To date, most marker trait-related analyzes have been demonstrated using QTL and genome-wide association studies (GWAS), demonstrating both their successes and limitations. A haplotype is a particular combination of alleles / markers observed in a particular population of chromosomal segments, making it possible to test the effects of multiple allele interactions. 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, sharing a similar minor allele frequency (MAF). Haplotype-based analysis simultaneously tests groups of SNPs rather than individual SNPs, so statistical detection of many aspects of both population and quantitative genetics, such as identifying signals for recent positive selections and performing GWAS. Power will improve. Haplotype-related mappings are more powerful than single-marker and multi-marker analysis because they take into account not only allelic heterogeneity, but also possible statistical interactions between proximity markers.
Recently, scientists at the INRA Center de Recherche PACA in France have used an innovative approach to better understand the genetic structure of tomato fruit quality characteristics and a haplotype-based approach for association and genomic prediction studies. I tested the possibility of. The core collection of tomato strains was studied and genotyped with SNP markers. The haplotype architecture of the tomato genome is explained, (1) better understanding of recent reproductive history, (2) testing the potential of haplotypes for the detection of new candidate QTL regions, and (3) predicting phenotypes in context. Of the genome selection used to. Several haplotype-based analyzes were performed to demonstrate the multiple benefits of using haplotypes in genetic analysis.This study was published in Horticultural research..
“We have shown the benefits of haplotypes and SNPs in many aspects, including identifying the association between markers and traits. Haplotype Branching patterns close to the most important relevant SNPs explain the lack of heritability and improve the accuracy of genomic prediction, “said Professor Causse, whose results apply to tomatoes as well as other crops. It certainly helps for focused breeders and researchers.
Jiantao Zhao et al, a multiple haplotype-based analysis, provides genetic and evolutionary insights into the weight and composition of tomato fruits. Horticultural research (2022). DOI: 10.1093 / hr / uhab009
Provided by Nanjing Agricultural University
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Multiple haplotype-based analyzes provide genetic and evolutionary insights into tomato fruit weight and composition
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