Linkage disequilibrium, genetic association mapping and gene localization in crop plants

Abstract

DNA-based molecular markers have been extensively utilized for a variety of studies in both plant and animal systems. One of the major uses of these markers is the construction of genome-wide molecular maps and the genetic analysis of simple and complex traits. However, these studies are generally based on linkage analysis in mapping populations, thus placing serious limitations in using molecular markers for genetic analysis in a variety of plant populations. Therefore, alternative approach has been suggested, linkage disequilibrium-based association analysis which detects and locates quantitative trait loci (QTL) by the strength of the correlation between a trait and a marker. Although association analysis has already been used for studies on genetics of complex traits in humans, its use in plants has newly started. In the present review, we describe what is known about variation in linkage disequilibrium (LD) and summarize published results on association studies in crop plant species. We give a list of different factors affecting LD, and discuss the current issues of LD research in plants. Later, we also describe the various uses of LD in crop plants research and summarize the present status of LD researches in different plant genomes. Finally, future key issues about the application of these studies on the localization of genes in these crop plants have been also discussed.

Peach genetic resources: diversity, population structure and linkage disequilibrium

“…A similar report on 104 Chinese landraces also found low levels of LD in northwest China and middle and lower reaches of the Changjiang River subpopulations [28]. Extremely low levels of LD in landrace and wild accessions have also been observed in other species, such as wild French grape (2.7 cM compared to 16.8 cM for cultivated French grape) [25,26] and maize (1 kb in landraces, 2 kb in diverse inbred lines and 100 kb in commercial elite inbred lines) [24]. A rapid decline of LD was observed in a wild, strictly self-incompatible, cherry subpopulation compared to a cultivated sweet cherry [37].…”

“…In contrast, outcrossing, high recombination rate, high mutation rate and gene conversion can decrease the LD [22,24]. The amount, extent and distribution of LD have been well described for common human diseases.…”

Potential for marker-assisted selection for forest tree breeding: lessons from 20 years of MAS in crops

“…Both factors have been extensively considered in many simulation and theoretical studies on MAS but the amount of LD that is captured through a given level of marker density is population-specific. Although it is assumed that LD declines with distance, this decline is known to be different within regions of the genome, between populations due to distinctive population histories and among species (Flint-Garcia et al 2003b;Gupta et al 2005;Sorkheh et al 2008).…”

Gene discovery in cereals through quantitative trait loci and expression analysis in water‐use efficiency measured by carbon isotope discrimination

“…As a valuable complementary tool in detecting markertrait associations, association mapping has been extensively utilized in cereals (Garris, McCouch & Kresovich 2003;Kraakman et al 2004;Skøt et al 2005;Breseghello & Sorrells 2006;Ravel et al 2006;Yu & Buckler 2006;Cockram et al 2008;Horvath et al 2009;Stracke et al 2009;Waugh et al 2009;Neumann et al 2011;Yan et al 2011). By utilizing all the historic recombination events from germplasm development, association mapping can provide a high resolution genetic map (fine mapping) and provide more precise locations of individual QTL (Oraguzie et al 2007;Maccaferri et al 2011;Neumann et al 2011), or a step towards positional cloning (Rafalski 2010), which is more challenging but more rewarding for quantitative traits (Sorkheh et al 2008). Major factors that affect association mapping include the level of linkage disequilibrium, population structure and stratification, familial relatedness and complexity of target traits (Abdurakhmonov & Abdukarimov 2008;Rafalski 2010).…”