This article presents an update on the development of molecular markers linked to late blight resistance genes or QTLs by utilization of Solanum species for MAS in potato.. Key words: la
Trang 1Molecular markers for late blight resistance breeding of potato: an update
JA G E S H K TI W A R I1,4, SU N D A R E S H A SI D D A P P A1, BI R PA L SI N G H1, SU R I N D E R K KA U S H I K2, SW A R U P K
CH A K R A B A R T I1,3, VI N A Y BH A R D W A J1and PO O N A M CH A N D E L1
1
Central Potato Research Institute, Shimla, 171 001, Himachal Pradesh India;2Central Potato Research Institute Campus, Modipuram, Meerut, 250 110, Uttar Pradesh India;3Present address: Director, Central Tuber Crop Research Institute, Thiruvananthapuram - 695
017, Kerala, India;4Corresponding author, E-mail: jageshtiwari@gmail.com
With 2 tables
Received October 29, 2011/Accepted January 19, 2013
Communicated by P Wehling
Abstract
Late blight is the most devastating disease of the potato crop that can be
effectively managed by growing resistant cultivars Introgression of
resis-tance (R) genes/quantitative trait loci (QTLs) from the Solanum
germ-plasm into common potato is one of the plausible approaches to breed
resistant cultivars Although the conventional method of breeding will
continue to play a primary role in potato improvement, molecular marker
technology is becoming one of its integral components To achieve rapid
success, from the past to recent years, several R genes/QTLs that
origi-nated from wild/cultivated Solanum species were mapped on the potato
genome and a few genes were cloned using molecular approaches As a
result, molecular markers closely linked to resistance genes or QTLs
offer a quicker potato breeding option through marker-assisted selection
(MAS) However, limited progress has been achieved so far through
MAS in potato breeding In near future, new resistance genes/QTLs are
expected to be discovered from wild Solanum gene pools and linked
molecular markers would be available for MAS This article presents an
update on the development of molecular markers linked to late blight
resistance genes or QTLs by utilization of Solanum species for MAS in
potato
Key words: late blight — molecular marker — MAS — potato
— resistance gene — Solanum species
Late blight caused by the oomycete (Phytophthora infestans
(Mont.) de Bary) is the most important disease of potato
produc-tion worldwide This disease caused devastating impact on
humanity in the mid-1840s when severe epidemics swept
through Europe and resulted in the Irish potato famine (Fry
2008) Consequently, given its significant importance, there have
been concerted global efforts for more than 100 years to develop
durable resistant potato cultivars against P infestans However,
evolution of new races of P infestans was able to conquer the
past resistance genes and resulted in susceptible cultivars
world-wide Durably resistant cultivars against a range of P infestans
isolates possessing multiple resistance genes are needed today,
which can be developed in less time by conventional and
molec-ular approaches Regardless of the fact that common potato lacks
significant sources of resistance, many wild Solanum species are
rich sources of resistance genes Globally breeders exploited
only a very limited scale of Solanum biodiversity in potato
breeding For example, the genetic base of modern Indian potato
cultivars is limited to 49 ancestors only involving the wild
spe-cies S rybinii and S demissum Late blight resistance genes
were introgressed from the wild species S demissum,
S stoloniferum and the cultivated S tuberosum subsp andigena and S phureja into common potato in different parts of the world (Bradshaw et al 2006c) Thus, it necessitates potato breeders to search for new sources of resistance in wild gene pools and their faster deployment into cultivars through marker-assisted selection (MAS).
Conventional breeding methods are of primary importance but are too slow (10 –15 years) because they are essentially based on several generations of back crossing, field evaluation and pheno-typic selection This is also not an easy task in potato due to its polyploidy (2n = 4x = 48), tetrasomic inheritance and chromatid segregation Particularly, breeding efforts are very much depen-dent on typical reproductive features of potato (Gopal 2006) Several hypotheses have been presented earlier for larger utiliza-tion of wild Solanum gene pools at tetraploid (4EBN) (endo-sperm balance number) and diploid (2EBN/1EBN) levels by designing specific crossing schemes The primary gene pool con-sists of the cultivated potato (4EBN), without any barrier to gene flow, and genotypes are freely crossable with each other The secondary gene pool includes most of the 2EBN or less common 4EBN wild species that can be sexually crossed with the culti-vated potato employing manipulation of ploidy level, 2n gametes
or modified breeding techniques The tertiary gene pool includes 1EBN wild species that are distantly related to cultivated crop and can be exploited through somatic hybridization For exam-ple, as of now the most important late blight resistance RB gene was isolated from a somatic hybrid regenerated from the 1EBN wild species S bulbocastanum (Carputo and Frusciante 2011).
