Abstract:
The objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the varieties. Initially, 92 SSR markers were genotyped in 20 Brazilian cotton cultivars. Of this total, 38 loci were polymorphic, two of which were amplified by one primer pair; the mean number of alleles per locus was 2.2. The values of polymorphic information content (PIC) and discrimination power (DP) were, on average, 0.374 and 0.433, respectively. The mean genetic distance was 0.397 (minimum of 0.092 and maximum of 0.641). A panel of 96 varieties originating from different regions of the world was assessed by 21 polymorphic loci derived from 17 selected primer pairs. Among these varieties, the mean genetic distance was 0.387 (minimum of 0 and maximum of 0.786). The dendrograms generated by the unweighted pair group method with arithmetic average (UPGMA) did not reflect the regions of Brazil (20 genotypes) or around the world (96 genotypes), where the varieties or lines were selected. Bootstrap resampling shows that genotype identification is viable with 19 loci. The polymorphic markers evaluated are useful to perform varietal identification in a large panel of cotton varieties and may be applied in studies of the species diversity.
Index terms:
Gossypium hirsutum; cultivar discrimination; intraspecific polymorphism; microsatellite
Resumo:
O objetivo deste trabalho foi identificar marcadores polimórficos de sequências simples repetidas (SSR) para identificação varietal de algodão e avaliação da distância genética entre as variedades. Inicialmente, 92 marcadores SSR foram genotipados em 20 cultivares de algodão do Brasil. Desse total, 38 locos foram polimórficos, dos quais dois deles foram amplificados por um único par de iniciadores; o número médio de alelos por loco foi 2,2. Os conteúdos de informação polimórfica (PIC) e de poder de discriminação (DP) foram, em média, 0,374 e 0,433, respectivamente. A distância genética média foi de 0,397 (mínima de 0,092 e máxima de 0,641). Um painel de 96 variedades originárias de diversas regiões do mundo foi avaliado por 21 locos polimórficos derivados a partir de 17 pares de iniciadores selecionados. Entre essas variedades, a distância genética média foi de 0,387 (mínima de 0 e máxima de 0,786). Os dendrogramas elaborados a partir de média aritmética não ponderada (UPGMA) não refletiram as regiões do Brasil (20 genótipos) ou do mundo (96 genótipos), onde as variedades ou linhagens foram selecionadas. O procedimento de reamostragem bootstrap mostra que a identificação dos genótipos é viável com 19 locos. Os marcadores polimórficos avaliados são úteis na identificação varietal de um painel amplo de variedades de algodão e podem ser aplicados em estudos de diversidade da espécie.
Termos para indexação:
Gossypium hirsutum; discriminação de cultivares; polimorfismo intraespecífico; microssatélite
Introduction
The genetic diversity of the genus Gossypium is high among
wild and domesticated cotton species. Wild cotton comprises 45 diploid
and 5 tetraploid species (Campbell et
al., 2010CAMPBELL, B.T.; SAHA, S.; PERCY, R.; FRELICHOWSKI, J.;
JENKINS, J.N.; PARK, W.; MAYEE, C.D.; GOTMARE, V.; DESSAUW, D.;
GIBAND, M.; DU, X.; JIA, Y.; CONSTABLE, G.; DILLON, S.;
ABDURAKHMONOV, I.Y.; ABDUKARIMOV, A.; RIZAEVA, S.M.; ABDULLAEV,
A.; BARROSO, P.A.V.; PÁDUA, J.G.; HOFFMANN, L.V.; PODOLNAYA, L.
Status of the global cotton germplasm resources. Crop Science,
v.50, p.1161-1179, 2010. DOI:
10.2135/cropsci2009.09.0551.
https://doi.org/10.2135/cropsci2009.09.0...
), of which four have been independently
domesticated in four different regions worldwide. Gossypium
hirsutum L., one of the tetraploid species, is
classified into seven different races: one wild and six domesticated
(Lacape et al., 2007LACAPE, J.-M.; DESSAUW, D.; RAJAB, M.; NOYER, J.-L.;
HAU, B. Microsatellite diversity in tetraploid
Gossypium germplasm: assembling a highly
informative genotyping set of cotton SSRs. Molecular Breeding,
v.19, p.45-58, 2007. DOI:
10.1007/s11032-006-9042-1.
https://doi.org/10.1007/s11032-006-9042-...
). The
G. hirsutum race
latifolium Hutch., or upland cotton, is
economically the most important one and, besides being broadly adapted,
is also the main fiber crop (Campbell et
al., 2010CAMPBELL, B.T.; SAHA, S.; PERCY, R.; FRELICHOWSKI, J.;
JENKINS, J.N.; PARK, W.; MAYEE, C.D.; GOTMARE, V.; DESSAUW, D.;
GIBAND, M.; DU, X.; JIA, Y.; CONSTABLE, G.; DILLON, S.;
ABDURAKHMONOV, I.Y.; ABDUKARIMOV, A.; RIZAEVA, S.M.; ABDULLAEV,
A.; BARROSO, P.A.V.; PÁDUA, J.G.; HOFFMANN, L.V.; PODOLNAYA, L.
Status of the global cotton germplasm resources. Crop Science,
v.50, p.1161-1179, 2010. DOI:
10.2135/cropsci2009.09.0551.
https://doi.org/10.2135/cropsci2009.09.0...
). However, there is evidence that cotton genetic
diversity has been declining in breeding programs (Paterson et al., 2004PATERSON, A.H.; BOMAN, R.K.; BROWN, S.M.; CHEE, P.W.;
GANNAWAY, J.R.; GINGLE, A.R.; MAY, O.L.; SMITH, C.W. Reducing the
genetic vulnerability of cotton. Crop Science, v.44, p.1900-1901,
2004. DOI: 10.2135/cropsci2004.1900.
https://doi.org/10.2135/cropsci2004.1900...
), which can also lead to a
reduction in yield gain through breeding, since diversity is required
for selection (Campbell et al.,
2010CAMPBELL, B.T.; SAHA, S.; PERCY, R.; FRELICHOWSKI, J.;
JENKINS, J.N.; PARK, W.; MAYEE, C.D.; GOTMARE, V.; DESSAUW, D.;
GIBAND, M.; DU, X.; JIA, Y.; CONSTABLE, G.; DILLON, S.;
ABDURAKHMONOV, I.Y.; ABDUKARIMOV, A.; RIZAEVA, S.M.; ABDULLAEV,
A.; BARROSO, P.A.V.; PÁDUA, J.G.; HOFFMANN, L.V.; PODOLNAYA, L.
Status of the global cotton germplasm resources. Crop Science,
v.50, p.1161-1179, 2010. DOI:
10.2135/cropsci2009.09.0551.
https://doi.org/10.2135/cropsci2009.09.0...
).
Diversity can be increased by using wild genotypes in breeding. However,
there are constraints related to crossing barriers (Pereira et al., 2012PEREIRA, G.S.; SOUSA, R.L.; HOFFMANN, L.V.; SILVA, E.F.;
BARROSO, P.A.V. Selective fertilization in interspecific crosses
of allotetraploid species of Gossypium. Botany,
v.90, p.159-166, 2012. DOI: 10.1139/b11-094.
https://doi.org/10.1139/b11-094...
) and mainly
to traits largely different from those required for commercial cotton
production. For this reason, cotton breeding has usually been performed
from a narrow genetic base. In this context, intraspecific polymorphic
markers can assist breeders, by easily displaying relevant genetic
diversity among cotton lineages from overlooked germplasm banks, for
instance.
