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Acta Agronomica Sinica ›› 2024, Vol. 50 ›› Issue (4): 932-943.doi: 10.3724/SP.J.1006.2024.34122

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genome-wide identification and expression analysis of AhGA3ox gene family in peanut (Arachis hypogaea L.)

LI Hai-Fen(), LU Qing, LIU Hao, WEN Shi-Jie, WANG Run-Feng, HUANG Lu, CHEN Xiao-Ping, HONG Yan-Bin, LIANG Xuan-Qiang()   

  1. Guangdong Provincial Key Laboratory of Crop Genetic Improvement / South China Peanut Sub-Center of National Center of Oilseed Crops Improvement / Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China
  • Received:2023-07-14 Accepted:2023-10-23 Online:2024-04-12 Published:2023-11-14
  • Contact: * E-mail: Liangxuanqiang@gdaas.cn
  • Supported by:
    Open Competition Program of Top Ten Critical Priorities of Agricultural Science and Technology Innovation for the 14th Five-Year Plan in Guangdong Province(2022SDZG05);Guangdong Provincial Key Research and Development Program- Modern Seed Industry(2020B020219003);Guangdong Provincial Key Research and Development Program- Modern Seed Industry(2022B0202060004);China Agriculture Research System of MOF and MARA(CARS-13);National Natural Science Foundation of China(32001442);National Natural Science Foundation of China(32172051);Guangdong Basic and Applied Basic Research Foundation(2021A1515010811);Guangdong Basic and Applied Basic Research Foundation(2023A1515010098);Technology Special Fund of Guangdong Province Agriculture and Rural Affairs Department(2019KJ136-02);Guangdong Province Overseas Master Teacher Program(207124505346);Agricultural Competitive Industry Discipline Team Building Project of Guangdong Academy of Agricultural Sciences(202104TD)

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Abstract:

Gibberellin 3-beta-dioxygenase (GA3ox) is one of the key enzymes involved in gibberellin biosynthesis, which can regulate plant growth and development by affecting gibberellin formation. There were no systematic studies in peanut genome. In this study, AhGA3ox family genes were identified from the genome database of cultivated peanut species by bioinformatics, and the distribution, structure, evolutionary characteristics, physical and chemical properties, promoter cis-acting elements were also analyzed. The relative expression pattern of AhGA3oxs in different peanut tissues was analyzed by qRT-PCR, and the relative expression level of in shell of two peanut lines with different pod size were also analyzed. The results showed that 7 AhGA3oxs were distributed on 7 chromosomes of peanut, all of which were composed of 1 intron and 2 exons. All the AhGA3ox proteins contained 1 DIOX_N domain and 1 2OG-FeII_Oxy domain. Phylogenetic analysis showed that they were closely related to GA3ox proteins of soybean,. The AhGA3oxs showed obvious tissue expression specificity in root, stem, leaf, flower and peg. The expression levels of AhGA3oxs were not only different in different development stages of the peanut shell, but also different at the same development stage of the two lines. Interestingly, the relative expression levels in large pod lines were significantly higher than those in small pod lines at most development stages. Therefore, we predict that the gene expression of AhGA3ox gene family may promote the formation of large pod.

Key words: peanut, GA3ox, the relative expression analysis, bioinformatics, functional analysis

Table 1

Primers used for qRT-PCR"

引物名称
Primer name		 引物序列
Primers sequence (5°-3°)		 引物名称
Primer name		 引物序列
Primers sequence (5°-3°)
actin-F CCATTGAGAAGACCTACGA Ahy_A09g046613-F CACATACGTCCACATCCAA
actin-R AATCATGGAAGGCTGGAA Ahy_A09g046613-R TGGTTCCAAGGTACTCATTC
Ahy_A06g030353-F TGGATCAAGTGGTTTCTC Ahy_B06g085507-F GTAGTTTCTCCTTTGGTTCCGAAT
Ahy_A06g030353-R CAAGGCTTTGTCAAGATAC Ahy_B06g085507-R GGCTTTGTCAAGATACTTGTCCTT
Ahy_A07g037374-F TGTCCACATGCGAAGCTA Ahy_B09g094759 -F TCCACATCCAAAGCTAATAGGC
Ahy_A07g037374-R TGGTGCCAAGGTACTCATT Ahy_B09g094759 -R GGTTCCAAGGTACTCATTCCAA
Ahy_A08g040809-F ATTCCCACGCATGGTTTCA Ahy_B08g089553-F CGTTACTCTTTGGCTTATTTCC
Ahy_A08g040809-R CGATGATGGGTATGGATGGAAT Ahy_B08g089553-R CTTCACACTAACCCTACGAAAT