To breed potato cultivars with durable resistance, it is now necessary to combine multiple resistance (R) genes and/or quan-titative trait loci (QTLs) against P infestans Single R genes are easily overcome by this rapidly evolving pathogen, whereas the presence of several R genes could probably prolong the rate of late blight resistance The large gene pool available within the Solanum species offers sufficient possibilities to explore new R genes conferring resistance to P infestans Earlier, Gebhardt and Valkonen (2001) reviewed the organization of genes controlling disease resistance in the potato genome including late blight resistance (R) genes/quantitative trait loci (QTLs) Since that time, significant progress has been achieved at molecular level
in mapping, cloning and MAS Recently, Park et al (2009b) reviewed a perspective of cisgenesis on molecular breeding for
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Trang 2resistance to P infestans However, limited progresses have been
achieved in the utilization of R genes of wild Solanum
germplasm in molecular breeding In recent years, intensified
molecular research has improved the insight of employing wild
Solanum species for late blight resistance (Vleeshouwers et al.
2011).
To augment conventional methods for accelerated breeding,
molecular markers closely linked to resistance genes may be
easy to apply in widely related genotypes when the target genes
are introgressed Despite whether genetic analysis is conducted
at the diploid or the tetraploid level or whether genetic control
of a trait is considered to be simple or complex, potato research
has been successful in identifying genetic factors related to the
target trait Tagging of resistance loci with molecular markers
offers a possibility for MAS in the early stages of selection to
partially substitute time-consuming and environmentally sensitive
trials Since, most of the molecular markers used previously in
mapping were either restriction fragment length polymorphism
(RFLP) or amplified fragment length polymorphism (AFLP)
found exclusively using diploid segregating populations
Ampli-fied fragment length polymorphism markers are a reliable but
expensive, labour intensive, long assay technique, whereas AFLP
and simple sequence repeat (SSR) systems are based on the
polyacylamide gel system, a long and laborious technique.
Hence, these markers are not easy assays and therefore not
suit-able for MAS On the other hand, sequence-characterized
ampli-fied region (SCAR) and cleaved amplified polymorphic
sequence (CAPS) are simple to use Sequence-characterized
amplified region markers make use of polymorphisms in the
pri-mer sites resulting in an absence or presence of an amplified
band, whereas CAPS markers make use of a restriction site
poly-morphism after PCR amplification Moreover, with the
advance-ment in molecular biology of potato, usability of molecular
markers linked to resistance genes in genotype selection has
been demonstrated To make MAS an integrated part of
conven-tional breeding, it will be necessary for breeders to recognize the
potential of marker technology Therefore, to encourage
breed-ers, an update on progress in molecular marker development for
late blight resistance genes/QTLs utilizing the wild Solanum
germplasm for MAS in potato breeding is presented here.
Resistance Source and Conventional Breeding
The genus Solanum offers a greatly diverse gene pool, which
can be utilized for late blight resistance breeding in potato The
wild and cultivated Solanum species reported in the literature
that show resistance to late blight are presented in Table 1 In
the past, a few wild potato species were exploited widely in
conventional breeding to introgress race-specific resistance into
the cultivated gene pool Among them, the late-blight-resistant
hexaploid Mexican species S demissum, a source of eleven
sin-gle dominant R genes (R1-R11), was crossed to S tuberosum
during the 1950s and 1960s to breed resistant cultivars
(Brad-shaw and Ramsay 2005) Primarily, potato breeding focussed
on the introgression of these 11 R genes through conventional
methods, and therefore, most of the current potato cultivars
have resistance genes from S demissum The gene R1 is one
of the P infestans race-specific 11 R genes introgressed into
cultivated potato using traditional breeding (Umaerus and
Uma-erous 1994) However, it proved not to be durable and was
quickly defeated by newly evolving races of P infestans.
Unfortunately, rapidly changing populations of new P infestans
tems (Hein et al 2009) The rapid breakdown of the R genes from S demissum stimulated breeders to reconsider their breeding goals and efforts were targeted towards improving durable field resistance to late blight, which is quantitative and race non-specific (van der Vossen et al 2003) Hence, there is
a renewed interest to combine multiple resistance genes to have durable resistant cultivars Consequently, at the beginning of the 21st century, contemporary potato breeding is heavily exploring the wealth of R gene diversity in Solanum species
to build up a collection of diverse R genes to confer broad-spectrum resistance against late blight Currently attention is mostly paid to the RB gene that originated from S bulbocasta-num, which is considered to be a highly resistant source for all known races of P infestans Series of crosses showed durable resistance (Song et al 2003).
