Yanjun Guo, Qianhua
Ji*, Liying Guo, Yapin Hu, Hui Jiang and Xiqin Zhou
Fruit Tree Research Institute, Zhaoqing University,
Guangdong 526061, China
*For correspondence: qhgee@163.com
Received 29 July 2020; Accepted 03 September 2020;
Published 10 December 2020
This study explored the genetic diversity of 35 citrus accessions using
start-codon targeted (SCoT) markers. Total 15 primers were used to amplify
products ranging in length from 100 to 2000 bp. A total of 133 fragments were
amplified and found that 126 (95%) were polymorphic. The genetic similarity
coefficients among the 35 accessions ranged from 0.67 to 1.00, indicating that
the SCoT markers could reveal high genetic diversity in the citrus germplasm. A
cluster analysis showed that local citrus breeds of Sihui city fell into one
cluster, possibly reflecting the geographical distribution of the tested
samples. The sizes of the fragments of eight local citrus cultivars amplified
by one of the primers ranged from 951 to 1001 bp, and the similitude was 95.17%
high. Both single-base mutations, insertions and
deletions were identified among the fragments and comparison with a sequence
database suggested that the amplified region was part of a ribosomal
protein-coding sequence. Using Scot marks combined with clonal sequencing,
each of the test samples had one or more mutation sites that could be used as
markers to differentiate from the other seven test samples. Thus, the
resolution of the genetic diversity among the local citrus breeds revealed by
the SCoT technique was enhanced by the subsequent sequencing analysis of
specific fragments. The experimental results also provide evidence that the
relationship between Citrus nobilis
Lour. ‘gonggan’ and C. haniana Hort.
ex Tseng ‘Sihuihanggan’ is that between parent and offspring hybrids and not
between bud-mutation strains. The SCoT marker is a targeted gene molecular
marker, based on the characteristic bands of primers, it can be used as a
marker to isolate genes of local citrus varieties and also for investigating
mutational hotspots of these gene. © 2021 Friends Science Publishers
Keywords: Citrus; SCoT; Local germplasm resources; Sequence alignment
Introduction
Start-codon targeted (SCoT) polymorphism is a technique
for developing functional DNA markers (Collard and Mackill 2009; Xiong et al. 2009) by amplifying the region
flanking the translation-initiation site (ATG) of a target gene by using a
single primer. The SCoT technique was first validated in rice and features
simple operation, easy establishment of technical systems for various species,
effective production of markers linked with phenotypic characters, and facilitation
of molecular marker-assisted breeding. SCoT primers generate reproducible
results, are easy to design for a variety of species, and can be used for
diversity analysis in plants, QTL mapping, bulked segregation analysis, and other applications. The SCoT technique has been used to generate
molecular markers for target genes in rice (Collard and Mackill 2009), peanut
(Xiong et al. 2010), mango (Luo et al. 2011), longan (Chen et al. 2010a, b), citrus (Han et al. 2011; Jiang et al. 2011), and other plants. These markers are especially useful for citrus plants because of
the many new local breeds and breeds with mutated genes that have been
generated through natural hybridization, artificial cultivation, selection, and
cultivation based on the likeliness of hybridization, open pollination, and asexual reproduction, all of which complicate its
classification.
Sihui city in the Zhaoqing region of Guangdong province has abundant
citrus resources and a long history of citrus cultivation that can be traced back to the Han dynasty. The citrus
breeds currently planted in the Zhaoqing region are mainly historical farm varieties
with unknown origins, and there is a lack of systematic research and breeding
experiments. The randomness of breed cultivation in different periods has
resulted in the loss of citrus genetic resources in the region, especially for
some farm varieties. In a previous study on citrus germplasm accessions of Sihui city, we studied the
classification status of the local citrus breeds by field cultivation, isozyme
analysis, quality analysis, and random amplified polymorphic DNA (RAPD) and
simple sequence repeat (SSR) marker-based analyses of the parental species of
existing natural hybrid cultivars based on chloroplast genes (Ji and Guo 2011; Ji
et al. 2007, 2010, 2011a, b, 2012,
2013; Guo et al. 2013).
In the present study, 35 citrus samples to determine the
genetic diversity and genetic relationships using SCoT analysis among the local
citrus breeds of Sihui city were collected. This study also sequenced target
fragments from different clones of local varieties to identify its genetic
variation, which can provide evidence of breeding patterns.
