Marker‑assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.)

Marker‑assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.) 
Publication Type 
Journal Article 
Varshney RK, Pandey MK, Janila P, Nigam SN, Sudini H, Gowda MVC, Sriswath M, Radhakrishnan T, Manohar SS, Nagesh P 
Year of Publication 
Theoretical and Applied Genetics 
Date Published 
AhXV, GM1536, GM2079, GM2301, GPBD 4, Groundnut, ICGV 91114, IPAHM103, JL 24, Leaf rust, MABC, marker-assisted backcrossing, Puccinia arachidis Speg, QTL, quantitative trait loci, TAG 24 
DOI 10.1007/s00122-014-2338-3 


Leaf rust, caused by Puccinia arachidis Speg, is one of the major devastating diseases in peanut (Arachis hypogaea L.). One QTL region on linkage group AhXV explaining upto 82.62 % phenotypic variation for rust resistance was validated and introgressed from cultivar ‘GPBD 4’ into three rust susceptible varieties (‘ICGV 91114’, ‘JL 24’ and ‘TAG 24’) through marker-assisted backcrossing (MABC). The MABC approach employed a total of four markers including one dominant (IPAHM103) and three co-dominant (GM2079, GM1536, GM2301) markers present in the QTL region. After 2–3 backcrosses and selfing, 200 introgression lines (ILs) were developed from all the three crosses. Field evaluation identified 81 ILs with improved rust resistance. Those ILs had significantly increased pod yields (56–96 %) in infested environments compared to the susceptible parents. Screening of selected 43 promising ILs with 13 markers present on linkage group AhXV showed introgression of the target QTL region from the resistant parent in 11 ILs. Multi-location field evaluation of these ILs should lead to the release of improved varieties. The linked markers may be used in improving rust resistance in peanut breeding programmes.


Peanut or groundnut (Arachis hypogaea L.) is one of the most important oilseed and food crops having a large impact on the livelihoods of poor farmers in the semi-arid tropics (SAT). It is cultivated on over 24 million hectares (M ha) with a global production of about 38 million tonnes (Mt) (FAOSTAT 2012). Several biotic and abiotic constraints limit the realization of the full genetic potential of modern improved peanut varieties. For instance, rust disease caused by Puccinia arachidis Speg. is one of the widespread diseases that severely affects peanut productivity in tropical countries. Many other species of this fungal pathogen are known to damage a majority of grain and forage legumes worldwide (Sillero et al. 2006). Several popular peanut varieties have been phased out of farmers’ fields in the recent past due to heavy yield losses caused by their susceptibility to foliar fungal diseases. In general, disease control is possible with fungicides (4–8 sprays based on disease severity) but a majority of farmers in the SAT cannot afford them since they lack the resources and technical expertise required to use them effectively (Subrahmanyam et al. 1984). Moreover, the use of fungicides is neither a cost-effective approach nor a healthy practice for the environment and human health. Under these circumstances, a genetic approach involving introgression of disease resistance into modern and popular cultivars seems to be ideal. Conventional breeding has been successful in introgressing resistance in peanut breeding programmes. However, it is labour intensive and time consuming. Recent advances in crop genomics facilitate the identification of molecular markers associated with target trait(s) that can be deployed to select a superior line in a breeding programme. This process, known as ‘genomics-assisted breeding’ (Varshney et al. 2005), has been used to improve several traits in some legume crops (Varshney et al. 2006, 2010). Two recombinant inbred line (RIL) mapping populations, namely ‘TAG 24’ (susceptible) × ‘GPBD 4’ (resistant) and ‘TG 26’ (susceptible) × ‘GPBD 4’ were used earlier to map rust resistance (Khedikar et al. 2010; Sujay et al. 2012). Initially, a partial genetic map comprising of 56 marker loci was developed on the ‘TAG 24’ × ‘GPBD 4’ RIL population and a major quantitative trait loci (QTL) for rust resistance explaining 55.20 % phenotypic variation (PV) was identified (Khedikar et al. 2010). The nearest marker to the QTL, IPAHM103 (developed by Cuc et al. 2008), was found to be tightly linked with rust resistance. Subsequently, saturation of genetic maps with additional 132 SSR marker loci and comprehensive QTL analyses provided not only additional linked co-dominant markers (GM2009, GM1536, GM2301and GM2079) but also increased the resolution of QTL with a more accurate estimation of QTL effect (82.96 % PV) (Sujay et al. 2012). The reliability of these linked markers was confirmed by validating them on a set of resistant and susceptible genotypes (Khedikar et al. 2010, unpublished data). This study was undertaken to introgress the QTL region controlling rust resistance into two elite peanut varieties (‘TAG 24’ and ‘ICGV 91114’) and one old but popular variety (‘JL 24’) through marker-assisted backcrossing (MABC). Four linked markers (IPAHM103, GM1536, GM2301 and GM2079) from the QTL region were used to select the lines to make backcrosses for the next generation in MABC. After making 2–3 backcrosses and selfing the backcross progenies, several backcross-derived introgression lines (ILs) with enhanced rust resistance and better yield compared to the respective recurrent parent genotype were developed.

Marker‑assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.)2 MB
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