Maize
Genetics Cooperation Newsletter vol 86 2012
Genetic relations among Tripsacum species revealed by genomic variation
Suketoshi Taba1
and Victor Chavez T1
1.
Maize genebank, Genetic Resources Program, International Maize
and Wheat Improvement Center (CIMMYT), El Bat�n,
Mexico.
2.
Email: [email protected]; [email protected]
Introduction
We studied genomic
variation among several Tripsacum
spp. and teosinte species in collaboration with Floragenex Inc., Portland, Oregon, USA. Materials were 18 Tripsacum clones from Mexico and South America,
seven teosinte race populations, and one tropical
maize inbred (tables 1, 3, and S1). A preliminary analysis revealed interesting
results for relationships between Zea and Tripsacum.
Sequencing
and SNP (polymorphism) discovery
Paired-end
Illumina / Solexa sequence
reads of the material were anchored to the Tripsacum clone sample 12 (table
S1) reference assembly, using custom short-read software with a Needleman-Wunsch alignment algorithm. Specified alignment thresholds allowed
approximately three base pair changes between the ~50 bp
Illumina / Solexa read and
the reference (>90 percent identity). Small gapped alignments (short indels) spanning one or two base pairs were also
permissible.
A total
of 25,878 contigs were constructed, with 5,705,986
base pairs. Contig sequence length ranged from 100 to
625 bp, with an average of 220.5 bp.
Using the Tripsacum clone 12 as the reference, the
number of contigs with at least one polymorphism was 11558.
Within the 11558 contigs, 7756 were aligned onto the
B73 genome, where 45449 polymorphic loci were anchored.
In
total, 72413 polymorphic loci were identified. Of these, 1036 were high-quality
polymorphic loci identified across all 26 lines; 10 of which were InDel genomic variation and 1026 were single nucleotide
polymorphisms (SNPs).
Clustering analysis of Tripsacum, Teosinte, and maize
Information
on all the material analyzed in this study is shown in tables 1, 2, and 3.
Table 1. Tripsacum clones sampled for this study at CIMMYT Tlaltizap�n station, 2009.
|
Clonal sample ID |
Collection No. |
Population No. |
Species classification |
chromosome
number |
Possible ploidy |
Country of origin |
Collection site and province or state |
Collection site altitude (m), latitude, longitude
|
|
01 |
T.1069 |
95 |
TMN (T. manisuroides de Wet and
Harlan) |
36 |
diploid |
Mexico |
Mirador, Los Chiapas,
Chiapas |
1200, 16:37; -91:85 |
|
02 |
T. 5243 |
613 |
TCD (T.cundinamarce de Wet and
Timothy) |
36 |
diploid |
Colombia |
Viota-Tamarindo, Cundinamarca |
1095, 4:42; -74:52 |
|
03 |
T. 5222 |
603 |
TMR (T.dactiloydes var.meridionale de Wet and Timothy) |
36 |
diploid |
Venezuela |
El Caimito-5km from Libertad, Tachira |
1400, 7:58; -72:32 |
|
04 |
T.7003 |
1 |
TZP (T. zopilotense Hernandez and
Randolph) |
36 |
diploid |
Mexico |
Ca�on de Zopilote,
Guerrero |
354, 18:35; -101:70 |
|
05 |
T. 5087 |
554 |
TMR (T.dactyloydes var.meridionale de Wet and Timothy) |
36 |
diploid |
Colombia |
Sota, 7km Carr. a Sota,
Boyaca |
1000, 6:32; -72:70 |
|
06 |
T.69 |
18 |
