Science - USA (2022-03-04)

were transiently induced in the hypocotyl
after removal of the root system [Fig. 3R;
( 42 )]. Both CRISPR-generated nulllbd17and
lbd29mutants had reduced number of roots
on cut hypocotyl. Similarly, both mutants ex-
hibited a reduction in the number of roots
developed on the hypocotyls of etiolated seed-
lings. However,lbd29mutants had a more
significant reduction in the number of these
roots (Fig. 3S and table S3;P< 0.001; TukeyÕs
honestly significant difference), suggesting sub-
functionalization of these paralogs. Finally, our
hypothesis is supported by the evolutionary
retention of subclass IIIB genes, because they
were lacking only in three angiosperm species,
two carnivorous plants,Aldrovanda vesiculosa
andUtricularia gibba, and the water plant
Ceratophyllum demersum(table S4). Common
to all three is that they lost their roots during
evolution. Taken together, our data indicate
that the initiation program of shoot-borne

roots and its specific regulation by subclass

IIIB LBDs is deeply conserved in angiosperms.

Deep conservation of an LBD superlocus

During the assembly of the phylogenetic

tree, we observed that subclass IIIB genes

were almost always located immediately next

to a closely related subclass IIIA gene in a

single superlocus that exists already in basal-

diverging angiosperms (fig. S13 and table S4).

Cis-regulatory conservation analysis of 80 plant

species from four families using the Conserv-

atory algorithm ( 43 ), revealed broad conser-

vation of noncoding regions within the locus,

including multiple auxin and cytokinin response

elements [Fig. 4A and table S5; ( 28 )], supporting

the existence of a conserved regulatory pro-

gram for the entire locus. To test whether the

function of this regulatory sequence is con-

served, we constructed a dual reporter of the

tomato regulatory sequences ofSBRLand its

syntenic subclass IIIA geneBROTHER OF SBRL

(BSBRL;pBSBRL:mNeonGreen-NLS-BSBRLterm

pSBRL:mScarleti-NLS-SBRLterm) and intro-

duced it intoArabidopsis. Despite these species

having diverged ~120 million years ago ( 39 ),

the tomato regulatory sequence was sufficient

to drivemScarletiexpression in root primordia

that formed on theArabidopsishypocotyl after

removal of the root system (fig. S12, A to I).

The sequence similarity of subclass IIIA

and IIIB genes suggests that they perform

similar functions, but neitherBSBRLnor its

Solanaceae-specific duplicationBSBRL2were

detected in our single-cell expression dataset.

RTCNandLBD16,themaizeandArabidopsis

subclass IIIA genes (table S4), respectively,

were previously linked to the regulation of

lateral root development ( 17 ), suggesting that,

similar to subclass IIIB function in shoot-borne

roots, subclass IIIA genes may play a con-

served role in lateral root initiation. To test

Omaryet al.,Science 375 , eabf4368 (2022) 4 March 2022 5of7

Fig. 4. A conserved superlocus
regulates lateral root initiation.
(A) Synteny and cis-regulatory
sequence conservation in the
SBRL-BSBRLsuperlocus. Black
triangles mark conserved noncoding
sequences. Red and blue squares
mark conserved cytokinin and auxin
response elements, respectively
(CytRE: TGATTA; AuxRE: TGTCTC/
CC/GG). (B) Expression of sub-
class IIIA/IIIB LBDs during tomato
lateral root development. (C) Aver-
age expression of tissue identity
markers during lateral root develop-
ment. (DtoG) Ten-day-old WT
(D) and mutant [(E) to (G)] tomato
seedlings. (H) Lateral root density in
10-day-old tomato seedlings (n= 50,
30, 25, 40, and 50 for WT,sbrl,
bsbrl,bsbrl2, andsbrlbsbrl, respec-
tively). (I) Gene structure of the
SBRL-BSBRLsuperlocus and
BSBRL2. Arrowheads mark gRNA
targets. (JandK) Ten-day-old
seedling (J) and cut hypocotyl
10 days after the cut (K) ofsbrlbsbrl
double mutants. (L) qRT-PCR
expression of subclass IIIA genes
during wound-induced root initiation
onsbrlhypocotyl (n= 5). (Mand
N) Ten-day-old seedling (M) and cut
hypocotyl 10 days after the cut
(N) ofsbrlbsbrlbsbrl2triple
mutants. (OandP) Three-month-old
pot-grown tomato plants.
(Q) Model for the initiation of
different root types in angiosperms.
Error bars indicate SE. Asterisks indicate statistically significant difference from baseline (WT or time 0 hours; *P< 0.05; **P< 0.001). Data in (H) and (L) were analyzed with
Tukey’s test; data in (B) were analyzed by Welch’s test. Scale bars: (D) to (G), (J), (K), (M), and (N), 1 cm; (O) and (P), 10 cm.

A

CNS CytRE AuxRE

D

WT sbrl

E

bsbrl bsbrl2

FG

LR Stage

C

Vasculature initials

Procambium

Transition

Stem Cells

Root cap 0

1

N

M

E

I BSBRL 8.4kb SBRL BSBRL2

H

P

sbrl

bsbrl

bsbrl2

O

sbrl

WT sbrl bsbrl

brl

bsbrl

bsbrl2

M

sbrl

bsbrl

bsbrl2

N

sbrl

bsbrl

J

sbrl

K

E

xpre

ss

ion

L

0

1

0h 24h 48h120h

BSBRL

BSBRL2

Time since cut

*

*

Root

meristem

IIIB

IIIB

IIIA2

Transition

S t ate

IIIB

IIIA

2

4

6

WTsbrl bsbrl bsbrl2 sbrl

bsbrl

Lateral Roots

Den

sity (root

/cm)

**

** *

**

B

Or

igi

n 1 2 3 4 5

Expression

0

20

40

60

SBRL BSBRL BSBRL2

*

*

*

Or

igi

n^12345

LR Stage

Fabaceae

Poaceae

Solanaceae

Brassicaceae

bsbrl

Wounding

Q

IIIA IIIB

s

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