Mapping and Cloning of Resistance Genes Linkage mapping is necessary to understand resistance genes and molecular markers Although the tetraploid nature of potato slowed early linkage mapping efforts, extensive linkage maps have been constructed Mapping has provided several markers linked to resistance loci However, their utilization in MAS still remains a work in progress Early maps were primarily based on RFLP markers and revealed a high degree of synteny of con-served markers between potato and tomato chromosomes Later, the potato map has been highly saturated by an ultra-high-density (UHD) map of 10 365 AFLPs markers (van Os et al 2006) Recently, diversity array technology (DArT) marker map-ping in the resistant wild species S bulbocastanum has yielded a genome-wide linkage map comprising of 439 markers and span-ning 403 cM (Bradeen et al 2010) Further, sequencing and in silico approaches resulted in a scaffold upon which late blight resistance genes can be anchored Now, single nucleotide poly-morphisms (SNP) are representing the ultimate molecular marker type that continued to evolve today against P infestans (Syver-son and Bradeen 2011).
Several wild and cultivated Solanum species were examined for late blight resistance and consequently used for genetic map-ping of R genes/QTLs As of 2011, R genes/QTLs originated from Solanum species and their location on the potato chromo-somes are presented in Table 1 A series of R genes was mapped from wild species including R1-R11 from S demissum; RB/Rpi-blb1, Rpi-blb2, Rpi-blb3, Rpi-bt1 and Rpi-abpt from S bulbocas-tanum; Rpi-bst1 from S brachistotrichum; Rpi-edn1.1 from
S edinense; Rpi-hjt1.1, Rpi-hjt1.2 and Rpi-hjt1.3 from S hjertin-gii; Rpi-mcd1 from S microdontum; Rpi-snk1.1 and Rpi-snk1.2 from S schenckii; Rpi-ver1 from S verrucosum; Rpi-pnt1 from
S pinnatisectum; Rpi-sto1 and Rpi-sto2 from S stoloniferum; Rpi-pta1 from S papita; Rpi-plt1 from S polytrichon; Rpi-mcq1 from S mochiquense; Rpi-phu1 from S phureja; Rpi-vnt1.1, Rpi-vnt1.2, Rpi-vnt1.3 from S venturii; Rpi-dlc1 from S dulca-mara; Rpi-ber1 and Rpi-ber2 from S berthaultii; Rpi-avl1 from
S avilesi; Rpi-cap1 from S capsicibaccatum; and Rpi-qum1 from S circaeifolium spp quimense Newly identified wild spe-cies that showed a high level of resistance, including S urubam-bae, S violaceimamoratum, S cantense, S cajamarquense,
S orophilum, S velaedei, have to be characterized yet (Herma-nova et al 2007) Moreover, recently Li et al (2012) investi-gated six conditional QTLs expressed under five environments
in Peru and mapped one each on chromosome 2, 7 and 12 and three on chromosome 9 in a complex potato hybrid Danan et al.
