Scientia Agricultura Sinica ›› 2021, Vol. 54 ›› Issue (14): 3097-3112.doi: 10.3864/j.issn.0578-1752.2021.14.015

• HORTICULTURE • Previous Articles     Next Articles

Genome-Wide Identification and Expression Pattern Analysis of LRR-RLK Gene Family in Apple

HUANG JinFeng1(),LÜ TianXing1,WANG Xu2,WANG YingDa1,WANG DongMei1,YAN ZhongYe1,LIU Zhi1()   

  1. 1Liaoning Institute of Pomology, Yingkou 115009, Liaoning
    2College of Horticultural Science and Engineering, Shangdong Agricultural University, Tai’an 271018, Shangdong
  • Received:2020-08-30 Accepted:2020-12-29 Online:2021-07-16 Published:2021-07-26
  • Contact: Zhi LIU E-mail:huangfeng1002@163.com;lnliuzhi@163.com

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Abstract:

【Objective】 The study was carried out to explore the whole genome characteristics and expression patterns ofLRR-RLKs in apple, to reveal the expression specificity of family members in different tissues and their responses to biological and abiotic stress, and further understand its biological function in apple. 【Method】 The members of LRR-RLK gene family in the whole genome of apple were identified based on the local BLAST database and Pfam database. The LRR-RLK amino acid sequence prediction, subcellular localization prediction, domain analysis, phylogenetic tree and chromosome localization were completed by software of ExPASy Proteomics Server, Cell-PLoc, CD-Search Tool, MEGAX and MG2C. In addition, the expression pattern of 12 LRR-RLK genes in different tissues and stress were analyzed by real-time fluorescent quantitative PCR (qRT-PCR).【Result】 A total of 378 LRR-RLKgenes were identified from apple genome. TheseLRR-RLKgenes encoded proteins containing 318-1 827 amino acid, and the theoretical isoelectric point ranged from 6.14 to 9.01. The prediction subcellular localization of apple LRR-RLK proteins was all distributed in the cell membrane. The gene family could be divided into 15 subgroups, containing 1-111 genes. The 378 genes in this family were distributed on all 17 chromosomes of the apple, and the chromosome 7 contained 40 genes. The LRR-RLK gene family had two conserved domains, namely the leucine-rich repeat structure and the protein kinase domain. Irregular curl and α-helix was the main secondary structure in the LRR-RLK gene family, and the rotation of β-turn was very small. It was found that the 12 selected family members were expressed in all tissues (except MD00G1105400), and most genes were expressed at relatively high levels in stem. Seven genes were up-regulated under low temperature conditions, and the expression of MD09G1153800 was the most obvious. The expression of MD09G1153800 was raised to 6.8 times of that under the control. While MD06G1170200 and MD05G1061600 were both down-regulated. Eight genes were up-regulated under drought conditions, and MD00G1105400 was the most obvious one. The expression of MD00G1105400 was raised to 9.6 times of that under the control; under salt conditions, MD04G1150400, MD13G1108000 and MD02G1071800 were always up-regulated. Among them, MD02G1071800 had the highest expression after 24 hours of salt stress treatment, which was 14.9 times of that under the control. After inoculating Botryosphaeria dothidea, the expression of 12 LRR-RLKgenes increased first and then decreased. After inoculating, the expression level of Wangshanhong was higher on the first day, however the expression level of Jiguan was higher on the third day. The expression of MD09G1153800 and MD05G1065800 were up-regulated significantly in Jiguan, in relative to have no change in Wangshanhong, suggesting that these twoLRR-RLKscould serve as candidate genes for further functional characterization. 【Conclusion】 A total of 378 LRR-RLK members were identified from apple whole genome sequences, which could be divided into 15 groups and distributed on 17 chromosomes, and the most of LRR-RLK genes were responsive to stress stimulus and Botryosphaeria dothidea.

Key words: apple, LRR-RLK, gene family, identification, expression analysis

Table 1

Primers sequences of real time fluorescent quantitative PCR"

登录号 Gene number 上游引物 Forward primer (5′-3′) 下游引物 Reverse primer (5′-3′)
MdActin TGACCGAATGAGCAAGGAAATTACT TACTCAGCTTTGGCAATCCACATC
MD09G1153800 TCTTCTTGAGCCATCTCC CGTCGGTCAGTATGTTTT
MD04G1150400 ACCGTTCATTGCTCCTTG GCGAGCCCTATTTCCATC
MD03G1138500 GAAGCCAACAGACGAGAT GGATAATAAGCAAACCCT
MD06G1170200 CCAGTGGACCCATCATTC GCTTGGAGCATTTCTTGTAT
MD03G1036900 GGAAAGGAGGAGCAGATT CAGGACCCAACAGAACAT
MD05G1061600 AGATGTCTACAGCTATGGGATA TGGTTAGTTCGCCTTTGA
MD13G1108000 TTCCCATAGACAGCAAGA GTGGCATCCAAGTAAAGC
MD05G1261100 GTCGAAACCAAGCTATTT TAGTTGAGGCGAACATTA
MD00G1105400 GACTGATAGGTTGGCACTG GACCCTCTGACTATGTCG
MD02G1071800 GAATCCATCATAGAAACT ATTAGCCATGTACTCGTA
MD05G1065800 TTCAATACCTCCGCAACT AAATCCCACTCAGCAAAT
MD15G1288500 GCCTTGAGGATGGCAGAT GTACCCTAACTTGAACAACGAC

