Exploiting Wild Relatives for Genomics-assisted Breeding of Perennial Crops

Abstract

Perennial crops are vital contributors to global food production and nutrition. However, the breeding of new perennial crops is an expensive and time-consuming process due to the large size and lengthy juvenile phase of many species. Genomics provides a valuable tool for improving the efficiency of breeding by allowing progeny possessing a trait of interest to be selected at the seed or seedling stage through marker-assisted selection (MAS). The benefits of MAS to a breeder are greatest when the targeted species takes a long time to reach maturity and is expensive to grow and maintain. Thus, MAS holds particular promise in perennials since they are often costly and time-consuming to grow to maturity and evaluate. Well-characterized germplasm that breeders can tap into for improving perennials is often limited in genetic diversity. Wild relatives are a largely untapped source of desirable traits including disease resistance, fruit quality, and rootstock characteristics. This review focuses on the use of genomics-assisted breeding in perennials, especially as it relates to the introgression of useful traits from wild relatives. The identification of genetic markers predictive of beneficial phenotypes derived from wild relatives is hampered by genomic tools designed for domesticated species that are often ill-suited for use in wild relatives. There is therefore an urgent need for better genomic resources from wild relatives. A further barrier to exploiting wild diversity through genomics is the phenotyping bottleneck: well-powered genetic mapping requires accurate and cost-effective characterization of large collections of diverse wild germplasm. While genomics will always be used in combination with traditional breeding methods, it is a powerful tool for accelerating the speed and reducing the costs of breeding while harvesting the potential of wild relatives for improving perennial crops.

The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition

“…Advanced and conventional breeding Marker-assisted selection is used widely in major crop development and has begun to be applied to orphan crops. Examples include the annual orphan crops of foxtail millet (Setaria italica; Jia et al, 2013) and pigeonpea (Cajanus cajan; Varshney et al, 2017) and, increasingly, a range of perennial plants (Iwata et al, 2016;Migicovsky & Myles, 2017). However, the relatively high costs of phenotyping remain a constraint in most cases (Varshney et al, 2012).…”

Fruits of wild and semi‐domesticated Diospyros tree species have contrasting phenological, metabolic, and antioxidant activity profiles

“…The second objective of this study was to explore whether fruits of D. rekoi , a wild relative of the domesticated D. digyna that is endemic of the Balsas region of México, possess chemical traits having the potential to be used for the improvement of commercial Diospyros fruits, including ‘black zapote’. The latter is supported by the proven premise that wild relatives frequently represent a largely unexplored source of desirable traits that can complement the limited genetic diversity often available for perennial plant improvement in aspects such as fruit quality . Representative examples are: (i) the introgression of the ‘foxy’ flavor from the wild grape, Vitis labrusca , into the domesticated Vitis vinifera ; (ii) the use genetic markers of wild red‐fleshed kiwifruits to facilitate breeding of the highly appreciated commercial red kiwis; (iii) the improvement of the antioxidant capacity (AOC) in cultivated raspberry and blackberry through the utilization wild genotypes having unusually high AOC and key antioxidants respectively; and (iv) the recognition that wild apple species are valuable donors of desirable traits for commercial and ornamental apple cultivars .…”

Using Living Germplasm Collections to Characterize, Improve, and Conserve Woody Perennials

“…Due to their extended juvenile phases, perennial crops and their wild relatives are particularly well suited to genomicsassisted breeding. Using genomics-assisted breeding, progeny with desirable genetic profiles can be selected at the seedling stage without needing to incur the large costs and excessive time required to grow the plants to maturity (McClure et al, 2014;Migicovsky and Myles, 2017). Germplasm collections can be used for genetic mapping using genome-wide association studies (GWAS).…”