Published online 1 August 2005
Published in Crop Sci 45:1750-1757 (2005)
© 2005 Crop Science Society of America
677 S. Segoe Rd., Madison, WI 53711 USA
GENOMICS, MOLECULAR GENETICS & BIOTECHNOLOGY
Genomic Constitution and Genetic Relationship among the Tropical and Subtropical Indian Sugarcane Cultivars Revealed by AFLP
A. Selvia,b,
N. V. Nairb,
J. L. Noyerc,
N. K. Singha,
N. Balasundaram,
K. C. Bansala,
K. R. Koundala and
T. Mohapatraa,*
a National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India
b N. Balasundraram, Sugarcane Breeding Institute, Coimbatore 641007, Tamilnadu, India
c CIRAD, UMR 1096 PIA, TA 40/03, F-34398 Montpellier, France
* Corresponding author (tm{at}nrcpb.org)
 |
ABSTRACT
|
|---|
Sugarcane (Saccharum spp.) is a tropical plant. In India, systematic breeding initiated early in the twentieth century led to the development of cultivars suitable for subtropical conditions. In spite of a long breeding history, no systematic effort has been made to understand the genetic constitution of these cultivars. The present study was performed to characterize 28 commercial sugarcane cultivars grown in the tropical and subtropical regions of India by means of amplified fragment length polymorphism (AFLP). Eleven of the 12 selective primer combinations used in the study could individually discriminate all the cultivars from each other, which suggested their usefulness in identification of sugarcane cultivars. Comparison of the AFLP profiles of the cultivars with that of their progenitor species revealed the presence of 78.8% of the 250 S. officinarum L. specific DNA fragments, whereas 28.85% of the 260 S. spontaneum L. specific fragments could be traced in the cultivars. Saccharum officinarum specific DNA fragments were found equally shared by the tropical and subtropical cultivars. The subtropical cultivars, however, retained significantly higher number of S. spontaneum specific DNA fragments than did the tropical cultivars, reflecting the breeding strategy followed in the development of these cultivars. The level of genetic diversity between the tropical and subtropical cultivars was much higher than most of the pair-wise diversity measures within each of these two adaptive groups. The AFLP-based clustering of the cultivars also corresponded well with their pedigree relationships.
Abbreviations: AFLP, amplified fragment length polymorphisms • RAPD, random amplified polymorphic DNA • RFLP, restriction fragment length polymorphisms • SSR, simple sequence repeats
|
INTRODUCTION
|
|---|
SUGARCANE is a tropical plant and grows well under tropical conditions all over the world. However in India, it is grown to a large extent in the Indo-Gangetic plains of the subtropical region that faces extreme climatic conditions resulting in a low cane yield. In the year 2004, the sugarcane area in the subtropical zone of India was 2.6 million hectares, while the area under the tropical zone was 1.3 million hectares. Attempts to breed superior cultivars of sugarcane for subtropical conditions were initiated early in the 20th century at the Sugarcane Breeding Institute, Coimbatore, India. Interspecific crosses were produced between S. officinarum, the high sugar-containing species, grown in the tropics and S. barberi Jesw., the north Indian species that was grown in the subtropics (Thuljaram Rao, 1987a). Since notable improvement was not observed, the wild species S. spontaneum, known for its hardiness, was utilized in the breeding programs to assist in the production of cultivars for the subtropical region. A breakthrough in the history of sugarcane breeding was made in 1912 by crossing S. officinarum (‘Vellai’) with S. spontaneum, generating the first hybrid (‘Co 205’) that yielded 50% more than the indigenous cultivars belonging to S. barberi (Thuljaram Rao, 1987a). This novel hybrid was found to be well adapted to the climatic and soil conditions in the subtropical zone. Subsequently a number of sugarcane cultivars were developed by interspecific hybridization involving S. officinarum and S. spontaneum followed by backcrossing with the S. officinarum parent. This process, called "nobilisation," resulted in the development of high sugar-containing clones with high productivity and stress tolerance. Breeding cultivars for the tropical regions of India began in 1926 with emphasis on selection for thicker canes (Thuljaram Rao, 1987b). A significant outcome of this effort was the development of the cultivar Co 419 in the year 1933 that was outstanding in yield and sucrose content. This cultivar soon occupied the entire tropical zone of India and dominated the scene for over three decades. Several cultivars with high productivity and suited for both the regions were bred subsequently. Thus sugarcane breeding in India has a history of being "region specific," including the choice of parents as well as selection and evaluation of the progeny resulting in distinct cultivars for the tropical and subtropical regions of the country (Thuljaram Rao, 1987b).