Materials and
Methods
Germplasm samples
The 35 germplasm samples (Table 1) included Citrus (33 samples), Poncirus (one sample) and Atalantia (one sample, used as an
outgroup) species collected from the Fruit Tree Research Institute of Zhaoqing
University, the Guangdong Province Academy of Agricultural Sciences, and the
Fruit Tree Research Institute of Chaozhou city. The represented samples were
existing cultivated breeds and accessions of Sinocitrus or related plant species collected in China, including
tangerines, oranges, pomelos, lemons, and other fruits. Those samples are
representative to some extent and can be applied in molecular marker research.
The citrus breeds historically cultivated in Sihui city
include Citrus haniana Hort. ex Tseng
‘Sihuihanggan’, C. flamea Hort. ex
Tseng shiyueju ‘Big fruit shape’, C.
flamea Hort. ex Tseng ‘bayueju’, C.
flamea Hort. ex Tseng ‘Mashiju’, C.
sinensis osbeck ‘Lanhuacheng No.4’, C. flamea Hort. ex Tseng
‘wuyueju’, C. nobilis Lour.
‘gonggan’, and C. haniana Hort. ex
Tseng ‘Sihuigan’. C. flamea Hort. ex
Tseng shiyueju and C. nobilis Lour.
‘gonggan’ are the dominant breeds currently planted in the Zhaoqing region. The
scientific names of “China Fruit notes:
Citrus research” (Zhou and Ye 2009) were adopted for all the test samples.
DNA extraction
A modified CTAB (hexadecyl trimethyl ammonium bromide)
method (Ji et al. 2011a) was used to
extract DNA. The quality of the extracted DNA was determined by 1.5%
agarose-gel electrophoresis and spectrophotometry. The samples were then
diluted to the required concentration and stored at −20°C for later use.
Fifteen selected
primers were synthesized by Shanghai Bioengineering Co., Ltd. (Table 2) according to the methods of Collard and Mackill
(2009). From the primers of a new gene-targeted marker developed in paddy rice
and published by these authors, and by referring to the frequency of references
by other researchers to fruits such as citrus, longan, grape, and pineapple,
15 primers were selected for this study.
Table
1: Samples tested
Material |
Sample
name (Latin or English) |
1 |
Citrus grandis
(L.) Osbeck‘kekouyou’ |
2 |
C. tangerina
Tanaka‘jiangxihongju’ |
3 |
C.
haniana Hort. ex Tseng ‘sichuan suanju’ |
4 |
C.
haniana Hort. ex Tseng ‘yanshanhongpi suanju’ |
5 |
C. limon
(L.) Burm.f.‘Eureka Lemon’ |
6 |
C. sinensis Osbeck
‘Newhall Navel Orange’ |
7 |
C. tangerina Gongneiyiyuan‘Miyauchi
Iyokan’ |
8 |
C. reticulata Blanco‘xinshengxi
NO. 3 Ponkan’ |
9 |
C. reticulata × C. sinensis
‘Moketeju (W.Murcott) tangor’ |
10 |
C. unshiu Marcow. ‘Nangan No.20’ |
11 |
Qiuhuijuyou
‘Fallglo Tangelo’ |
12 |
C. reticulata Blanco
‘No.830 ponkan’ |
13 |
Nowajuyou
‘Nova tangelo’ |
14 |
C. sinensis Osbeck
‘Seike Navel orange’ |
15 |
Atalantia buxifolia
(Poir.) Oliv. |
16 |
Fortunella
Swing |
17 |
C.
haniana Hort. ex Tseng ‘deqing suanju’ |
18 |
C.
limonia Osbeck ‘Honglimeng’ |
19 |
C. sinensis Osbeck
‘Valencia Orange’ |
20 |
C. nobilis Lour.
Xingjinwenzhoumigan‘okitsu wase’ |
21 |
Poncirus
trifoliata (L.) Raf. ‘changyangzhicheng’ |
22 |
C. haniana
Hort. ex Tseng ‘Sihuihanggan’ |
23 |
C.
