Download Comparative Genomics of the Genomic Region Controlling

 GSTF International Journal of BioSciences (JBio) Vol.2 No.2, May 2013
Comparative Genomics of the Genomic
Region Controlling Resistance to Puccinia
Polysora Underw. in Zea Mays L.
Bhavani P1., Harini Kumar K. M1., Lohithaswa H. C2., Shashidhar H. E1., and Pandurange Gowda K. T2.
1
Department of Biotechnology, UAS, G.K.V.K., Bengaluru – 97
2
College of Agriculture, V.C. Farm, Mandya -571402
Abstract - Polysora rust (Southern Corn Rust) is a major
disease of maize in tropical and subtropical region
causing yield loss in excess of 45%. The loci governing
resistance (Rpp9, RppQ and RppD) have been mapped to
10.01 bins on short arm of maize chromosome 10, which
also has genes for common rust resistance like Rp1 and
Rp5. With the publication of maize draft genomic
sequence we tried to annotate the region spanning these
genes using comparative genomic tools. We constructed a
physical map using the various loci and the
corresponding markers, BAC clones and contigs reported
from the previous researchers and using MaizeGDB. The
sequence for this region was downloaded from
maizesequence.org. The sequence was scanned for coding
regions using GENSCAN and the CDS and peptides
obtained along with the whole sequence (in bits of 1 MB)
was subjected to BLAST analysis in NCBI-nBLAST,
NCBI-pBLAST, COGE-BLAST and MaizeGDB BLAST.
The region when located on a physical map, had all the
loci governing Polysora rust resistance in a overlapping
position and was around 3 MB size. Two loci RppQ and
RppD covered large portion of the 3MB region whereas
Rpp9 was 82769 bp long. The BLAST results indicated
the similarity of the region to many loci responsible for
disease resistance like PR protein, Serine/threonine
kinase protein, rust resistance protein (rp3-1), receptor
kinases and zein cluster. The region shared homology
with rice, sorghum and brachypodium grass and we
found some orthologs having NB-LRR domain. Hence
from this analysis it could be concluded that the region is
responsible for disease resistance and host many other
genes linked with resistance to various diseases.
Polysora rust (PR) or Southern Corn Rust
(SCR) is one among several diseases afflicting maize.
It is a major disease worldwide across tropical and
subtropical regions. Though it is regarded as minor
disease of corn, it has a huge destructive potential. It is
severe in warm growing conditions and grain yield
losses in excess of 45% have been recorded [2][3][4].
It occurs throughout the tropical and subtropical
regions of the world including Africa, Southeast Asia,
Australia, Central and South America, southern regions
of the United States and countries surrounding South
Indian Ocean. Polysora rust caused by Puccinia
polysora was first identified in Alabama in 1891 on
Tripsacum dactyloides L. Since then it was regarded as
minor pathogen of corn until it was found in the Corn
Belt in 1949, 1958 and North Carolina in 1972 and
1973 causing epiphytotics [2][3]. Soon the occurrence
and the losses due to Polysora rust were reported
worldwide. Losses of upto 50-70% were reported in
West Africa [5][6], upto 60-80% in Pennysylvania and
Maryland in America [7], 42-53% loss in northern
China reaching epiphytotic levels [8]. In India, the
disease was first noticed in 1991 in Byelkuppa of
Mysore district and Arabhavi of Dharwad district in
Karnataka [9][10].
At least three single dominant, race-specific
PR resistance genes have been discovered. Completely
dominant gene Rpp1 confer resistance to P. polysora
race EA1 and incompletely dominant gene Rpp2 confer
resistance to races EA1 and EA2 [11]. But genes Rpp1
and Rpp2 were not effective against third race EA3
found in Kenya in 1961 [12]. Genes Rpp3 - Rpp8
governs resistance against P. polysora races PP3-PP8
[13]. Gene Rpp9 confers resistance to race 9 in Indiana
[14], whose location is very near to that of the Rp1
resistance gene (conferring resistance to common rust)
on the short arm of chromosome 10. Rpp10 and Rpp11
have been identified in Columbian corn and Mexican
corn [12]. A study on inheritance of the disease
resistance gene to PR using P25 (immune inbred line),
F349 (susceptible inbred line) and the derived
Keywords: Disease resistance - genetic map - maize physical map- polysora rust
I. INTRODUCTION
Maize, the most important crop after rice and
wheat, has its significance as a source of a large
number of industrial products besides its use as human
food and animal feed. Diversified uses of maize are
edible corn, starch, oil production, babycorn, popcorn,
etc. Potential for exports has added to the demand of
maize all over world [1].
