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Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (8): 1437-1449.doi: 10.3724/SP.J.1006.2021.01077


Genome-wide identification and expression analysis of B-box gene family in wheat

WANG Yan-Peng(), LING Lei, ZHANG Wen-Rui, WANG Dan, GUO Chang-Hong*()   

  1. Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province/College of Life Science and Technology, Harbin Normal University, Harbin 150025, Heilongjiang, China
  • Received:2020-09-18 Accepted:2021-01-13 Online:2021-08-12 Published:2021-02-22
  • Contact: GUO Chang-Hong E-mail:13694609045@163.com;kaku3008@126.com
  • Supported by:
    Preliminary Research Project of the National Basic Research Program of China (973 Program)(2011CB111500);Graduate innovation fund of Harbin Normal University(HSDSSCX2020-08)


B-box (BBX) is a class of zinc finger proteins that contain one or two B-box domains and play important roles in plant growth and development. The number, gene structure and phylogenetic relationship of wheat B-box transcription factors, as well as their expression specificity in different tissues and response to abiotic stress were investigated. A total of 87 members of B-box gene family were identified from wheat genome and all contained the B-box domain. TaBBXs encoded 146 to 489 amino acids and the isoelectric points ranged from 4.32 to 10.42. Chromosome mapping showed that these genes were distributed on 18 wheat chromosomes except 1A, 1B, and 1D. Based on phylogenetic analysis, TaBBXs were divided into five subfamilies, with 0-4 introns. The members of the subfamily in the same phylogenetic tree branch in the same group had highly similar gene structures. The qRT-PCR revealed that the investigated 20 genes had different expression patterns, and most genes were highly expressed in leaves, and TaBBX10 and TaBBX39 were only highly expressed in leaves, while TaBBX74 was expressed in spikes, TaBBX43 was specifically expressed in roots. These genes showed different expression patterns under different stress. 11 genes were up-regulated after low temperature stress, 13 genes were down-regulated after ABA treatment, 10 genes were up-regulated after salt stress, and 7 genes were down-regulated after drought stress. TaBBX10, TaBBX39, TaBBX60, TaBBX67, and TaBBX74 were significantly up-regulated under two or more stresses.

Key words: wheat, genome-wide, B-box gene family, abiotic stress, gene expression

Table 1

Primers used in this study"

Forward primer (5′-3′)
Reverse primer (5′-3′)

Table S1

TaBBX genes information identified in the wheat genome"

