Supporting Information
Piperno 10.1073/pnas.1703658114
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Teosinte Gene Expression. In teosinte, other genes that were differen-
tially expressed in early Holocene vs. modern conditions and not
previously identified as domestication candidates nonetheless have
functions known or suggested in maize and other grasses to mediate
the following key trait differences observed in the experimental grow-
outs (see refs. 27, 59 for further details): (i) vegetative architecture:
phytohormone genes such as auxins were differentially expressed, and
they are known to influence this trait, possibly through interactions
with the tb1 gene; (ii) inflorescence sexuality: recently discovered
hormones called “Brassinosteroids” that now are known to control
this trait partially in maize were differentially expressed; (iii) plant
height: phytohormones, including gibberellins, and gibberellin regu-
lators called “DELLA” that modulate plant growth and responses to
abiotic stressors, such as cold, in maize were differentially expressed.
Studying GA in Maize Domestication.Approaches increasingly used by
investigators to study possible incidences of GA use a comparative
transcriptome analysis that correlates changes in phenotype with
possible differential expression of genes in the inducing and non-
inducing environment (63, 64). Here we had the advantage of being
able to work with both the ancestral and derived plant, because the
former presumably would exhibit more plasticity than the latter, and
selected traits can be placed in an evolutionary context (e.g., refs. 19,
33). Domestication studies typically will provide this beneficial cir-
cumstance, because wild progenitors of many important crops have
been identified and are still found onmodern landscapes. Therefore,
to study GA, we grew traditional land races of Mexican maize in the
same early Holocene and modern conditions of atmospheric CO2
and temperature used for teosinte. RNAseq analysis was carried out
on the maize to determine if DE genes in teosinte were invariant in
expression in maize in the contrasting environments; we inferred
such invariability would represent GA at those loci. The compara-
tive gene expression results do suggest that a substantial loss of
plasticity occurred during maize domestication, because numerous
genes that were differentially expressed in teosinte were not dif-
ferentially expressed in maize, including 83 with previous evidence
of selection and that mediate diverse traits. Moreover, a number of
genes that were differentially expressed in teosinte (discussed in
part above), that were not previously identified as targets of selec-
tion but that nonetheless have relationships to vegetative architec-
ture, inflorescence sexuality, plant height, and yield, were invariant
in maize, thus also suggesting GA.
Other Current Examples of Crop Plant Plasticity. The plants discussed
thus far exemplify examples of trait plasticity that was lost during
domestication; it may turn out that plasticity was lost in a majority of
cases, because farmers would be expected to decrease environ-
mental sensitivity in their crops. However, there were instances in
which plasticity was maintained in the domesticated species, re-
ducing fitness in some environmental contexts. For example, man-
ioc (Manihot esculenta Crantz) retained plasticity from its wild
ancestor in growth form (shrub or liana depending on savanna or
forested environment), but stem brittleness, which apparently was
favored by farmers for ease of harvesting, limits growth of the liana
form in abandoned fields (109). Another less well-documented
example of plasticity in traditional cultivars concerns fruit bitter-
ness, considered a premier wild trait in the Cucurbitaceae, a family
that gave rise to many Old and NewWorld domesticates (squashes,
gourds, cucumbers, and others) including some of the earliest crops
of the Americas. However, recent evidence indicates the trait is
plastic in some varieties of domesticated cucumber (Cucumis sativus
L.), because nonbitter fruits become bitter when exposed to cold
temperature stress, a process controlled in part by a newly discov-
ered transcription factor (110). Bitterness in all economic cucurbits
is conferred by the triterpenoids cucurbitacins. Therefore, a possible
association of plasticity and temperature variability in the evolution
of nonbitter fruits would lend itself to study in other Cucurbitaceae,
including Cucurbita spp. squashes, which in Mesoamerica and South
America were domesticated at the beginning of the Holocene.
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Fig. S1. A map depicting known or likely centers of plant domestication. Black outlines surround the most widely accepted independent centers of do-
mestication, and sources of major diffusions of domesticates are indicated by arrows. Green and purple regions are those where the domestication process
took place during the late Pleistocene to early Holocene transition (12,000–8,200 y B.P.) and in the middle Holocene (8,200–4,200 y B.P.), respectively. Brown
regions represent areas where, at present, the evidence for domestication is interpreted based on the presence of domestic forms indigenous to these regions
found outside their native distributions. The letters A–H correspond to the following: A, Southwest Asia (wheat, barley, lentil, pea, chickpea); B, India [rice
(indica), millets, mungbean]; C, China [broomcorn millet, foxtail millet, rice (japonica), soybean, melon]; D, New Guinea (banana, taro, yam); E, Africa (date
palm, sorghum, pearl millet, African rice, oil palm); F, Eastern North America (acorn and spaghetti squash, sunflower, sumpweed, goosefoot); G, Mexico (maize,
pumpkin squash, common and lima beans, avocado, chili pepper); H, South America [chili peppers, peanut, cotton, squashes (butternut and Hubbard), common
and lima beans, manioc, sweet potato, white potato, yam, quinoa]. Reproduced from ref. 2.
Fig. S2. Maize’s wild ancestor teosinte in its natural habitat in Guerrero, Mexico growing in poor, shallow soils. It responded with plasticity to produce maize
traits in vegetative architecture and inflorescence sexuality as described in the legend of Fig. 1 caption. Image courtesy of Anthony J. Ranere.
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Table S1. Some known and potential examples of plasticity for important domestication traits in domesticated plants and wild
ancestors
Species Plastic change Environmental factor (refs.)
Zea mays ssp parviglumis (wild maize) Vegetative architecture, flower sexuality Shade, poor soils, little moisture (55, 58 )
Past low CO2 and temperature (experimental) (27)
Triticum monococcum (einkorn wheat) Seed size increase Enriched soils of early cultivation? (69)
Hordeum vulgare (barley) Seed size increase Enriched soils of early cultivation? (69)
Cucumis sativa (cucumber) Fruit bitterness Temperature (110)
Chenopodium berlandieri (goosefoot) Seed dormancy traits Age at flowering related to soil moisture? (66, 67)
Polygonum erectum (erect knotweed) Seed morphology Unspecified growing conditions (28)
Manihot esculenta ssp. flabellifolia
(Pohl) Cifferi (wild manioc)
Growth form (shrub vs. liana) Savanna vs. forest (109)
Manihot esculenta ssp. esculenta
(domesticated manioc)
Growth form (shrub vs. liana) Cultivated field vs. forest (109)
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