chuana Hort. ex Tseng ‘Nanfengmiju’ |
24 |
C. sinensis
osbeck ‘tangcheng’ |
25 |
C. sinensis osbeck
‘hongjiangcheng’ |
26 |
C. flamea
Hort. ex Tseng shiyueju‘Big fruit shape’ |
27 |
C. grandis (L.)
osbeck ‘shatianyou’ |
28 |
C. flamea
Hort. ex Tseng ‘bayueju’ |
29 |
C. flamea Hort.
ex Tseng ‘Mashiju’ |
30 |
C. sinensis osbeck
‘Lanhuacheng No.4’ |
31 |
C. junons Sieb.
ex Tanaka |
32 |
C.
flamea Hort. ex Tseng wuyueju |
33 |
C. nobilis
Lour. ‘gonggan’ |
34 |
C. haniana
Hort. ex Tseng ‘Sihuigan’ |
35 |
Poncirus trifoliata
(L.) Raf |
Table 2: SCoT primer used
SCoT primer |
Primer sequence |
S1 |
CAACAATGGCTACCACCA |
S3 |
CAACAATGGCTACCACCG |
S8 |
CAACAATGGCTACCACGT |
S9 |
CAACAATGGCTACCAGCA |
S11 |
AAGCAATGGCTACCACCA |
S12 |
ACGACATGGCGACCAACG |
S17 |
ACCATGGCTACCACCGAG |
S19 |
ACCATGGCTACCACCGGC |
S22 |
AACCATGGCTACCACCAC |
S23 |
CACCATGGCTACCACCAG |
S24 |
CACCATGGCTACCACCAT |
S25 |
ACCATGGCTACCACCGGG |
S26 |
ACCATGGCTACCACCGTC |
S34 |
ACCATGGCTACCACCGCA |
S36 |
GCAACAATGGCTACCACC |
SCoT fragments were amplified in a 20 μL optimized PCR system as
described by Jiang et al. (2011). The
reaction system contained 80 ng DNA template, 1.6 mM Mg2+,
0.3 mM dNTPs, 0.2 μM primers, and 1.6 U TaqDNA
polymerase. The reaction conditions were as follows: pre-denaturation
at 94°C for 4 min; 35 cycles of denaturation at 94°C for 1
min, annealing at 50°C for 45 s, and extension at
72°C for 1 min; and extension at 72°C for 8 min after the cycling. The PCR
products were stored at 4°C and later verified by 1.5% agarose-gel
electrophoresis.
SCoT fragment amplification, cloning, and sequencing
Eight samples for
SCoT fragment amplification, cloning, and sequencing were all from local citrus
breeds of Sihui city [(1) C. haniana
Hort. ex Tseng ‘Sihuihanggan’, (2) C.
flamea Hort. ex Tseng shiyueju ‘Big fruit shape’, (3) C. flamea Hort. ex Tseng ‘bayueju’, (4) C. flamea Hort. ex Tseng ‘Mashiju’, (5) C. sinensis osbeck ‘Lanhuacheng No.4’, (6) C. flamea Hort. ex Tseng ‘wuyueju’, (7) C. nobilis Lour. ‘gonggan’, and (8) C. haniana Hort. ex Tseng ‘Sihuigan’].
There were two reasons for selecting primer S19 for
amplification, cloning and sequencing of SCoT fragments. Reference 8 applied
this primer to the bud mutation identification of citrus varieties with close
genetic relationships, and it was speculated that the eight local varieties may
be closely related. If S19 amplified a common characteristic band, it was
proposed to try to discover some rules from its sequence.
The amplification products of the eight samples
amplified by SCoT primer S19 were verified by 1.5% agarose gel electrophoresis.
The T1Angel Midi Purification Kit (T1ANGEN) was used to recycle and purify the
characterized bands for TA cloning, then for connection using the pMD19T
cloning vector (Takara Biotechnology (Dalian) Co., Ltd., China) as the carrier,
and the connection products were transformed into competent TOP10 cells.
Positive clones were identified by dye PCR amplification of templates from
single colonies and sent to Shanghai Bioengineering Co., Ltd. for sequencing.
Chromas1.45 was used to view the traces of the sequencing results.
Artificial proofreading and editing were used to ensure that the sequences were
correct, and then the ContigExpress software was used for sequence splicing.
After the sequences were determined, Clustalx 1.81 was used for comparative
analysis of multiple sequences (http:
//www.hgmp.mrc.ac.uk/Registered/Option/clustalx.html), and BLAST was used to
identify comparative similarities (National Center for Biotechnology
Information of USA, NCBI website: http://www.ncbi.nlm.nih.gov/).
