Benefit of Introgression Depends on Level of Genetic Trait Variation in Cereal Breeding Programmes

Abstract

We investigated the benefit from introgression of external lines into a cereal breeding programme and strategies that accelerated introgression of the favourable alleles while minimising linkage drag using stochastic computer simulation. We simulated genomic selection for disease resistance and grain yield in two environments with a high level of genotype-by-environment interaction (G × E) for the latter trait, using genomic data of a historical barley breeding programme as the base generation. Two populations (existing and external) were created from this base population with different allele frequencies for few (N = 10) major and many (N ~ 990) minor simulated disease quantitative trait loci (QTL). The major disease QTL only existed in the external population and lines from the external population were introgressed into the existing population which had minor disease QTL with low, medium and high allele frequencies. The study revealed that the benefit of introgression depended on the level of genetic variation for the target trait in the existing cereal breeding programme. Introgression of external resources into the existing population was beneficial only when the existing population lacked variation in disease resistance or when minor disease QTL were already at medium or high frequency. When minor disease QTL were at low frequencies, no extra genetic gain was achieved from introgression. More benefit in the disease trait was obtained from the introgression if the major disease QTL had larger effect sizes, more selection emphasis was applied on disease resistance, or more external lines were introgressed. While our strategies to increase introgression of major disease QTL were generally successful, most were not able to completely avoid negative impacts on selection for grain yield with the only exception being when major introgression QTL effects were very large. Breeding programmes are advised to carefully consider the level of genetic variation in a trait available in their breeding programme before deciding to introgress germplasms.

A study of pod constriction in a peanut population with mixed wild and cultivated genetics

“…When incorporating new traits from wild germplasm into elite lines, it is common to unintentionally introgress agronomically unadapted characteristics due to linkage drag (D. J. Bertioli et al., 2011; Li et al., 2022). Additionally, the use of wild species can reintroduce undesired traits that were selected against during domestication (Lippman et al., 2007).…”

Diamonds in the not-so-rough: Wild relative diversity hidden in crop genomes

“…Each desirable allele will reside in a region of the genome that may contain numerous maladapted alleles, and the combination of recombination rate and haplotype structure (whether beneficial and deleterious alleles are on the same or different haplotypes) will determine the likelihood of breaking up linkage blocks ( Fig 2 ). In the end, the merits and consequences of introgression will depend on several factors, including variation present in the breeding program and the number and effect size of the loci underlying the trait to be introgressed [ 54 ].…”

Characteristics of Progenies Derived from Bidirectional Avena sativa L. and Avena fatua L. Crosses

“…Linkage drag is a severe limitation on the use of potentially beneficial alleles accumulated in wild species and may not always be removed, even by multiple backcrossing to the recurrent parents [26]. By narrowing the starting material, breeders do not need to eliminate the undesirable features, significantly speeding up the breeding process, but this attempt leads to meeting only short-term breeding goals and narrowing the cultivated oat gene pool [27]. Therefore, prebreeding programmes are conducted by scientific institutions to support breeders and provide preliminary evaluated and selected lines.…”