Moreover, the identification of cotton varieties is important during
breeding and registration processes, and during seed production, trade,
and inspection. The identification of intraspecific polymorphic markers
for varietal and cultivar discrimination is necessary, considering the
narrow cotton genetic base and consequent insufficiency of morphological
descriptors (Zhu et al., 2014ZHU, Q.-H.; SPRIGGS, A.; TAYLOR, J.M.; LLEWELLYN, D.;
WILSON, I. Transcriptome and complexity-reduced, DNA-based
identification of intraspecies single-nucleotide polymorphisms in
the polyploid Gossypium hirsutum L. G3-Genes
Genomes Genetics, v.4, p.1893-1905, 2014.).
The use of molecular markers serves as a modern and suitable approach to
varietal and cultivar identification as it is more rapid and cost
effective (Korir et al., 2013KORIR, N.K.; HAN, J.; SHANGGUAN, L.F.; WANG, C.; KAYESH,
E.; ZHANG, Y.Y.; FANG, J.G. Plant variety and cultivar
identification: advances and prospects. Critical Reviews in
Biotechnology, v.33, p.111-125, 2013. DOI:
10.3109/07388551.2012.675314.
https://doi.org/10.3109/07388551.2012.67...
).
In addition, breeding efforts are facilitated by information on the
genetic diversity of available germplasm resources, including those from
commercial seeds.
Currently, most of the available polymorphic molecular markers for cotton
varieties are interspecific, and genetic diversity, as well as molecular
mapping in cotton, has frequently been done with more than one species
or race (Blenda et al., 2006BLENDA, A.; SCHEFFLER, J.; SCHEFFLER, B.; PALMER, M.;
LACAPE, J.-M.; YU, J.Z.; JESUDURAI, C.; JUNG, S.; MUTHUKUMAR, S.;
YELLAMBALASE, P.; FICKLIN, S.; STATON, M.; ESHELMAN, R.; ULLOA,
M.; SAHA, S.; BURR, B.; LIU, S.; ZHANG, T.; FANG, D.; PEPPER, A.;
KUMPATLA, S.; JACOBS, J.; TOMKINS, J.; CANTRELL, R.; MAIN, D.
CDM: a cotton microsatellite database resource for
Gossypium genomics. BMC Genomics, v.7,
article ID 132, 2006. DOI:
10.1186/1471-2164-7-132.
https://doi.org/10.1186/1471-2164-7-132...
;
Menezes et al., 2008MENEZES, I.P.P. de; HOFFMANN, L.V.; ALVES, M.F.;
MORELLO, C. de L.; BARROSO, P.A.V. Distância genética entre
linhagens avançadas de germoplasma de algodão com uso de
marcadores de RAPD e microssatélites. Pesquisa Agropecuária
Brasileira, v.4, p.1339-1347, 2008. DOI:
10.1590/S0100-204X2008001000012.
https://doi.org/10.1590/S0100-204X200800...
).
Despite the high diversity of SSR markers in Gossypium
genomes (Lacape et al., 2007LACAPE, J.-M.; DESSAUW, D.; RAJAB, M.; NOYER, J.-L.;
HAU, B. Microsatellite diversity in tetraploid
Gossypium germplasm: assembling a highly
informative genotyping set of cotton SSRs. Molecular Breeding,
v.19, p.45-58, 2007. DOI:
10.1007/s11032-006-9042-1.
https://doi.org/10.1007/s11032-006-9042-...
),
the documentation of markers that are intraspecifically polymorphic in
G. hirsutum is still
incipient.
The objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the species varieties.
Materials and Methods
Two collections of plant material were used. The first one was composed by 20 Brazilian genotypes. Of these, 5 were commercial cultivars, identified by the BRS prefix, and 15 were inbred lines, identified by the prefix of the state in which they were selected: two from Bahia (BA), five from Goiás (GO), five from Mato Grosso (MT), and three from Paraíba identified by (CNPA). This collection represents genotypes of the breeding programs of Embrapa Algodão, developed for the main producing areas in the country. Genomic DNA was isolated from the endosperm of one seed for each genotype, placed in microtubes with sodium dodecyl sulfate extraction buffer (McDonald et al., 1994MCDONALD, M.B.; ELLIOT, L.J.; SWEENEY, P.M. DNA extraction from dry seeds for RAPD analyses in varietal identification studies. Seed Science and Technology, v.22, p.171-176, 1994.) and grinded with beadbeater equipment (BioSpec Products, Inc., Bartlesville, OK, USA).
The second plant material, also from the germplasm bank of Embrapa Algodão,
was composed by 96 worldwide genotypes: 22 current Brazilian varieties,
51 obsolete varieties (17 from Brazil, 17 from the USA, 7 from Mexico, 2
from Argentina, 1 from Venezuela, 2 from India, 2 from China, 1 from
Uzbekistan, and 2 from Africa), and 23 lineages of unknown-origin
selected or maintained for having special traits (mainly disease
resistance and superior fiber traits). Genomic DNA was extracted from
young leaves through the CTAB method (Plant..., 2014PLANT DNA extraction protocol for DArT. Camberra:
Diversity Arrays Technology, 2014. Available at: <Available at: https://www.
diversityarrays.com/files/DArT_DNA_isolation.pdf
>. Accessed on: 10 Dec. 2014.
https://www.
...
). After both extraction batches, DNA was
quantified for comparison with well-known amounts of lambda phage DNA
(Invitrogen, Carlsbad, CA, USA) in 0.8% (w/v) agarose gels stained by
Sybr Gold (Invitrogen, Carlsbad, CA, USA).
For polymorphism screening in the collection of 20 genotypes, 92 SSR markers
were included: 37 BNL (Liu et al.,
2000LIU, S.; SAHA, S.; STELLY, D.; BURR, B.; CANTRELL, R.G.
Chromosomal assignment of microsatellite loci in cotton. Journal
of Heredity, v.91, p.326-332, 2000. DOI:
10.1093/jhered/91.4.326.
https://doi.org/10.1093/jhered/91.4.326...
; Lacape et al.,
2007LACAPE, J.-M.; DESSAUW, D.; RAJAB, M.; NOYER, J.-L.;
HAU, B. Microsatellite diversity in tetraploid
Gossypium germplasm: assembling a highly
informative genotyping set of cotton SSRs. Molecular Breeding,
v.19, p.45-58, 2007. DOI:
10.1007/s11032-006-9042-1.
https://doi.org/10.1007/s11032-006-9042-...
), 40 CIR (Nguyen et
al., 2004NGUYEN, T.-B.; GIBAND, M.; BROTTIER, P.; RISTERUCCI,
A.-M.; LACAPE, J.-M. Wide coverage of the tetraploid cotton
genome using newly developed microsatellite markers. Theoretical
and Applied Genetics, v.109, p.167-175, 2004. DOI:
10.1007/s00122-004-1612-1.
https://doi.org/10.1007/s00122-004-1612-...
), 4 JESPR (Reddy
et al., 2001REDDY, O.U.K.; PEPPER, A.E.; ABDURAKHMONOV, I.; SAHA,
S.; JENKINS, J.N.; BROOKS, T.; BOLEK, Y.; EL-ZIK, K.M. New
dinucleotide and trinucleotide microsatellite marker resources
for cotton genome research. Journal of Cotton Science, v.5,
p.103-113, 2001.), and 11 NAU (Han et al., 2004HAN, Z.-G.; GUO, W.-Z.; SONG, X.-L.; ZHANG, T.-Z.
Genetic mapping of EST-derived microsatellites from the diploid
Gossypium arboreum in alloteraploid
cotton. Molecular Genetic Genomics, v.272, p.308-327, 2004. DOI:
10.1007/s00438-004-1059-8.
https://doi.org/10.1007/s00438-004-1059-...
). These SSR loci are summarized in Table
1 according to information available at the CottonGen database (Yu et al., 2014YU, J.; JUNG, S.; CHENG, C.H.; FICKLIN, S.P.; LEE, T.;
ZHENG, P.; JONES, D.; PERCY, R.; MAIN, D. CottonGen: a genomics,
genetics and breeding database for cotton research. Nucleic Acids
Research, v.42, p.D1229-D1236, 2014. DOI:
10.1093/nar/gkt1064.
https://doi.org/10.1093/nar/gkt1064...