Results
All 15 primers generated clear polymorphic bands (Fig.
1). The number of amplified bands ranged from 1 to 11. A total of 133 bands
were amplified, of which 126 were polymorphic. With each primer producing eight
polymorphic bands on average, the average polymorphism rate was 95%.
1 and 0 data regarding all bands
were clustered analysis by Hierarchical clustering method, and then dendrogram
was constructed (Fig. 2). Using a genetic similarity coefficient of 0.73 as the
criterion, the test samples were divided into three groups. Group 1 consisted
of Atalantia buxifolia (Poir.) Oliv,
group 2 Fortunella Swing, Poncirus
trifoliata (L.) Raf, and P. trifoliata (L.) Raf. ‘Changyangzhicheng’
and group 3 mandarin, tangerine, orange, lemon, pomelo, and other varieties.
Using a genetic similarity coefficient of 0.81 as the criterion, the lemon, pomelo, and mandarin,
tangerine, and orange in group 3 could be divided into different subgroups. In
this group 3, the local citrus breeds of the Zhaoqing region formed a single
cluster, indicating a high degree of genetic relatedness. The similarity
coefficients between C. nobilis Lour.
‘Gonggan’ and C. haniana Hort. ex
Tseng ‘Sihuihanggan’, C. flamea Hort.
ex Tseng shiyueju and C. flamea Hort. ex Tseng wuyueju, and C. flamea Hort. ex Tseng ‘bayueju’ and C.
chuana Hort. ex Tseng ‘Nanfengmiju’ were 0.91, 0.97, and 0.97,
respectively; and those between C. haniana Hort.ex Tseng ‘Sihuigan’, C.
flamea Hort. ex Tseng ‘Mashiju’, C. haniana Hort. ex Tseng ‘sichuan
suanju’, C. haniana Hort. ex Tseng ‘yanshanhongpi suanju’ and C.
haniana Hort. ex Tseng ‘deqing suanju’, were all 1.0.
SCoT fragment sequencing
The results show that specific
primers can amplify characteristic fragments of some citrus plants and can be
used in further studies. The primer S19 was selected, as it amplifies a common,
obvious characteristic band in eight Sihui local citrus varieties, and it was
also applied in reference 8 to identify bud mutation in citrus plants. The
selection of S19 was appropriate for the present study and for comparative
analysis in other studies.
The DNA fragments from the local citrus breeds of Sihui city [(1) C. haniana Hort. ex Tseng
‘Sihuihanggan’, (2) C. flamea Hort. ex
Tseng shiyueju ‘Big fruit shape’, (3) C.
flamea Hort. ex Tseng ‘bayueju’, (4) C.
flamea Hort. ex Tseng ‘Mashiju’, (5) C.
sinensis osbeck ‘Lanhuacheng No.4’, (6) C. flamea Hort. ex Tseng
‘wuyueju’, (7) C. nobilis Lour.
‘gonggan’, and (8) C. haniana Hort. ex
Tseng ‘Sihuigan’] amplified by primer S19 were
recycled for TA cloning and sequencing. The total lengths of the amplified
fragments ranged from 951 to 1001 bp. Alignment analysis revealed that the SCoT
sequences of the eight local breeds were highly similar, with identity as high
as 95.17%. There were a total of 39 mutation sites, including A>G,
T>C, and C>T conversions as well as T>G, G>T, and A>T
transversions, a (G) deletion, and insertions at different sites (Table 3).
The BLAST results showed that the second halves
(starting between nucleotides 720 and 950) of the amplified fragments of C. haniana Hort. ex Tseng
‘Sihuihanggan’, C. flamea Hort. ex
Tseng ‘bayueju’, C. sinensis osbeck
‘Lanhuacheng No.4’, C. flamea Hort. ex Tseng ‘wuyueju’, and C. haniana Hort. ex Tseng ‘Sihuigan’
were of the same origin and presented in a positive permutation. The first
halves (starting between nucleotides 1 and 370) of the amplified fragments of C. flamea Hort. ex Tseng shiyueju ‘Big
fruit shape’, C. flamea Hort. ex Tseng
‘Mashiju’, and C. nobilis Lour.
‘gonggan’ were of the same origin and presented in a reversed permutation.
