Genetic Resources and Crop Evolution (2006) 53: 1145–1152
Springer 2005

DOI 10.1007/s10722-005-1304-y

Genetic diversity of Asian cotton (Gossypium arboreum L.)

in China evaluated by microsatellite analysis

Diqiu Liu , Xiaoping Guo , Zhongxu Lin, Yichun Nie and Xianlong Zhang*
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei
430070, China; *Author for correspondence (e-mail: xlzhang@mail.hzau.edu.cn; phone: +86-27-87283955;
fax: +86-27-87280016)

Received 2 July 2004; accepted in revised form 21 January 2005

Key words: Cotton, Genetic diversity, Gossypium arboreum, Microsatellite, Simple sequence repeats, SSR

Abstract

Asian cotton (Gossypium arboreum L.) was once widely cultivated in China. It has also been a valuable
source of genetic variation in modern cotton improvement. In this study, the genetic diversity of selected
G. arboreum accessions collected from different regions of China was evaluated by microsatellite (simple
sequence repeats, SSRs) analysis. Of the 358 microsatellite markers analyzed, 74 primer pairs detected 165
polymorphic DNA fragments among 39 G. arboreum accessions examined. Twelve accessions could be
fingerprinted with one or more SSR markers. With the exception of two accessions, DaZiJie and
DaZiMian, genetic similarity coefficients among all accessions ranged from 0.58 to 0.87 suggesting high
level of genetic variation in the G. arboreum collections. The UPGMA dendrogram constructed from
genetic similarity coefficients revealed positive correlation between cluster groupings and geographic dis-
tances. In addition, comparison of the microsatellite amplification profiles of the diploid G. arboreum and
tetraploid Gossypium hirsutum L. found that size distribution of amplified products in G. arboreum was
dispersive and that of G. hirsutum was relatively concentrated. The information on the genetic diversity and
SSR fingerprinting from this study is useful for developing mapping populations for constructing diploid
cotton genetic linkage map and tagging economically important traits.

Introduction believed that the tetraploid cotton was originated

Cotton (Gossypium L.) is a leading fiber crop
in the world. Although the genus Gossypium L.
has approximately 50 species, only four of
them are cultivated, which include two dip-
loids (2n = 2x = 26): G. arboreum L. (A2A2)
and G. herbaceum L. (A1A1), as well as two
allotetraploids (2n = 4x = 52): G. hirsutum L.
(AADD) and G. barbadense L. (AADD). It was
These two authors contributed equally to this work.
from an interspecific hybridization of an Old
World diploid species that was closely related with
G. arboreum or G. herbaceum (A genome donor)
and a New World diploid species relative to
G. raimondii Ulbrich or G. gossipioides Standley
(D genome donor), which occurred about
1–2 million years ago (Beasley 1940). The putative
A and D genome diploid ancestors of tetraploid
cotton species were thought to have diverged from
a common ancestor 4–10 million years prior to
polyploidization (Seelanan et al. 1997).
1146