). Polymerase
chain reactions (PCR) were performed on 20 μL solutions containing PCR
buffer (10 mmol L-1 Tris-HCl pH 8.3, 50 mmol L-1
KCl, and 0.1% Triton X-100), 0.2 mmol L-1 of each dNTP, 1.0 U
of Taq DNA polimerase, 0.15 μmol L-1 of each primer, and 20
ng (for BNL primers) or 25 ng (for CIR, JESPR, and NAU primers) of
genomic DNA. Magnesium chloride was added to each primer according to
the developer's specifications (Table
1).
Information on repeat motifs, MgCl2 concentration (mmol L-1), annealing temperature (AT, ºC), and chromosome location for all simple sequence repeat (SSR) markers used in the intraspecific polymorphism screening of the collection of 20 upland cotton (Gossypium hirsutum race latifolium Hutch.) genotypes(1).
The amplification reaction for the BNL primers was performed by an initial denaturation at 95°C for 12 min, followed by 30 cycles at 93°C for 1 min, 55°C for 2 min, and 72°C for 3 min, with a final extension at 72°C for 7 min. For the CIR, JESPR, and NAU primers, the initial denaturation was at 94°C for 5 min, followed by 35 cycles at 94°C for 30 s, annealing temperature recommended for each primer pair (Table 1) at 1 min, and 72°C for 1 min, with a final extension at 72°C for 8 min. PCR products were electrophoresed on 6% (w/v) polyacrylamide gels and stained with silver nitrate. SSR data were scored visually, and fragment size estimates were based on their mobility relative to a 50-bp ladder size standard (Invitrogen, Carlsbad, CA, USA).
Two measures of marker informativeness were obtained for each polymorphic
SSR loci in the collection of 20 genotypes. Polymorphic information
content (PIC) and discrimination power (DP) values were calculated as
proposed by Botstein et al. (1980)BOTSTEIN, D.; WHITE, R.L.; SKOLNICK, M.; DAVIS, R.W.
Construction of a genetic linkage map in man using restriction
fragment length polymorphisms. American Journal of Human
Genetics, v.32, p.314-331, 1980.
and Tessier et al. (1999)TESSIER, C.; DAVID, J.; THIS, P.; BOURSIQUOT, J.M.;
CHARRIER, A. Optimization of the choice of molecular markers for
varietal identification in Vitis vinifera L.
Theoretical and Applied Genetics, v.98, p.171-177, 1999. DOI:
10.1007/s001220051054.
https://doi.org/10.1007/s001220051054...
,
respectively. Furthermore, individual observed heterozygozity
(Hi), i.e. the percentage of heterozygous SSR loci,
was calculated for each G. hirsutum
cultivar.
For varietal identification, a number of markers was defined by performing
1,000 bootstrap resampling over an increasing number of polymorphic loci
using the GenClone software, version 2.0 (Arnaud-Haond & Belkhir, 2007ARNAUD-HAOND, S.; BELKHIR, K. GENCLONE: a computer
program to analyse genotypic data, test for clonality and
describe spatial clonal organization. Molecular Ecology Notes,
v.7, p.15-17, 2007. DOI:
10.1111/j.1471-8286.2006.01522.x.
https://doi.org/10.1111/j.1471-8286.2006...
). Afterwards, genotyping
was carried out in a panel of 96 genotypes for varietal identification.
Amplification was performed according to the recommendations of the
respective developers, as described before, multiplexing up to five
primer pairs with similar annealing temperature and amplifying fragments
of contrasting molecular weights. One primer of each pair was labeled
with either 6-FAM, HEX, or NED (Applied Biosystems Inc., Foster City,
CA, USA) and was combined to another in batches. Initial denaturation
was at 95°C for 15 min, followed by 40 cycles at 94°C for 1 min,
annealing temperature at 51 or 55°C for 90 s (depending on the primer
combination), and 72°C for 90 s, with a final extension at 72°C for 8
min. The obtained PCR products were run in the ABI 3500xL sequencer and
scored using the GeneMapper software (Applied Biosystems Inc., Foster
City, CA, USA).
Posteriorly, the GenClone software, version 2.0 (Arnaud-Haond & Belkhir, 2007ARNAUD-HAOND, S.; BELKHIR, K. GENCLONE: a computer
program to analyse genotypic data, test for clonality and
describe spatial clonal organization. Molecular Ecology Notes,
v.7, p.15-17, 2007. DOI:
10.1111/j.1471-8286.2006.01522.x.
https://doi.org/10.1111/j.1471-8286.2006...
), was used to
reevaluate the 1,000 bootstrap resampling over the number of markers
scored in the collection of 96 genotypes. This was done in order to
verify the reliability of this number of markers in discriminating the
so-called multilocus genotypes (MLG).
For both collections of genotypes, genetic distances, defined as the
proportion of shared alleles (Bowcock et
al., 1994BOWCOCK, A.M.; RUIZ-LINARES, A.; TOMFOHRDE, J.; MINCH,
E.; KIDD, J.R.; CAVALLI-SFORZA, L.L. High resolution of human
evolutionary trees with polymorphic microsatellites. Nature,
v.368, p.455-457, 1994. DOI: 10.1038/368455a0.
https://doi.org/10.1038/368455a0...
), were calculated over the means of 1,000
bootstrap resampling in the Microsat software, version 1.5 (Stanford
University, Stanford, CA, USA). Cluster analysis was done using the
unweighted pair group method with arithmetic average (UPGMA) in the Mega
software, version 5.05 (Tamura et al.,
2011TAMURA, K.; PETERSON, D.; PETERSON, N.; STECHER, G.;
NEI, M.; KUMAR, S. MEGA5: molecular evolutionary genetics
analysis using maximum likelihood, evolutionary distance, and
maximum parsimony methods. Molecular Biology and Evolution, v.28,
p.2731-2739, 2011. DOI: 10.1093/molbev/msr121.
https://doi.org/10.1093/molbev/msr121...
).
Results and Discussion
Ninety-two primer pairs amplified 93 loci in the collection of 20 genotypes.
From this total, 38 loci were polymorphic, totaling 40.8% (Table 2). The polymorphic loci
presented a total of 84 alleles, with 2.2 alleles per locus in average,
ranging from two to four alleles. The most polymorphic marker was
BNL1551, which presented four different alleles. The highest PIC values
(≥0.5) were those calculated for the CIR055, CIR165, and CIR249 loci,
and the PIC average was 0.374. However, BNL1551, CIR249, and JESPR153b
showed the highest DP values (>0.9), and the DP average was 0.433.
The PIC values show the degree of marker informativeness within the
latifolium race, which was smaller than the ones
obtained using different cotton species (Liu et al., 2000LIU, S.; SAHA, S.; STELLY, D.; BURR, B.; CANTRELL, R.G.
Chromosomal assignment of microsatellite loci in cotton. Journal
of Heredity, v.91, p.326-332, 2000. DOI:
10.1093/jhered/91.4.326.
https://doi.org/10.1093/jhered/91.4.326...
; Lacape
et al., 2007LACAPE, J.-M.; DESSAUW, D.; RAJAB, M.; NOYER, J.-L.;
HAU, B. Microsatellite diversity in tetraploid
Gossypium germplasm: assembling a highly
informative genotyping set of cotton SSRs. Molecular Breeding,
v.19, p.45-58, 2007. DOI:
10.1007/s11032-006-9042-1.
https://doi.org/10.1007/s11032-006-9042-...
). However, DP seems to be more useful than
PIC to select primer pairs for varietal identification, since it
considers the number of evaluated individuals and shows the probability
of randomly-selected genotypes being discriminated by each marker.
Characterization of 38 polymorphic microsatellite loci amplified in the evaluated upland cotton (Gossypium hirsutum race latifolium Hutch.) genotypes(1).