Comparative analysis and alignment following the reverse complementation of
sequences of C. flamea Hort. ex Tseng
shiyueju ‘Big fruit shape’, C. flamea Hort.
ex Tseng ‘Mashiju’, and C. nobilis
Lour. ‘gonggan’ revealed high similarity (Fig. 3).
The similar sequence in the fragments from the eight samples had the
same origin as the mitochondrial 60s ribosomal protein gene sequence on rice
chromosome 12, with 90% identity with the sequences in this study. It also had
the same origin as the gene for the mitochondrial S3 ribosomal protein of beet,
with 90% identity with the sequences, origin was also similar as genes in the
mitochondrial genomes of apple, tobacco, and petunia. These results suggest
that the SCoT primers amplified part of a gene encoding a ribosomal protein
that may originate in the mitochondrial genome. However, these results do not
exclude the possibility that the amplified fragment originated in the nuclear
genome.
Discussion
Samples of three citrus-related genera (Citrus, Poncirus, and Atalantia)
were selected in this study. The clustering results showed that the SCoT
technique revealed genetic diversity among the tested samples, clustering
samples of different genera separately, a result largely consistent with
previous studies using RAPD and SSR markers (Ji et al. 2011c, 2012). In this study, as the hybrid (P. trifoliata × C. sinensis) of Fructus aurantii and sweet orange, citrange (Poncirus trifoliata (L.) Raf.
Changyangzhicheng), is categorized as citrus using RAPD and SSR markers, and
its SCoT clustering result is the same as for Fructus aurantii,
suggesting homology with trifoliate orange.
The citrus breeds of Sihui city clustered into one category when the
genetic coefficient was 0.80, and the genetic relationship was closer,
indicating that geographical factors strongly influence the study of genetic
relationships among citrus. In ancient China, the exchange of citrus plants among
different areas was relatively rare; therefore, citrus varieties display
typical geographical distributions. For citrus plants, distant hybridization by
intergeneric and interspecific crossing is easy to achieve and has generated
many distant natural hybrids in nature. The circulation of citrus varieties in
different regions in modern times and the rapid promotion of citrus breeding
are beneficial to citrus germplasm diversity (Deng and Peng 2013). Some local
varieties in Sihui are not large-scale cultivated varieties with small external
circulation, and most of them are farm varieties, hybrids or natural bud
mutations that were not intentionally developed; for this reason the SCoT
clustering result still shows common geographical distributions.
SCoT molecular markers have been successfully applied to plant genetic
diversity, genetic relationship identification and genetic map construction (Zhai et al. 2018). It has been pointed out
that the SCoT marker was suitable for interspecific genetic analysis and identification
of distant hybrid progenies, but unsuitable for genetic analysis of different
types of common tobacco species (Liu et
al. 2013). Through SCoT study, there was no significant difference among
the bud-mutation varieties of sweet orange, and the same bands were amplified
by single primer in some bud-mutation varieties (Jiang et al. 2011). In this study, primer S19 amplified the same specific
band in all the citrus breeds of Sihui city, suggesting a region of homology
among the test samples. However, recycling the bands amplified by the S19
primer for TA cloning and sequencing showed that all the samples had a very
high degree of sequence identity and some differences. Each of the test samples
had one or more mutation sites that could be used as markers to differentiate
from the other seven test samples. The similar genetic backgrounds among the
citrus breeds of Sihui city could result from the communication of partial
genetic materials via natural hybridization or the formation of different
breeds and strains via bud mutations. However, the sequencing results showed that over years of cultivation,
Table
3: Variation among
