Genomics-Assisted Breeding

Abstract

Since the Arabidopsis genome was sequenced, hundreds of plant genomes have either been sequenced or are in sequencing progress. Reference genome sequences and large-scale genome sequencing technologies have initiated a new era in molecular breeding. The fi eld of genomics is progressing rapidly and has already provided invaluable practical products for plant molecular breeding. Here, we review progress in genome sequencing technology and its application to plant breeding. We introduce various genomics tools and discuss how next-generation genome sequencing and genotyping technologies have been applied to high-throughput molecular breeding. We also describe the use of epigenome analysis to interpret phenotypic variations that cannot be explained by simple genetics based on the underlying DNA sequence alone, but rather by epigenetically-controlled mechanisms.

Comparing Single‐SNP, Multi‐SNP, and Haplotype‐Based Approaches in Association Studies for Major Traits in Barley

“…This approach exploits the existing genetic diversity and historical recombination events captured within a population to examine the degree of association between thousands or millions of SNPs with a trait of interest (Varshney and Tuberosa, 2007; Lee et al, 2015; Beilsmith et al, 2019). It is based on linkage disequilibrium (LD), defined as the nonrandom segregation of SNPs and QTLs leading to associations between them (Hayes, 2013; Choi et al, 2015; Bartoli and Roux 2017). These associations exist because there are portions of the genome in the population being studied that trace back to a common ancestor without being separated by recombination.…”