Gossypium arboreum has been domesticated and The objectives of this study are to (1) evaluate the
cultivated for almost 2000 years in China since it genetic diversity among selected G. arboreum
was first introduced from India (Xiang and Shen accessions; and (2) identify G. arboreum accessions
1989). G. arboreum possesses many favorable traits with high genetic diversity that will be used to
for cotton production, which the upland cotton develop mapping populations for constructing
cultivars lack. For example, the drought tolerance, diploid cotton linkage maps and marker-assisted
resistance to diseases like root rot, and insect pests molecular tagging of economically important traits.
like bollworms and aphids (Mehetre et al. 2003)
make G. arboreum well adapted to dry land con-
ditions and low input cultivation practices. Natu-
Materials and methods
ral G. arboreum fibers display various colors (e.g.,
white, milky, beige and brown). Many Chinese
Germplasm collection
G. arboreum accessions produce fibers with high
strength and seeds with high oil content and seed
The 39 G. arboreum accessions used in this study
index. Over 300 G. arboreum accessions have been
were randomly selected from the more than 300
collected and conserved in the Cotton Germplasm
G. arboreum accessions preserved in the Cotton
Center located in the Chinese Academy of Agri-
Research Institute, Chinese Academy of Agricul-
cultural Science. These G. arboreum collections are
tural Sciences (CRI, CAAS), which were kindly
invaluable gene pool for cotton improvement.
provided by Dr X.M. Du of CRI, CAAS. With the
However, they have not been well characterized at
exception of two accessions that were originated
the molecular level. Understanding of the genetic
from Japan and the USA, respectively, all others
relationships of G. arboreum would facilitate effi-
were collected from different provinces of China.
cient use of these resources in developing superior
The additional materials from the authors’ labo-
cotton cultivars with favorable agronomic traits.
ratory, G. hirsutum cv. ‘Jinmian6’ (JM6), one
Molecular markers, especially PCR-based
G. herbaceum accession and G. raimondii were also
markers such as RAPD (random amplified poly-
used. Relevant information of the 39 G. arboreum
morphic DNA), AFLP (amplified fragment length
accessions and the G. herbaceum accession was
polymorphism) and SSRs (simple sequence
presented in Table 1 and Figure 1.
repeats) have been extensively used to study
genetic diversity, genetic relationships and molec-
ular phylogeny in Gossypium species (Tatineni et
al. 1996; Khan et al. 2000; Abdalla et al. 2001; Microsatellite analysis
Iqbal et al. 2001; Xu et al. 2001; Gutiérrez et al.
2002; Lu and Myers 2002; Zhu et al. 2003). Total genomic DNA was isolated from leaf tissue
Recently, the SSR marker has received much more of each material according to Paterson et al.
attention in phylogenetic studies in cotton. The (1993). Totally 358 SSR primer pairs were used for
PCR-based, co-dominant microsatellite markers the present study. All primer sequences were
are highly polymorphic and preferentially associ- downloaded from the UK CropNet website
ated with non-repetitive DNA in plant genomes (http://ukcrop.net/perl/ace/search/CottonDB) and
(Morgante et al. 2002). These features make it were synthesized commercially. Procedure of SSR
ideal to use microsatellite markers for genetic analysis followed Mei et al. (2004).
diversity studies and marker-assisted selection in
cotton breeding.
In this study, the genetic diversity within 37 Data analysis
representative G. arboreum accessions from differ-
ent regions of China was analyzed using microsat- After silver staining, all major DNA band sizes
ellite markers. In addition, two G. arboreum were recorded using 100 bp DNA ladder as the
accessions, one from Japan and the other from the reference. The amplified DNA fragments were
United States of America, as well as a G. herbaceum scored as either 1 or 0, respectively, representing
accession were also included in this study for presence or absence of the band. Each polymorphic
comparison of genetic variation of these materials. SSR fragment was considered a different locus as it
 1147

Table 1. Description of 39 Gossypium arboreum accessions and one G. herbaceum sample used in this study.

Code numbera Germplasm Abbreviation Geographic origin (province)

1 G. herbaceum L. Unknown
2 Pingdongxiaohua PDXH Guizhou (GZ)
3 Changfengheizi CFHZ Jiangsu (JS)
4 Qingjinghuanghuayouhongxin QJHHYHX Unknown
5 Wuanzhongmian WAZM Hebei (HeB)
6 Dazijie DZJ Hebei (HeB)
7 Zijingzihuazhongmian ZJZHZM Unknown
8 Dazimian DZM Hebei (HeB)
9 Shanghaizhongmian SHZM Shanghai (SH)
10 Jiangxixiushuizhongmiamaozi JXXSZMMZ Jiangxi (JX)
11 Wanxianxiaobaihua WXXBH Hebei (HeB)
12 Shanxianxiaozihua SXXZH Shandong (SD)
13 Shiyaxi1 SYX1 Hebei (HeB)
14 Nonglin6 NL6 Japan
15 Huazhongziganzhongmian HZZGZM Hubei (HuB)
16 Jiadingzhongmian JDZM Shanghai (SH)
17 Baoshangzihua BSZH Shanghai (SH)
18 Zhejianghuangdidabu ZJHDDB Zhejiang (ZJ)
19 Meiguozhongmian971 MGZM971 USA
20 Tiemuchi TMC Liaonin (LN)
21 Hexianzizhumianhua HXZZMH Anhui (AH)
22 Changshudabaizi CSDBZ Jiangsu (JS)
23 Xiazhaixiaohua 3 XZXH3 Guizhou (GZ)
24 Chaoxianzihuaxiaozi CXZHXZ Anhui (AH)
25 Sangjiangguandongzongxuzhongmian SJGDZXZM Guangxi (GX)
26 Jinxianzhongmian JXZM Hebei (HeB)
27 Dingyuanxiaohuamian DYXHM Anhui (AH)
28 Qingyangdazihuamaozi QYDZHMZ Anhui (AH)
29 Rudongjijiaoyaguo RDJJYG Jiangsu (JS)
30 Anhuifuyangxinjidahua AHFYXJDH Anhui (AH)
31 Luodianguantianxiaomianhua LDGTXMH Guizhou (GZ)
32 Shulubaihuabai SLBHB Hebei (HeB)
33 Guizhouzhongmian GZZM Guizhou (GZ)
34 Yuxi 3–3 YX3-3 Hebei (HeB)
35 Changshundaihuaxiaohua CSDHXH Guizhou (GZ)
36 Changrongzhongmian CRZM Hubei (HuB)
37 Wangmosanglangdamianhua WMSLDMH Guizhou (GZ)
38 Wuzhaixiaohua WZXH Guizhou (GZ)
39 Xiabaxiaohua2 XBXH2 Guizhou (GZ)
40 Dongtaixiaobaihua DTXBH Jiangsu (JS)
a
Code number = designated sample number for accessions in SSR analysis.