The expansion of sugarcane cultivation to marginal and low fertility regions poses a challenge to the sugarcane breeding programs. The parental clones used early in the history of sugarcane breeding were very few and repeated intercrossing of the hybrids has led to a relatively narrow genetic base in sugarcane cultivars (Arceneaux, 1965; Daniels and Roach, 1987). The use of S. spontaneum clones, the most variable species in the Saccharum complex (Mukherjee, 1957) as one of the parents to incorporate tolerance to biotic and abiotic stresses is considered responsible for most of the genetic variation existing in sugarcane cultivars (Lu et al., 1994). Sugarcane cultivars, however, are complex polyploids, usually aneuploids and highly heterozygous, with chromosome numbers ranging from 100 to 120. Understanding the extent of variation at the molecular level and determining the contribution of the parental species to the observed variation among the existing cultivars is essential for devising new strategies for sugarcane improvement. Although systematic breeding of sugarcane started in India that led to the development of genotypes suitable for tropical and subtropical regions of the country, the Indian cultivars remain largely uncharacterized in this regard.
Modern sugarcane cultivars possess large genome with a 2C value of around 11 pg DNA which is equivalent to about 10000 Mbp (D'Hont and Glaszmann 2001). Characterization of such a large genome requires a robust DNA marker system like AFLP that provides extensive genome coverage. AFLP markers have been used to study the diversity existing among Brazilian sugarcane cultivars (Lima et al., 2002) and in Erianthus, a related genus of Saccharum (Besse et al., 1998). These markers have also been employed for constructing linkage maps of sugarcane and to tag a gene for rust resistance (Hoarau et al., 2001; Asnaghi et al., 2004). The present study was undertaken with the objectives of (i) evaluating the potential of AFLP for discriminating between tropical and subtropical Indian sugarcane cultivars, (ii) determining their genetic constitution with respect to the progenitor species used in early hybridization programs, and (iii) establishing correspondence of molecular marker based classification of the cultivars with their pedigree and adaptive environment.
|
MATERIALS AND METHODS
|
|---|
Plant Materials
A total of 28 cultivars of sugarcane developed during the period from 1933 to 1998 and suitable for commercial cultivation in the tropical (14) and subtropical (14) regions of India were used for the study (Table 1). These cultivars were chosen because they (i) represent Indian breeding efforts over six decades, (ii) are economically important as cultivars, and/or (iii) are valued as potential parents in breeding programs. For instance, the cultivar Co 419 that was developed in the year 1933 has been used as one of the parents of many present day cultivars, and Bo 91 is widely grown in the subtropical zone of India particularly in the states of Uttar Pradesh, Bihar, and West Bengal. The list of cultivars, their immediate parents, year of release and the region of cultivation are presented in Table 1.
AFLP Profiling
Total DNA was extracted from fresh leaves of a single plant by the method described by Walbot (1988). The quality and concentration of the extracted DNA were estimated on a 0.8% (w/v) agarose gel with diluted uncut lambda DNA as a size standard. AFLP profiles were generated on the basis of the protocol of Vos et al. (1995) with the AFLP Analysis System I (Invitrogen Corporation, Grand Island, NY) following the manufacturer's instructions. The size of the fragments was estimated using a 20-bp DNA ladder (MBI Fermentas, Lithuania).