Trang 3Table 1: Late blight resistance (R) genes/QTLs identified in various Solanum species
Species (ploidy/EBN) Chromosome Resistant/R gene/QTL References
S acaule (4x/2EBN) – Resistant Budin (2002)
S ajanhuiri (2x/2EBN) – Resistant Gabriel et al (2007)
S alandiae (2x/2EBN) – Resistant Bradshaw and Ramsay (2005)
S astleyi (2x/2EBN) – Resistant Galarreta et al (1998)
S avilesi (2x/2EBN) 11 Rpi-avl1 Verzaux (2010)
S berthaultii (2x/2EBN) 10 Rpi-ber1and
Rpi-ber2
Rauscher et al (2006); Park et al (2009a)
S bolivense (2x/2EBN) – Resistant Budin (2002)
S brachistotrichum (2x/1EBN) 4 Rpi-bst1 Hein et al (2009)
S brachycarpum (6x/4EBN) – Resistant Budin (2002)
S bulbocastanum (2x/1EBN) 8 (Rpi-blb1 and Rpi-bt1),
6 (Rpi-blb2), and
4 (Rpi-blb3 and Rpi-abpt)
RB/Rpi-blb1, Rpi-blb2, Rpi-blb3, Rpi-abpt and Rpi-bt1
Naess et al (2000); van der Vossen
et al (2003, 2005); Park et al (2005a, b); Lokossou et al (2009); Oosumi et al (2009)
S capsicibaccatum (2x/1EBN) 11 Rpi-cap1 Jacobs et al (2010)
S caripense (2x)* 9 – Nakitandwe et al (2007)
S cardiophyllum (2x, 3x/1EBN) – Resistant Thieme et al (2010)
S chacoense (2x/2EBN) – Pi_QTL Bradshaw and Ramsay (2005)
S circaeifolium spp quimense (2x/1EBN) 11 Rpi-qum1 Verzaux (2010)
S commersonii (2x/1EBN) – Resistant Bradshaw and Ramsay (2005)
S demissum (6x/4EBN) 5 (R1),
4 (R2 and Rpi-dmsf1),
11 (R3-R11 except R8),
9 (R8)
R1, R2, R3 (R3 & R3b), R4, R5, R6, R7, R8, R9, R10, R11 and Rpi-dmsf1
Huang et al (2005); Bradshaw et al (2006b, c); Hein et al (2009); Vleeshouwers et al (2011); Jo et al (2011)
S dulcamara (2x)* 9 Rpi-dlc1 Golas et al (2010)
S edinense (5x)* 4 Rpi-edn1.1 Champouret (2010)
S fendleri (4x/2EBN) – Resistant Bradshaw and Ramsay (2005)
S hjertingii (4x/2EBN) 4 Rpi-hjt1.1,
Rpi-hjt1.2 and Rpi-hjt1.3
Champouret (2010)
S hougasii (6x/4EBN) – Resistant Bradshaw and Ramsay (2005)
S iopetalum (6x/4EBN) – Resistant Bradshaw and Ramsay (2005)
S juzepczukii (3x)* – Resistant Gabriel et al (2007)
S kurtzianum (2x/2EBN) – Pi_QTL Budin (2002)
S leptophyes (2x/2EBN); (4x/4EBN) – Resistant Budin (2002)
S megistacrolobum (2x/2EBN) – Resistant Budin (2002)
S michoacanum (2x)* – Resistant Szczerbakowa et al (2010)
S microdontum (2x/2EBN), 3x 4 Rpi-mcd1 Tan (2008)
S mochiquense (2x/1EBN) 9 Rpi-mcq1 Smilde et al (2005)
and Rpi-pta2
Vleeshouwers et al (2008), Wang et al (2008)
S paucissectum (2x/2EBN) 10, 11 and 12 QTLpcs10,
QTLpcs11, QTLpcs12
Villamon et al (2005)
S phureja (2x/2EBN) 9 Rpi-phu1 Sliwka et al (2006)
S pinnatisectum (2x/1EBN) 7 Rpi-pnt1 Kuhl et al (2001)
S polyadenium (2x/1EBN) – Resistant Budin (2002)
S polytrichon (4x/2EBN) 8 Rpi-plt1 Wang et al (2008)
S raphanifolium (2x/2EBN) – Resistant Galarreta et al (1998)
S sanctae-rosae (2x/2EBN) – Resistant Budin (2002)
S schenckii (6x/4EBN) 4 Rpi-snk1.1
and Rpi-snk1.2
Jacobs et al (2010); Champouret (2010)
S sparcipilum (2x/2EBN) 10 Pi_QTL Danan et al (2009)
S spegazzini (2x/2EBN) 10 Pi_QTL Danan et al (2009)
S stenotomum (2x/2EBN) – Pi_QTL Gabriel et al (2007)
S stoloniferum (4x/2EBN) 8 (Rpi-sto1) and
11 (Rpi-sto2)
Rpi-sto1 and Rpi-sto2
Champouret (2010); Wang et al (2008); Vleeshouwers et al (2008, 2011)
S sucrense (4x/4EBN) – Resistant Gabriel et al (2007)
S tarijense (2x/2EBN) – Pi_QTL Budin (2002)
S tarnii (2x/2EBN) – Resistant Thieme et al (2008)
S toralapanum (2x)* – Resistant Budin (2002)
S trifidum (2x/1EBN) – Resistant Budin (2002)
S tuberosum subsp tuberosum (4x/4EBN) 3–6, 8, 9 and 11 Pi_QTL Costanzo et al (2005);
Bradshaw et al (2006a)
S tuberosum subsp andigena (4x/4EBN) – Pi_QTL Gabriel et al (2007)
(continued)
Trang 4meta-analysis to investigate the genetic architecture of late blight
resistance and plant maturity traits They observed late blight
resistance QTLs on every chromosome and maturity
meta-QTLs on six chromosomes only.