corresponds to a unique position in the genome. Results

The coefficients of genetic similarities (Nei and Li
1979) were calculated using the SIMQUAL
program of the Numerical Taxonomy Multivariate
Analysis System (NTSYS-pc) software package
(Version 2.10) (Rohlf 2000). Subsequently, an
unweighted pair group method of arithmetic means
(UPGMA) trees (Sokal and Michener 1958) were
generated by NTSYS-pc based on the above-men-
tioned genetic similarity matrices.
SSR polymorphism level and SSR fingerprinting
Of the 358 SSR primer pairs applied to the 40
materials listed in Table 1, 200 detected mono-
morphic products in each sample and 84 produced
very faint or indecipherable bands. The remaining
74 primer pairs yielded totally 165 polymorphic
bands. The number of polymorphic fragments
1148

Figure 1. Geographic origin of 37 Gossypium arboreum accessions collected from China. For germplasm name and province name in
brackets, see Table 1. The remaining two accessions were from Japan and the USA, respectively, which were not shown here.

generated by each primer pair ranged from 1 to 8,
with an average of 2.33. For example, the micro-
satellite markers BNL2634 and BNL2569 detected
eight and six polymorphic loci respectively, among
the 40 accessions.
Accession-specific microsatellite markers were
identified based on the SSR band patterns. There
were twelve accessions possessing one or more
specific SSR markers (here referred to SSR prim-
ers) to distinguish each of them from other 38
accessions (Table 2). Remarkably, NL6 had eight
accession-specific SSR markers. LDGTXMH had
four, both QYDZHMZ and HXZZMH had two.
The other eight accessions, WAZM, WXXBH,
MGZM971, CSDBZ, XZXH3, GZZM,
CSDHXH and CRZM had one each.
Genetic diversity analysis
Genetic similarity coefficients among all 39
G. arboreum accessions and one G. herbaceum
ranged from 0.58 to 0.99, and the maximum 0.99
was between two G. arboreum, DZJ and DZM,

Table 2. Gossypium arboreum accessions fingerprinted by specific SSR markers.

Accessions Name of primers producing specific SSR markers

NL 6 BNL 347 BNL 852 BNL 1317 BNL 2634 BNL 2884 BNL 3264
LDGTXMH BNL 269 BNL 1395 BNL 1897 BNL 2440
HXZZMH BNL 116 BNL 2569
QYDZHMZ BNL 2967 BNL 4094
WAZM BNL 1395
WXXBH BNL 3971
MGZM971 BNL 256
CSDBZ BNL 2569
XZXH3 BNL 1897
GZZM BNL 2440
CSDHXH BNL 116
CRZM BNL 2569

For abbreviations of germplasm names, see Table 1.