DOI: 10.5176/2251-3140_2.2.33
1
© 2013 GSTF
GSTF International Journal of BioSciences (JBio) Vol.2 No.2, May 2013
populations F1, F2, B1 and B2 reported major resistance
gene P25 in the inbred line P25 [15]. Major genes for
resistance to PR on the short arm of chromosome 10
and quantitative trait loci (QTLs) on chromosomes 3
and 4 [16], 3, 4 and 9 [17] and 9 [18] have been
reported by using different sets of maize germplasm
across the world [3][4][14][15][19][20]; but linkage or
allelic relationships and race specificity were not
established. Yet another gene RppD controlling
resistance to PR rust was located to bin 10.00-10.01
[21]. The completion of the maize genomic sequence
provides the much-needed information to study the
genotype-phenotype
interrelations
and
interdependencies [22]. Integration of genetic maps
and QTL locations onto reference genome map is
widely applied to position both QTL and markers on a
single consensus map [23]. With the ocean of
information on maize genome, genomic sequences,
gene models and annotations, the rust controlling
region on the chromosome 10 was targeted for further
analysis and to extract the functional relevance of the
region.
SSR markers were earmarked using the MaizeGDB
Locuslookup. The sequences of each of these loci
(RppD, Rpp9, RppQ, Rp1) were also downloaded and
analyzed separately by conducting BLAST.
II. STRATEGY FOLLOWED
A. Identification of the region controlling disease
resistance
Fig. 1: Flowchart of the bioinformatics approach
followed to identify the disease resistance region on
Maize chromosome
An extensive survey of literature (print and
electronic) was carried out to explore all the
information related to polysora rust. Reports located
the gene/QTL contributing towards resistance against
Puccinia polysora to different chromosomes of Zea
mays L. viz., a single dominant gene Rpp9 on
chromosome 10 [14], chromosome 3 and 4 [16],
chromosome 3, 4, and 9 [17], chromosome 9 [18],
chromosome 10 [4][21], chromosome 3, 8, 9 and 10
[20]. Among these, most of the genetic elements
(Rpp9, RppQ, RppD, Rpp25) were found to be
concentrated on chromosome 10.00-10.01.
B. Gene prediction and annotation
Gene prediction and annotation was done
using the gene prediction programs FGENESH and
GENSCAN
(http://www.softberry.
com;
http://genes.mit.edu/GENSCAN.html). To complement
the gene prediction programs and determine sequence
similarity, the whole sequence was fragmented in silico
into 1kb fragments with 200bp overhangs and
subjected to BLASTn and BLASTx searches [24]
against the GenBank database. Furthermore, the
protein domains of the gene clusters on the BAC
sequence were determined by conserved domain
database (CDD) v2.16 [25]. Sequences that were
identical to known genes in GenBank were assigned
relevant gene name.
Further, the literature was explored for the
information on the linked SSRs in the region. The
SSRs obtained were searched in the maizeGDB for the
location and the primer sequence. SSRs and BACs
associated between 10.00-10.01 identified and
collected from the reviews were located on the
chromosome 10. The information on the Physical
location of the genes/QTLs, SSRs and BACs was
collected from www.maizegdb.org.
The
spanning the
downloaded
analysis. The
C. BLAST
The genomic sequence of the region targeted was
subjected
to
NCBI-nBLAST
MaizeGDB
(http://blast.ncbi.nlm.nih.gov/Blast.cgi),
(http://blast.maizegdb.org/home.php?a=BLAST_UI)
and
COGEBLAST
(http://genomevolution.org/CoGe/CoGeBlast.pl). The
sequence of the chromosomal region
markers umc1380 and bnlg1451 was
from maizesequence.org for further
regions for these gene loci flanked by
2
© 2013 GSTF
GSTF International Journal of BioSciences (JBio) Vol.2 No.2, May 2013
Table 1. Output obtained after submitting the 3 Mb
region to gene prediction tools
genes obtained by the gene prediction tools were also
subjected for BLAST analysis against NCBI-nBLAST.