Exclusive alleles indicate a certain differentiation and can be used as a
direct tool for varietal identification, as well as to check genetic
purity (Schuster et al., 2006SCHUSTER, I.; VIEIRA, E.S.N.; PADILHA, L. Marcadores
moleculares no pós-melhoramento. In: BORÉM, A.; CAIXETA, E.T.
(Ed.). Marcadores moleculares. Viçosa: Ed. da UFV, 2006.
p.205-230.)
and hybridization for that specific genotype (Selvakumar et al., 2010SELVAKUMAR, P.; RAVIKESAVAN, R.; GOPIKRISHNAN, A.;
THIYAGU, K.; PREETHA, S.; BOOPATHI, N.M. Genetic purity analysis
of cotton (Gossypium spp.) hybrids using SSR
markers. Seed Science and Technology, v.38, p.358-366, 2010. DOI:
10.15258/sst.2010.38.2.09.
https://doi.org/10.15258/sst.2010.38.2.0...
). Two loci, BNL786 and
JESPR153b, revealed exclusive alleles for the CNPA 5052 inbred line,
whereas two other loci, BNL1551 and CIR246, revealed exclusive alleles
for the BRS Cedro commercial variety. The commercial variety BRS Seridó,
the only one in the collection developed to be planted in Northeast
Brazil, showed exclusive alleles revealed by BNL3994 and CIR105. In
addition, JESPR153 amplified two polymorphic loci, each one presenting
sets of alleles with different sizes, both identified on previous cotton
linkage maps (Ali et al., 2009ALI, M.A.; KHAN, I.A.; NAWAB, N.N. Estimation of genetic
divergence and linkage for fibre quality traits in upland cotton.
Journal of Agricultural Research, v.47, p.229-236,
2009.),
as a consequence of cotton allopolyploidization and the presence of
homeologous loci from the A and D genomes (Lacape et al., 2009LACAPE, J.-M.; JACOBS, J.; ARIOLI, T.; DERIJCKER, R.;
FORESTIER-CHIRON, N.; LLEWELLYN, D.; JEAN, J.; THOMAS, E.; VIOT,
C. A new interspecific, Gossypium hirsutum x
G. barbadense, RIL population: towards a
unified consensus linkage map of tetraploid cotton. Theoretical
and Applied Genetics, v.119, p.281-292, 2009. DOI:
10.1007/s00122-009-1037-y.
https://doi.org/10.1007/s00122-009-1037-...
).
The individual observed heterozygosity of the collection of 20 genotypes was
relatively high (Table 3), with a
mean of 4.8%. The expected rate for advanced lines was Hi =
0.0%, observed in five genotypes, and unexpectedly of Hi =
16.2% for two genotypes. The individual observed heterozigosity of 15
plants was relatively high, i.e. Hi>2% (Table 3), which was not expected
since the plants are lineages and, therefore, supposed to be derived
from successive self-pollinations. The occurrence of heterozygotes among
advanced lines may be explained by a limited number of self-pollination,
by variety release of genotypes selected in the first steps of the
breeding program (Lacape et al.,
2007LACAPE, J.-M.; DESSAUW, D.; RAJAB, M.; NOYER, J.-L.;
HAU, B. Microsatellite diversity in tetraploid
Gossypium germplasm: assembling a highly
informative genotyping set of cotton SSRs. Molecular Breeding,
v.19, p.45-58, 2007. DOI:
10.1007/s11032-006-9042-1.
https://doi.org/10.1007/s11032-006-9042-...
), or by pollen contamination on seed production
fields. Heterozygotes should facilitate individual identification,
although they were not supposed be found very often within lineages or
cultivars.
Observed individual heterozygosity (Hi) of 20 upland cotton (Gossypium hirsutum race latifolium Hutch.) genotypes by 38 polymorphic microsatellite loci.
The number of markers required for varietal discrimination was 19, estimated by resampling 38 polymorphic loci from the collection of 20 genotypes; when the number of loci tends towards 19, asymptotic behavior is observed (Figure 1A). The resampling strategy allowed testing random combinations of increasing numbers of markers. This generated minimum, average, and maximum number of discriminated MLG for each class number of sampled loci, ensuring that the chosen set of loci allows for a good estimate of the real number of MLG in the analyzed sample. Because of the arbitrary property of resampling loci, in theory, any subset of the 38 polymorphic loci could be used for exclusive identification of the collection of 20 genotypes.
Minimum, average, and maximum numbers of distinct multilocus genotypes (MLG) identified by bootstrap resampling of 38 (A) and 21 (B) polymorphic microsatellite loci genotyped in the collections of 20 and 96 upland cotton (Gossypium hirsutum race latifolium Hutch.) genotypes, respectively. Nineteen markers can be successfully used for varietal identification in cotton.
The number of loci needed for varietal discrimination was confirmed through
17 selected markers evaluated in the collection of 96 cotton genotypes
(Figure 1B). Out of these 17
markers, the following 12 were selected based on the polymorphism
screening performed in the present study, considering the highest PIC
and DP values: BNL2499, BNL3482, CIR030, CIR055, CIR081, CIR099, CIR165,
CIR170, CIR249, CIR373, JESPR153, and JESPR292. Moreover, five SSRs
evaluated in previous studies were also included in the present study
due to shared specific interests: BNL3661, for resistance to the
root-knot nematode, Meloidogyne incognita (Gutiérrez et al., 2010GUTIÉRREZ, O.A.; JENKINS, J.N.; MCCARTY, J.C.; WUBBEN,
M.J.; HAYES, R.W.; CALLAHAN, F.E. SSR markers closely associated
with genes for resistance to root-knot nematode on chromosomes 11
and 14 of upland cotton. Theoretical and Applied Genetics, v.121,
p.1323-1337, 2010. DOI:
10.1007/s00122-010-1391-9.
https://doi.org/10.1007/s00122-010-1391-...
); CIR316,
for resistance to M. incognita (Ulloa et al., 2010ULLOA, M.; WANG, C.; ROBERTS, P.A. Gene action analysis
by inheritance and quantitative trait loci mapping of resistance
to root-knot nematodes in cotton. Plant Breeding, v.129,
p.541-550, 2010. DOI:
10.1111/j.1439-0523.2009.01717.x.
https://doi.org/10.1111/j.1439-0523.2009...
); JESPR101,
related to four production or fiber traits (Zhang et al., 2013ZHANG, T.; QIAN, N.; ZHU, X.; CHEN, H.; WANG, S.; MEI,
H.; ZHANG, Y. Variations and transmission of QTL alleles for
yield and fiber qualities in upland cotton cultivars developed in
China. PLoS One, v.8, article e57220, 2013. DOI:
10.1371/journal.pone.0057220.
https://doi.org/10.1371/journal.pone.005...
); JESPR110, related to fiber
traits (Wang et al., 2011WANG, F.; GONG, Y.; ZHANG, C.; LIU, G.; WANG, L.; XU,
Z.; ZHANG, J. Genetic effects of introgression genomic components
from Sea Island cotton (Gossypium barbadense L.)
on fiber related traits in upland cotton (G.
hirsutum L.). Euphytica, v.181, p.41-53, 2011.
DOI: 10.1007/s10681-011-0378-1.
https://doi.org/10.1007/s10681-011-0378-...
); and
JESPR304, for resistance to Fusarium oxysporum wilt
(Wang et al., 2009WANG, P.; SU, L.; QIN, L.; HU, B.; GUO, W.; ZHANG, T.
Identification and molecular mapping of a Fusarium wilt resistant
gene in upland cotton. Theoretical and Applied Genetics, v.119,
p.733-739, 2009. DOI: 10.1007/s00122-009-1084-4.
https://doi.org/10.1007/s00122-009-1084-...
).
