Sphagnopsida

Plants for all experiments were grown under standard conditions with 10-hr day cycles in Percival A100 growth chambers (Percival Scientific, Perry, IA) planted in 98-well trays with all edge positions filled with inbred B73. Soil media was a 1:1 mixture of Turface MVP (PROFILE Products LLC, Buffalo Grove, IL) and LM111 (Lambert Peat Moss, Qc, Canada). All plants were harvested 14 days after planting and quickly trimmed to small SAM-containing tissue cassettes and fixed in FAA (3.7% formalin, 5% acetic acid and 50% ethanol in water) on ice, overnight.
For initial modelling, 10 kernels from inbred B73 and 10 kernels from inbred W22 were planted as above. To map the maize SAM morphospace, kernels from 384 inbred varieties (Supplementary Data 1) were planted in randomized positions in 4 biological replicates. For RNA in situ hybridization, 10 kernels from select lines were grown as above in 2 biological replicates. To estimate SAM cell count and ASCS, 4 kernels from 14 inbred varieties were planted with 3 biological replicates: 3 ZmSDA1-ALT lines and 5 ZmBAK1-like1 ALT lines with remaining lines randomly chosen to equally represent the lower quartile (small), middle quartiles (intermediate) and upper quartile (large) of SAM volume with COM from ZmSDA1 and ZmBAK1-like1.

All plants used in this study were grown in Huazhong Agricultural University, Wuhan. Fern and peat moss were collected on campus and identified according to FRPS (http://frps.eflora.cn/). Potato, citrus, palm, populous and bamboo were obtained from college of Horticulture and Forestry Sciences. Arabidopsis, tobacco and crops were grown in greenhouse. Thirteen plant species leaf samples and tuber of potato were collected using liquid nitrogen with two biological replicate sets. The freeze-dried samples were crushed using a mix mill (MM 400, Ratsch) with a zirconia bead for 1 min at 30 Hz, 100 mg dried power were weighted and extracted overnight at 4 °C with 1.0 mL 70% aqueous methanol containing 0.1 mg L⁻¹ lidocaine (internal standard) before analysis using an LC-ESI-MS/MS system^{34 (link)}. Qualification of metabolites was carried out using a scheduled multiple reaction monitoring method^{34 (link)}. The relative signal intensities of flavonoids were standardized by firstly dividing them by the intensities of internal standard and then log 2 transforming them to generate the final data matrix. Flavonoids were quantified based on comparison with standards of apigenin, tricin, apigenin 5-O-glucoside and apigenin 7-O-glucoside.

The world core collection of quinoa accessions (N = 334) and 26 entries in the 2018 WSU quinoa variety trial, were planted in a randomized complete block design with four replicates in each of two greenhouses on the WSU-Pullman campus. Additional information for the accessions is provided in Supplementary Table S1. Replicates were oriented in the greenhouse perpendicular to the direction of cooling (swamp cooler-exhaust fan axis). The greenhouses were planted approximately one month apart; greenhouse A (i.e. 7B) was planted on May 17th, 2018 and greenhouse B (i.e. 34B) was planted on June 14, 2018. Each greenhouse received 16 hours of light and 8 hours of dark, supplied through supplemental lighting, for the duration of the study. The temperature was maintained at 20°C during the day and 15°C at night, with relative humidity ranging from 40-70%. Three seeds of each accession were sown approximately 5mm below the surface of a soil-less media in each pot (2.6L). The pots were prepared with the same volume of media, which includes dolomitic limestone remnants and 70-80% Canadian Sphagnum peat moss (Sunshine Professional Growing, Agawam, MA, USA, www.agawam.ma.us). Plants were watered to saturation every other day.
Once two sets of true leaves were fully expanded on one plant in each pot, the remaining plants were removed by cutting the stem at the surface of the media. This resulted in a single plant per pot. Therefore, “plant” or “plants” refers to either a single replicate of one accession, or the collective replicates of accessions. This process was initiated approximately 14 days after sowing (DAS) for each greenhouse, and pots that did not have emerged plants were replanted. Each plant was fertilized with 2 g of Osmocote^® classic (13‐13‐13; Everris, NA). Even with a delay in sowing dates between the two greenhouses, fertilizer application occurred at approximately the same growth stage. For greenhouse A, fertilizer application occurred 28 days after sowing, while fertilizer application for greenhouse B occurred 27 days after sowing. Throughout the growing period, biological and chemical controls were applied to manage pest populations (all treatments listed in Supplementary Table S2). To mitigate the risk of stem breaking, plants were secured to a bamboo stake using a plastic-coated wire once they reached a height of approximately 90cm.

After the elongation phase, shoots of at least 20–25 mm long were used for root induction. The explants were cultivated into baby food jars with Magenta TM b-cap lids containing 25 mL of root induction medium, which consisted of HLP supplemented with three different auxins: (A) 5 µMNAA; (B) 10 µM NAA; and (C) a mixture of 5 µM NAA and 5 µM IBA; all media were supplemented with 3% (w/v) sucrose and solidified with 8.5 gL⁻¹ Plant Agar^®. The different light conditions were the same as described above. After four weeks of culture in medium A or two weeks in medium B and C, explants were cultured in baby food jars with Magenta TM b-cap lids containing 25 mL of root expression medium (REM), which consisted of hormone-free HLP supplemented with 2 gL⁻¹ activated charcoal, 3% (w/v) sucrose, and 8.5 gL⁻¹ Plant Agar^® for six weeks. Growth chamber temperature and photoperiod were the same as those described above.
After six weeks in REM, explants with visible roots (Figure 7e) were transferred to wet peat moss (Pindstrup, Ryomgård, Denmark): vermiculite (8:2, v/v) and acclimatized in the greenhouse under controlled conditions at 21 ± 1 °C with progressively decreasing humidity for one month from 95% to 80% (Figure 7f). Prior to acclimatization, and following the procedure described in Castander et al. [66 (link)], the plants that developed a poor root system were transferred to Ecoboxes (Eco2box/green filter: a polypropylene vessel with a “breathing” hermetic cover, Duchefa^®, Duchefa Biochemie, Haarlem, Netherlands) containing perlite:peat (1:1, v/v) moistened with liquid HLP.