The BLAST output was compared for shortlisting the
disease related genes.
The NCBI-BLASTn search was conducted against
“nucleotide collection (nr/nt)” and MaizeGDB BLAST
was conducted against “B73 RefGen_v2 (MGSC)”. In
COGEBLAST, organism name was specified as “Zea
mays L.,” organism description as “Zea mays (maize;
corn)” against the genome as “Maizesequence.org:
refgen_v2 assembly (working gene set annotations:
5a), v2 unmasked 2,065,722,704nt” at E-value of
“0.001” for the conduct of blast search.
FGENESH
Region
Gene
Exon
Mb
Plus strand
Minus strand
Gene
Exon
Gene
Exon
2-3
186
649
87
292
99
357
3-4
168
700
78
332
90
368
4-5
165
659
73
265
92
394
GENSCAN
III. RESULTS AND DISCUSSION
A. Genes in bin 10.01
The majority of the major genes reported for
resistance to polysora rust were found in bin 10.0010.01 of contig 392 on B73 maize reference
genome_V2
(B73
RefGen_v1)
(http://www.maizegdb.org/). Subsequently, Reference
20, reported that this region contribute about 82% of
variation
towards
disease
resistance
while
chromosomal regions on 4, 8 and 9 accounted for only
1.6, 2.0, and 1.5 per cent respectively. Therefore,
further analysis was restricted to bin 10.00-10.01.
Mb
Genes/Exons
Plus strand
(Genes/Exons)
Minus strand
(Genes/Exons)
2-3
214
95
109
3-4
211
97
114
4-5
186
77
109
C. BLAST
The smallest locus among these was Rp1 with
3896 bp. When Rp1 CDS obtained from GENSCAN
comprising of 690 bases was BLAST aligned with
NCBI-nBLAST resulted in hits with100% homology
with Rp1-D gene, its protein and pseudogenes with
maximum identity ranging from 100-90% (e = 0.0) and
maximum score ranging from 1273-691. The hits
covered sequence from Zea mays ssp. parviglumis, Zea
luxurians, Zea diploperennis. Homologous sequences
were also observed on Sorghum bicolor genome
specific to RP1-like protein. When orthologous
(AY369028- 3891 bp) (GI34541997) gene was BLAST
aligned using NCBI-nBLAST, hits were conformed to
sorghum and Zea with 84-100% homology. All of
them showed match with Rp1 locus and it was
homologous across three subspecies luxurians,
parviglumis and diploperennis.
The Rp1 gene responsible for rust resistance
of maize bearing GI34541997 when BLAST aligned
with MaizeGDB indicated 100% match with sequences
specific to chromosome 10. A few hits ranging from 15 were also manifested on other chromosomes with per
cent identity ranging from 85.15% to 94.2%. When the
Rp1 sequence was BLAST aligned using CoGeBLAST
for Zea mays, it showed homology on chromosome
10. Rp6 and Rpp9 region are congruent based on their
position on the physical map. Both of them locate to
the region between 4591964 and 4674733 flanked by
IDP258 (58.84 cM) and TIDP2853 (63.88 cM), but
Rp6 is separated from Rpp9 (59.99cM) locus by 1.6
crossovers (cM) (www.maizegdb.org).
Few other genes present in the region were
pyruvate
kinase,
Alp1,
rp5
and
Gdc
(www.maizegdb.org, June 2012). Other SSR markers
in the region 10.00-10.01 umc1318, p-umc1319, pumc1152, p-umc2018 [4][21] and BACs AC195216
and AC198290 [21] were reported to be having linkage
with the trait. This adds up to a region of ~3Mb and
this region spanning from 2255062 upto 4875758 bp in
the B73 RefGen_v2 sequence. This 3 Mb region
included genes for common rust (Rp1, Rp5, Rp6) and
polysora rust (Rpp9, RppQ, RppD).
B. Gene Prediction and Annotation
The result obtained from the gene prediction
tool is presented in table 1.
