To date, most marker-trait associations have been revealed using QTL and genome-wide association studies (GWAS), demonstrating both their successes and their limitations. Haplotypes are the particular combinations of alleles/markers observed on a chromosomal segment in a given population, and they make it possible to test multiple allelic interaction effects. Haplotypes can also increase the statistical power of GWAS by reducing the number of tests compared to using all SNPs. Alleles within the same haplotype block are more likely to be inherited together, while sharing a similar minor allele frequency (MAF).
Recently, scientists from the INRA Centre de Recherche PACA in France used an innovative approach to better understand the genetic architecture of tomato fruit quality traits and test the potential of haplotype-based approaches for association and genomic prediction studies.
"We demonstrated the benefits of haplotypes versus SNPs in many aspects, including identifying marker-trait associations, revealing the haplotype bifurcation patterns near the most significantly associated SNPs, explaining more missing heritability and increasing the genomic prediction accuracy", Prof Causse said. These results will certainly be helpful for breeders and researchers focusing not only on tomatoes but also on other agronomic crops.
Read the complete research at www.phys.org.
Jiantao Zhao et al, Multiple haplotype-based analyses provide genetic and evolutionary insights into tomato fruit weight and composition, Horticulture Research (2022). DOI: 10.1093/hr/uhab009