Analysis of Data
AFLP bands in the size range of 100 to 700 bp were scored for their presence (1) and absence (0) for each primer pair– cultivar combination. The phenetic analysis was performed by calculating the genetic dissimilarities between Cultivars i and j as di–j by the Sokal and Michener index di–j = 1 – (n11 + n00)/(n11 + n10 + n01 + n00) where n11 is the number of shared fragments between i and j, n10 and n01 are the number of fragments present in one cultivar and absent in the other, and n00 is the number of fragments absent in both. The matrix of pairwise di–j values was used to construct a phenogram with the Neighbor Joining method (Saitou and Nei, 1987) as undertaken by Darwin 3.5 software (Perrier et al., 2003). The clustering was validated by bootstrap analysis. One thousand bootstrap replicates were computed and a bootstrap 50% majority rule consensus tree was constructed using the bootstrap procedure of the PAUP 4b6 software program (Swofford, 2000).
To identify the most informative primer pair, the discrimination rate (DR) was calculated by the following formula: DR = the number of polymorphic pairs/total number of pairs. The usefulness of individual informative primer combinations was further assessed by comparing the Jaccards coefficient of similarity determined for each primer with that obtained with all the primers by a Mantel test (Mantel, 1967) using the MxCOMP module of NTSYS-PC (Rohlf, 1990). The probability of DNA fingerprints of two cultivars being identical by chance was calculated as described by Ramakrishna et al. (1994) employing the formula (XD)n where, XD = average similarity index and n = the average number of fragments per cultivar. The average similarity index was calculated by dividing the sum of all the pair-wise similarity indices by the total number of pairs.
|
RESULTS AND DISCUSSION
|
|---|
AFLP Profiles and Their Use in Cultivar Discrimination
Twelve primer combinations were used to screen 28 cultivars of which 14 each were from tropical and subtropical zones. Distinct bands in the size range of 100 to 700 bp were scored for the analysis. A total of 989 fragments were obtained and the number of bands per primer ranged from 54 (E-ACA/M-CTA) to 109 (E-ACC/M-CTA) with an average of 82.4 fragments per primer. The complex AFLP profiles obtained in sugarcane (Fig. 1), even with the use of six selective bases, are expected owing to a large genome size and high levels of heterozygosity. Similar complex AFLP patterns in sugarcane have also been reported earlier by Besse et al. (1998). In the present study, 621 of the 989 fragments were polymorphic. Primer combination E-ACA/M-CTG (67) produced the most polymorphic fragments and E-ACA/M-CTA the lowest (28) with an average of 51.75 polymorphic fragments per primer combination (Table 2). The percent polymorphisms obtained with individual primer pairs ranged from 50.0 to 78.9% with an average of 62.8% (Table 2). An earlier study on the genetic similarity in a collection of 79 Brazilian sugarcane cultivars using AFLP markers, revealed 2331 bands of which 1121 were polymorphic giving an average polymorphism rate of 48% (Lima et al., 2002). This comparison reveals higher levels of polymorphism detected among the Indian sugarcane cultivars than among the Brazilian sugarcane cultivars.
View larger version (159K):
[in this window]
[in a new window]
|
Fig. 1. AFLP profile obtained with primer combination E-ACA/M-CTT. Lanes 1–14: subtropical cultivars, Lanes 15–28: tropical cultivars as in Table 1.
