Quantitative trait locus analysis and construction of consensus genetic map for drought tolerance traits based on three recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.)

Abstract

Groundnut (Arachis hypogaea L.) is an important food and cash crop grown mainly in semi-arid tropics (SAT) regions of the world where drought is the major constraint on productivity. With the aim of understanding the genetic basis and identification of quantitative trait loci (QTL) for drought tolerance, two new recombinant inbred line (RIL) mapping populations, namely ICGS 76 × CSMG 84-1 (RIL-2) and ICGS 44 × ICGS 76 (RIL-3), were used. After screening of 3,215 simple sequence repeat (SSR) markers on the parental genotypes of these populations, two new genetic maps were developed with 119 (RIL-2) and 82 (RIL-3) SSR loci. Together with these maps and the reference map with 191 SSR loci based on TAG 24 × ICGV 86031 (RIL-1), a consensus map was constructed with 293 SSR loci distributed over 20 linkage groups, spanning 2,840.8 cM. As all these three populations segregate for drought-tolerance-related traits, a comprehensive QTL analysis identified 153 main effect QTL (M-QTL) and 25 epistatic QTL (E-QTL) for drought-tolerance-related traits. Localization of these QTL on the consensus map provided 16 genomic regions that contained 125 QTL. A few key genomic regions were selected on the basis of the QTL identified in each region, and their expected role in drought adaptation is also discussed. Given that no major QTL for drought adaptation were identified, novel breeding approaches such as marker-assisted recurrent selection (MARS) and genomic selection (GS) approaches are likely to be the preferred approaches for introgression of a larger number of QTL in order to breed drought-tolerant groundnut genotypes.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-011-9660-0) contains supplementary material, which is available to authorized users.

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“…Furthermore, they have also been mapped on different linkage groups from the consensus groundnut maps created to identify QTLs associated with foliar disease resistance and drought tolerance (Table 4). Marker GM1911 in this study is, for example, linked to a drought tolerance QTL (Ravi et al, 2011;Gautami et al, 2012), while markers GM1577 and GM1991 are linked to QTLs associated with tolerance to late leaf spot disease (Sujay et al, 2012). No doubt, the…”

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“…SSR markers have been found most successful in identifying molecular variation within the cultivated peanut species (Hopkins et al 1999;Ferguson et al, 2004aFerguson et al, , 2004bMace et al, 2006Mace et al, , 2007Cuc et al, 2008;Varshney et al, 2009;Khedikar et al, 2010;Mondal and Badigannavar, 2010;Gautami et al, 2011;Shirasawa, 2012;Sujay et al, 2012). However, a few RAPD markers have been successfully used in the identification of candidate genes of interest in peanut (Burow et al, 1996;Garcia et al, 1996;Mondal et al, 2007).…”

“…In contrast, SSRs are codominant PCR-based markers and more polymorphic in cultivated peanut than RAPDs. In the recent past, good progress was made in the development of SSRs as well as in tagging of economically important genes in peanut (Selvaraj et al, 2009;Varshney et al, 2009;Hong et al, 2010;Mondal and Badgannavar, 2010;Gautami et al, 2011;Ravi et al, 2011;Mondal et al, 2012;Qin et al, 2012;Sujay et al, 2012).…”

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“…Resistance to biotic stresses Angular leaf spot QTL 22-64 Oblessuc et al, 2012;Teixeira et al, 2005 (Khedikar et al, 2010;Liang et al, 2009a;Qin et al, 2012;Sujay et al, 2012;Wang et al, 2013 (Gautami et al, 2012b;Ravi et al, 2011;Varshney et al, 2009b) Gautami et al, 2012a;Liang et al, 2009;Ravi et al, 2011;Selvaraj et al, 2009;Shirasawa et al, 2012;Varshney et al, 2009b) (Continued on next page) (Liang et al, 2009;Pandey et al, 2012c;Sarvamangala et al, 2011;Selvaraj et al, 2009;Shirasawa et al, 2012) Pea Plant height QTL 19-65 (Tullu et al, 2008;Tar'an et al, 2003b;Dirlewanger et al, 1994) (Atibalentja et al, 2005;Guo et al, 2006;Guo et al, 2008;Han et al, 2008;Huynh et al, 2010;Kazi et al, 2008;Ruben et al, 2006;Shi et al, 2008;Silva and Danielle, 2008;Vuong et al, 2008;Wang et al, 2010;Winter et al, 2007) (Continued on next page) Funatsuki et al, 2005;Githiri et al, 2006;Githiri et al, 2007;…”