TLT (T.latifolium Hitchc.) |
54 |
triploid |
Mexico |
Pluma Hidalgo, Oaxaca |
1100, 15:92; -96:42 |
|
07 |
T.7146 |
4 |
TMZ (T. maizar Hernandes
and Randolph) |
54 |
triploid |
Mexico |
San Jose II, Nayarit |
30, 22.47: -105:30 |
|
08 |
T.552 |
6 |
TBV (T. bravum Gray) |
72 |
tetraploid |
Mexico |
Rancho Nuevo, 87.7 km from Iguala, Guerrero |
780, 18:17; -101:40 |
|
09 |
T.569 |
9 |
TDH (T. dactyloydes var. hispidum (Hitchc.) de Wet
and Harlan) |
72 |
tetraploid |
Mexico |
Zacazonapan, 2 km N. of Zacazonapan, Mexico |
1450, 19:07; -100:20 |
|
10 |
T.139 |
24 |
TDM (T.dactyloides var.mexicanum de Wet and Harlan) |
72 |
tetraploid |
Mexico |
Aguascaliente, 13km S. of Acatl�n de Juarez, Jalisco |
1420, 19:98; -104:00 |
|
11 |
T.210 |
31 |
TIT (T. intermedium de Wet and
Harlan) |
72 |
tetraploid |
Mexico |
Ojo de Agua, 1km W. of Ojo
de Agua, Colima |
170, 19:32; -103:80 |
|
12 |
T.1070 |
96 |
TJL (T.Jalapense de Wet et
Brink) |
72 |
tetraploid |
Mexico |
La Coyota, km 14.9 Carr. Sumidero,
Chiapas |
1150, |
|
13 |
T.7221 |
1 |
TPL (T.pilosum Scribner and
Merrill) |
72 |
tetraploid |
Mexico |
Jilotl�n, Jalisco |
740, 19:22; -103:01 |
|
14 |
T.1610 |
39 |
TDM (T.dactyloydes var.mexicanum de Wet and Harlan) |
72 |
tetraploid |
Mexico |
La Toma, 3 km W. of Tequila, Jalisco |
1200, 20:90; -103.80 |
|
15 |
T.2131 |
142 |
LC (T.lanceolatum Ruprecht
ex Fournir) |
72 |
tetraploid |
Mexico |
Rio Chico, Carr. Mazatl�n, Durango |
2100, 23:93; -104.80 |
|
16 |
T.2368 |
153 |
TDD (T. dactyloides (L.) L.) |
72 |
tetraploid |
Mexico |
Lamasinta, Carr. Chilapa-Tlapa, Guerrero |
1500, 17:60; -99:17 |
|
17 |
T.5081 |
550 |
TPR (T.peruvianum de Wet and Timothy) |
90 |
pentaploid |
Peru |
Tingode Saposoa, San Martin |
299, -7:12; -76:62 |
|
18 |
T. 5023 |
522 |
TAD (T.andersonii Gray) |
64 |
hybrid (64) |
Brazil |
Campinas Institute of Agronomy, Sao Paulo |
661, -22:88; -46:07 |
Table 2. Plant
traits measured for the Tripsacum clones analyzed
in this study and for some additional clones at CIMMYT Tlaltizap�n station.
|
Clonal Sample ID |
Collection No. |
Popultion No. |
Species
classification |
Plant height (m) |
Leaf length (cm) |
Leaf width (cm) |
Culm width (cm) |
Culm thickness
(cm) |
|
Tripsacum clones used for phylogenetic study in A1 plot at
Tlaltizap�n, Morelos. Mexico |
||||||||
|
01 |
T.1069 |
95 |
TMN (T. manisuroides de Wet and
Harlan) |
3.28 |
152 |
3.3 |
1.5 |
1.35 |
|
02 |
T. 5243 |
613 |
TCD (T.cundinamarce de Wet and
Timothy) |
3.15 |
158 |
4.2 |
2.15 |
1.65 |
|
03 |
T. 5222 |
603 |
TMR (T.dactiloydes var.meridionale de Wet and Timothy) |
|||||
|
04 |
T.7003 |
1 |
TZP (T. zopilotense Hernandez and
Randolph) |
2.39 |
144 |
1.6 |
0.6 |
0.4 |
|
05 |
T. 5087 |
554 |
TMR (T.dactyloydes var.meridionale de Wet and Timothy) |
2.5 |
127 |
2 |
1.2 |
1 |
|
06 |
T.69 |
18 |
TLT (T.latifolium Hitchc.) |
1.8 |
135 |
4.1 |
2.3 |
2 |
|
07 |
T.7146 |
4 |
TMZ (T. maizar Hernandes
and Randolph) |
2.07 |
128 |
6 |
2.3 |
2.15 |
|
08 |
T.552 |
6 |
TBV (T. bravum Gray) |
1.68 |
114 |
1.9 |
1.4 |
1.15 |
|
09 |
T.569 |
9 |
TDH (T. dactyloydes var. hispidum (Hitchc.) de Wet