Considering that four primer pairs (BNL3661, CIR165, CIR316, and
JESPR101) amplified two distinct loci each in the collection of 96
genotypes, 21 loci were produced for varietal identification, i.e., two
more than recommended for the collection of 20 genotypes. Bootstrap
resampling over the 21 polymorphic loci from the collection of 96
genotypes indicated that these were sufficient to identify each variety
(Figure 1B). For 19 loci, a
minimum of 94 genotypes could be discriminated properly. A maximum of 96
genotypes was achieved by a combination of at least ten loci.
For the collection of 20 genotypes, the genetic distances measured by the 38 polymorphic loci ranged from 0.092 to 0.641, with an average of 0.397 (Figure 2). The smallest genetic distance was observed between the GO 8022 and CNPA 2571 lines, and the highest between the BA33 line and the BRS Buriti commercial variety. For the collection of 96 genotypes, the average of genetic distance was 0.387, ranging from 0 to 0.786. The most divergent genotype pair was Hopiacala (USA) and Silvermine (unknown origin), whereas the less divergent ones were Roella (unknown origin) and SA 2628 (USA), and Coodetec 403 and Epamig 4 (both from Brazil). The analysis of the calculated genetic distance distributions of all genotype pairs showed a higher frequency of distances at the classes from 0.4 to 0.5 (Figure 2), representing 78 and 64% of the results for the collections of 20 and 96 genotypes, respectively.
Relative frequency distribution of genetic distances obtained for 20 (black bars) and 96 (shaded bars) upland cotton (Gossypium hirsutum race latifolium Hutch.) genotypes by 38 and 21 polymorphic microsatellite loci, respectively.
Varieties selected in the same region were not placed in separate clusters in the grouping pattern shown by the UPGMA dendrograms (Figures 3 and 4). This may be explained by the genealogy of the lines, since some of them originated from the same crossings in the same breeding program and were then distributed to be evaluated in various regions. Another factor to be considered in this case are the similarities between selection parameters among the regions, as well as the lack of association between those selection parameters and the SSR markers. Since distances were small, all genotypes from both collections could be considered a single group; for the collection of 20 genotypes, lineages could be subgrouped into two clusters based on distance 0.22 - one including 4 genotypes and another, the 16 remaining genotypes (Figure 3).
Clustering assessment obtained by the unweighted pair group method with arithmetic average (UPGMA), based on the genetic distances among 20 Brazilian cotton genotypes.
Clustering assessment obtained by the unweighted pair group method with arithmetic average (UPGMA), based on the genetic distances among 96 worldwide cotton genotypes.
The recent discovery and advances on the analysis of polymorphism in cotton
SSRs (Blenda et al., 2006BLENDA, A.; SCHEFFLER, J.; SCHEFFLER, B.; PALMER, M.;
LACAPE, J.-M.; YU, J.Z.; JESUDURAI, C.; JUNG, S.; MUTHUKUMAR, S.;
YELLAMBALASE, P.; FICKLIN, S.; STATON, M.; ESHELMAN, R.; ULLOA,
M.; SAHA, S.; BURR, B.; LIU, S.; ZHANG, T.; FANG, D.; PEPPER, A.;
KUMPATLA, S.; JACOBS, J.; TOMKINS, J.; CANTRELL, R.; MAIN, D.
CDM: a cotton microsatellite database resource for
Gossypium genomics. BMC Genomics, v.7,
article ID 132, 2006. DOI:
10.1186/1471-2164-7-132.
https://doi.org/10.1186/1471-2164-7-132...
; Chen & Du, 2006CHEN, G.; DU, X.-M. Genetic diversity of source
germplasm of upland cotton in China as determined by SSR marker
analysis. Acta Genetica Sinica, v.33, p.733-745, 2006. DOI:
10.1016/S0379-4172(06)60106-6.
https://doi.org/10.1016/S0379-4172(06)60...
; Kebede et al., 2007KEBEDE, H.; BUROW, G.; DANI, R.G.; ALLEN, R.D. A-genome
cotton as a source of genetic variability for upland cotton
(Gossypium hirsutum). Genetic Resources
and Crop Evolution, v.54, p.885-895, 2007. DOI:
10.1007/s10722-006-9157-6.
https://doi.org/10.1007/s10722-006-9157-...
; Lacape et al., 2007LACAPE, J.-M.; DESSAUW, D.; RAJAB, M.; NOYER, J.-L.;
HAU, B. Microsatellite diversity in tetraploid
Gossypium germplasm: assembling a highly
informative genotyping set of cotton SSRs. Molecular Breeding,
v.19, p.45-58, 2007. DOI:
10.1007/s11032-006-9042-1.
https://doi.org/10.1007/s11032-006-9042-...
) led to the
choice of high polymorphic markers. Microsatellites may be chosen
instead of markers based on random PCR amplification because they are
relatively easy to reproduce and their location in the genome can also
be determined (Blenda et al.,
2006BLENDA, A.; SCHEFFLER, J.; SCHEFFLER, B.; PALMER, M.;
LACAPE, J.-M.; YU, J.Z.; JESUDURAI, C.; JUNG, S.; MUTHUKUMAR, S.;
YELLAMBALASE, P.; FICKLIN, S.; STATON, M.; ESHELMAN, R.; ULLOA,
M.; SAHA, S.; BURR, B.; LIU, S.; ZHANG, T.; FANG, D.; PEPPER, A.;
KUMPATLA, S.; JACOBS, J.; TOMKINS, J.; CANTRELL, R.; MAIN, D.
CDM: a cotton microsatellite database resource for
Gossypium genomics. BMC Genomics, v.7,
article ID 132, 2006. DOI:
10.1186/1471-2164-7-132.
https://doi.org/10.1186/1471-2164-7-132...
). Furthermore, microsatellites are easy to perform and
cost-effective, in comparison to SNP high-throughput technologies,
because they are multiallelic (Gupta et
al., 2005GUPTA, P.K.; RUSTGI, S.; KULWAL, P.L. Linkage
disequilibrium and association studies in higher plants: present
status and future prospects. Plant Molecular Biology, v.57,
p.461-485, 2005. DOI: 10.1007/s11103-005-0257-z.
https://doi.org/10.1007/s11103-005-0257-...
) and only a small number of markers are required
for the analyses. Genomic SSRs are also more recommended than
genic-derived SSRs, because gene regions tend to be less polymorphic
(Kalia et al., 2011KALIA, R.K.; RAI, M.K.; KALIA, S.; SINGH, R.; DHAWAN,
A.K. Microsatellite markers: an overview of the recent progress
in plants. Euphytica, v.177, p.309-334, 2011. DOI:
10.1007/s10681-010-0286-9.
https://doi.org/10.1007/s10681-010-0286-...
).
The usefulness of the markers is shown by the relatively high polymorphism
level obtained (40.8%). Polymorphic primer pairs were distributed along
22 of the 26 amphidiploid cotton chromosomes; these markers were equally
distributed on the chromosomes of both the A and D genomes, with 18 and
20 polymorphic loci, respectively. An equivalent distribution in
diversity among the A and D genomes was also observed by Lacape et al. (2007)LACAPE, J.-M.; DESSAUW, D.; RAJAB, M.; NOYER, J.-L.;
HAU, B. Microsatellite diversity in tetraploid
Gossypium germplasm: assembling a highly
informative genotyping set of cotton SSRs. Molecular Breeding,
v.19, p.45-58, 2007. DOI:
10.1007/s11032-006-9042-1.
https://doi.org/10.1007/s11032-006-9042-...
, and seems
to contradict a previous belief that the D genome would be more diverse
than the A genome (Adams & Wendel,
2004ADAMS, K.L.; WENDEL, J.F. Exploring the genomic
mysteries of polyploidy in cotton. Biological Journal of the
Linnean Society, v.82, p.573-581, 2004. DOI:
10.1111/j.1095-8312.2004.00342.x.
https://doi.org/10.1111/j.1095-8312.2004...
