Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding

Abstract

BackgroundPolyploidy can result in genetic bottlenecks, especially for species of monophyletic origin. Cultivated peanut is an allotetraploid harbouring limited genetic diversity, likely resulting from the combined effects of its single origin and domestication. Peanut wild relatives represent an important source of novel alleles that could be used to broaden the genetic basis of the cultigen. Using an advanced backcross population developed with a synthetic amphidiploid as donor of wild alleles, under two water regimes, we conducted a detailed QTL study for several traits involved in peanut productivity and adaptation as well as domestication.ResultsA total of 95 QTLs were mapped in the two water treatments. About half of the QTL positive effects were associated with alleles of the wild parent and several QTLs involved in yield components were specific to the water-limited treatment. QTLs detected for the same trait mapped to non-homeologous genomic regions, suggesting differential control in subgenomes as a consequence of polyploidization. The noteworthy clustering of QTLs for traits involved in seed and pod size and in plant and pod morphology suggests, as in many crops, that a small number of loci have contributed to peanut domestication.ConclusionIn our study, we have identified QTLs that differentiated cultivated peanut from its wild relatives as well as wild alleles that contributed positive variation to several traits involved in peanut productivity and adaptation. These findings offer novel opportunities for peanut improvement using wild relatives.

Quantitative Trait Locus Analysis of Late Leaf Spot Resistance and Plant-Type-Related Traits in Cultivated Peanut (Arachis hypogaea L.) under Multi-Environments

“…Therefore, these four QTLs were repeatedly detected in different populations. With respect to the QTLs for plant-type-related traits, no similar segment was found between our study and previously studies [26,27,55,56]. …”

Yield, market quality, and leaf spots partial resistance of interspecific peanut progenies

“…In the 2011/12 progenies evaluation, the estimated broad-sense heritability, the coefficients of genotypic determination and CVg/CVe ratio for pod yield and W100S were high (Table 1). These values are similar to those obtained with the BC 3 F 2 interspecific population reported by Fonceka et al (2012), and superior to those observed for advanced cultivated lines (Gomes and Lopes 2005), indicating a favorable condition for selecting superior genotypes for these traits under the current experimental conditions. Segregating plants for yield, pod uniformity and pod shape were selected in the interspecific progenies evaluated in the 2011/12 crop season, resulting in the introduction of new 43 runner type lines in the peanut breeding program of Embrapa.…”

“…In the present study, high yielding interspecific progenies of runner market type with seed size for different markets were identified in the first backcross generation, attesting the potential for economic exploitation of the wild species reported by Stalker et al (1979) and Fonceka et al (2012). Partial resistant, high yield runner lines were selected and crossed with high yield/partial resistant cultivars to generate new breeding populations.…”

“…The same was observed by Stalker et al (1979), who reported that some interspecific lines (A. hypogaea x A. cardenasii) presented high yield and transgressive segregation for seed size. Fonceka et al (2012) detected high levels of variability for yield component traits in the BC 3 F 2 interspecific population A. hypogaea cv. Fleur 11 x (A. ipaënsis x A. duranensis) 4x ; however, the genotypes that had better performances than the cultivated parent in number of pods per plant had similar W100S.…”

Co-localization of major quantitative trait loci for pod size and weight to a 3.7 cM interval on chromosome A05 in cultivated peanut (Arachis hypogaea L.)

“…For example, Selvaraj et al [4] identified two SSR markers, PM375 and Seq8D09, linked with pod length using bulked segregant analysis. Similarly, Shirasawa et al [18] identified three QTLs for pod length and two for pod width in an F 2 population while Fonceka et al [19] mapped three QTLs for pod length, six for pod width and two for hundred-pod weight in an advanced backcross population. More recently, Huang et al [15] detected one QTL for pod length, two QTLs for pod width and three QTLs for hundred-pod weight in an F 2:3 population.…”