Crops ›› 2024, Vol. 40 ›› Issue (3): 23-31.doi: 10.16035/j.issn.1001-7283.2024.03.004

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Genomic SSR Loci Mining and Genetic Diversity Analysis of Camellia oleifera Based on Genome Sequences

Dai Han1(), Shen Tie1(), Shi Taoxiong2, Li Ruiyuan1()   

  1. 1Guizhou Provincial Key Laboratory of Information and Computing Science, Guizhou Normal University, Guiyang 550001, Guizhou, China
    2College of Life Sciences / Buckwheat Industry Technology Research Center, Guizhou Normal University, Guiyang 550001, Guizhou, China
  • Received:2023-07-10 Revised:2023-08-26 Online:2024-06-15 Published:2024-06-18

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Abstract:

SSR (Simple Sequence Repeat) loci were excavated from the whole genome sequence of Camellia oleifera Abel available in the NCBI database. Primer pairs were designed using Primer 3.0 software, and those with high polymorphism were selected for genetic diversity evaluation. A total of 1 661 881 SSR loci were detected with a cumulative length of 2 889 508 820 bp, occurring at a frequency of 63.22%. Mono-nucleotide repeats were the most abundant (61.72%), followed by di-nucleotide repeats (28.59%) and tri-nucleotide repeat units (6.90%). Analysis of repeat sequence motifs revealed the presence of 337 types of repeat elements, with A/C being the predominant repeat unit, followed by A/T (60.46%), AG/TC (13.88%), AT/TA (12.09%), AC/TG (2.86%), and AAT/TTA (2.54%). The 10 pairs of primers per chromosome (a total of 150 pairs of primers) were synthesized and assessed for polymorphism. The results indicated that 129 primer pairs successfully amplified target bands, with 25 primer pairs displaying specificity among different materials. The utilization of the whole genome sequence of C.oleifera enabled the large-scale development of SSR markers, which could be employed for genetic diversity analysis, construction of genetic maps, variety identification, and other related research in C.oleifera.

Key words: Camellia oleifera, Genome, SSR, Germplasm resource, Genetic diversity

Table 1

Origins of 15 samples"

样品编号
Sample number		 采集地点
Sampling site		 树龄
Tree age
X1-1 铜仁市松桃县正大镇长征村 70
X2-1 铜仁市松桃县正大镇长征村 70
X3-1 铜仁市松桃县正大镇长征村 70
X4-1 铜仁市松桃县正大镇长征村 70
X5-1 铜仁市松桃县正大镇长征村 70
X6-1 铜仁市松桃县正大镇丫山塘村 12
X7-1 铜仁市松桃县正大镇丫山塘村 12
X8-1 铜仁市松桃县正大镇丫山塘村 12
X9-1 铜仁市松桃县正大镇丫山塘村 12
X10-1 铜仁市松桃县正大镇丫山塘村 12
X11-1 铜仁市碧江区滑石乡新寨村 6
X12-1 铜仁市碧江区滑石乡新寨村 6
X13-1 铜仁市碧江区滑石乡新寨村 6
X14-1 铜仁市碧江区滑石乡新寨村 6
X15-1 铜仁市碧江区滑石乡新寨村 6

Fig.1

Distribution of SSRs on C.oleifera chromosomes"

Fig.2

Distribution characteristics of SSR Loci in C.oleifera genome"

Fig.3

The number of motifs in SSRs of different length repeat unit"

Fig.4

The number of repeat unit SSRs of different lengths"

Fig.5

Frequency of SSR in different length repeat units"

Table 2

Screening of primers of SSR-PCR"