which might mean they were closely related. With
the exception of DZJ and DZM, pairwise genetic
similarity coefficients ranged from 0.58 to 0.87,
indicating that a vast genetic base is present in
Chinese G. arboreum. The least similarity coeffi-
cient of 0.58 was generated between NL6 and
WXXBH, the former was introduced from Japan
and the latter from Hebei province of China. NL6
was outstanding because its average similarity to
other accessions was 0.66, showing large variabil-
ity in genomic constitution. PDXH and WZXH,
MGZM971 and DYXHM were included in the
accessions with maximum similarity index of 0.87.
The first two were both collected from Guizhou
province of China while the latter two were from
far away regions, the USA and Anhui province of
China, respectively.
The UPGMA dendrogram generated from
genetic similarity coefficients is shown in Figure 2.
Cluster analysis resulted in seven groups
(A through G). Group A consisted of four
G. arboreum accessions and the G. herbaceum
accession. There were nine members in group B.
Accessions in groups A and B were mainly from
northern and northeastern regions of China, such
as Hebei and Shandong provinces (Figure 1).
Eighteen members constituted group C, and most
of them were from provinces in the middle and
Figure 2. An UPGMA dendrogram of 39 Gossypium arboreum accessions and one G. herbaceum sample based on SSR data. For
abbreviations of germplasm names, see Table 1.
1149
lower Yangtze Valley such as Hubei, Anhui,
Jiangsu and Shanghai. The US introduction,
MGZM971 was also in group C. Group D was
composed of five G. arboreum accessions. Basal
position of the phylogenic tree was occupied by
three accessions, QYDZHMZ, LDGTXMH and
NL6, which made up groups E, F and G, respec-
tively. As shown above, the three accessions hap-
pened to have the highest polymorphism as
revealed by microsatellite analysis in this study.
Not all accessions from the same regions were
clustered in the same group. For example, the
eight accessions originated from the Guizhou
province of southwestern China dispersed in
groups B, D and F indicating high local genetic
diversity within this region.
Comparison of microsatellite performance
between G. arboreum and G. hirsutum
In this study, 84 SSR primer pairs failed to amplify
decipherable products among the 40 G. arboreum
or G. herbaceum accessions listed in Table 1.
However, when the PCR profiles of these micro-
satellite markers were compared among three
Gossypium species: G. arboreum (A2), G. raimondii
(D) and G. hirsutum cv. ‘Jinmian 6’ (AD), 17 SSR
1150
primers of the 84 primer pairs did not clearly
produce distinct fragments in all three species and
the remaining 67 produced distinct bands in D and
AD genomes, but not in the A2 genome. There-
fore, the loci detected by these 67 primer pairs may
be located in the D genome. According to chro-
mosomal assignment of microsatellite loci or
linkage relationship (Liu et al. 2000; Lacape et al.
2003; Mei et al. 2004), 17 primer pairs out of the 67
produced distinct bands in D and AD genomes,
but not in the A2 genome, had been reported to be
located in specific D subgenome of tetraploid
cotton.
It was interesting to find that the sizes of many
amplified fragments for G. arboreum were different
from those of tetraploid cotton. Hence, variation
in amplified fragments sizes between the diploid
G. arboreum and tetraploid G. hirsutum was sys-
tematically investigated by SSR analysis. Total
genomic DNA of JM6 was amplified using the
same 358 SSR primer pairs. Distribution of frag-
ment sizes of G. arboreum and JM6 are compared
in Figure 3. The sizes of most amplified fragments
in both G. arboreum and G. hirsutum ranged from
100 to 500 basepair (bp). However, the percentage
of fragments within 200 bp and 801–1000 bp in
G. arboreum was obviously higher than that in
G. hirsutum. Meanwhile, G. hirsutum had
more bands ranging from 201 to 500 bp than
G. arboreum. The fragment sizes of G. arboreum
showed two peaks, 101–200 bp and 901–1000 bp,
whereas JM6 has only one peak at 301–400 bp. In
other words, size distribution of G. arboreum
amplified fragments was dispersive and that of
G. hirsutum was relatively concentrated. Never-
theless, more G. hirsutum accessions should be
examined to confirm this observation.
Figure 3. Sizes distribution of DNA fragments amplified by
SSR primers.
Discussion
Gossypium arboreum is an invaluable gene pool for
improving modern cotton cultivars. A systematic
genetic assessment of the gene resources will help
to decrease the redundancy and construct a core
germplasm collection, which is important for effi-
cient use of these gene resources in cotton breed-
ing. In this study, 37 G. arboreum accessions
collected from different regions of China and two
accessions from other countries were evaluated for
their genetic diversity. One G. herbaceum accession
as an outgroup was also included in analysis.
Calculation of pairwise genetic similarity coeffi-
cients suggested that except for DZJ and DZM
which were closely related with a genetic similarity
coefficient 0.99, most of the G. arboreum acces-
sions examined were genetically diversified (the
coefficients varied from 0.58 to 0.87 with an
average of 0.74). In contrast, genetic variation is
extremely limited in G. hirsutum especially among
the elite cultivated types (Iqbal et al. 2001; Lu and
Myers 2002; Zhu et al. 2003). These suggested that
there is higher level of genetic variation at the
DNA level among the G. arboreum accessions
than that among G. hirsutum accessions. There-
fore, the G. arboreum accessions may be an
important source of novel genes for genetic
improvement of cotton. These data may also serve
as a guide in selecting the core germplasm pool of
G. arboreum.
Gossypium herbaceum was on the top of the
UPGMA dendrogram (Figure 2). Nei’s similarity
between G. herbaceum and 39 G. arboreum acces-
sions ranged from 0.62 to 0.78 with an average of
0.71. Cytogenetic data indicated that both species
possess the Gossypium A genome (Beasley 1942),
and they differed by a reciprocal translocation
(Gerstel 1953). In Khan et al’s (2000) analysis based
on RAPD marker, G. arboreum and G. herbaceum
were clustered into the same group with the Nei’s
similarity of 0.79. Results from this study sup-
ported their conclusion. The lower genetic similar-
ity in our result suggested that microsatellites were
more informative than the RAPD markers.
In the dendrogram assembled for the 39
G. arboreum accessions (Figure 2), there was a
positive correlation between cluster groupings and
geographic distances. For example, most of the
G. arboreum accessions from the northern and
northeastern provinces of China were clustered into

