Hidden variation in polyploid wheat drives local adaptation

Abstract

Abstract:Wheat has been domesticated into a large number of agricultural environments and has a remarkable ability to adapt to diverse environments. To understand this process, we survey genotype, repeat content and DNA methylation across a bread wheat landrace collection representing global genetic

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

“…The addition of novel data types such as epigenetics and chromatin conformation may contribute to improved wheat phenotypic prediction. Initial studies reveal epigenetic differences amongst landraces (Gardiner et al ., 2018b), which are likely to also be observed in elite material. Incorporating diverse data types (genomics, epigenomics and environmental data) may enable more accurate predictions of phenotypes.…”

“…This collection has been purified by single‐seed descent from which many genomic and genetic resources have been developed. Genotyping of this collection revealed extensive novel genetic (Winfield et al ., ) and epigenetic (Gardiner et al ., 2018b) diversity, which was absent from modern cultivars. A core set of 107 accessions was used to generate nested association mapping populations (Wingen et al ., ), all of which were genotyped, have genetic maps available, and are free to access (http://wisplandracepillar.jic.ac.uk/).…”

“…As 99% of the wheat genome is non‐protein coding, variation in these regions is likely to account for a significant proportion of phenotypic variation. DNA methylation and histone mark variation both within and across cultivars is only beginning to be studied in wheat (Gardiner et al ., 2018b; Ramírez‐González et al ., ), and is likely to provide a wealth of information on gene regulation for traits of agronomic importance. Natural epigenetic variation is known to impact on agronomically relevant traits such as fruit ripening and plant height, and was found to underpin artificially selected variation for increased energy use efficiency in canola (Springer, 2013; for review, see Gallusci et al ., ).…”

Elucidating the genetic basis of biomass accumulation and radiation use efficiency in spring wheat and its role in yield potential

“…In the last decades, exotic parents have been used in breeding programmes with the aim of introducing greater diversity into elite gene pools (Singh et al ., ). The exotic parents that are most frequently used are those from the primary gene pool represented by germplasm that share a common genome but that have become isolated from mainstream gene pools such as landraces (Reynolds et al ., ,b), which have been shown to be not only genetically, but epigenetically diverse (Gardiner et al ., ). The secondary gene pool that has also been used is represented by closely related genomes that can be utilised through inter‐specific hybridisation, and would include the development of so‐called ‘synthetic’ or ‘re‐synthesised’ wheat, where a tetraploid durum wheat has been hybridised with Aegilops tauschii , the ancestral donor of the D genome, to recreate hexaploid bread wheat (Mujeeb‐Kazi et al ., ).…”

Conservation and trans-regulation of histone modification in the A and B subgenomes of polyploid wheat during domestication and ploidy transition

“…Indeed, an array of investigations in diverse plants have documented that allopolyploidization induces a cascade of rapid epigenetic modifications such as altered DNA methylation via differential titration of non-coding RNAs [17][18][19][20][21]. Analyses of homoeologous DNA methylation pattern in hexaploid wheat suggested that tri-genome methylation is significantly more conserved across the accessions compared to uni-and bigenome methylation [22,23]. Beside DNA methylation, histone modifications also play important roles in polyploid formation and stabilization [21,24].…”