Fig. 1

Phylogenetic tree of LRR-RLK gene family in apple"

Table 2

The information of LRR-RLK gene family in apple"

亚家族
Subclade 		基因数量
No.of genes 		氨基酸数目
Number of amino acids 		范围Range
等电点 Isoelectric point 分子量 Molecular weight (Kd) LRR数量 No. of LRRs
I-1 10 697-1022 5.34-8.39 78.68-111.91 1-11
II 39 595-1054 5.16-8.49 66.69-116.19 1-6
III 50 400-1063 5.61-9.66 43.51-115.39 2-9
IV 5 681-683 6.16-7.76 73.96-74.16 3-5
V 12 551-801 5.57-9.39 60.88-86.53 2-6
VI-1 10 700-794 7.61-9.46 77.79-87.25 2-8
VI-2 5 655-716 5.50-5.92 71.84-78.63 1-3
VII-1 7 886-1010 5.28-6.26 96.77-110.12 5-12
VII-2 2 861-862 5.8-6.15 94.58-94.84 7
VII-3 3 1141-1146 5.61-7.56 106.07-123.50 11-16
VIII 9 794-964 5.84-7.24 87.52-105.10 3-7
IX 8 851-977 5.62-8.63 93.01-103.52 5-9
Xa 4 601-627 6.14-8.09 66.09-124.65 1-4
Xb-1 12 1021-1301 5.42-6.74 122.83-141.35 9-19
Xb-2 2 1071-1090 5.76-6.80 117.55-119.70 6
XI 74 614-1258 5.28-9.09 67.92-138.67 4-20
XII 111 318-1827 5.22-9.75 34.95-199.33 2-19
XIII-a 5 532-606 5.44-6.15 58.27-67.22 2-3
XIII-b 1 989 6.05 108.91 8
XIV 4 899-911 6.50-8.10 97.60-98.43 5-9
XV 5 441-1145 6.15-8.37 47.94-125.05 6-10

Fig. 2

Chromosome location of the LRR-RLK gene family in apple "

Fig. 3

Gene structure analysis of LRR-RLK family members in apple"

Fig. 4

Conserved motifs and sequence logo of III subfamily A: III subfamily motif analysis; B: Logo of 15 conserved motif"

Fig. 5

Conservative domains of III subfamily"

Table 3

The secondary structure of LRR-RLK proteins in apple"

登录号 Gene number α-螺旋 α-helix (%) β-转角 β-turn (%) 无规则卷曲 Random coil (%) 延长链 Extended strand (%)
MD04G1019100 34.88 5.98 43.74 15.39
MD04G1079600 36.80 4.25 44.13 14.81
MD04G1150400 36.25 4.86 43.83 15.06
MD04G1174900 37.82 2.18 45.39 14.61
MD05G1065800 37.14 3.85 46.92 12.09
MD05G1153300 32.27 3.67 45.21 18.85
MD05G1261100 33.66 2.41 52.14 11.79
MD05G1299200 41.63 5.44 41.63 11.30
MD06G1198600 34.16 2.39 49.86 13.59
MD07G1259500 39.01 3.34 45.90 11.75
MD08G1017800 36.67 2.28 47.46 13.60
MD09G1014600 33.97 3.30 46.26 16.48
MD09G1153800 40.07 5.08 39.35 15.50
MD09G1168400 38.16 7.75 38.59 15.49
MD11G1047400 37.23 1.91 48.42 12.44
MD12G1192800 28.75 4.62 52.26 14.38
MD13G1108000 26.88 4.21 49.43 19.48
MD15G1152400 33.84 2.79 51.05 12.33
MD15G1288500 29.64 5.73 50.00 14.63
MD16G1288500 39.36 4.33 42.37 13.94
MD17G1060000 33.74 1.80 51.47 12.99

Fig. 6

Relative expression of LRR-RLKin different tissues of apple Different lowercase letters indicate significant difference (P<0.05). The same as below "

Fig. 7

Relative expression of apple LRR-RLK under different abiotic stresses "

Fig. 8

Expression pattern of LRR-RLKin response to B. dothidea in apple "

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