Gene cloning efforts in potato have been aided by an
improved understanding of the molecular architecture of R
genes The first late blight resistance gene R1 was cloned in the
year 2002 and derived from S demissum and made a significant
achievement in understanding the molecular basis of R genes
(Ballvora et al 2002) Unfortunately, the effectiveness of the R1
gene was overcome long ago by new races of P infestans, and
it is likely to be of limited future agricultural use The RB gene,
which originated from S bulbocastanum, is conferring broad
spectrum of resistance to potato late blight and was cloned in
the year 2003 from the somatic hybrid of S bulbocastanum (+)
S tuberosum (Song et al 2003) Subsequently, several
function-ally equivalent homologs of RB were cloned, and the RB gene
still is the most promising late blight resistance gene in potato
yet As far as known in 2011, a total of 13 late blight resistance
genes are cloned namely Rpi-blb1 (van der Vossen et al 2003),
R3a (Huang et al 2005), Rpi-blb2 (van der Vossen et al 2005),
RBver (Liu and Halterman 2006), Rpi-stol1 and Rpi-pta1
(Vleeshouwers et al 2008), Rpi-vnt1.1 and Rpi-vnt1.3 (Foster
et al 2009, Pel et al 2009), Rpi-blb3, Rpi-abpt, R2 and R2-like
(Lokossou et al 2009) and Rpi-bt1 (Oosumi et al 2009).
Approximately 75% of all R genes cloned to date belong to the
nucleotide-binding site (NBS) –leucine-rich repeats (LRR)
super-family Therefore, a construction of resistance gene analogue
(RGA) libraries and NBS profiling holds significant promise for
R gene cloning (Bradeen 2011) Many more R genes are
expected to be cloned in coming years so that multiple R genes
could be deployed in potato breeding.
Marker-Assisted Selection
Molecular markers and genome sequencing information are
expected to play a significant role in MAS The typical marker
considerations for MAS include ease of use, robustness, low
costs, linkage to gene controlling trait of interest and the amount
2004) Molecular marker-assisted introgression offers the possi-bility of faster progress and allow breeders to track the introgres-sion of desirable genes from wild species Marker-assisted selection is now becoming more economically feasible because easy marker assays based on PCR are being developed Potato breeding will benefit from emerging technologies and research initiatives aimed at delivering reliable, high-throughput markers that can be applied at reasonable costs In Table 2, R genes/ QTLs-wise information on successful MAS application in potato breeding and primer sequences of markers is presented briefly Primarily late blight resistance breeding relied upon the 11 dominant R genes (R1 to R11) which originated from S demis-sum and molecular markers linked to those dominant genes were developed for MAS Recently, Kim et al (2012) showed broad-spectrum late blight resistance in potato differential set plant MaR9, conferred by multiple stacked MAS of seven R genes including Rpi-abpt, R1, R3a, R3b, R4, R8, and R9 It was shown that in MaR8 and MaR9, at least four (R3a, R3b, R4 and R8) and seven (R1, Rpi-abpt1, R3a, R3b, R4, R8 and R9) R genes were present, respectively Sokolova et al (2011) developed three SCAR markers namely R1-1205, R3-1380 and Sdms-523 recognizing the race-specific genes R1 and R3 These markers were validated in screening 209 accessions of 21 wild Solanum species for MAS application Sedlak et al (2005) validated the R1 gene in Czech potato genetic resources employing previously developed markers SPUD237 and GP21 (De Jong et al 1997), and R1F/R (76-2sf2/76-2SR) (Ballvora et al 2002) by MAS The DNA markers, viz BA47f2 and CosA (Gebhardt et al 2004), GP179 (Meksem et al 1995) and GP76 (Oberhagemann
et al 1999), were useful in MAS for late blight resistance con-ferred by the R1 gene (Gebhardt et al 2004).