Gene name
Gene ID
Chromosome location
Length (bp)
Length (aa)
Isoelectric point (pI)
Molecular weight (kD)
Exon number
Domain type
TaBBX01 TraesCS2A02G119600 2A:70102039-70104699 1149 382 5.73 40010.83 4 1BBX + CCT
TaBBX02 TraesCS2A02G348900 2A:587750669-587751938 765 254 4.95 27209.52 2 2BBX
TaBBX03 TraesCS2A02G353900 2A:594579959-594581671 951 316 5.56 33724.51 2 2BBX+ CCT
TaBBX04 TraesCS2A02G366100 2A:610710308-610712939 789 262 4.79 28237.51 2 2BBX
TaBBX05 TraesCS2A02G388500 2A:635722864-635724553 777 258 5.82 27357.5 3 2BBX
TaBBX06 TraesCS2B02G140300 2B:106954443-106956656 1164 387 5.44 40384.32 4 1BBX + CCT
TaBBX07 TraesCS2B02G367300 2B:523760095-523761742 774 257 4.89 27492.85 2 2BBX
TaBBX08 TraesCS2B02G372000 2B:530306217-530307895 960 319 5.56 33908.66 2 2BBX+ CCT
TaBBX09 TraesCS2B02G406600 2B:575903665-575905255 795 264 5.82 27823.99 3 2BBX
TaBBX10 TraesCS2D02G121400 2D:70622968-70625567 1146 381 5.72 39968.91 4 1BBX + CCT
TaBBX11 TraesCS2D02G347300 2D:445396017-445397519 777 258 4.81 27494.76 2 2BBX
TaBBX12 TraesCS2D02G351900 2D:450234732-450236192 960 319 5.56 33936.74 2 2BBX+ CCT
TaBBX13 TraesCS2D02G386300 2D:491429370-491431171 789 262 5.82 27600.81 3 2BBX
TaBBX14 TraesCS3A02G139300 3A:117227850-117230216 1050 349 5.15 37168.47 3 2BBX
TaBBX15 TraesCS3B02G156900 3B:150154692-150156947 1050 349 5.22 37477.8 3 2BBX
TaBBX16 TraesCS3D02G139600 3D:99748881-99751184 1050 349 5.32 37482.8 3 2BBX
TaBBX17 TraesCS4A02G140600 4A:216145053-216148012 1239 412 5.5 45256.44 5 1BBX + CCT
TaBBX18 TraesCS4A02G268500 4A:580733925-580736107 1233 410 5.85 44829.19 2 1BBX + CCT
TaBBX19 TraesCS4B02G045700 4B:32896523-32898695 1236 411 6.04 44870.33 2 1BBX + CCT
TaBBX20 TraesCS4B02G155800 4B:281732350-281735921 1194 397 6.06 43627.8 3 1BBX + CCT
TaBBX21 TraesCS4D02G046200 4D:21774703-21776886 1233 410 5.85 44816.25 2 1BBX + CCT
TaBBX22 TraesCS4D02G167300 4D:288428472-288432595 1194 397 6.1 43454.51 3 1BBX + CCT
TaBBX23 TraesCS5A02G166100 5A:355071283-355072804 981 326 5.78 35576.36 2 1BBX + CCT
TaBBX24 TraesCS5A02G317100 5A:528110873-528114741 636 211 5.74 23146.7 5 2BBX
TaBBX25 TraesCS5A02G336000 5A:545058736-545059411 540 179 5.29 19206.94 2 1BBX
TaBBX26 TraesCS5A02G336100 5A:545073760-545074317 441 146 4.57 15371.44 2 1BBX
TaBBX27 TraesCS5A02G339000 5A:546563819-546564523 705 234 9.27 24319.82 1 1BBX
TaBBX28 TraesCS5A02G339100 5A:546575974-546576576 603 200 10.42 21432.56 1 1BBX
TaBBX29 TraesCS5B02G163500 5B:302753429-302754975 978 325 5.96 35477.32 2 1BBX + CCT
TaBBX30 TraesCS5B02G317700 5B:501954375-501958483 636 211 5.85 23088.66 5 2BBX
TaBBX31 TraesCS5B02G335200 5B:518472466-518473347 468 155 5 16721.09 2 1BBX
TaBBX32 TraesCS5B02G335300 5B:518481548-518484145 1107 368 6.23 39645.26 4 1BBX + CCT
TaBBX33 TraesCS5B02G337400 5B:520970152-520970850 699 232 9.02 24101.56 1 1BBX
TaBBX34 TraesCS5B02G337500 5B:521031958-521032572 615 204 9.65 21590.87 1 1BBX
TaBBX35 TraesCS5D02G170700 5D:267762539-267764201 978 325 5.96 35519.42 2 1 1BBX + CCT
TaBBX36 TraesCS5D02G323400 5D:415613354-415617623 636 211 5.85 23084.67 5 2BBX
TaBBX37 TraesCS5D02G341000 5D:429289528-429291886 1083 360 6.33 38690.35 4 1BBX + CCT
TaBBX38 TraesCS5D02G343300 5D:431251824-431252543 720 239 9.03 25267.96 1 1BBX
TaBBX39 TraesCS6A02G143900 6A:121616223-121619829 645 214 4.72 22147.27 2 2BBX
TaBBX40 TraesCS6A02G150900 6A:134947729-134949478 1095 364 5.68 37982.35 3 2BBX+ CCT
TaBBX41 TraesCS6A02G216400 6A:398252913-398254425 771 256 5.14 27782.32 2 2BBX
TaBBX42 TraesCS6A02G218900 6A:405166583-405168134 966 321 5.24 33625.42 2 2BBX+ CCT
TaBBX43 TraesCS6A02G239300 6A:449584187-449585880 711 236 5.77 25104.96 3 2BBX
