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

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)

Microsatellites and agronomic traits for assessing genetic relationships among 18 New Rice for Africa (NERICA) varieties

The Africa Rice Center (WARDA) has developed several interspecific rice varieties by crossing the high yielding Asian rice (Oryza sativa subsp. japonica) with the locally adapted African rice (Oryza glaberrima). Eighteen varieties were named with the prefix NERICA (New Rice for Africa) but theirgenetic difference and patterns of relationship is largely unknown. A total of 102 polymorphic microsatellite markers were used to genotype 18 NERICAs. A subset of seven NERICAs (NERICA 1 to 7) was further characterized for 10 agronomic traits. The microsatellites data revealed no genetic difference between NERICA 8 and 9. The absence of genetic distance and identical SSR haplotype distribution (banding pattern) observed between NERICAs 8 and 9 is highly likely to be due to lack molecular difference at the DNA level but the possibility for seed admixture remains to be explored. This study, however, revealed the presence of a wide range of genetic differences among all other NERICAs, with the highest being between NERICA 6 and 17. Cluster and principal component analyses of the SSR data revealed distinct separation of NERICA 1 to 7 from NERICA 8 to 18. The possible reasons for such separation and the implications for breeding programs are discusse

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

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

Genetic diversity analysis in tropical maize germplasm for stem borer and storage pest resistance using molecular markers and phenotypic traits

One hundred maize inbred lines and eighty four hybrids were characterized for resistance to maize stem borer and post-harvest insect pests. This was achieved using genetic distance and population structure based on simple sequence repeat (SSR) markers and biophysical traits. The test materials were evaluated for stem borer, maize weevil and larger grain borer (LGB) resistance. Leaf samples were harvested from 10 healthy plants per genotype and bulked. Genomic DNA was extracted using a modified version of mini-prep Cetyl Trimethyl Ammonium Bromide (CTAB) method. The samples were genotyped with 55 SSRs makers. Univariate analysis of variance was done using the general linear model procedure of SAS statistical package. Rodgers genetic distance was calculated for all data sets as a measure of genetic distance using NTSYS-pc for Windows. The distance matrices were used to generate phenograms using the unweighted pair group method based on arithmetic average (UPGMA) method in MEGA5. The genotypes were assigned into different populations using population structure software. The data was further subjected to discriminant and principal component analysis to group the gnotyoes. Analysis of molecular variance within and among the different populations was done using arlequin. There were significant differences (P ≤ 0.001) for all the biophysical traits evaluated. The SSR marker data estimated successfully the close relationship among different hybrids and inbred lines within clusters. Comparisons of the different multivariate analyses revealed high concordance among the different approaches of analyses. The results of this study can be directly used by breeding programs to develop resistant genotypes

Rotational diversity effects in a triticale-based cropping system

Research indicates that not all crops respond similarly to cropping diversity and the response of triticale (× Triticosecale ssp.) has not been documented. We investigated the effects of rotational diversity on cereals in cropping sequences with canola (Brassica napus L.), field pea (Pisum sativum L.), or an intercrop (triticale:field pea). Six crop rotations were established consisting of two, 2-yr low diversity rotations (LDR) (continuous triticale (T-T_LDR) and triticale-wheat (Triticum aestivum L.) (T-W_LDR)); three, 2-yr moderate diversity rotations (MDR) (triticale-field pea (T-P_MDR), triticale-canola (T-C_MDR), and a triticale: field pea intercrop (T- in P_MDR)); and one, 3-yr high diversity rotation (HDR) (canola-triticale-field pea (C-T-P_HDR)). The study was established in Lethbridge, Alberta (irrigated and rainfed); Swift Current (rainfed) and Canora (rainfed), Saskatchewan, Canada; and carried out from 2008 to 2014. Triticale grain yield for the 3-yr HDR was superior over the LDR rotations and the MDR triticale-field pea system; however, results were similar for triticale-canola, and removal of canola from the system caused a yield drag in triticale. Triticale biomass was superior for the 3-yr HDR. Moreover, along with improved triticale grain yield, the 3-yr HDR provided greater yield stability across environments. High rotational diversity (C-T-P_HDR) resulted in the highest soil microbial community and soil carbon concentration, whereas continuous triticale provided the lowest. Net economic returns were also superior for C-T-P_HDR ($670 ha–1) and the lowest for T-W_LDR ($458 ha–1). Overall, triticale responded positively to increased rotational diversity and displayed greater stability with the inclusion of field pea, leading to improved profitability and sustainability of the system

Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice

Previous studies conducted on limited number of accessions have reported very low genetic variation in African rice (Oryza glaberrima Steud.) as compared to its wild progenitor (O. barthii A. Chev.) and to Asian rice (O. sativa L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and O. barthii (115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of O. barthii, respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1–32.1 and 16.3–37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10−4, which is not only 20-fold smaller than the value estimated from all genomewide SNPs (π = 1.6 × 10−2), but also accounted for just 4.1%, 0.9% and 2.1% of that of O. barthii, lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use