).
The cultivated cotton race, G. hirsutum
race latifolium, is less diverse than the other races
(Bertini et al., 2006BERTINI, C.H.C. de M.; SHUSTER, I.; SEDIYAMA, T.;
BARROS, E.G. de; MOREIRA, M.A. Characterization and genetic
diversity analysis of cotton cultivars using microsatellites.
Genetics and Molecular Biology, v.29, p.321-329, 2006. DOI:
10.1590/S1415-47572006000200021.
https://doi.org/10.1590/S1415-4757200600...
).
Lacape et al. (2007)LACAPE, J.-M.; DESSAUW, D.; RAJAB, M.; NOYER, J.-L.;
HAU, B. Microsatellite diversity in tetraploid
Gossypium germplasm: assembling a highly
informative genotyping set of cotton SSRs. Molecular Breeding,
v.19, p.45-58, 2007. DOI:
10.1007/s11032-006-9042-1.
https://doi.org/10.1007/s11032-006-9042-...
found
a relatively low dissimilarity value of 0.20 within
latifolium genotypes, but greater than when
measured in other DNA marker studies, including those with RFLP (Brubaker & Wendel, 1994BRUBAKER, C.L.; WENDEL, J.F. Reevaluating the origin of
domesticated cotton (Gossypium hirsutum;
Malvaceae) using nuclear restriction fragment length
polymorphisms (RFLPs). American Journal of Botany, v.81,
p.1309-1326, 1994. DOI: 10.2307/2445407.
https://doi.org/10.2307/2445407...
) or
SSRs (Rungis et al., 2005RUNGIS, D.; LLEWELLYN, D.; DENNIS, E.S.; LYON, B.R.
Simple sequence repeat (SSR) markers reveal low levels of
polymorphism between cotton (Gossypium hirsutum
L.) cultivars. Australian Journal of Agricultural Research, v.56,
p.301-307, 2005. DOI: 10.1071/AR04190.
https://doi.org/10.1071/AR04190...
; Tyagi et al., 2014TYAGI, P.; GORE, M.A.; BOWMAN, D.T.; CAMPBELL, B.T.;
UDALL, J.A.; KURAPARTHY, V. Genetic diversity and population
structure in the US upland cotton (Gossypium
hirsutum L.). Theoretical and Applied Genetics,
v.127, p.283-295, 2014. DOI:
10.1007/s00122-013-2217-3.
https://doi.org/10.1007/s00122-013-2217-...
). A decrease
in the diversity of cultivated genotypes, when compared to the wild
ones, is mostly related to the selection for crop domestication, which
may be accompanied by a dispersal bottleneck (Van de Wouw et al., 2010VAN DE WOUW, M.; KIK, C.; VAN HINTUM, T.; VAN TREUREN,
R.; VISSER, B. Genetic erosion in crops: concept, research,
results and challenges. Plant Genetic Resources, v.8, p.1-15,
2010. DOI: 10.1017/S1479262109990062.
https://doi.org/10.1017/S147926210999006...
). For cotton, an
additional bottleneck occurred when just a few genotypes were
transported from Mexico to the United States during the 19th
century, from which the genotypes currently cultivated were derived
(Paterson et al.,
2004PATERSON, A.H.; BOMAN, R.K.; BROWN, S.M.; CHEE, P.W.;
GANNAWAY, J.R.; GINGLE, A.R.; MAY, O.L.; SMITH, C.W. Reducing the
genetic vulnerability of cotton. Crop Science, v.44, p.1900-1901,
2004. DOI: 10.2135/cropsci2004.1900.
https://doi.org/10.2135/cropsci2004.1900...
).
The intraspecific polymorphism of the markers may be significant for
marker-assisted selection, since breeding programs might have to use
some form of monitoring of allelic richness. The molecular basis of the
cultivated cotton are reduced, but can be amplified by landraces or
exotic germplasm introduction (Van de
Wouw et al., 2010VAN DE WOUW, M.; KIK, C.; VAN HINTUM, T.; VAN TREUREN,
R.; VISSER, B. Genetic erosion in crops: concept, research,
results and challenges. Plant Genetic Resources, v.8, p.1-15,
2010. DOI: 10.1017/S1479262109990062.
https://doi.org/10.1017/S147926210999006...
). The markers selected in the present
study may be used to monitor genetic diversity among Brazilian or
foreign genotypes and their crosses, as well as to select the most
distant parental crosses that could foster genetic variance and,
consequently, genetic gains, as shown for cotton by Gutiérrez et al. (2002)GUTIÉRREZ, O.A.; BASU, S.; SAHA, S.; JENKINS, J.N.;
SHOEMAKER, D.B.; CHEATHAM, C.L.; MCCARTY, J.C. Genetic distance
among selected cotton genotypes and its relationship with F2
performance. Crop Science, v.42, p.1841-1847, 2002. DOI:
10.2135/cropsci2002.1841.
https://doi.org/10.2135/cropsci2002.1841...
.
The 19 SSRs chosen by permutation and resampling, combined with loci
informativeness measures (Arnaud-Haond
& Belkhir, 2007ARNAUD-HAOND, S.; BELKHIR, K. GENCLONE: a computer
program to analyse genotypic data, test for clonality and
describe spatial clonal organization. Molecular Ecology Notes,
v.7, p.15-17, 2007. DOI:
10.1111/j.1471-8286.2006.01522.x.
https://doi.org/10.1111/j.1471-8286.2006...
), can be used to discriminate upland
cotton genotypes, with or without additional trait-linked markers.
Genotypic discrimination should be used in germplasm banks and breeding
programs to monitor the germplasm bank, to support breeders in variety
protection or in monitoring the genetic variability of the genotypes
used for crossings in the breeding program, and to understand reports of
increased disease susceptibility in crops, as observed in a wheat
variety (Simpfendorfer et al.,
2013SIMPFENDORFER, S.; MARTIN, A.; SUTHERLAND, M.W. Use of
SSR markers to determine the genetic purity of a popular
Australian wheat variety and consequences for stripe rust
reactions. Seed Science and Technology, v.41, p.98-106, 2013.
DOI: 10.15258/sst.2013.41.1.09.
https://doi.org/10.15258/sst.2013.41.1.0...
). Furthermore, the use of distinct multilocus
genotypes should ensure variety protection in the world seed market and
can be extended to experimental or commercial breeding when maximum
genetic distances are required, as in the selection of parents for
mapping or for other crossing purposes.
Conclusions
-
Genotype identification in upland cotton (Gossypium hirsutum race latifolium Hutch.) is viable with 19 SSR markers.
-
The geographical region where a commercial genotype is obtained by breeding does not influence clustering by the unweighted pair group method with arithmetic average (UPGMA) in cotton.
Acknowledgments
To Embrapa Algodão and to Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), for financial support and fellowships granted; to the researchers Camilo de Lelis Morello, Francisco José Correia Farias, and Francisco Vidal from Embrapa Algodão, for supplying the cotton seeds analyzed in the present study; and to Francisco Alves Neto, Fábia Suelly Lima Pinto, and Eliane Cristina Pereira, for technical support
References
- ADAMS, K.L.; WENDEL, J.F. Exploring the genomic mysteries of polyploidy in cotton. Biological Journal of the Linnean Society, v.82, p.573-581, 2004. DOI: 10.1111/j.1095-8312.2004.00342.x.
» https://doi.org/10.1111/j.1095-8312.2004.00342.x - ALI, M.A.; KHAN, I.A.; NAWAB, N.N. Estimation of genetic divergence and linkage for fibre quality traits in upland cotton. Journal of Agricultural Research, v.47, p.229-236, 2009.
- ARNAUD-HAOND, S.; BELKHIR, K. GENCLONE: a computer program to analyse genotypic data, test for clonality and describe spatial clonal organization. Molecular Ecology Notes, v.7, p.15-17, 2007. DOI: 10.1111/j.1471-8286.2006.01522.x.