Table 2

Prediction of physicochemical properties of AhGA3ox family proteins"

基因编号
Gene ID		 CDS大小
CDS size (bp)		 外显子
数目
No. of exons		 亚细胞定位
Subcellular
localization		 等电点
pI		 不稳定
参数
Instability index		 脂溶指数
Aliphatic index		 亲水性
平均数
GRAVY		 带正电荷残基数
Asp + Glu		 带负电荷残基数Arg+Lys
Ahy_A06g030353 1047 2 细胞核 Nucleus 5.53 39.42 82.66 -0.358 46 36
Ahy_A07g037374 1125 2 细胞核 Nucleus 8.11 37.63 86.29 -0.221 31 33
Ahy_A08g040809 1056 2 细胞质 Cytoplasm 7.30 36.94 77.87 -0.434 40 40
Ahy_A09g046613 1068 2 细胞质和细胞核
Cytoplasm and nucleus		 7.68 39.04 87.08 -0.231 30 31
Ahy_B06g085507 1047 2 细胞骨架 Cytoskeleton 5.53 39.09 82.66 -0.370 46 36
Ahy_B08g089553 1062 2 细胞质 Cytoplasm 6.49 37.31 75.79 -0.462 43 39
Ahy_B09g094759 1092 2 细胞核 Nucleus 8.08 39.45 85.71 -0.287 31 33

Fig. 1

Chromosomal distribution GA3ox gene family in peanut genome The black bars represent the chromosomes. GA3ox genes are marked to the right of the chromosomes. The scale bar on the left indicates the length of the chromosomes."

Fig. 2

Phylogenetic and structural analysis of AhGA3ox gene family and encoded proteins in peanut (A) phylogenetic tree is constructed with amino acid sequences of AhGA3ox; (B) the structure of AhGA3ox genes. Green rectangles, yellow rectangles, and black line represent UTR, CDS, and introns; (C) the structure of AhGA3ox protein. Blue and purple rectangles represent DIOX_N and 2OG-FeII_Oxy domains."

Fig. 3

Phylogenetic analysis of GA3ox family The light blue background was tetraploid wild peanut (Arachis moticolar), the green area was cultivated soybean (Glycine max), the blue area was rice (Oryza sativa), the light gray area was Arabidopsis (Arabidopsis thaliana), the yellow area was A genomic diploid wild peanut (Arachis duranensis), the brown area was wild peanut with B genome diploid (Arachis ipaensis), the purple area was wild soybean (Glycine soja), the red area was tetraploid cultivated peanut (Arachis hypogaea L.). Phylogenetic relationships among 71 GA3ox proteins in peanut, arabidopsis, rice, soybean and wild soybean. GA3ox proteins were divided into 4 classes. The phylogenetic tree is built on the basis of the complete amino acid sequences of GA3ox proteins by MEGA-X with maximum likelihood method. Bootstrap=1000."

Fig. 4

Distribution of conserved motifs in GA3ox proteins Phantom analysis is performed by MEME program. The height of different amino acid represents repeatability. The scale bar at the bottom indicates the length of the motif protein sequence. On the left are the names of the protein series. The different colors on the right correspond to the positions of different conserved motifs on the series, respectively."

Fig. 5

Prediction of cis-acting elements in the promoters of AhGA3ox gene family Different colored boxes represent different cis-elements, and the scale at the bottom represents the length of the promoter sequence."

Table 3

Comparison of agronomic traits of two peanut lines"

性状Trait P92 P92-1
株高 Plant height (cm) 36.59±1.11 38.33±1.82
分枝数 Branching number 10.33±0.47 9.67±0.47
结果数 Pod number 39.00±0.83 36.00±0.50
荚壳厚度 Pod shell thickness(mm) 1.15±0.06 1.48±0.22*
荚果长 Pod length (mm) 19.21±1.03 35.11±1.59**
荚果宽 Pod width (mm) 12.73±0.19 15.39±0.26**

Fig. 6

Relative expression pattern of AhGA3ox genes family in different plant tissues of P92 and P92-1 Different lowercase letters means significant difference at the 0.05 probability level in peanut tissue."

Fig. 7

Relative expression pattern of AhGA3ox gene family in the shell of two peanut lines with different pod size S1-S5 represents the 10th, 17th, 24th, 31st, and 38th day after the gynophore enters the soil, respectively. *, ** mean significant difference at the 0.05 and 0.01 probability levels, respectively."

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