Currently, the genes blb (blb1/RB, blb2 and Rpi-blb3) are the most important R genes in potato yet that were developed from S bulbocastanum for recognizing broad spec-trum of late blight resistance Marker-assisted selection has been successfully applied in the gene RB in potato breeding The SCAR markers RB-629/638, Sblb-509 (Sokolova et al 2011), RB-1223 and RB-629 (Pankin et al 2011) linked to the RB gene (Rpi-blb1) of S bulbocastanum were validated for MAS Earlier,
Table 1 (continued)
Species (ploidy/EBN) Chromosome Resistant/R gene/QTL References
S venturii (2x/2EBN) 9 Rpi-vnt1.1,
Rpi-vnt1.2 and Rpi-vnt1.3
Foster et al (2009); Pel et al (2009)
S verrucosum (2x/2EBN) 6 Rpi-ver1 Jacobs et al (2010)
S vigultorum (2x)* – Resistant Galarreta et al (1998)
S phureja9 S stenotomum 3, 5, 11 and 12 QTL_phu-stn Wickramasinghe et al (2009);
Costanzo et al (2005)
S tuberosum ssp andigena9 S phureja 9
S stenotomun9 S acaule 9
S bulbocastanum
2, 7, 9 and 12 Pi_QTL Li et al (2012)
S tuberosum ssp tuberosum9 S chacoense 9
S kurtzianum9 S stenotomum 9 S vernei 1 to 12 Pi_QTL Oberhagemann et al (1999)
S tuberosum ssp tuberosum9 S chacoense 9
S verrucosum9 S microdontum 9
S gourlayi (2x/2EBN; 4x/4EBN)9
S yungasense (2x, 3x)*
3, 4, 5 and 10 Pi_QTL Sliwka et al (2007)
QTL, quantitative trait loci
*EBN (Endosperm Balance Number) is not known
Trang 5Table 2: Molecular markers of late blight resistance (R) genes/QTLs for MAS in potato (IUPAC code is used)
Gene/QTL Chr Marker/primer Marker type Primer sequence (5′ ? 3′) References
R1 5 R1-1205 SCAR CACTCGTGACATATCCTCACTA
GTAGTACCTATCTTATTTC TGCAAGAAT
Sokolova et al (2011)
BA47f2 SCAR TAACCAACATTATCTTCTTTGCC
GAATTTGGAGAGGGGTTTGCTG
Gebhardt et al (2004) CosA SCAR CTCATTCAAAATCAGTTTTGATC
GAATGTTGAATCTTTTTGTGAAGG
Gebhardt et al (2004) R1F/R
(76-2sf2/
76-2SR)
AS CACTCGTGACATATCCTCACTA
CAACCCTGGCATGCCACG
Ballvora et al 2002,
GP76 SCAR ATGAAGCAACACTGATGCAA
TTCTCCAATGAACGCAAACT
Oberhagemann et al (1999) SPUD237 (AluI) CAPS TTCCTGCTGATACTGACT
AGAAAACC AGCCAAGGAAAAGCTAGCATCCAAG
De Jong et al (1997)
GP21 (AluI) CAPS AGTGAGCCAGCATAGCATTACTTG
GGTTGGTGGCCTATTAGCCATGC
De Jong et al (1997) GP179 SCAR GGTTTTAGTGATTGTGCTGC
AATTTCAGACGAGTAGGCACT
Meksem et al (1995) R3 (R3a & R3b) 11 R3-1380 SCAR TCCGACATGTATTGATCTCCCTG
AGCCACTTCAGCTTCTTAC AGTAGG
Sokolova et al (2011)
SHa-F/SHa-R AS ATCGTTGTCATGCTATGAGATTGTT
CTTCAAGGTAGTGGGCAGTATGCTT
Huang et al (2005) R3bF4/R3bR5 AS GTCGATGAATGCTATGTTTCTCGAGA
ACCAGTTTCTTGCAATTCCAGATTG
Rietman (2011) RB/Rpi-blb1 8 RB-629/638 SCAR AATCAAATTATCCACCCCAA
CTTTTAAAT CAAGTATTGGGAGGACTGAAAGGT
Sokolova et al (2011)
RB-1223 SCAR ATGGCTGAAGCTTTCATTCAAGTTCTG
CAAGTATTGGGAGGACTGAAAGGT
Pankin et al (2011) CT88 (Primer
1/primer 1′) SCAR CACGAGTGCCCTTTTCTGACACAATTGAATTTTTAGACTT
Colton et al (2006) Rpi-abpt 4 R2-F1/R2-R3 AS GCTCCTGATACGATCCATG
ACGGCTTCTTGAATGAA
Kim et al (2012) Th2 CAPS AGGATTTCAGTATGTCTCG
TCCATTGTTGATTGCCCCT
