An overview of molecular marker methods for plants

The development and use of molecular markers for the detection and exploitation of DNA polymorphism is one of the most significant developments in the field of molecular genetics. The presence of various types of molecular markers, and differences in their principles, methodologies, and applications require careful consideration in choosing one or more of such methods. No molecular markers are available yet that fulfill all requirements needed by researchers. According to the kind of study to be undertaken, one can choose among the variety of molecular techniques, each of which combines at least some desirable properties. This article provides detail review for 11 different molecular marker methods: restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), inter-simple sequencerepeats (ISSRs), sequence characterized regions (SCARs), sequence tag sites (STSs), cleaved amplified polymorphic sequences (CAPS), microsatellites or simple sequence repeats (SSRs), expressedsequence tags (ESTs), single nucleotide polymorphisms (SNPs), and diversity arrays technology (DArT)

Principles, requirements and prospects of genetic mapping in plants

Genetic mapping (also known as linkage mapping or meiotic mapping) refers to the determination of the relative position and distances between markers along chromosomes. Genetic map distancesbetween two markers are defined as the mean number of recombination events, involving a given chromatid, in that region per meiosis. Genetic map construction requires that the researcher developappropriate mapping population, decide the sample size and type of molecular marker(s) for genotyping, genotype the mapping population with sufficient number of markers, and perform linkageanalyses using statistical programs. The construction of detailed genetic maps with high levels of genome coverage is a first step for localizing genes or quantitative trait loci (QTL) that are associatedwith economically important traits, marker assisted selection, comparative mapping between different species, a framework for anchoring physical maps, and the basis for map-based cloning of genes.Highly reproducible, high throughput, codominant, and transferable molecular markers, especially developed from expressed regions, are sought to increase the utility of genetic maps. This articlereviews the principles, requirements, and future prospects of genetic mapping in plants

Progress and prospects of marker assisted backcrossing as a tool in crop breeding programs

Marker assisted backcrossing (MAB) is one of the most anticipated and frequently cited benefits of molecular markers as indirect selection tools in breeding programs. However, routine implementationsof MAB in ongoing plant breeding programs are still scarce. Currently MAB of single gene is perhaps the most powerful approach that uses DNA markers effectively. Improvement of quantitative traits loci(QTLs) through MAB resulted to variable results ranging from limited success and/or even a failure to a few highly successful stories. A major constraint to the implementation of MAB in pragmatic breedingprograms has been the high relative cost compared to conventional phenotypic selection. It is a popular misconception that a ‘DNA fingerprint’ is always to be preferred. To be useful to plant breeders,gains made from MAB must be more cost-effective than gains through traditional breeding or MAB must generate significant time savings, which justifies the additional cost involved. Currently, mostnational agricultural research systems (NARS) in Africa have either no or very limited facilities, skilled manpower, and financing for integrating molecular markers as part of their breeding programs. Therefore, conventional breeding methods remain the main option for NARS for many years to come, but targeted use of MAB may become a supplement if well-validated markers are developed or availablethrough collaboration with the international agricultural research centers. This paper provides detail review of the current literature on MAB, including requirements and selected experimental results

Suitability of a selected set of simple sequence repeats (SSR) markers for multiplexing and rapid molecular characterization of African rice (Oryza glaberrima Steud.)

African rice (Oryza glaberrima) was neglected for a long time by researchers but gained attention with the success of NERICA varieties. While AfricaRice holds a collection of about 2,500 O. glaberrima samples only four accessions have been used as NERICA parents. This collection needs to be characterized using rice descriptors and molecular markers to fully exploit the whole diversity of this species. To allow a quick and accurate molecular characterization of African rice, a set of 30 SSR markers were identified and tested on a subset of 74 African rice samples. The results showed that these markers were highly polymorphic, could be multiplexed in 8 panels without overlapping alleles and were able to distinguish the genetic groups of African rice; the two major ecotypes and intermediates between Oryza sativa and O. glaberrima species.Key words: Rice, Oryza glaberrima, simple sequence repeats (SSR) markers, genetic diversity, NERICA (New Rice for Africa)

