Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species

Abstract

Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (Zea mays), rice (Oryza sativa), Brassica (Brassica spp.), and soybean (Glycine max) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species.

Breeding crops for drought-affected environments and improved climate resilience

“…While progress toward this end has been made and continues, there are still many issues to be resolved to predict the complex response surfaces of multi-trait phenomes and yield reaction-norms for the TPE of agricultural ecosystems based on the characterization of plant genomes, and to enable the ambition of prediction-based design of drought tolerant crops for current and future climates ( Messina et al, 2011 , 2018 , 2022a ; Cooper et al, 2014a , 2014b ; Technow et al, 2015 ; Bustos-Korts et al, 2019a , 2019b , 2021 ; Millet et al, 2019 ; Ramstein et al, 2019 ; Voss-Fels et al, 2019a ; Langridge et al, 2021 ; Varshney et al, 2021a , 2021b ; Diepenbrock et al, 2022 ; Powell et al, 2022 ; Welcker et al, 2022 ; Zhao et al, 2022 ). Through the ongoing advances in genome sequencing capabilities to enable the investigation of trait genetic diversity within breeding populations, together with combinations of novel trait mapping studies and targeted genetic manipulation strategies, key regions of plant genomes have been identified that contain genes and natural sequence variation that underpins the expression of trait phenotypic variation at different scales ( Yu and Buckler, 2006 ; Yu et al, 2006 , 2008 ; Salvi et al, 2007 ; Buckler et al, 2009 ; Myles et al, 2009 ; Dong et al, 2012 ; Mace et al, 2013 ; Guo et al, 2014 ; Thoen et al, 2016 ; Wisser et al, 2019 ; Voss-Fels et al, 2019b ; Bayer et al, 2020 ; Simmons et al, 2021 ; Massel et al, 2021 ; Tao et al, 2021 ; Liu and Qin, 2021 ; Diepenbrock et al, 2022 ; Tay Fernandez et al, 2022a , 2022b ; Welcker et al, 2022 ). These genomic regions represent target entry points to further investigate and model at different scales the properties and contributions of the gene networks that are responsible for trait genetic variation and expression of phenot...…”

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

“…In recent years, advances in genome sequencing and bioinformatic tool development have extended the means to fully catalogue genetic variation among domestication and CWR populations through the construction of pangenomes ( Bayer et al., 2020 ; Jayakodi et al., 2021 ; Tay Fernandez et al., 2022 ). Pangenomes achieve this by providing a comprehensive genomic reference to which both small variants, including single-nucleotide polymorphisms (SNPs), and structural variants, including presence/absence variation of large nucleotide sections (PAVs), can be identified across diverse populations ( Danilevicz et al., 2020 ).…”

Studies on Lotus Genomics and the Contribution to Its Breeding

“…Pan-genome contains the totality of genome sequence information of the target species and covers more comprehensive variant information. Pan-genomes have been constructed in many plants, such as rice, maize, brassica, and soybean, and applied to identify causal genes [12][13][14][15]. Pan-genome or graph pan-genome is obtaining new references along with the upgrading of sequencing.…”