Park et al (2005b) Rpi-ber1 10 CT214 (DdeI) CAPS GAACGCGAAAGAGTGCTGATAG
CCCGCTGCCTATGGAGAGT
Tan et al (2010) TG63
(Bme1390I)
CAPS TCCAATTGCCAGACGAA
TAGAGAAGGCCCTTGTAAGTTT
Tan et al (2010) Q133 SCAR ATCATCTCCTCAAAGAATCAAG
ATCTCCCCATTGACAACCAA
Tan et al (2010) Rpi-mcd1 4 TG339 (MnlI) CAPS GCTGAACGCTATGAGGAGATG
TGAGGTTATCACGCAGAAGTTG
Tan et al (2010) Rpi-phu1 9 GP94 (OPB07
+ TG/GT) RAPD GAAACGGGTG+ TG/GT Sliwka et al (2006) QTL_phu-stn 3 OPA17 RAPD GACCGCTTGT Wickramasinghe et al (2009)
OPA03 RAPD AGTCAGCCAC Wickramasinghe et al (2009) GP198F/R SCAR GTAATTTGCGAGGAAGGAGAAG
TCACTTTGGTGCTTCTGTCG
Wickramasinghe et al (2009) GP198F-1/R AS TTTGCTTACTCTTGTTGTATG
TCACTTTGGTGCTTCTGTCG
Wickramasinghe et al (2009) Rpi-sto1 8 Ssto-448 SCAR GTGGAACGCCGTCCATCCTTAG
TGCATAGGTGGTTAGATGTA TGTTTGATTA
Sokolova et al (2011)
Rpi-avl1 N2527 AS GAAACACAGGGGAATATTCACC
CCATRTCTTGWATTAAGTCATGC
Verzaux (2010) Rpi-cap1 11 CP58 (MspI) CAPS ATGTATGGTTCGGGATCTGG
TTAGCACCAACAGCTCCTCT
Jacobs et al (2010) Rpi-dlc1 9 GP101 (AluI) CAPS GGCATTTCTATGGTATCAGAG
GCTTAACATGCAAAGGTTAAA
Golas et al (2010) S1d5-a AS CGCCTCTTTCTCTGAATTTC
GATCTGGGATGGTCCATTC
Golas et al (2010) Rpi-mcq1 9 TG328 (AluI) CAPS AATTAAATGGAGGGGGTATC
GTAGTATTCTAGTTAAACTACC
Smilde et al (2005) Rpi-snk1.1 and
Rpi-snk1.2
4 Th21 (MboI) CAPS ATTCAAAATTCTAGTTCCGCC
AACGGCAAAAAAGCACCAC
Jacobs et al (2010)
(continued)
Trang 61/primer 1 ′) of RB gene conferring broad-spectrum late blight
resistance through MAS Recently, Kim et al (2012)
demon-strated the marker R2-F1/R2-R3 linked to gene Rpi-abpt in
mul-tiple R gene stacking using MAS Earlier, Park et al (2005b)
developed a CAPS marker Th2 from the AFLP marker PAT/
MAGA_307 cosegregating with the Rpi-abpt for MAS In
addition, several molecular markers were discussed earlier for the
RB gene, which can be effective in selecting resistant genotypes
(van der Vossen et al 2003, 2005, Park et al 2005a,b, Lokossou
et al 2009) In recent studies, Syverson and Bradeen (2011)
devel-oped a set of markers for the RB gene using a mismatch
amplifica-tion mutaamplifica-tion assay (MAMA)-PCR approach for tapping the
potential of SNPs Pajerowska-Mukhtar et al (2009) identified
nine SNPs associated with the allene oxide synthase 2 gene on
chromosome 11, which likely controls late blight resistance.
Researchers have successfully demonstrated MAS for other R
genes as well, namely Rpi-ber, Rpi-mcd1, Rpi-phu1 and Rpi-sto1;
and QTL_phu-stn Tan et al (2010) developed CAPS and
SCAR markers linked to the gene Rpi-ber for MAS Effect of
pyramiding of the genes Rpi-ber and Rpi-mcd1 was investigated
using CAPS markers CT214 (DdeI), TG63 (Bme1390I), TG339
(MnlI) and SCAR marker Q133 Sliwka et al (2010)
introgres-sed the gene Rpi-phu1 into S tuberosum using the linked marker
GP94250 (6.4 cM) in mapping population 97 –30 This marker
was shown to be useful in selecting resistant genotypes, and it
showed an example of successful application of MAS in potato.