3
© 2013 GSTF
GSTF International Journal of BioSciences (JBio) Vol.2 No.2, May 2013
Table 2. Genes obtained after BLAST analysis of
nucleotide sequence of bin 10.01 of maize
GeneID
AY466202.2
AY530951.1
DQ002406.1
included
phosphate/phosphate
translocator
(Brachypodium distachyon), tyrosine-specific protein
phosphatase-like (Oryza sativa Japonica Group),
retrotransposon protein, gag-pol precursor, kinase,
ornithine carbamoyltransferase (Zea mays) and many
others. The genes having relevance with disease
resistance have been chosen and listed in Table 4. The
region shared homology with rice, sorghum and
brachypodium grass and some orthologs having NBLRR domain and NB-ARC domain characteristic of
resistance genes were found. The selected genes will
be used for further study for identifying the gene/s
linked with disease resistance.
Function
pol-protein gene
Zea mays growth regulating factor 1
Copia retrotransposons and helitron
DNA binding protein, DNA repair,
peroxisome synthetase
22kDa alpha zein gene cluster
B73 teosinte glume architecture 1 gene
B73 pathogenesis-related protein 2 and
GASA-like protein genes
heme
oxygenase,
anthocyanin
biosynthesis regulatory protein, receptor
protein kinase
Zea mays gypsy retrotransposon, huck
and copia retrotransposon
Zea mays copia type retroelement PREM2 gag gene
Zea mays transposase
Zea mays B73 serine/threonine kinase
protein expressed RNA-dependent RNA
polymerase
Zea mays B transcriptional activator (D1)
gene B' allele
Zea mays rust resistance protein rp3-1
gene
Zea mays AP2 domain transcription
factor (Rap2.7)
Zea mays chloroplast phytoene synthase
(Y1) gene
Zea mays alcohol dehydrogenase 1
(adh1A) gene
The
BLA
ST
HQ234502.1
resul
AF090447.2
ts
AY883559.2
(Tabl
DQ417752.1
e 2)
of
this
AY530952.1
3 Mb
DQ002408.1
regio
n
U41000.1
indic
AF466646.1
ated
the
DQ417753.1
prese
nce
AY078063.2
of
man
AY574035.1
y
EF659468
loci
respo
AY455286.1
nsibl
e for
AY691949.1
disea
se resistance like PR proteins, serine/threonine kinase
protein, receptor kinases (reviewed by Afzal et al.,
2008), rust resistance protein (RP3-1), and zein cluster.
The rp3 gene showed 100% identity towards the query
covering 45% of query (e value = 0.0). The hits also
included Zea mays chloroplast phytoene synthase (Y1)
gene, AP2 domain transcription factor, putative heme
oxygenase 1, serine/threonine kinase protein, teosinte
glume architecture 1, pathogenesis-related protein 2
and GASA-like protein. Similarly, nBLAST of each
genetic element RppQ, RppD, Rpp9 [2713838:4246404
bp length, 27864 hits (e value = 0) 27-50% query
coverage, 100% maximum identity; 4591464:4675233
bp length 20198 hits (e value = 0), 13-35%, 100%
maximum identity] yielded almost similar hits with
additions like rust resistance protein (RP3-1), Zea mays
B transcriptional activator (b1) gene, b1-B' allele
which is involved in biosynthesis of flavonoids,
anthocyanin biosynthesis regulatory protein, putative
receptor protein kinase and also a promoter
(US20020115849) that is activated by a fungal
infection.
Acceleration in rate of discovery of QTL
variation is expected with the adoption of linkage
disequilibrium and candidate gene strategies for QTL
fine mapping and cloning [26]. With the growing
information on genomics and availability of
bioinformatics tools it is possible to reach a gene with
more accuracy, rapidly and with less investment. The
strategy to integrate QTL mapping information across
different studies onto a single reference map has
advantages as to localize all markers and QTL against
common framework and synthesise all the information
related to a cluster of QTL by identifying consensus or
meta-QTL [23].
