Association mapping in forest trees and fruit crops

• Published in: Journal of experimental botany Vol. 63; no. 11; pp. 4045 - 4060
• Main Authors: Khan, M. Awais, Korban, Schuyler S
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press [etc.] 01.06.2012; Oxford University Press
• Subjects: Agronomy. Soil science and plant productions; Biological and medical sciences; Chromosome Mapping; Crops, Agricultural - genetics; Crops, Agricultural - growth & development; Crops, Agricultural - metabolism; DNA; Evolutionary genetics; Forest trees; Forestry; forests; Fruit - genetics; Fruit - growth & development; Fruit - metabolism; fruit crops; Fundamental and applied biological sciences. Psychology; gene pool; Genetic variation; Genetics and breeding of economic plants; genome; Genomes; Genomics; genotyping; high-throughput nucleotide sequencing; Linkage Disequilibrium; Medical genetics; microsatellite repeats; phenotype; phenotypic correlation; Phenotypic traits; Plant genetics; Plant physiology and development; Plant Proteins - genetics; Plant Proteins - metabolism; Plants; Quantitative Trait Loci; REVIEW PAPER; Sequencing; single nucleotide polymorphism; Trees - genetics; Trees - growth & development; Trees - metabolism; Quantitative trait loci; Cartography; Association mapping; Fruit crop; Botany; Genetic linkage; Perennial plant; Forest tree; linkage disequilibrium; perennial plants
• ISSN: 0022-0957; 1460-2431
• DOI: 10.1093/jxb/ers105

Association mapping (AM), also known as linkage disequilibrium (LD) mapping, is a viable approach to overcome limitations of pedigree-based quantitative trait loci (QTL) mapping. In AM, genotypic and phenotypic correlations are investigated in unrelated individuals. Unlike QTL mapping, AM takes advantage of both LD and historical recombination present within the gene pool of an organism, thus utilizing a broader reference population. In plants, AM has been used in model species with available genomic resources. Pursuing AM in tree species requires both genotyping and phenotyping of large populations with unique architectures. Recently, genome sequences and genomic resources for forest and fruit crops have become available. Due to abundance of single nucleotide polymorphisms (SNPs) within a genome, along with availability of high-throughput resequencing methods, SNPs can be effectively used for genotyping trees. In addition to DNA polymorphisms, copy number variations (CNVs) in the form of deletions, duplications, and insertions also play major roles in control of expression of phenotypic traits. Thus, CNVs could provide yet another valuable resource, beyond those of microsatellite and SNP variations, for pursuing genomic studies. As genome-wide SNP data are generated from high-throughput sequencing efforts, these could be readily reanalysed to identify CNVs, and subsequently used for AM studies. However, forest and fruit crops possess unique architectural and biological features that ought to be taken into consideration when collecting genotyping and phenotyping data, as these will also dictate which AM strategies should be pursued. These unique features as well as their impact on undertaking AM studies are outlined and discussed.