|
|
No two accessions used in this study possessed an identical DNA profile, indicating that it was possible to uniquely fingerprint all the genotypes. The number of polymorphic fragments between pairs of cultivars ranged from 97 to 269 when the whole data set was considered (data not shown), indicating a very high level of distinctness established by all the AFLP markers. Under the hypothesis of nonlinkage between the markers, the probability of fingerprints of two cultivars being identical by chance was 1.76 x 10–97 when all 12 primer combinations were considered, thus providing a very high confidence level to the varietal identity. All the primer combinations, except one (E-ACC/M-CTG), individually differentiated the cultivars from each other. The primer combination E-ACC/M-CTG, in spite of giving the second highest percentage (78.2%) of polymorphic fragments and also higher PIC value (0.35) than three other primer combinations (Table 2), had the lowest discrimination rate (0.99). The other 11 primer combinations gave a discrimination rate of 1.0 irrespective of the PIC values (Table 2). Two of these primer combinations, viz., E-ACA/M-CTG and E-ACC/M-CTA, when used together, were found more useful than the rest on the basis of two important considerations. First, the probability of identical match by chance calculated by using the profiles obtained with these two primer combinations together was quite low that suggested unequivocal discrimination of 1021 sugarcane cultivars. Second, the similarity matrix obtained from the profiles of these two primer combinations gave the highest correlation (r = 0.82) with that based on all the 12 primers. The correlation observed between the similarity matrices generated with these two primers was low (r = 0.45), emphasizing that their amplification products could provide complementary information (Van Droogenbroeck et al., 2002). Thus the primer combinations E-ACA/M-CTG and E-ACC/M-CTA could be recommended for fingerprinting and generating reliable similarity estimates for sugarcane cultivars. The high efficiency of AFLP primer combinations in discriminating cultivars and genotypes has also been demonstrated in several other species including Vitis vinifera L. (Cervera et al., 1998), Cynodon spp. (Zhang et al., 1999), Cassava (Fregene et al., 2000), Nicotiana (Ren and Timko 2001), and Oryza sativa L. (Prashanth et al., 2002).
More S. spontaneum Alleles in the Subtropical Cultivars
The AFLP profiles of the cultivars obtained in this study were compared with those of S. officinarum (8 clones) and S. spontaneum (6 clones) generated in a previous study (Selvi et al., 2005) to determine the genomic contribution of the progenitor species to the commercial cultivars. Markers that were present in at least two clones of one species and completely absent in the other were considered species specific (Jannoo et al., 1999a) and were traced back to the cultivars for their presence and absence. Out of 510 markers that differentiated the progenitor species clones, 250 were specific to S. officinarum and 260 specific to S. spontaneum. The S. spontaneum specific alleles could be traced in the cultivars only in respect of 75 (28.85%) of the 260 S. spontaneum specific markers. In contrast, 197 (78.8%) of the 250 S. officinarum specific fragments were found distributed across all the 28 cultivars. This is in line with the observations made in sugarcane cultivars bred in the Barbados and Mauritius where about 80% of the S. officinarum specific markers were shared by the cultivars (Jannoo et al., 1999b). This is also in agreement with the results obtained from genomic in situ hybridization studies (D'Hont et al., 1996). The 2n transmissions from S. officinarum in the early interspecific hybrids (Bhat and Gill 1985; Bremer 1961) combined with rigorous selection for high sugar yield over generations would have led to the retention of more S. officinarum alleles. However, there was no difference between the tropical and subtropical cultivars with regard to the fragments inherited from S. officinarum. The number of these fragments ranged from 137 (54.8%) to 169 (67.6%) with a mean 155.57 (62.23%) in the subtropical cultivars and 135 (54%) to 160 (64%) with a mean 148.78 (59.51%) in the tropical cultivars, the difference between the two mean values being nonsignificant.
