Association mapping of leaf traits, flowering time, and phytate content inBrassica rapa

Abstract

Association mapping was used to investigate the genetic basis of variation within Brassica rapa, which is an important vegetable and oil crop. We analyzed the variation of phytate and phosphate levels in seeds and leaves and additional developmental and morphological traits in a set of diverse B. rapa accessions and tested association of these traits with AFLP markers. The analysis of population structure revealed four subgroups in the population. Trait values differed between these subgroups, thus defining associations between population structure and trait values, even for traits such as phytate and phosphate levels. Marker-trait associations were investigated both with and without taking population structure into account. One hundred and seventy markers were found to be associated with the observed traits without correction for population structure. Association analysis with correction for population structure led to the identification of 27 markers, 6 of which had known map positions; 3 of these were confirmed in additional QTL mapping studies.

Association Mapping of Quantitative Disease Resistance in a Natural Population of Loblolly Pine (Pinus taeda L.)

“…An association genetic approach relies on the premise that historical, unrecorded re-combination events over many generations have reduced LD between markers and quantitative trait loci such that only those marker-trait pairs that are tightly linked remain detectable; this may enable ''fine mapping'' to identify genes underlying quantitative variation (Flint-Garcia et al 2003;Neale and Savolainen 2004). Association-based approaches have been used to identify candidate genes underlying traits in plants (Zhao et al 2007;Stich et al 2008;Wang et al 2008;Yahiaoui et al 2008;Inostroza et al 2009;Stracke et al 2009), based in part on applications in humans (D'alfonso et al 2002;McGuffin et al 2003;Easton et al 2007; Lee et al 2007), livestock (Martinez et al 2006;Charlier et al 2008;Goddard and Hayes 2009), and Drosophila (Kennington et al 2007;Norry et al 2007;Jiang et al 2009). Recent association studies in tree species have evaluated single candidate genes or a modest number of candidate genes for association (Thumma et al 2005;Gonzalez-Martinez et al 2007, 2008Ingvarsson et al 2008;Eckert et al 2009a).…”

Breeding Brassica napus for Shatter Resistance

“…AM approach is based upon the principle that linkage disequilibrium is maintained between loci over many generations in a given gene pool. Association mapping has been used for discovery and validation of trait-marker associations identified in the classical quantitative trait loci (QTL) mapping for loci associated with blackleg resistance, flowering time, leaf traits, seed phytate content in rapeseed (Jestin et al, 2010;Raman et al, 2010;Raman et al, 2011;Zhao et al, 2007). AM overcomes the major limitations of the QTL analysis that utilize bi-parental populations such as doubled haploids and recombinant inbred lines, as it surveys a large number of alleles at one locus and saves resources and time required to construct purpose designed 'mapping and validation' populations derived from structured biparental crosses.…”

Genetics, Genomics and Metabolomics

“…That said, many of the metabolic traits that have been mapped suggest that such studies could greatly benefit from the advantages afforded by this approach, namely, that they generally have higher mapping resolution, a greater allele number and a lesser research time in establishing association than linkage analysis (Yu & Buckler, 2006). To date, association mapping has successfully pinpointed associations between genomic regions and kernel composition and starch content, pigment content, provitamin A content, phytate and sugar content (Wilson et al, 2004;Zhao et al, 2007;Li et al, 2008;Stich et al, 2008) at the metabolite level as well as with the activity of the crucial photosynthetic enzyme RubisCo (Sulpice et al, 2007) However, as yet the number of cultivars or accessions that have been examined, at high-throughput within a single study, is relatively limited. This fact notwithstanding, several prototype studies assessing the combination of associating mapping at the metabolomic level are currently underway worldwide and it seems likely to be only a matter of time before their efficacy can be assessed.…”