Application of crop wild relatives in modern breeding: An overview of resources, experimental and computational methodologies

Abstract

Global agricultural industries are under pressure to meet the future food demand; however, the existing crop genetic diversity might not be sufficient to meet this expectation. Advances in genome sequencing technologies and availability of reference genomes for over 300 plant species reveals the hidden genetic diversity in crop wild relatives (CWRs), which could have significant impacts in crop improvement. There are many ex-situ and in-situ resources around the world holding rare and valuable wild species, of which many carry agronomically important traits and it is crucial for users to be aware of their availability. Here we aim to explore the available ex-/in- situ resources such as genebanks, botanical gardens, national parks, conservation hotspots and inventories holding CWR accessions. In addition we highlight the advances in availability and use of CWR genomic resources, such as their contribution in pangenome construction and introducing novel genes into crops. We also discuss the potential and challenges of modern breeding experimental approaches (e.g. de novo domestication, genome editing and speed breeding) used in CWRs and the use of computational (e.g. machine learning) approaches that could speed up utilization of CWR species in breeding programs towards crop adaptability and yield improvement.

Diversifying agrifood systems to ensure global food security following the Russia–Ukraine crisis

“…They have been nurtured as native crops agriculturally suited to local or regional climates and grown in domesticated forms or introduced centuries ago and are now established in their local environments. NUS are breeding candidates for advanced food crops with great economic potential (Mabhaudhi et al, 2019;Tirnaz et al, 2022). NUS cover a wide range of crop types, including cereals, roots and tubers, legumes, fruits and vegetables, seeds and spices, and were often traditionally grown by indigenous people and smallholder farmers as food for home consumption or a source of income at local markets (Padulosi et al, 2019;Heindorf et al, 2021).…”

Supporting crop plant resilience during climate change

“…Including wild relatives in a pangenome provides a way to retrieve genes previously lost during domestication and breeding that may be related to abiotic and biotic stress. Because crop wild relatives usually grow in a more diverse environment, they may host genes that may be absent or silenced in the cultivated crop varieties and are important for adaptation (Petereit et al., 2022; Tirnaz et al., 2022). By the genomic analysis of crop wild relatives, the genetic diversity of crops could be improved with the introgression of climate‐resilience genes from wild relatives (Cantila et al., 2020; Migicovsky & Myles, 2017; Zhang & Batley, 2020).…”

Crop Wild Relatives (CWRs) a Genetic Pool for Crop Improvement: A Review

“…Lee.) but due to their genetic incompatibility and ploidy, breeders were unable to use these resources (Tirnaz et al 2022). 2.…”