» https://doi.org/10.1111/j.1471-8286.2006.01522.x - BERTINI, C.H.C. de M.; SHUSTER, I.; SEDIYAMA, T.; BARROS, E.G. de; MOREIRA, M.A. Characterization and genetic diversity analysis of cotton cultivars using microsatellites. Genetics and Molecular Biology, v.29, p.321-329, 2006. DOI: 10.1590/S1415-47572006000200021.
» https://doi.org/10.1590/S1415-47572006000200021 - BLENDA, A.; SCHEFFLER, J.; SCHEFFLER, B.; PALMER, M.; LACAPE, J.-M.; YU, J.Z.; JESUDURAI, C.; JUNG, S.; MUTHUKUMAR, S.; YELLAMBALASE, P.; FICKLIN, S.; STATON, M.; ESHELMAN, R.; ULLOA, M.; SAHA, S.; BURR, B.; LIU, S.; ZHANG, T.; FANG, D.; PEPPER, A.; KUMPATLA, S.; JACOBS, J.; TOMKINS, J.; CANTRELL, R.; MAIN, D. CDM: a cotton microsatellite database resource for Gossypium genomics. BMC Genomics, v.7, article ID 132, 2006. DOI: 10.1186/1471-2164-7-132.
» https://doi.org/10.1186/1471-2164-7-132 - BOTSTEIN, D.; WHITE, R.L.; SKOLNICK, M.; DAVIS, R.W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, v.32, p.314-331, 1980.
- BOWCOCK, A.M.; RUIZ-LINARES, A.; TOMFOHRDE, J.; MINCH, E.; KIDD, J.R.; CAVALLI-SFORZA, L.L. High resolution of human evolutionary trees with polymorphic microsatellites. Nature, v.368, p.455-457, 1994. DOI: 10.1038/368455a0.
» https://doi.org/10.1038/368455a0 - BRUBAKER, C.L.; WENDEL, J.F. Reevaluating the origin of domesticated cotton (Gossypium hirsutum; Malvaceae) using nuclear restriction fragment length polymorphisms (RFLPs). American Journal of Botany, v.81, p.1309-1326, 1994. DOI: 10.2307/2445407.
» https://doi.org/10.2307/2445407 - CAMPBELL, B.T.; SAHA, S.; PERCY, R.; FRELICHOWSKI, J.; JENKINS, J.N.; PARK, W.; MAYEE, C.D.; GOTMARE, V.; DESSAUW, D.; GIBAND, M.; DU, X.; JIA, Y.; CONSTABLE, G.; DILLON, S.; ABDURAKHMONOV, I.Y.; ABDUKARIMOV, A.; RIZAEVA, S.M.; ABDULLAEV, A.; BARROSO, P.A.V.; PÁDUA, J.G.; HOFFMANN, L.V.; PODOLNAYA, L. Status of the global cotton germplasm resources. Crop Science, v.50, p.1161-1179, 2010. DOI: 10.2135/cropsci2009.09.0551.
» https://doi.org/10.2135/cropsci2009.09.0551 - CHEN, G.; DU, X.-M. Genetic diversity of source germplasm of upland cotton in China as determined by SSR marker analysis. Acta Genetica Sinica, v.33, p.733-745, 2006. DOI: 10.1016/S0379-4172(06)60106-6.
» https://doi.org/10.1016/S0379-4172(06)60106-6 - COTTON genome database. Washington: United States Department of Agriculture, 2011. Available at: <Available at: http://www.cottondb.org/wwwroot/cdbhome.php >. Accessed on: 10 Dec. 2014.
» http://www.cottondb.org/wwwroot/cdbhome.php - GUPTA, P.K.; RUSTGI, S.; KULWAL, P.L. Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Molecular Biology, v.57, p.461-485, 2005. DOI: 10.1007/s11103-005-0257-z.
» https://doi.org/10.1007/s11103-005-0257-z - GUTIÉRREZ, O.A.; BASU, S.; SAHA, S.; JENKINS, J.N.; SHOEMAKER, D.B.; CHEATHAM, C.L.; MCCARTY, J.C. Genetic distance among selected cotton genotypes and its relationship with F2 performance. Crop Science, v.42, p.1841-1847, 2002. DOI: 10.2135/cropsci2002.1841.
» https://doi.org/10.2135/cropsci2002.1841 - GUTIÉRREZ, O.A.; JENKINS, J.N.; MCCARTY, J.C.; WUBBEN, M.J.; HAYES, R.W.; CALLAHAN, F.E. SSR markers closely associated with genes for resistance to root-knot nematode on chromosomes 11 and 14 of upland cotton. Theoretical and Applied Genetics, v.121, p.1323-1337, 2010. DOI: 10.1007/s00122-010-1391-9.
» https://doi.org/10.1007/s00122-010-1391-9 - HAN, Z.-G.; GUO, W.-Z.; SONG, X.-L.; ZHANG, T.-Z. Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in alloteraploid cotton. Molecular Genetic Genomics, v.272, p.308-327, 2004. DOI: 10.1007/s00438-004-1059-8.
» https://doi.org/10.1007/s00438-004-1059-8 - HAN, Z.; WANG, C.; SONG, X.; GUO, W.; GOU, J.; LI, C.; CHEN, X.; ZHANG, T. Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theoretical and Applied Genetics, v.112, p.430-439, 2006. DOI: 10.1007/s00122-005-0142-9.
» https://doi.org/10.1007/s00122-005-0142-9 - KALIA, R.K.; RAI, M.K.; KALIA, S.; SINGH, R.; DHAWAN, A.K. Microsatellite markers: an overview of the recent progress in plants. Euphytica, v.177, p.309-334, 2011. DOI: 10.1007/s10681-010-0286-9.
» https://doi.org/10.1007/s10681-010-0286-9 - KEBEDE, H.; BUROW, G.; DANI, R.G.; ALLEN, R.D. A-genome cotton as a source of genetic variability for upland cotton (Gossypium hirsutum). Genetic Resources and Crop Evolution, v.54, p.885-895, 2007. DOI: 10.1007/s10722-006-9157-6.
» https://doi.org/10.1007/s10722-006-9157-6 - KORIR, N.K.; HAN, J.; SHANGGUAN, L.F.; WANG, C.; KAYESH, E.; ZHANG, Y.Y.; FANG, J.G. Plant variety and cultivar identification: advances and prospects. Critical Reviews in Biotechnology, v.33, p.111-125, 2013. DOI: 10.3109/07388551.2012.675314.
» https://doi.org/10.3109/07388551.2012.675314 - LACAPE, J.-M.; DESSAUW, D.; RAJAB, M.; NOYER, J.-L.; HAU, B. Microsatellite diversity in tetraploid Gossypium germplasm: assembling a highly informative genotyping set of cotton SSRs. Molecular Breeding, v.19, p.45-58, 2007. DOI: 10.1007/s11032-006-9042-1.
» https://doi.org/10.1007/s11032-006-9042-1 - LACAPE, J.-M.; JACOBS, J.; ARIOLI, T.; DERIJCKER, R.; FORESTIER-CHIRON, N.; LLEWELLYN, D.; JEAN, J.; THOMAS, E.; VIOT, C. A new interspecific, Gossypium hirsutum x G. barbadense, RIL population: towards a unified consensus linkage map of tetraploid cotton. Theoretical and Applied Genetics, v.119, p.281-292, 2009. DOI: 10.1007/s00122-009-1037-y.
» https://doi.org/10.1007/s00122-009-1037-y - LIU, S.; SAHA, S.; STELLY, D.; BURR, B.; CANTRELL, R.G. Chromosomal assignment of microsatellite loci in cotton. Journal of Heredity, v.91, p.326-332, 2000. DOI: 10.1093/jhered/91.4.326.