the S19 sequences of eight Citrus species
No. |
material |
|||||||
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
|
167 |
- |
- |
- |
- |
- |
- |
T |
- |
171 |
- |
- |
- |
- |
- |
- |
A |
- |
183 |
- |
- |
- |
- |
- |
- |
G |
- |
190 |
- |
- |
- |
- |
- |
- |
A |
- |
199 |
T |
T |
T |
T |
T |
T |
G |
T |
205 |
- |
- |
- |
- |
- |
- |
C |
- |
214 |
G |
G |
G |
G |
G |
G |
T |
G |
216 |
- |
- |
- |
- |
- |
- |
A |
- |
225 |
- |
- |
- |
- |
- |
- |
C |
- |
227 |
G |
G |
G |
G |
G |
G |
T |
G |
232 |
C |
T |
T |
T |
T |
T |
T |
T |
237 |
- |
- |
- |
- |
- |
- |
A |
- |
239 |
C |
C |
C |
C |
C |
C |
T |
C |
247 |
- |
- |
- |
- |
- |
- |
A |
- |
261 |
- |
- |
- |
- |
- |
- |
C |
- |
270 |
- |
- |
- |
- |
- |
- |
C |
- |
321 |
A |
G |
A |
A |
A |
A |
A |
A |
374 |
A |
A |
A |
A |
A |
T |
A |
A |
447 |
C |
T |
T |
T |
T |
T |
T |
T |
468 |
G |
- |
G |
G |
G |
G |
G |
G |
556 |
T |
T |
T |
T |
T |
T |
C |
T |
571 |
A |
G |
A |
A |
A |
A |
A |
A |
604 |
G |
A |
A |
A |
A |
A |
A |
A |
625 |
T |
T |
T |
T |
T |
C |
T |
C |
675 |
T |
T |
T |
T |
T |
T |
C |
T |
718 |
A |
A |
A |
G |
A |
A |
A |
A |
792 |
A |
A |
A |
A |
A |
A |
T |
A |
893-895 |
TTA |
TTA |
--- |
TTA |
--- |
TTA |
TTA |
TTA |
897-899 |
--- |
--- |
--- |
--- |
--- |
--- |
TAT |
--- |
913 |
A |
A |
A |
A |
A |
A |
A |
G |
928 |
- |
- |
- |
- |
- |
- |
- |
C |
945 |
- |
- |
- |
- |
- |
- |
- |
G |
947 |
T |
T |
T |
T |
T |
T |
T |
T |
961 |
- |
- |
- |
- |
- |
- |
- |
C |
Note:
Numbers 1–8 are the test materials, see Materials and methods section
Fig.
3: Dendrogram of eight local Citrus species based on sequencing of S19 fragments
Note:
The species are numbered 1-8;
see Materials and Methods
differences have appeared among the breeds owing to
internal mutations in the same functional gene. Thus, the resolution of the
genetic diversity among the local citrus breeds revealed by the SCoT technique
was enhanced by the subsequent sequencing analysis of specific fragments.
C. nobilis Lour. ‘gonggan’, one of the
dominant citrus breeds planted in the Zhaoqing region, is thought to be a
natural hybrid of tangerine and orange. Previously, using RAPD and SSR markers it
was shown that C. nobilis Lour.
‘gonggan’ and C. haniana Hort. ex
Tseng ‘Sihuihanggan’ have the closest genetic relationship among the local
breeds (Ji et al. 2012, 2013), consistent with the results of
the present study. Some researchers speculate that C. haniana Hort. ex Tseng ‘Sihuihanggan’ is the female parent of C. nobilis Lour. ‘gonggan’ according to
evidence based on the trnl chloroplast
gene (Ji et al. 2010). Therefore, C. nobilis Lour. ‘gonggan’ is probably a
hybrid of C. haniana Hort. ex Tseng
‘Sihuihanggan’ and orange. The possibility that it is instead a bud-mutation
strain of C. haniana Hort. ex Tseng
‘Sihuihanggan’ is not excluded, although there is currently no evidence
supporting this hypothesis. The sequencing results showed that the SCoT
sequence amplified by primer S19 contains 20 single-base polymorphism and a
three-base polymorphism between C.
nobilis Lour. ‘gonggan’ and C.
haniana Hort. ex Tseng ‘Sihuihanggan’. Sixteen of the single-base mutations
were concentrated between nucleotide positions 160 and 270, indicating a high
mutation frequency in the region. Similar results are displayed between C. nobilis Lour. ‘gonggan’ and several
other samples. The base sequence in this region forms mutational hotspots in
this gene of this variety and is mainly dominated by insertion mutation,
followed by transversion and then transition mutation. The cause of mutational
hotspots of citrus is still unclear. Theoretically, there is a higher frequency
of transition in mutational hotspots and it is much easier for insertion and
deletion mutation to occur in short tandemly duplicated sequence. Given that
the SCoT marker is a targeted gene molecular marker, the characteristic bands
of primers can be used as a marker to isolate genes of local citrus varieties
in Sihui city and for investigating mutational hotspots of this gene. It can
also be used to recognize and analyze potential mutational hotspots.