Wickramasinghe et al (2009) developed two RAPD markers:
OPA17559 and OPA03576, and one allele-specific marker
GP198F-1/GP198R linked to QTL_phu-stn for late blight
resis-tance in a diploid potato hybrid population of Solanum
phur-eja 9 S stenotomum Two QTLs were mapped on the
chromosomes 3 and 12 using the markers OPA17559 and
OPA03576, respectively A third marker GP198F-1, derived from
the original RFLP marker GP198, was linked to a QTL on
chro-mosome 3 These three PCR-based markers were used to screen
late-blight-resistant genotypes and validated for MAS
Further-more, Sokolova et al (2011) developed a SCAR marker
Ssto-448 for the gene Rpi-sto1, which originated from S
stolo-niferum This SCAR marker Rpi-sto1 was validated in a progeny
derived from a cross between cultivated and wild species.
There are many more molecular markers of SCAR, CAPS and
allele-specific types developed, closely linked/cosegregating to
genes Rpi-avl1, Rpi-dlc1, Rpi-mcq1, Rpi-cap1, Rpi-snk, Rpi-ver1
and Rpi-vnt that have to be proven for MAS yet Verzaux
(2010) developed the tightly linked allele-specific marker N2527
to the gene Rpi-avl1, which originated from S avilesii Golas
et al (2010) identified a new gene Rpi-dlc1 in S dulcamara
using the marker interval spanned by CAPS marker GP101
observed the gene Rpi-mcq1 in S mochiquense linked to the RFLP marker TG328 and the CAPS marker TG328 (AluI) Jacobs et al (2010) identified cosegregating CAPS markers, viz CP58 (MspI) with gene Rpi-cap1, marker Th21 (MboI) with gene Rpi-snk1.1 and Rpi-snk1.2 and marker CD67 (HpyCH4IV, SsiI) with gene Rpi-ver1 for MAS Pel et al (2009) identified the allele-specific marker NBS3B closest at 0.2 cM to gene vnt1.1 and CAPS marker TG35 that co-segregated with Rpi-vnt1.3 These closely linked SCAR, CAPS and allele-specific markers may be useful for MAS in potato breeding.
Conclusion Conventional breeding is on the top of potato improvement, and molecular marker technology is becoming one of its integral components in future With the advent of DNA markers used in mapping and cloning of late blight resistance loci, a number of markers have been demonstrated successfully for MAS applica-tion There is no longer doubt about the utility of this technology
in potato breeding It leads to a considerable reduction in time and efforts for the development of cultivars In all marker sys-tems, PCR-based molecular markers, which may be easily resolved on simple agarose gel, require less labour and are more feasible and economic than polyacrylamide gel markers Unlike RFLP, AFLP and SSR, easy markers such as SCAR and CAPS markers are low in costs, robust and convenient to use for MAS With the development of high-throughput marker genotyping technology, costs are no longer an issue for the utilization of this technology in potato breeding Recent advances in marker tech-nology, large-scale whole-genome sequencing and a high-density mapping of the potato chromosomes have expanded the database
of marker lists Indeed, without the problems of genetic drag that limit exploitation of these precious genetic resources through conventional breeding, the available marker lists may lead the development of more precise, accurate and easy-assay molecular markers linked to target genes in potato for MAS In the future genomics era, isolation of new R genes, development of closely linked markers and subsequent introgression into existing potato cultivars could be a much faster way of exploiting late blight resistance sources from wild Solanum species for genomics-assisted breeding.
Acknowledgement
The authors are grateful to the Director, Central Potato Research Insti-tute (Indian Council of Agricultural Research), Shimla, for providing the necessary facilities for the preparation of this review article We also thank the anonymous reviewers and the editors for important
Table 2 (continued)
Gene/QTL Chr Marker/primer Marker type Primer sequence (5′ ? 3′) References
Rpi-ver1 6 CD67
(HpyCH4IV, SsiI)
CAPS CCCCTGCAAATCCGTACATA
CCATACGAGTTGAGGGATCG
Jacobs et al (2010)
Rpi-vnt1.1 9 TG35
(HhaI/XapI)
CAPS CACGGAGACTAAGATTCAGG
TAAAGGTGATGCTGATGGGG
Pel et al (2009) Rpi-vnt1.3 9 NBS3B AS CCTTCCTCATCCTCACATTTAG
GCATGCCAACTATTGAAACAAC
Pel et al (2009)
CAPS, cleaved amplified polymorphic sequence; MAS, marker-assisted selection; NBS, nucleotide-binding site; SCAR, sequence-characterized ampli-fied region; QTL, quantitative trait loci
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