US Department of Agriculture-Agricultural Research Service, Crop Protection and Management Research Unit, Tifton, GA USA

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

[ ]Department of Plant Pathology, University of Georgia, Tifton, GA USA

[ ]US Department of Agriculture-Agricultural Research Service, Plant Genetic Resources Conservation Unit, Griffin, GA USA

[ ]College of Life Science, Qingdao Agricultural University, Qingdao, China

[ ]College of Bioscience and Biotechnology, Qiongzhou University, Sanya, China

[ ]Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China

[ ]Department of Agronomy, University of Florida, Gainesville, FL USA

[ ]US Department of Agriculture-Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA USA

Article

Publisher ID: 133

DOI: 10.1186/s12863-014-0133-4

PMC ID: 4278341

PubMed ID: 25491595

SO-VID: 849be9e1-914f-4659-a1c6-2ee6743a7ecd

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 25 July 2014

Date accepted : 20 November 2014

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ScienceOpen disciplines: Genetics

Keywords: peanut,genetic map,qtl analysis,oil content,oleic acid,linoleic acid,o/l ratio,fad2 genes

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ScienceOpen disciplines: Genetics

Keywords: peanut, genetic map, qtl analysis, oil content, oleic acid, linoleic acid, o/l ratio, fad2 genes

Identification of QTLs associated with oil content and mapping FAD2 genes and their relative contribution to oil quality in peanut ( Arachis hypogaea L.)

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Abstract

Background

Results

Conclusions

Electronic supplementary material

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G3: Genes|Genomes|Genetics

Most cited references 39

The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.).

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

Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.)

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