and Harlan) |
1.15 |
122 |
1.43 |
0.7 |
0.55 |
|
10 |
T.139 |
24 |
TDM (T.dactyloides var.mexicanum de Wet and Harlan) |
3.2 |
177 |
3.13 |
1.7 |
1.25 |
|
11 |
T.210 |
31 |
TIT (T. intermedium de Wet and
Harlan) |
3.28 |
179 |
3.66 |
0.95 |
0.8 |
|
12 |
T.1070 |
96 |
TJL (T.Jalapense de Wet et
Brink) |
3.24 |
178 |
3.6 |
1.25 |
1.1 |
|
13 |
T.7221 |
1 |
TPL (T.pilosum Scribner and Merrill) |
3.53 |
223 |
4.1 |
2.2 |
1.7 |
|
14 |
T.1610 |
39 |
TDM (T.dactyloydes var.mexicanum de Wet and Harlan) |
2.77 |
155 |
3.67 |
1.8 |
1.5 |
|
15 |
T.2131 |
142 |
LC (T.lanceolatum Ruprecht
ex Fournir) |
1.64 |
129 |
1.65 |
0.7 |
0.5 |
|
16 |
T.2368 |
153 |
TDD (T. dactyloides (L.) L.) |
2.5 |
150 |
0.76 |
0.65 |
0.45 |
|
17 |
T.5081 |
550 |
TPR (T.peruvianum de Wet and Timothy) |
2.73 |
140 |
4.1 |
1.5 |
1.1 |
|
18 |
T. 5023 |
522 |
TAD (T.andersonii Gray) |
2.08 |
163 |
6.73 |
2.5 |
2.1 |
|
Additional Tripsacum
clones measured in A0 plot at Tlaltizap�n, Morelos,
Mexico |
||||||||
|
A01 |
TZP-DEC- 0506 |
TZP (T. zopilotense Hernandez and
Randolph) |
2.18 |
142 |
0.9 |
0.35 |
0.3 |
|
|
A02 |
T.5085 |
553 |
TPR (T.peruvianum de Wet and Timothy) |
2.14 |
129 |
2.96 |
0.7 |
0.55 |
|
A03 |
TLX-DEC-05-72 |
TLX(T. laxum Nash) |
4.4 |
144 |
5.1 |
2.15 |
1.65 |
|
|
A04 |
TLT-DEC-05-70 |
TLT (T.latifolium Hitchc.) |
2.95 |
203 |
3.46 |
1.85 |
1.05 |
|
Table
3. Maize
and teosinte samples included in this
study.
|
Sample ID |
CIMMYT Bank ID |
Race name |
Population |
Collection site or seed origin |
|
Maize line |
16417 |
Tuxpe�o pool |
CML 247 |
G24F119*G24F54-6-4-1-1-BB,CIMMYT |
|
Teosinte 01 |
8765 |
Balsas |
K67-22 |
Tinganbato, Michoac�n, Mexico |
|
Teosinte 02 |
8768 |
Chalco |
K68-1 |
Milpa Alta, M�xico, Mexico |
|
Teosinte 03 |
9478 |
Guatemala |
Chiquimula, Guatemala |
|
|
Teosinte 04 |
9479 |
Huehuetenango |
Jacaltanango, Huehuetenango, Guatemala |
|
|
Teosinte 05 |
10003 |
Diploperennis |
San Miguel |
Cautitl�n, Jalisco, Mexico |
|
Teosinte 06 |
11367 |
Central Plateau |
K69-5 |
Chacandiro, Michoac�n, |
|
Teosinte 07 |
11403 |
Balsas |
W.S.92-12 |
Ixcapzalco, Guerrero, Mexico |
0.02 MR ( T.dact.var.meridionale )2 Venezuela MR ( T.dact.var.meridionale )1 Colombia CD ( T.cundinamarc a ) Colombia ZP ( T.zopilotense Herna.and R.) M�xico PR ( T.peruvianum ) Ecuador Zea Mexicana Mcenter Mexico Zea Mexicana Chalco Mexico Zea Huehuet Guatemala Zea Parviglumis Balsas1 Mexico Zea Parviglumis Balsas2 Mexico Zea Diploperennis Mexico Zea Luxurians Guatemala CML247, CIMMYT AD ( T.andersonii ) Brazil LT ( T.latifolium Hitchc .) Oaxaca, Mexico DD ( T.dactiloides (L.) L .) Mexico LC ( T.lanceolatum ) Mexico DM ( T.dact.var.mexicana )2 Mexico MN( T.manisuroides ) Chiapas, Mexico MN ( T.manisuroides ) Chiapas, Mexico DH ( T. dact . Var. hispidum ) Mexico MZ ( T. maizar Hern.and Rand .) Mexico DM ( T.dact.var.mexicana )1 Mexico IT ( Tripsacum intermedium ) Mexico BV ( T. bravum Gray ) Mexico PL ( T.pilosum Scribner and M ) Mexico
Figure 1 shows that the among
the Tripsacum species studied,
those from South America (i.e., T. peruvianum, T. cundinamarc, and T.