序号
Number		 名称
Name		 重复基序
Repeat
motif		 引物序列
Primer sequence		 扩增片段大小
Amplified fragment
size (bp)		 等位
基因数
Na		 杂合度
He		 多态性
信息含量
PIC		 基因多样性
Gene
diversity
1 CoAb086 (CAT)5 F: CCCTGAAGATATCCGCACCC 257 4 1.00 0.57 0.63
R: TTCTTCCACCGGGTTCCATG
2 CoAb089 (AAAT)5 F: CGAAACACCGGCCCATATCT 268 1 0.00 0.52 0.67
R: TTCTTCTTCGGGGTTCCGTG
3 CoAb090 (TTTTC)5 F: GGCCGCAATGTGTTAGCTTT 339 6 1.00 0.66 0.70
R: TTGTTGTGGGGGGTTACTCT
4 CoAb091 (TTATT)5 F: AACTGGAGATTGCGACACGT 294 9 1.00 0.78 0.80
R: TTATTATTAAGGGTTCCACA
5 CoAb095 (GCT)5 F: GCTGCCTAGCCTTGACTGAA 265 3 0.67 0.58 0.66
R: TTGTTGAGGCGGGTTAGTAA
6 CoAb096 (ACA)7 F: ACACAACACACAACGGATGA 228 6 0.73 0.74 0.78
R: TTATTACCACGGGTTAGGGT
7 CoAb097 (TGA)10 F: CCACGTTGGATCTTGAGGCT 292 8 0.73 0.64 0.68
R: TTCTTCGACCGGGTTAGAGA
8 CoAb098 (AAC)5 F: TGCACACAGCCACAAATCCT 254 3 0.60 0.38 0.46
R: TTTTTTACTGGGGTTTGGCA
9 CoAb099 (CAT)6 F: TCCGATTCGACGCATCATCA 319 1 0.00 0.32 0.00
R: TTTTTTGCTCGGGTTTGACC
10 CoAb100 (AAC)5 F: GGGCAGGTCTACACCAACAA 296 3 0.73 0.41 0.50
R: TTGTTGATGGGGGTTCCAAC
11 CoAb101 (GCT)7 F: TACTGGCACTGCTTTCGGAG 286 2 0.87 0.37 0.49
R: TTTTTTAATAGGGTTCTCAG
12 CoAb110 (GCT)5 F: AATTCTGCTGGTCTGCTGGC 127 7 1.00 0.70 0.73
R: TTATTATTAAGGGTTAAACT
13 CoAb111 (TGA)5 F: TTATAGGCGTGACTCCCGGT 241 2 1.00 0.38 0.50
R: TTTTTTTGTTGGGTTCTGAG
14 CoAb114 (AAC)5 F: TGCCAGGAGGAGAATTTGGG 276 4 1.00 0.50 0.58
R: TTTTTTTCTGGGGTTGGCAA
15 CoAb134 (TAAA)5 F: TCGCTGAAACAAACAGACCT 193 6 1.00 0.66 0.70
R: TTTTTTGCTCGGGTTACAAA
16 CoAb148 (ATAA)5 F: GGCTGAGTGGGCATGTTAGT 145 5 1.00 0.56 0.63
R: TTGTTGGGGGGGGTTGAGCA
17 CoAb169 (AATA)5 F: GCATGCAGAGGGAAGAGTGT 114 3 1.00 0.55 0.62
R: TTGTTGGTGCGGGTTCGCCA
18 CoAb176 (TTTTA)5 F: TCCCACCTGCTACACCTTCA 243 6 1.00 0.76 0.79
R: TTTTTTAATCGGGTTCCGCC
19 CoAb179 (ATTTT)5 F: TCCGACAATTTGAAGCACCT 183 5 1.00 0.62 0.67
R: TTTTTTGCTCGGGTTCATGA
20 CoAb183 (TTATT)5 F: CTTCCATCGTTCGAGGACCA 136 7 1.00 0.75 0.78
R: TTCTTCGGCTGGGTTGTCGG
21 CoAb211 (TTATT)5 F: TCATGCTTTGCCTCCAAACC 324 4 1.00 0.57 0.64
R: TTTTTTCCTCGGGTTAGGGC
22 CoAb214 (AAACC)6 F: TCGAAACCAAGTGACCTGGA 186 4 1.00 0.50 0.59
R: TTTTTTTGTCGGGTTAATCA
23 CoAb225 (TTGGT)7 F: CATCTCCAGCCCGTACTCAC 187 8 1.00 0.67 0.71
R: TTCTTCACCAGGGTTGCCGA
24 CoAb230 (AAACC)5 F: AAATGTGCCTACCCTTGTGG 178 6 1.00 0.73 0.77
R: TTATTATGAAGGGTTGATCG
25 CoAb235 (TTGGT)6 F: GGAGAGAGAAGGGAGAGCCA 130 6 1.00 0.74 0.77
R: TTGTTGAAGGGGGTTAAAAC
均值Mean 4.76 0.85 0.58 0.63

Fig.6

Distribution of SSR markers on chromosomes"

Fig.7

Cluster analysis of 15 C.oleifera samples"

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