The SCoT study of Jiang et al. (2011)
on bud-mutation strains of sweet orange showed that their genetic backgrounds
are very narrow and differences between the aligned sequences amplified by a
single SCoT primer can be minimal. There were very few differences between some
breeds, indicating that the mutation range of the bud-mutation strains is
narrow.
In the present study, the SCoT genetic similarity coefficient of C. nobilis Lour. ‘gonggan’ and C. haniana Hort. ex Tseng ‘Sihuihanggan’
was high, indicating a close genetic relationship. There were obvious
differences among the fragments amplified by some SCoT primers, and the
sequencing of the same characteristic sequence amplified by the single primer
S19 showed multiple mutation sites, suggesting that the relationship between C. nobilis Lour. ‘gonggan’ and C. haniana Hort. ex Tseng ‘Sihuihanggan’
is between parent and offspring hybrids and not between bud-mutation strains.
Thus, it is speculated that based on the homologous-sequence alignment
results, the fragment amplified by primer S19 is part of a ribosomal
protein-coding sequence, which may originate in the mitochondrial or nuclear
genome. The evidence based on the chloroplast trnl genes of C. nobilis
Lour. ‘gonggan’ and C. haniana Hort.
ex Tseng ‘Sihuihanggan’ suggests that C.
haniana Hort. ex Tseng ‘Sihuihanggan’ is the female parent of C. nobilis Lour. ‘gonggan’. Based on the
SCoT sequencing results, however, the C.
haniana Hort. ex Tseng ‘Sihuihanggan’ sequence had a higher mutational frequency
than the C. nobilis Lour. ‘gonggan’
sequence, indicating that the sequence encoding ribosomal protein is more
likely from the nuclear than from the mitochondrial genome and is probably from
the male parent of C. nobilis Lour.
‘gonggan’. The ribosomal protein may participate in ribosome structure and
translation, which plays an important role in plant development. Its protein
synthesis starts from the N terminus and its sequence composition has a large
effect on its biological function. Study of the protein and its N end sequence
is beneficial for the analysis of protein structure and the revelation of the
biological function of the protein. Base mutations in the tested accessions may
account for amino acid variation at the N end, a subject that awaits further
research.
Several types of
target-gene molecular markers have been developed and used in recent years. As
a new method, SCoT markers are an effective supplement to RAPD, ISSR, and other
conventional random DNA markers (Collard and Mackill 2009), which can produce
markers linked with phenotypic characters to facilitate molecular
marker-assisted breeding. Given that only 15 SCoT primers were studied, and
detection analysis was performed only on one primer combining some single
genes, the information obtained is limited. In future research, further
development of other polymorphic SCoT primers should be performed, combining
sequencing results from fragments amplified by multiple SCoT primers, for the
study of local citrus germplasm resources in Sihui city. Several types of
target-gene molecular markers have been developed and used in recent years. As
a new method, SCoT markers are an effective supplement to RAPD, ISSR, and other
conventional random DNA markers (Collard and Mackill 2009), which can produce
markers linked with phenotypic characters to facilitate molecular
marker-assisted breeding. Therefore, it will play a significant role in the
development of excellent genes of local citrus varieties.
Conclusion
The SCoT markers could reveal high genetic diversity in
the citrus germplasm and could be used to study the regional distribution of
citrus. Each of the test samples
had one or more mutation sites that could be used as markers to differentiate
from the other seven test samples, thus, the resolution of the genetic
diversity and research on gene hotspots among the local citrus breeds revealed
by the SCoT technique was enhanced by the subsequent sequencing analysis of
specific fragments. The relationship between C. nobilis Lour. ‘gonggan’ and C.
haniana Hort. ex Tseng ‘Sihuihanggan’ is that between parent and offspring
hybrids and not between bud-mutation strains. The SCoT technique combined with
clonal sequencing can provide a reference for the collection, protection, and
effective use of the local citrus germplasm resources of the Sihui region. It
can be applied to research into mechanisms, functions, and phylogenies of
citrus genes and the development of target genes used as markers in citrus
breeding in future.
Acknowledgements
This study was
supported by China Agriculture (Citrus) Research System Building Project
(cars-26); Rural Sci-tech Commissioner Project (2019-18).
Author Contributions
YG and QJ planned the experiments, YG, LG and HJ
interpreted the results, YG and YH made the write up and YH and XZ
statistically analyzed the data and made illustrations
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