Molecular profiling of interspecific lowland rice populations derived from IR64 (Oryza sativa) and Tog5681 (Oryza glaberrima)

Several lowland NERICAs (New Rice for Africa) were derived from crosses between IR64 (an Oryza sativa subsp. indica variety) and Tog5681 (an Oryza glaberrima variety) that possess useful traitsadapted to lowland conditions in West Africa. The proportion of parental genomic contribution and extent of genetic differences among these sister lines is unknown at the molecular level. The objectivesin this study were therefore to determine, with 60 SSR markers that cover 1162 cM of the rice genome, the frequency and magnitude of deviations from the expected parental contributions among 21 BC2F10,17 BC3 F8 and 10 BC4F8 lines and determine patterns of their genetic relationships. The estimated average O. glaberrima genome coverage was 7.2% (83.5 cM) at BC2F10, 8.5% (99.3 cM) at BC3F8 and 8.1%(93.8 cM) at BC4F8 lines. The O. sativa parent accounted for 73.2% (851.3 cM) at BC2F10, 82.6% (959.5 cM) at BC3F8 and 78.2% (908.6 cM) at BC3F8. Non-parental alleles were detected at all 3 backcross generations but the frequency of such alleles at BC2 (8.8%) was twice that of BC3F8 (3.4%) and nine times that of BC4F8 (0.9%). Both cluster and principal component analyses revealed two major groups irrespective of the level of backcross generations and the proportion of parental genome contribution

Molecular profiling of an interspecific rice population derived from a cross between WAB 56-104 (Oryza sativa) and CG 14 (Oryza glaberrima)

NERICA rices are interspecific inbred progeny derived from crosses between Oryza sativa x O. glaberrima. In this study, we evaluated 70 BC2 interspecific lines, developed by crossing a tropicaljaponica variety (WAB 56-104) as the recurrent parent to an O. glaberrima variety (CG 14) as the donor parent, followed by the use of anther culture to derive doubled haploids (DH) (26 lines) or eightgenerations of inbreeding to fix the lines (44 lines). Seven of these BC2 derived inbred lines have been released as NERICA 1 - NERICA 7. This study examined the relative contribution of each parent and theextent of genetic differences among these 70 sister lines using 130 well-distributed microsatellite markers which cover 1725 cM of the rice genome. The average proportion of O. sativa recurrent parentgenome was 87.4% (1,508 cM), while the observed average proportion of O. glaberrima donor genome was 6.3% (108 cM). Non-parental alleles were detected in 83% of the lines and contributed an average of38 cM per line (~2.2% of genomic DNA). Lines that had undergone eight generations of inbreeding in the field contained significantly more non-parental alleles (av. 2.7%) compared to the DH lines (av. 1.3%)that were developed from BC2 anthers. Using both cluster and principal component analyses, two major groups were detected in these materials. The NERICA varieties (NERICA 1 to 7) clustered in one group while the remaining 63 lines clustered in another group, suggesting that the second group may offer significant opportunities for further selection and variety development

Identification and differentiation of three Nigerian Orseolia sp. by RAPD markers

Identification and differentiation of three Nigerian Orseolia sp. (Orseolia nwanzei, Orseolia bonzii and Orseolia oryzivora) was carried out using Random Amplified Polymorphic DNA (RAPD) markers. Ninety operon primers were screened, from which 6 showed polymorphism among the three species tested, generating 54 bands, 69% of which were polymorphic with sizes ranging between 1000 and 3000 bp. DNA fingerprints of adults and pupae of each species were genetically identical. O. oryzivora and O. bonzii are identified as most closely related, while O. nwanzei is distinct. The DNA fingerprints identified for each Orseolia sp. will be useful for entomological survey for the identification of new species within the context of the effective development of rice cultivars with durable resistance to AfRGM