In the 14 subtropical cultivars which were analyzed in this study, the number of S. spontaneum specific markers varied from 20 to 30 (mean 24.35), which accounted for 7.69 to 11.54% (mean 9.37%) of the S. spontaneum specific markers (260). In contrast, the S. spontaneum specific fragments varied from 10 (3.85%) to 23 (8.85%) with an average of 15.71 (6.0%) in the 14 tropical cultivars. Test of significance suggested that the mean S. spontaneum specific fragments were significantly higher in the subtropical cultivars than in the tropical cultivars of India (P < 0.01). Analysis of the distribution of the 75 S. spontaneum fragments revealed that 15 of them were specific to the subtropical cultivars. Though eight of the S. spontaneum fragments were also found specific to tropical cultivars, the presence of seven individual fragments obtained with the primer combination E-ACC/M-CAA was restricted to only one cultivar each. S. spontaneum has always been used as a source of genes for hardiness and high tillering. Conscious selection for such traits possibly had contributed to retention of more S. spontaneum specific fragments in the subtropical cultivars than the tropical ones. It would be of interest to associate the S. spontaneum specific fragments present only in the subtropical cultivars with useful traits introgressed from this wild progenitor species through a QTL mapping approach. The present study, thus, has provided an insight into the genomic constitution of the Indian sugarcane cultivars in relation to the progenitor species.
Genetic Base of the Indian Cultivars
The estimated genetic distance between the cultivars ranged from 0.17 to 0.48 (Table 3) with a mean of 0.38. The average distance between the subtropical and tropical cultivars (0.38) was slightly higher than the average distances within each group (0.36 within subtropical and 0.35 within tropical). Of all the pair-wise distance measures between cultivars of these two groups, 40.31% were greater than 0.40, whereas only 9.81 and 16.48% of the pair wise distances were >0.40 within the subtropical and tropical cultivars, respectively. This suggested higher levels of diversity between some of the cultivars belonging to these two groups, while the diversity is comparatively lower within each group. This could be partly due to differential contribution of the S. spontaneum genome to the tropical and subtropical cultivars. Studies on genomic in situ hybridizations indicated the presence of 15 to 25% of S. spontaneum genome in the cultivars through introgression of minor chromosome segments (D'Hont et al., 1996; Lu et al., 1994) that could have resulted in the observed diversity. The parental clones of S. officinarum could also have qualitatively contributed to the observed diversity, although the mean contribution of alleles from this species to the two groups of cultivars was not significantly different. An investigation of the diversity of S. officinarum using mapped RFLP markers has detected higher than expected diversity in the S. officinarum clones, most of this variability being retained in the cultivars (Jannoo et al., 1999b).
Correspondence of Molecular Relationship among the Cultivars with Their Pedigree
The present study revealed that the AFLP markers were informative and reflected the existing pedigree relationships between the cultivars. Most of the tropical and subtropical cultivars with common parents were placed together in the tree (Fig. 2). Among the subtropical cultivars, Co 1148 is a male parent of CoS 8436 and both the cultivars clustered together (100% occurrence). CoPant 84212, with Co 1148 as its female parent, also remained in the same subcluster. Co 86249, a tropical cultivar, was included in this subcluster, since its female parent CoJ 64 is a subtropical cultivar and CoA 7601, its male parent, had Co 301 in its genealogy, which was also the male parent of the subtropical cultivar Co 1148. Thus, grouping of these cultivars supported by 86% bootstrap values, was clearly influenced by a common ancestry involving Co 1148. Similarly, the tropical cultivar Co 62175 clustered with its male parent Co 419 with a high bootstrap value (95%). Co 7717 and Co 6304 have Co 419 as their female parent and were also placed close to Co 419 in the tree. Of the three cultivars Co 8021, Co 8371 and Co 7704 derived from the cross Co 740 x Co 6806, two cultivars Co 8021 and Co 8371 clustered together whereas Co 7704 was placed farther in a separate cluster along with the subtropical cultivars. Interestingly, Co 6806, the male parent of these cultivars, had Co 419 in its ancestry. On the whole, all the tropical cultivars in this sub-cluster had Co 419 in their ancestry, which could have highly influenced their clustering. Cultivars Co 85002, Co 86032, and Co 87025 sharing Co 62198 as either male or female parent were included in the same cluster. Interestingly, Co 62198 had Co 775 as its male parent in its immediate ancestry and CoC 671, present in this subcluster, also had Co 775 as its male parent. The strong clustering of the four tropical cultivars (CoC 671, Co 87025, Co 86032, and Co 85002) supported with high boot strap values (93%), was influenced clearly by Co 775 that was used as a progenitor parent. Thus the use of AFLP markers in the present study resulted in a definitive grouping of the cultivars that corresponded well with their pedigree relationships. A study on molecular investigation of the genetic base of sugarcane cultivars with RFLP markers showed that the molecular data confirms the genealogy data to some extent. The clones that occurred in the genealogy of many cultivars were close to the cultivars (Jannoo et al., 1999b). Similarly, the AFLP analysis of the Brazilian cultivars indicated that there was a tendency of the cultivars to group together with others obtained from the same cross (Lima et al., 2002). In contrast, the parentage of the cultivars did not correlate significantly to the clustering pattern obtained with RAPD and maize SSR markers (Nair et al., 2002; Selvi et al., 2003). The possibility of screening a higher number of anonymous loci than is possible with any other method makes AFLP more efficient in establishing genetic relatedness existing among the cultivars of this complex crop with high certainty.
