Discovery and Study of Modified Genes

Domesticated genes can be identified and isolated by using technologies as quantitative trait locus (QTL) analysis, genome-wide association studies (GWAS) and whole genome resequencing studies. GWAS identifies significant associations between genes and phenotypic traits by using markers, focusing on single-nucleotide polymorphisms  (SNPs) in the genome and linkage disequilibrium to provide full coverage (Meyer and Purugganan, 2013).

Quantitative Trait Locus (QTL) mapping (or Linkage mapping) 

is a technique that is among the first used in the study of domesticated traits (Doebley et al., 2006; Gross and Olsen, 2010). According to Meyer and Purugganan (2013), QTL is defined as a “genomic region with a gene (or multiple linked genes) that contains mutations which result in phenotypic variation in populations” (Meyer and Purugganan, 2013). And the main goal of the QTL mapping is to help study less understood phenotypes by characterizing (number, location, and impact) the determinants involved in the inheritance of variable traits (Paterson, 2002). The methodology consists in, starting with the crossing of F0 strains genetically and phenotypically different in the trait of interest (the wild-type and the domesticated). Then develop a mapping population of the F1 genetically marked generation (using techniques such as double haploid lines, backcross, or recombinant inbred lines for example), followed by the construction of a linkage map that characterize the segregation of markers in the chromosomes, and finally a statistical study to relate the genetic and phenotypic variance (Kearsey, 1998; Miles and Wayne, 2008; Sehgal et al., 2016). First, we map the markers and then we relate the markers and the trait (Kearsey and Farquhar, 1998). Some of the problems associated with this technique are the small individual QTL effects; don’t work well with certain crops, like perennial’s for example; some statistical difficulties; lack of specificity; and the need of a phenotype identification beforehand (Kearsey, 1998; Doebley et al., 2006; Ross-Ibarra et al., 2007).

Linkage Disequilibrium (LD), or Association, mapping

Mackay and Powell (2007) define linkage disequilibrium as “the non-random association of alleles at separate loci located on the same chromosome”, and this process can be caused by several factors such as mutations, migrations, and selection for example (Mackay and Powell, 2007). This technique, first used in human genetics, can be made in various ways (Multiparent Advanced Generation Intercross or Transmission Disequilibrium Test), but, they all have the same basis, by relying in the LD decay, and comparing genome variation with phenotype variations and the more in-dept analysis of the responsible genetic alterations, making use of molecular markers and statistical analysis (Mackay and Powell, 2007; Ross-Ibarra et al., 2007; Sehgal et al., 2016). Although more rapid and with better mapping resolution than QTL mapping, due to the lack of necessity of doing crossovers, there is a need for a large sample size and some problems associated with the geographic origin of the studied individuals, that can affect the veracity of the results (Ross-Ibarra et al., 2007; Sorkheh et al., 2008; Sehgal et al., 2016).

Made by : Celso Santos and Patrícia Cruz

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