TaBBX44 TraesCS6A02G286400 6A:518666410-518670650 972 323 6.65 35122.47 3 2BBX+ CCT
TaBBX45 TraesCS6A02G289400 6A:521451709-521454099 1110 369 5.91 41051.82 2 2BBX+ CCT
TaBBX46 TraesCS6A02G293200 6A:524718099-524720326 1281 426 6.81 46496.91 2 1BBX + CCT
TaBBX47 TraesCS6B02G172300 6B:184884215-184886653 645 214 4.89 22154.35 2 2BBX
TaBBX48 TraesCS6B02G179000 6B:198984566-198986312 1125 374 5.28 38846.14 3 2BBX+ CCT
TaBBX49 TraesCS6B02G246500 6B:439021199-439022376 783 260 4.98 28026.56 2 2BBX
TaBBX50 TraesCS6B02G248400 6B:445852206-445853977 966 321 5.34 33887.8 2 2BBX+ CCT
TaBBX51 TraesCS6B02G285200 6B:514117744-514119320 717 238 6.04 25141.06 3 2BBX
TaBBX52 TraesCS6B02G315400 6B:563320471-563324616 1173 390 4.96 42531.41 4 2BBX+ CCT
TaBBX53 TraesCS6B02G319500 6B:567397520-567399497 1113 370 5.58 41154.91 2 2BBX+ CCT
TaBBX54 TraesCS6B02G323400 6B:572391940-572393940 1287 428 6.4 46597.09 2 1BBX + CCT
TaBBX55 TraesCS6D02G133100 6D:100871867-100874382 645 214 4.97 22054.19 2 2BBX
TaBBX56 TraesCS6D02G140900 6D:110442898-110444721 1095 364 5.68 38019.41 3 2BBX+ CCT
TaBBX57 TraesCS6D02G199200 6D:277099701-277101029 783 260 5.14 28221.83 2 2BBX
TaBBX58 TraesCS6D02G202000 6D:284849813-284850866 954 317 5.17 33352.08 2 2BBX+ CCT
TaBBX59 TraesCS6D02G221700 6D:312763126-312764854 717 238 5.77 25258.08 3 2BBX
TaBBX60 TraesCS6D02G267100 6D:377220309-377224969 1179 392 4.79 43027.95 4 2BBX+ CCT
TaBBX61 TraesCS6D02G269500 6D:379572086-379574125 1110 369 5.5 40998.72 2 2BBX+ CCT
TaBBX62 TraesCS6D02G274100 6D:382588127-382590143 1305 434 6.12 47026.54 2 1BBX + CCT
TaBBX63 TraesCS7A02G108400 7A:65969778-65975971 1080 359 5.1 38311.73 3 2BBX
TaBBX64 TraesCS7A02G108700 7A:66173971-66174456 486 161 8.98 17172.82 1 1BBX
TaBBX65 TraesCS7A02G132100 7A:85159979-85160728 750 249 7.65 25502.35 1 1BBX + CCT
TaBBX66 TraesCS7A02G206200 7A:168812422-168813720 1299 432 5.32 47132.21 1 1BBX + CCT
TaBBX67 TraesCS7A02G211300 7A:174203246-174205720 1158 385 6.06 42218.87 2 2BBX+ CCT
TaBBX68 TraesCS7A02G218600 7A:185642724-185648145 1191 396 4.92 43615.36 4 2BBX+ CCT
TaBBX69 TraesCS7A02G263500 7A:261221617-261225670 1473 490 6.1 52005.04 4 1BBX + CCT
TaBBX70 TraesCS7A02G383400 7A:558402604-558404184 852 283 5.04 29956.59 3 2BBX
TaBBX71 TraesCS7A02G497200 7A:686936894-686938479 1119 372 5.96 39566.55 2 2BBX+ CCT
TaBBX72 TraesCS7B02G006400 7B:3684186-3689427 1017 338 4.83 36159.24 4 2BBX
TaBBX73 TraesCS7B02G113400 7B:131376607-131378427 1299 432 5.3 47173.18 1 1BBX + CCT
TaBBX74 TraesCS7B02G118300 7B:137793769-137796142 1152 383 6.24 42114.89 2 2BBX+ CCT
TaBBX75 TraesCS7B02G125500 7B:146898679-146904866 1014 337 4.32 36449.17 3 2BBX
TaBBX76 TraesCS7B02G161500 7B:220866464-220870459 1467 488 6.44 51810.89 4 1BBX + CCT
TaBBX77 TraesCS7B02G286300 7B:521577849-521579171 936 311 5.69 33195.49 2 2BBX
TaBBX78 TraesCS7B02G400600 7B:667070044-667071768 1119 372 5.9 39407.46 2 2BBX+ CCT
TaBBX79 TraesCS7D02G103300 7D:63325536-63331403 1092 363 5.03 38772.21 3 2BBX
TaBBX80 TraesCS7D02G131700 7D:83472836-83474058 753 250 6.09 25596.33 1 1BBX + CCT
TaBBX81 TraesCS7D02G209000 7D:167228163-167229829 1299 432 5.26 47125.17 1 1BBX + CCT
TaBBX82 TraesCS7D02G213000 7D:171311981-171314465 1119 372 6.31 41073.77 2 2BBX+ CCT
TaBBX83 TraesCS7D02G220300 7D:180685905-180691434 1191 396 4.92 43609.35 4 2BBX+ CCT
TaBBX84 TraesCS7D02G264300 7D:244952312-244956390 1470 489 6.21 51903.89 4 1BBX + CCT
TaBBX85 TraesCS7D02G379900 7D:492148581-492150240 858 285 5.02 30133.81 3 2BBX
TaBBX86 TraesCS7D02G484400 7D:594729348-594730950 1119 372 5.86 39527.57 2 2BBX+ CCT
TaBBX87 TraesCSU02G091500 Un:81434193-81437118 1110 369 6.21 40011.43 4 1BBX + CCT