View larger version (29K):
[in this window]
[in a new window]
|
Fig. 2. NJ tree showing genetic relationships among the Indian sugarcane cultivars grown under subtropical and tropical zones of India based on Sokal and Michener dissimilarity indices on 12 primer combinations. Numbers shown above different branches represent percentage confidence obtained in the bootstrap analysis. The scale bar represents simple matching distance. The number in the parenthesis given against each cultivar on the right margin of the tree corresponds to the serial number of the cultivar as in the Table 1, whereas, T and ST represent tropical and subtropical adaptation, respectively.
|
|
As evident from the above description, the pedigree of the cultivars used in the study had confounding effects on the grouping according to the adaptive environments. Most of the subtropical and tropical cultivars tended to remain in different clusters (Fig. 2) as influenced by their pedigree. Sugarcane cultivars originating from Barbados and Mauritius could also be differentiated on the basis of their breeding origins in spite of the profuse exchange of parental materials between the two sugarcane-breeding stations. One explanation that has been suggested is the possible relationship between the parent specific markers and adaptation to local environments, which is expected if strong linkage disequilibrium exists within the genome, particularly between the markers and the adaptive gene loci (Jannoo et al., 1999a). Such possibilities of linkage disequilibrium and preferential allele associations maintained through generations have been observed in modern sugarcane cultivars (Jannoo et al., 1999a). However, contribution of S. spontaneum specific alleles linked with the genes for adaptation to the molecular classification of the Indian sugarcane cultivars performed in the present study remains to be established.
In conclusion, the present study describes the genomic constitution of the commercial Indian sugarcane cultivars in relation to their progenitor species. AFLP markers provided a realistic estimate of genetic diversity that reflected pedigree relationship of the cultivars. Such objective measurements of genetic diversity would help define priorities, reduce costs and optimize the choice of parents for crossing. Unambiguous discrimination and identification of cultivars using single AFLP primer combinations are of significance in the context of establishing clonal fidelity and authenticity of the planting materials, and granting protection to the elite genotypes.
|
ACKNOWLEDGMENTS
|
|---|
The authors are highly thankful to Dr. Angelique D'Hont, CIRAD, France for critically evaluating the manuscript and providing useful suggestions for its improvement. This work was carried out in the National Agricultural Technology Project funded Team of Excellence Project of the Indian Council of Agricultural Research, New Delhi.
|
NOTES
|
|---|
This work was carried out in the National Agricultural Technology Project funded Team of Excellence Project of the Indian Council of Agricultural Research, New Delhi.
Received for publication September 10, 2004.
|
REFERENCES
|
|---|
- Arceneaux, G. 1965. Cultivated sugarcanes of the world and their botanical derivation. Proc. Int. Soc. Sugarcane Technol. 12:844–854.
