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We exploited the newly developed amplified fragment length polymorphism (AFLP) technique to study the polymorphism, distribution and inheritance of AFLP markers with a doubled haploid rice population derived from 'IR64'/'Azucena'. Using only 20 pairs of primer combinations, we detected 945 AFLP bands of which 208 were polymorphic. All 208 AFLP markers were mapped and distributed over all 12 chromosomes. When these were compared with RFLP markers already mapped in the population, we found the AFLP markers to be highly polymorphic in rice and to follow Mendelian segregation. As linkage map of rice can be generated rapidly with AFLP markers they will be very useful for marker-assisted backcrossing.

Seed shattering is an important trait that distinguishes crop cultivars from the wild and weedy species. The genetics of seed shattering was investigated in this study to provide insights into rice domestication and the evolution of weedy rice. Quantitative trait locus (QTL) analysis, conducted in 2 recombinant inbred populations involving 2 rice cultivars and a weedy rice accession of the southern United States, revealed 3-5 QTLs that controlled seed shattering with 38-45% of the total phenotypic variation. Two QTLs on chromosomes 4 and 10 were consistent in both populations. Both cultivar and weedy rice contributed alleles for increased seed shattering. Genetic backgrounds affected both QTL number and the magnitude of QTL effects. The major QTL qSH4 and a minor QTL qSH3 were validated in near-isogenic lines, with the former conferring a significantly higher degree of seed shattering than the latter. Although the major QTL qSH4 overlapped with the sh4, the presence of the nonshattering single nucleotide polymorphism allele in the weedy rice accession suggested involvement of a linked locus or an alternative molecular genetic mechanism. Overlapping of several QTLs with those from earlier studies indicated that weedy rice may have been derived from the wild species Oryza rufipogon. Natural hybridization of rice cultivars with the highly variable O. rufipogon present in different geographic regions might be responsible for the evolution of a wide range of phenotypic and genotypic variabilities seen in weedy rice populations worldwide.

Seed dormancy (SD) is a key domestication trait closely related to preharvest sprouting tolerance. Wild and weedy rices ißryza spp.) exhibit higher degrees of seed dormancy compared to the cultivated rice. Red rice {Oryza sativa L.), a major weed in the rice growing areas of the southern United States, was used to elucidate the genetic architecture of SD. Quantitative trait loci (QTL) analysis conducted in two recombinant inbred line (RIL) populations developed from the crosses involving two rice cultivars (Bengal and Cypress) and a red rice accession (PSRR-1) revealed six to seven QTL for seed dormancy, which accounted for 49 to 52% of the total phenotypic variance. The magnitude of the QTL contribution to phenotypic variance was influenced by genetic backgrounds. The majority of QTL had minor effects, except the QTL linked to Re and Sdr4. The genetic architecture for seed dormancy in U.S. red rice was distinct compared with the earlier reported weedy accessions. Four QTL were mapped onto similar positions in both populations. Both cultivars and red rice contributed alleles for increased SD. Most of the digenic epistatic interactions involved loci other than the QTL with main effects. The nucleotide polymorphisms at the Sdr4 locus could not explain the phenotypic variation for seed dormancy in our materials. The variation in SD among the rice cuitivars could be attributed to segregation of minor QTL, which may be exploited to improve preharvest sprouting tolerance.

Rice has become a model cereal plant for molecular genetic research. Rice has the most comprehensive molecular linkage maps with more than 2000 DNA markers and shows synteny and colinearity with the maps of other cereal crops. Until

Brown rust, caused by the fungus Puccinia melanocephala, poses an increasing threat to sugarcane industries worldwide. Recently, markers R12H16 and 9020-F4 were developed for a major resistance gene Bru1 that contributes to a significant proportion of brown rust resistance in multiple sugarcane industries. Marker-assisted screening of Louisiana sugarcane germplasm showed a low frequency (4.3%, five out of 117 clones) of Bru1 among sugarcane cultivars and elite breeding clones. Likewise, among progeny of crosses involving wild/exotic germplasm, only 14 of 208 clones (6.7%) tested Bru1 positive. However, Bru1 frequency was higher (28.7%, 52 of 181 clones) in wild/exotic germplasm, which indicated that diverse genetic resources are available for Bru1 introgression. Commercial Bru1-positive cultivar, 'L 01-299', was resistant to brown rust. However, Bru1-positive cultivar, 'L 10-146', was susceptible while Bru1-negative cultivars, such as 'L 99-233', showed resistance to brown rust. Bru1-negative clones with brown rust resistance offer an opportunity to identify alternate sources of resistance, which can be pyramided with Bru1 for effective and durable resistance in sugarcane against the changing pathogen.

In addition to the cultivation of sugarcane for sugar, the crop is considered seriously as an important bioenergy grass crop for its high biomass production ability. But, lignin is a serious bottleneck in the bioconversion of lignocellulosic biomass to ethanol. Hence, genetic relationships among 64 genotypes within the Saccharum complex were studied with respect to lignin-related genes using target region amplified polymorphic (TRAP) primers derived from caffeic acid O-methyltransferase (COMT), cinnamoyl alcohol dehydrogenase (CAD), cinnamoyl coA reductase (CCR), and ferrulate 5-hydroxylase (F5H) genes. While the average polymorphism detected by the TRAP markers was 43%, the markers derived from F5H gene (34%) were less polymorphic in comparison to those derived from COMT (46%), CCR (44%), and CAD (46%) genes. The lignin gene-based TRAP markers differentiated members of the Saccharum complex broadly according to previously established genetic relationships in the order of Miscanthus>Erianthus>Saccharum spontaneum>Saccha-rum robustum/Saccharum barberi/Saccharum sinense> Saccharum officinarum/cultivars. Principal coordinate analysis showed that 29% of the total variation was explained by the genotypes with respect to the lignin-related genes. The association of genetic variation revealed in this study with the biomass composition-related genes of the genotypes within a species will be helpful to design breeding strategies to develop superior energy cane cultivars with improved biomass quality of the sugarcane.

Chromosome segment substitution lines (CSSLs) are a powerful alternative for locating quantitative trait loci (QTL), analyzing gene interactions, and providing starting materials for map-based cloning projects. We report the development and characterization of a CSSL library of a U.S. weedy rice accession ‘PSRR-1’ with genome-wide coverage in an adapted rice cultivar ‘Bengal’ background. The majority of the CSSLs carried a single defined weedy rice segment with an average introgression segment of 2.8 % of the donor genome. QTL mapping results for several agronomic and domestication traits from the CSSL population were compared with those obtained from two recombinant inbred line (RIL) populations involving the same weedy rice accession. There was congruence of major effect QTLs between both types of populations, but new and additional QTLs were detected in the CSSL population. Although, three major effect QTLs for plant height were detected on chromosomes 1, 4, and 8 in the CSSL population, the latter two escaped detection in both RIL populations. Since this was observed for many traits, epistasis may play a major role for the phenotypic variation observed in weedy rice. High levels of shattering and seed dormancy in weedy rice might result from an accumulation of many small effect QTLs. Several CSSLs with desirable agronomic traits (e.g. longer panicles, longer grains, and higher seed weight) identified in this study could be useful for rice breeding. Since weedy rice is a reservoir of genes for many weedy and agronomic attributes, the CSSL library will serve as a valuable resource to discover latent genetic diversity for improving crop productivity and understanding the plant domestication process through cloning and characterization of the underlying genes.