Fig. 1

Conserved domains of B-box genes family in wheat"

Fig. S1

Phylogenetic tree of B-box genes in wheat, A. thaliana and Oryza sativa"

Fig. 2

Phylogenetic tree of B-box genes family in wheat"

Fig. 3

Chromosome location and gene duplications of the B-box gene family in wheat Each colored bar represents a chromosome, gene names are labeled on the basis of their positions on the chromosomes, segmental duplication genes are linked by colored lines."

Fig. S2

Phylogenetic tree of B-box homoeologs genes in wheat Red: gene on chromosome 2A, 2B and 2D; Black: gene on chromosome 3A, 3B and 3D; Yellow: gene on chromosome 4A, 4B and 4D; Brown: gene on chromosome 5A, 5B and 5D; Blue: gene on chromosome 6A, 6B and 6D; Orange: gene on chromosome 7A, 7B and 7D."

Fig. 4

Gene structure of B-box gene family in wheat"

Table 2

Putative regulatory cis-elements in wheat B-box family gene promoters"

Number of genes
Functions of cis-elements
CAAT-box 87 Common cis-acting element in promoter and enhancer regions
TATA-box 87 Core promoter element around -30 of transcription start
CGTCA-motif 75 cis-acting regulatory element involved in the MeJA-responsiveness
TGACG-motif 75 cis-acting regulatory element involved in the MeJA-responsiveness
ABRE 84 cis-acting element involved in the abscisic acid responsiveness
ARE 67 cis-acting regulatory element essential for the anaerobic induction
MBS 49 MYB binding site involved in drought-inducibility
LTR 57 cis-acting element involved in low-temperature responsiveness
W box 51 Wounding and pathogen responsiveness.
TGA-element 42 Auxin-responsive element
GC-motif 51 Enhancer-like element involved in anoxic specific inducibility
CCAAT-box 24 MYBHv1 binding site
TCA-element 30 cis-acting element involved in salicylic acid responsiveness
P-box 31 Gibberellin-responsive element
WUN-motif 20 Wound-responsive element
ERE 18 Ethylene-responsive element
GARE-motif 23 Gibberellin-responsive element
TC-rich repeats 27 cis-acting element involved in defense and stress responsiveness
AuxRR-core 18 cis-acting regulatory element involved in auxin responsiveness

Fig. 5

Expression profile of B-box gene family in different tissues of wheat"

Fig. 6

Expression profile of B-box gene family under different treatments in wheat A: control; B: six hours of 20% PEG treatment; C: six hours of 4℃ treatment; D: six hours of 0.2 mol L-1 NaCl treatment; E: six hours of 100 μmol L-1 ABA treatment. * and ** indicate significantly different at P < 0.05 and P < 0.01, respectively."

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