- Asnaghi, C., D. Roques, S. Ruffel, C. Kaye, J.Y. Hoarau, H. Telismart, J.C. Girard, L.M. Raboin, A.M. Risterucci, L. Grivet, and A. D'Hont. 2004. Targeted mapping of a sugarcane rust resistance gene (Bru1) using bulked segregant analysis and AFLP markers Theor. Appl. Genet. 108:759–764.[CrossRef]
- Besse, P., G. Taylor, B. Carroll, N. Berding, D. Burner, and C.L. McIntyre. 1998. Assessing genetic diversity in a sugarcane germplasm collection using an automated AFLP analysis. Genetica (The Hague) 104:143–153.
- Bhat, S.R., and B.S. Gill. 1985. The implication of 2n egg gametes in nobilisation and breeding of sugarcane. Euphytica 34:377–384.[CrossRef]
- Bremer, G. 1961. Problems in breeding and cytology of sugarcane. Euphytica 10:59–78.[CrossRef]
- Cervera, M.T., J.A. Cabezas, J.C. Sancha, F. Martinez de Toda, and J.M. Martinez-Zapater. 1998. Applications of AFLPs to the characterization of grapevine Vitis vinifera L. Genetic resources. A case with accessions from Rioja (Spain). Theor. Appl. Genet. 97:51–59.
- Daniels, J., and B.T. Roach. 1987. Taxonomy and evolution. p. 7–84. In D.J. Heinz (ed.) Sugarcane improvement through breeding. Elsevier Press, Amsterdam.
- D'Hont, A., and J.C. Glaszmann. 2001. Sugarcane genome analysis with molecular markers; A first decade of research. Proc. Int. Soc. Sugar Cane Technol. 24:556–559.
- D'Hont, A., L. Grivet, P. Feldmann, S. Rao, N. Berding, and J.C. Glaszmann. 1996. Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics. Mol. Gen. Genet. 250:405–413.[ISI][Medline]
- Fregene, M., A. Bernal, M. Dugue, A. Dixon, and J. Thome. 2000. AFLP analysis of African cassava (Manihot esculenta Crantz) germplasm resistant to the cassava mosaic disease (CMD). Theor. Appl. Genet. 100:678–685.[CrossRef]
- Hoarau, J.Y., B. Offmann, A. D'Hont, A.M. Risterucci, D. Roques, J.C. Glaszmann, and L. Grivet. 2001. Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). I. Genome mapping with AFLP markers. Theor. Appl. Genet. 103:84–97.[CrossRef][ISI]
- Jannoo, N., L. Grivet, A. Dookun, A. D'Hont, and J.C. Glaszmann. 1999a. Linkage disequilibrium among modern sugarcane cultivars. Theor. Appl. Genet. 99:1053–1060.[CrossRef]
- Jannoo, N., L. Grivet, M. Seguin, F. Paulet, R. Domaingue, P.S. Rao, A. Dookun, A. D'Hont, and J.C. Glaszmann. 1999b. Molecular investigation of the genetic base of sugarcane cultivars. Theor. Appl. Genet. 99:171–184.[CrossRef]
- Lima, M.L.A., A.A.F. Garcia, K.M. Oliveira, S. Matsuoka, H. Arizono, C.L. de Souza, Jr., and A.P. de Souza. 2002. Analysis of genetic similarity detected by AFLP and coeffecient of parentage among genotypes of sugar cane (Saccharum spp.). Theor. Appl. Genet. 104:30–38.[CrossRef][ISI][Medline]
- Lu, Y.H., A. D'Hont, D.J.T. Walker, P.S. Rao, P. Feldmann, and J.C. Glaszmann. 1994. Relationships among ancestral species of sugarcane revealed with RFLP using single-copy maize nuclear probes. Euphytica 78:7–18.[CrossRef]
- Mantel, N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Res. 27:209–220.[ISI][Medline]
- Mukherjee, S.K. 1957. Origin and distribution of Saccharum. Bot. Gaz. 119:55–61.[CrossRef]
- Nair, N.V., A. Selvi, T.V. Sreenivasan, and K.N. Pushpalatha. 2002. Molecular diversity in Indian sugarcane cultivars as revealed by randomly amplified DNA polymorphisms. Euphytica 127:219–225.[CrossRef]
- Perrier, X., A. Flori, and F. Bonnot. 2003. Methods of data analysis. p. 43–76. In P. Hamon et al. (ed.) Genetic diversity of cultivated tropical plants. CIRAD, Montpellier, France.