groups A and B whereas the four accessions, SYX1,
DZJ, DZM and JXZM from Hebei Province fell
into group B. The majority of group C accessions
were collected from provinces in the middle and
lower Yangtze Valley. Similar results were found by
Monte et al. (1993) and Sharma et al. (2000).
Vergara and Bughrara (2003) also found that
bentgrass accessions from geographically adjacent
countries commonly clustered together, but those
from distant locations were clustered into different
groups with low similarity coefficients. The
G. arboreum had been cultivated in China for over
2000 years. It is likely that the widely different
environment of China had contributed significantly
to the diversity of G. arboreum. Nonetheless, eight
accessions from Guizhou were dispersed in groups
B, D, and F, indicating that they possess large ge-
netic diversity. The G. arboreum spread into China
from ancient India along the line of Punjab, Indian
peninsula, Burma and Vietnam and firstly culti-
vated in Chinese southern and southwestern re-
gions, subsequently spread to the drainage areas of
Yangtze and Yellow Rivers. Hence, the southern
and southwestern regions of China including
Yunnan and Guizhou provinces may be the sub-
biodiversity centre of G. arboreum. Several peren-
nial G. arboreum were found in Yunnan Province
(Xiang and Shen 1989) which may well explain the
high-level genetic diversity of G. arboreum acces-
sions from Guizhou that borders Yunnan Province.
In the present study, 74 SSR primer pairs yiel-
ded a total of 165 polymorphic loci with each
marker detecting 1–8 polymorphic fragments
among the 40 accessions. It seems that microsat-
ellite analysis is a method of choice to study
genetic diversity, varietal relationships and gen-
ome evolution in Gossypium. However, little is
known about the origin and evolution of them in
the Gossypium genomes. Syed et al. (2001) ana-
lyzed differences among dinucleotide microsatellite
repeats in diploid A or D genome and polyploid
AD genome of cotton, and concluded that among
107 SSR loci examined, 30–50% had similar allele
sizes in all three genomes, but over half of the loci
had either longer or shorter sequences in the tet-
raploids. They analyzed sequences of SSR loci and
discovered that not only the number of dinucleo-
tide repeats but also sequences flanking the repeats
caused the variation in allele sizes. Therefore, Syed
et al. (2001) speculated that after polyploidization,
the microsatellite alleles might evolve rapidly in
1151
polyploids, and through contraction or expansion,
the imperfect dinucleotide repeats converted to the
perfect repeats. Jiang et al. (1998) concluded that
during polyploidization, 52 chromosomes in tet-
raploids have diverged further from their ancestral
genomes, especially D subgenome. The same
phenomenon was observed in the present study
(Figure 3), but more detailed studies seem neces-
sary for making any conclusion.
So far all SSR markers (BNL series) were
developed from tetraploid cotton genome. Liu
et al. (2000) estimated that annealing between
primers and templates would be affected when
tetraploid cotton-derived primers were used to
amplify templates from diploid A or D genome
species. If this is true, it is not surprising that 84
SSR primer pairs out of 358 did not yield unam-
biguous and characteristic DNA fragments among
the 40 Gossypium diploid species in this assay.
Through farther validation, 67 SSR primer pairs
might relate to D genome with 17 primer pairs
previously reported to be located in D genome
(Liu et al. 2000; Lacape et al. 2003; Mei et al.
2004). Abdalla et al. (2001) detected 84 D-related
DNA bands using AFLP. It is more possible that
D-related markers were derived from the D-gen-
ome progenitor. The next objective of our work is
to make sure that the other 50 SSR primer pairs
(excluding 17 SSR primer pairs reported to be
located in D genome) are specific markers of D
genome.
Acknowledgements
We thank the Cotton Research Institute, Chinese
Academy of Agricultural Sciences for providing
the 39 G. arboreum accessions used in this study.
We also thank Drs L.F. Zhu, D.H. He and Y.X.
Zhang for technical help. Financial support of this
research from the National High Technology
Project (2004AA211171) and National Basic
Research Program of China (2004CB117301) was
appreciated.
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