The genes obtained through GENSCAN (no. of genes
obtained in GENSCAN is more than the FGENESH)
were submitted to BLAST (Table 3). The results
4
© 2013 GSTF
GSTF International Journal of BioSciences (JBio) Vol.2 No.2, May 2013
Table 3. List of genes obtained based on FGeneSH gene
prediction software
Gene ID
NP_001151894.1
NP_001066040.1
ABA91286.2
XP_003577864.1
BAD05711.1
BAC84194.1
ABG22544.1
XP_003575644.1
XP_003577143.1
ABA94507.1
BAC84194.1
ABA94507.1
BAC84194.1
XP_003579010.1
XP_003577128.1
NP_001175215.1
AAL58234.1
NP_001149012.1
ABA91295.1
XP_002530955.1
NP_001149114.1
XP_003527081.1
NP_190126.1
Function
secondary cell wall-related
glycosyltransferase family
47
secondary cell wall-related
glycosyltransferase family
47
secondary cell wall-related
glycosyltransferase family
47
PREDICTED:
probable
glycosyltransferase
putative RGH1A
putative
CC-NBS-LRR
resistance protein MLA13
NB-ARC domain containing
protein, expressed
PREDICTED:
disease
resistance protein RPM1-like
PREDICTED:
putative
disease resistance RPP13like protein 2-like
NB-ARC domain containing
protein, expressed
putative
CC-NBS-LRR
resistance protein MLA13
NB-ARC domain containing
protein, expressed
putative
CC-NBS-LRR
resistance protein MLA13
PREDICTED:
disease
resistance protein RPM1-like
PREDICTED:
putative
disease resistance RPP13like protein 2-like
putative stripe rust resistance
protein Yr10
putative disease resistance
gene
NB-ARC domain
containing protein
bifunctional
aspartokinase/homoserine
dehydrogenase
MATE efflux family protein,
expressed
multidrug resistance pump,
putative
GAST1 protein precursor
PREDICTED:
xylogalacturonan beta-1,3xylosyltransferase-like
exostosin family protein
similarity to those involved in disease resistance in
other crops like rice and sorghum as well. Hence from
this analysis it could be concluded that the region is
responsible for disease resistance and host many other
genes linked with resistance to various diseases.
Species
Zea mays
IV. ACKNOWLEDGMENT
Oryza
sativa
Japonica Group
We are thankful to Department of Science &
Technology, Govt. of India for providing financial
assistance in the form of PURSE fellowship to carry
out the research work.
Oryza
sativa
Japonica Group
Brachypodium
distachyon
Oryza
sativa
Japonica Group
Oryza
sativa
Japonica Group
Oryza
sativa
Japonica Group
Brachypodium
distachyon
Brachypodium
distachyon
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Dr. K. M. Harinikumar is working as an Associate
Professor in the Department of Biotechnology, University of
Agricultural Sciences, GKVK, Bengaluru. He has rich
experience in the field of biofuels and has pioneered many
research projects on biofuels in the University. He has also
worked in The Mysore Sugar Factory and contributed his
skills and knowledge for the development of rural farmers
during his tenure in the Sugar factory.
Dr. H. E. Shashidhar is a Professor in the Department of
Biotechnology, University of Agricultural Sciences, GKVK,
Bengaluru. He has extensive experience in the field of
Molecular Breeding and Rice Genetics. He is one such
scientist who can feel the farmers’ pulsation. He has released
an aerobic rice variety, which can be grown in rainfed
condition.
Dr. H.C. Lohithaswa is an Associate Professor and Head in
the Department of Plant Breeding and Genetics, College of
Agriculture, V.C. Farm Mandya. He has also served as
Senior Scientist in ZARS, VC Farm, Mandya and has added
many valuable resources to Forage breeding.
Dr. Bhavani Puttaswamy Gowda is working as a Research
Associate in Sugarcane Breeding Division, Zonal
Agricultural Research Station, V.C. Farm, Mandya. She has
worked on maize genetics and disease resistance during her
doctoral degree and has research implication towards
improving plant resistance to pests and diseases.
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© 2013 GSTF
GSTF International Journal of BioSciences (JBio) Vol.2 No.2, May 2013
Dr. Pandurange Gowda K.T is the Dean (Agri), College of
Agriculture, VC Farm, Mandya. He has also served as
Associate Director of Agriculture in ZARS, VC Farm,
Mandya. He is a renowned pathologist who contributed
extensively to National Maize Breeding for Resistance to
Puccinia polysora and Turcicum Leaf Blight. He has made
many farmer friendly programmes during his tenure as ADR.
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© 2013 GSTF