dactyloides) were genetically
closest to Zea (teosinte and maize, though T. zopilotense (Mexico) had similar
results. The next closest species to Zea were T. latifolium and T. andersonii.
The teosinte
species were clustered as
shown in Figure 1. T. zopilotense reportedly crosses well with maize (Savidan et al. 1993) and with T. australe (Raymundo
Q. C. 1993). T. dactylodes
is also known to cross well with maize. Unfortunately we did not have T. australe
and T. jalapense in our study.
From the current relationship
among the taxa of Tripsacum,
teosinte, and maize, we recommended that
inter-specific gene pools of Tripsacum species and Tripsacum X maize
gene pools are made to exploit useful genes and allelic diversity (Li et al.
1999; Dewald and Kindiger
1998) that may exist in Tripsacum.
It took
many days to curate a Tripsacum
garden in Tlaltizap�n station. The passport data of exiting
clones are updated. Some clones from the South American highlands
of South America suffered from high temperatures at the station.
Acknowledgements
The
authors would like to acknowledge Dr. Weiwei Wen,
former visiting scientist at CIMMYT maize genebank
and currently at the National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China, for
her help with data analysis and valuable discussions. Also Floragenex
Company, Oregon, USA for their work in sequencing DNA samples. A part of the
work was conducted under CGIAR genebank upgrading
projects of The World Bank. Finally, we thank CIMMYT editors Emma Quilligan and Mike Listman for
help polishing this text.
References
Savidan,Y., J.Berthaud,
and O.Leblanc. 1993. New Maize x Tripsacum
F1 hybrids for gene transfers to maize. Apomixis Newsletter 6:19-20.
Raymundo Q. C.
1993. MS thesis, Colegio de Postgraduados, Montecillo, Mexico
Li,
Y.G., C.L.Dewald, and P.L. Sims. 1999. Genetic
relationships within Tripsacum
as detected by RAPD variation. Annals of
Botany 84: 695-702.
Dewald, C.L.
and B.K. Kindiger. 1998. Cytological and molecular
evaluation of the reproductive behavior of Tripsacum andersonii
and a female fertile derivative (Poaceae). American Journal of Botany 85: 1237-1242.
Table S1. Number of Illumina
Sequence Reads obtained in Tripsacum and Zea accessions in this study
|
Accession
(DNA sample ID) |
Number
of reads |
|
maize
line-CML247 |
1,527,024 |
|
Teosinte01 |
179,916 |
|
Teosinte02 |
208,823 |
|
Teosinte03 |
249,833 |
|
Teosinte04 |
330,936 |
|
Teosinte05 |
269,964 |
|
Teosinte06 |
350,930 |
|
Teosinte07 |
806,423 |
|
Tripsacum01 |
2,052,542 |
|
Tripsacum02 |
639,275 |
|
Tripsacum03 |
480,868 |
|
Tripsacum04 |
484,349 |
|
Tripsacum05 |
609,107 |
|
Tripsacum06 |
457,786 |
|
Tripsacum07 |
692,378 |
|
Tripsacum08 |
573,691 |
|
Tripsacum09 |
844,068 |
|
Tripsacum10 |
858,477 |
|
Tripsacum11 |
729,792 |
|
Tripsacum12 |
4,183,737 |
|
Tripsacum13 |
2,367,395 |
|
Tripsacum14 |
3,715,711 |
|
Tripsacum15 |
82,867 |
|
Tripsacum16 |
230,727 |
|
Tripsacum17 |
96,609 |
|
Tripsacum18 |
158,771 |
|
Total |
23,181,999 |
Please Note: Notes
submitted to the Maize Genetics Cooperation Newsletter may be cited only with
consent of authors.