GWAS identifies candidate regulators of in planta regeneration in Populus trichocarpa

Abstract

Plant regeneration is an element of natural and horticultural plant propagation, and a key step in the production of transgenic plants. However, regeneration capacity varies widely among genotypes and species, the molecular basis of which is largely unknown. To shed light on the causes of variation in natural regeneration capacity, we undertook a GWAS of shoot regeneration from dormant cut stems in Populus trichocarpa. Using estimates of callus and shoot regeneration provided by a novel computer vision system, and using a variety of GWAS pipelines and statistical approaches, our analyses revealed over 200 candidate genes. The candidates each explained small fractions of the total genetic variance and many appeared to be members of genetic regulatory networks, showing regeneration to be a highly polygenic trait. The top candidates included regulators of cell adhesion, stress signaling, and hormone signaling pathways, as well as other diverse functions. These candidates provide new insights into the biological complexity of plant regeneration, and may serve as new reagents for improving regeneration and transformation of recalcitrant genotypes and species.

GWAS identifies candidate genes controlling adventitious rooting in Populus trichocarpa

“…Several possible roles for JA in adventitious rooting of Populus have been discussed in a recent review; in summary, these roles may include cross-talk with auxin signaling among others, and are evidenced to vary across genera (Bannoud & Bellini, 2021). Our previous GWAS of in planta regeneration in poplar support a major role for JA signaling in callus and shoot regeneration (Nagle et al, 2022; and sources cited within), via pathways that are likely to be relevant to adventitious rooting considering the previously discussed emergence of basal ARs from callus.…”

“…We used a P. trichocarpa GWAS population that was recently expanded to include a total of 1,323 genotypes (Yates et al ., 2021); subsets of this population were used in previous GWAS projects (Tuskan et al ., 2018; Bdeir et al ., 2019; Weighill et al ., 2019; Chhetri et al ., 2020; Chen et al ., 2021; Nagle et al ., 2022). This population is comprised of variation in wild P. trichocarpa spanning regions of British Columbia, Washington, Oregon, Idaho and northern California.…”

“…Clone banks for this GWAS population were produced in multiple locations, among which a replicate in a Corvallis, OR field location was utilized to obtain cuttings for this study. This study was performed using materials collected as described in previous work (Nagle et al ., 2022). In summary, dormant cuttings were collected in the winters of 2018, 2019 and 2020, then rooted up to a year later and grown in a greenhouse.…”

“…This study was performed using materials collected as described in previous work (Nagle et al, 2022). In summary, dormant cuttings were collected in the winters of 2018, 2019 and 2020, then rooted up to a year later and grown in a greenhouse.…”

“…Association mapping of all traits was performed in parallel with traits in our published GWAS of in planta regeneration, using methods and SNP sets detailed in this previous work (Nagle et al, 2022). To summarize, four GWAS methods were used: 1) Genome-wide Efficient analyzed with GEMMA and FarmCPU, while binarized traits were analyzed with GMMAT and untransformed traits with MTMC-SKAT using resampling to avoid violations of linear model assumptions for high-confidence associations.…”