- Prashanth, S.R., M. Parani, B.P. Mohanty, V. Talame, R. Tuberosa, and A. Parida. 2002. Genetic diversity in cultivars and landraces of Oryza sativa subsp. indica as revealed by AFLP markers. Genome 45:451–459.[Medline]
- Ramakrishna, W., M.D. Lagu, V.S. Gupta, and P.K. Ranjekar. 1994. DNA fingerprinting in rice using oligonucleotide probes specific for simple repetitive DNA sequences. Theor. Appl. Genet. 88:402–406.
- Ren, N., and M.P. Timko. 2001. AFLP analysis of genetic polymorphism and evolutionary relationships among cultivated and wild Nicotiana species. Genome 44:559–571.[Medline]
- Rohlf, F.J. 1990. NTSYS-PC. Numerical taxonomy and multivariate analysis system. Version1.60. Applied Biostatistics, New York
- Saitou, N., and M. Nei. 1987. The Neighbor-Joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406–425.[Abstract]
- Selvi, A., N.V. Nair, N. Balasundaram, and T. Mohapatra. 2003. Evaluation of maize microsatellite markers for genetic diversity analysis and fingerprinting in sugarcane. Genome 46:394–403.[Medline]
- Selvi, A., N.V. Nair, J.L. Noyer, N.K. Singh, N. Balasundaram, K.C. Bansal, K.R. Koundal, and T. Mohapatra. 2005. AFLP analysis of the phenetic organization and genetic diversity in the sugarcane complex, Saccharum and Erianthus. Genet. Resources Crop Evol. (in press).
- Swofford, D.L. 2000. PAUP: Phylogenetic analysis using parsimony. Sinauer Associates, Sunderland, MA.
- Thuljaram Rao, J. 1987a. The sugarcane wizard Sir T S Venkataraman. In The Platinum Jubilee Souvenir, Vol. 1. Sugarcane Breeding Institute, Coimbatore, India.
- Thuljaram Rao, J. 1987b. Sugarcane origin, taxonomy, breeding and varieties. In M. Naidu et al. (ed.) Sugarcane varietal improvement. Sugarcane Breeding Institute, Coimbatore, India.
- Van Droogenbroeck, B., P. Breyne, P. Goetghebeur, E. Romeijn Peeters, T. Kyndt, and G. Gheysen. 2002. AFLP analysis of genetic relationships among papaya and its wild relatives (Caricaceae) from Ecuador. Theor. Appl. Genet. 105:289–297.[CrossRef][ISI][Medline]
- Vos, P., R. Hogers, M. Bleeker, M. Reijans, T. Van de Lee, M. Hornes, A. Freijters, J. Pot, J. Peleman, M. Kuiper, and M. Zabeau. 1995. AFLP: A new technique for DNA fingerprinting. Nucleic Acids Res. 23:4407–4414.[Abstract/Free Full Text]
- Walbot, V. 1988. Preparation of DNA from single rice seedlings. Rice Genet. Newsl. 5:149–151.
- Zhang, L.H., P. Ozias-Akins, G. Kochert, S. Kresovich, R. Dean, and W. Hanna. 1999. Differentiation of bermudagrass (Cynodon spp.) genotypes by AFLP analyses. Theor. Appl. Genet. 98:895–902.[CrossRef]
Related articles in Crop Science:
- THIS ISSUE IN CROP SCIENCE
Crop Science 2005 45: x.
[Full Text]
TOP
ABSTRACT
INTRODUCTION