» https://doi.org/10.1093/jhered/91.4.326 - MCDONALD, M.B.; ELLIOT, L.J.; SWEENEY, P.M. DNA extraction from dry seeds for RAPD analyses in varietal identification studies. Seed Science and Technology, v.22, p.171-176, 1994.
- MENEZES, I.P.P. de; HOFFMANN, L.V.; ALVES, M.F.; MORELLO, C. de L.; BARROSO, P.A.V. Distância genética entre linhagens avançadas de germoplasma de algodão com uso de marcadores de RAPD e microssatélites. Pesquisa Agropecuária Brasileira, v.4, p.1339-1347, 2008. DOI: 10.1590/S0100-204X2008001000012.
» https://doi.org/10.1590/S0100-204X2008001000012 - NGUYEN, T.-B.; GIBAND, M.; BROTTIER, P.; RISTERUCCI, A.-M.; LACAPE, J.-M. Wide coverage of the tetraploid cotton genome using newly developed microsatellite markers. Theoretical and Applied Genetics, v.109, p.167-175, 2004. DOI: 10.1007/s00122-004-1612-1.
» https://doi.org/10.1007/s00122-004-1612-1 - PATERSON, A.H.; BOMAN, R.K.; BROWN, S.M.; CHEE, P.W.; GANNAWAY, J.R.; GINGLE, A.R.; MAY, O.L.; SMITH, C.W. Reducing the genetic vulnerability of cotton. Crop Science, v.44, p.1900-1901, 2004. DOI: 10.2135/cropsci2004.1900.
» https://doi.org/10.2135/cropsci2004.1900 - PEREIRA, G.S.; SOUSA, R.L.; HOFFMANN, L.V.; SILVA, E.F.; BARROSO, P.A.V. Selective fertilization in interspecific crosses of allotetraploid species of Gossypium Botany, v.90, p.159-166, 2012. DOI: 10.1139/b11-094.
» https://doi.org/10.1139/b11-094 - PLANT DNA extraction protocol for DArT. Camberra: Diversity Arrays Technology, 2014. Available at: <Available at: https://www. diversityarrays.com/files/DArT_DNA_isolation.pdf >. Accessed on: 10 Dec. 2014.
» https://www. diversityarrays.com/files/DArT_DNA_isolation.pdf - REDDY, O.U.K.; PEPPER, A.E.; ABDURAKHMONOV, I.; SAHA, S.; JENKINS, J.N.; BROOKS, T.; BOLEK, Y.; EL-ZIK, K.M. New dinucleotide and trinucleotide microsatellite marker resources for cotton genome research. Journal of Cotton Science, v.5, p.103-113, 2001.
- RUNGIS, D.; LLEWELLYN, D.; DENNIS, E.S.; LYON, B.R. Simple sequence repeat (SSR) markers reveal low levels of polymorphism between cotton (Gossypium hirsutum L.) cultivars. Australian Journal of Agricultural Research, v.56, p.301-307, 2005. DOI: 10.1071/AR04190.
» https://doi.org/10.1071/AR04190 - SCHUSTER, I.; VIEIRA, E.S.N.; PADILHA, L. Marcadores moleculares no pós-melhoramento. In: BORÉM, A.; CAIXETA, E.T. (Ed.). Marcadores moleculares. Viçosa: Ed. da UFV, 2006. p.205-230.
- SELVAKUMAR, P.; RAVIKESAVAN, R.; GOPIKRISHNAN, A.; THIYAGU, K.; PREETHA, S.; BOOPATHI, N.M. Genetic purity analysis of cotton (Gossypium spp.) hybrids using SSR markers. Seed Science and Technology, v.38, p.358-366, 2010. DOI: 10.15258/sst.2010.38.2.09.
» https://doi.org/10.15258/sst.2010.38.2.09 - SIMPFENDORFER, S.; MARTIN, A.; SUTHERLAND, M.W. Use of SSR markers to determine the genetic purity of a popular Australian wheat variety and consequences for stripe rust reactions. Seed Science and Technology, v.41, p.98-106, 2013. DOI: 10.15258/sst.2013.41.1.09.
» https://doi.org/10.15258/sst.2013.41.1.09 - TAMURA, K.; PETERSON, D.; PETERSON, N.; STECHER, G.; NEI, M.; KUMAR, S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, v.28, p.2731-2739, 2011. DOI: 10.1093/molbev/msr121.
» https://doi.org/10.1093/molbev/msr121 - TESSIER, C.; DAVID, J.; THIS, P.; BOURSIQUOT, J.M.; CHARRIER, A. Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L. Theoretical and Applied Genetics, v.98, p.171-177, 1999. DOI: 10.1007/s001220051054.
» https://doi.org/10.1007/s001220051054 - TYAGI, P.; GORE, M.A.; BOWMAN, D.T.; CAMPBELL, B.T.; UDALL, J.A.; KURAPARTHY, V. Genetic diversity and population structure in the US upland cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics, v.127, p.283-295, 2014. DOI: 10.1007/s00122-013-2217-3.
» https://doi.org/10.1007/s00122-013-2217-3 - ULLOA, M.; WANG, C.; ROBERTS, P.A. Gene action analysis by inheritance and quantitative trait loci mapping of resistance to root-knot nematodes in cotton. Plant Breeding, v.129, p.541-550, 2010. DOI: 10.1111/j.1439-0523.2009.01717.x.
» https://doi.org/10.1111/j.1439-0523.2009.01717.x - VAN DE WOUW, M.; KIK, C.; VAN HINTUM, T.; VAN TREUREN, R.; VISSER, B. Genetic erosion in crops: concept, research, results and challenges. Plant Genetic Resources, v.8, p.1-15, 2010. DOI: 10.1017/S1479262109990062.
» https://doi.org/10.1017/S1479262109990062 - WANG, F.; GONG, Y.; ZHANG, C.; LIU, G.; WANG, L.; XU, Z.; ZHANG, J. Genetic effects of introgression genomic components from Sea Island cotton (Gossypium barbadense L.) on fiber related traits in upland cotton (G. hirsutum L.). Euphytica, v.181, p.41-53, 2011. DOI: 10.1007/s10681-011-0378-1.
» https://doi.org/10.1007/s10681-011-0378-1 - WANG, P.; SU, L.; QIN, L.; HU, B.; GUO, W.; ZHANG, T. Identification and molecular mapping of a Fusarium wilt resistant gene in upland cotton. Theoretical and Applied Genetics, v.119, p.733-739, 2009. DOI: 10.1007/s00122-009-1084-4.
» https://doi.org/10.1007/s00122-009-1084-4 - YU, J.; JUNG, S.; CHENG, C.H.; FICKLIN, S.P.; LEE, T.; ZHENG, P.; JONES, D.; PERCY, R.; MAIN, D. CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic Acids Research, v.42, p.D1229-D1236, 2014. DOI: 10.1093/nar/gkt1064.
» https://doi.org/10.1093/nar/gkt1064 - ZHANG, T.; QIAN, N.; ZHU, X.; CHEN, H.; WANG, S.; MEI, H.; ZHANG, Y. Variations and transmission of QTL alleles for yield and fiber qualities in upland cotton cultivars developed in China. PLoS One, v.8, article e57220, 2013. DOI: 10.1371/journal.pone.0057220.
» https://doi.org/10.1371/journal.pone.0057220 - ZHU, Q.-H.; SPRIGGS, A.; TAYLOR, J.M.; LLEWELLYN, D.; WILSON, I. Transcriptome and complexity-reduced, DNA-based identification of intraspecies single-nucleotide polymorphisms in the polyploid Gossypium hirsutum L. G3-Genes Genomes Genetics, v.4, p.1893-1905, 2014.
Publication Dates
-
Publication in this collection
July 2015
History
-
Received
27 Nov 2014 -
Accepted
26 May 2015