Evidence of selection on fatty acid biosynthetic genes during the evolution of cultivated sunflower

Abstract

The identification of genes underlying the phenotypic transitions that took place during crop evolution, as well as the genomic extent of resultant selective sweeps, is of great interest to both evolutionary biologists and applied plant scientists. In this study, we report the results of a molecular evolutionary analysis of 11 genes that underlie fatty acid biosynthesis and metabolism in wild and cultivated sunflower (Helianthus annuus). Seven of these 11 genes showed evidence of selection at the nucleotide level, with 1 (FAD7) having experienced selection prior to domestication, 2 (FAD2-3 and FAD3) having experienced selection during domestication, and 4 (FAB1, FAD2-1, FAD6, and FATB) having experienced selection during the subsequent period of improvement. Sequencing of a subset of these genes from an extended panel of sunflower cultivars revealed little additional variation, and an analysis of the genomic region surrounding one of these genes (FAD2-1) revealed the occurrence of an extensive selective sweep affecting a region spanning at least ca. 100 kb. Given that previous population genetic analyses have revealed a relatively rapid decay of linkage disequilibrium in sunflower, this finding indicates the occurrence of strong selection and a rapid sweep.

Genome-wide association mapping and Identification of candidate genes for fatty acid composition in Brassica napus L. using SNP markers

“…In an association block on chromosome A2, four genes were ascribed to fatty acid within the asscociated regions (Table 4). For example, the A. thaliana gene LACS9 could catalyzes the formation of acyl-CoA from fatty acids, ATP, and CoA, which is involved in Arabidopsis seed oil biosynthesis [71], KCR1 is a functional KCR isoform involved in a multiprotein membrane-bound fatty acid elongation system [72], FAB1 could be involved in the elongation of C16:0-ACP to C18:0-ACP, which is the key step for fatty acid synthesis [73], and LPAT4 is the member of LPAT gene family, which is an essential candidate for oil composition and increase the seed oil [74]. Moreover, the another orthologous gene FAB1 ( BnaC01g26460D ) was also identified in the block on chromosome C1 (Table 4).…”

Improving grain quality: ecophysiological and modeling tools to develop management and breeding strategies

“…Since sunflower was initially domesticated for its edible seeds (putt, 1997), as opposed to explicit selection for oil content and/or composition, selective pressures may have affected palatability or germinability (chapman and Burke, 2012). More recently, the cultivated sunflower gene pool has been subjected to intense selection for high oil content and specific oil composition (Burke et al, 2005;putt, 1997).…”

Sequence Validation of Candidates for Selectively Important Genes in Sunflower

“…Notably, we focused our sequence-based analyses on a set of individuals from six landraces, whereas the SSR-based analyses utilized population-level sampling from a total of eight landraces. Given that the sunflower landraces are genetically quite diverse [24], [32], [40], a larger sample size in the initial analyses could have diluted the effects of more divergent landraces, resulting in significant tests in the wild-landrace comparisons in the earlier, SSR-based study but not in the present analysis of sequence diversity. In this context, it is worth noting that for three of the genes the showed evidence of selection during improvement in the current study (c1258, c1533 and c2963), the Maiz Negro landrace harbors an allele that was divergent from all other landrace and improved lines.…”

“…In the present study, we attempted to amplify portions of the 30 remaining genes from a panel of individuals (Table S1) representing eight wild, six landrace, and six improved sunflower accessions plus an outgroup ( H. petiolaris ). This was the same panel of individuals that was used to investigate patterns of DNA sequence variation in the original six genes, as well as in an analysis of selection on genes in the fatty acid biosynthetic pathway (see [24], [32]). Briefly, polymerase chain reaction (PCR) primers were designed by downloading unigene sequences from the Compositae Genome Project EST database (http://compgenomics.ucdavis.edu/), comparing them against genomic sequences from Arabidopsis , rice, grape, and poplar to infer the likely intron positions, and then using primer3 [33] to design primers that flanked regions spanning ca.…”