Construction, characteristics and high throughput molecular screening methodologies in some special breeding populations: a horticultural perspective

Advanced marker technologies are widely used for evaluation of genetic diversity in cultivated crops, wild ancestors, landraces or any special plant genotypes. Developing agricultural cultivars requires the following steps: (i) determining desired characteristics to be improved, (ii) screening genetic resources to help find a superior cultivar, (iii) intercrossing selected individuals, (iv) generating genetically hybrid populations and screening them for agro-morphological or molecular traits, (v) evaluating the superior cultivar candidates, (vi) testing field performance at different locations, and (vii) certifying. In the cultivar development process valuable genes can be identified by creating special biparental or multiparental populations and analysing their association using suitable markers in given populations. These special populations and advanced marker technologies give us a deeper knowledge about the inherited agronomic characteristics. Unaffected by the changing environmental conditions, these provide a higher understanding of genome dynamics in plants. The last decade witnessed new applications for advanced molecular techniques in the area of breeding,with low costs per sample. These, especially, include next-generation sequencing technologies like reduced representation genome sequencing (genotyping by sequencing, restriction site-associated DNA). These enabled researchers to develop new markers, such as simple sequence repeat and single- nucleotide polymorphism, for expanding the qualitative and quantitative information onpopulation dynamics. Thus, the knowledge acquired from novel technologies is a valuable asset for the breeding process and to better understand the population dynamics, their properties, and analysis methods

Candidate screening of blast resistance donors for rice breeding

Rice blast is one of the most serious diseases in the world. The use of resistant cultivars is the most preferred means to control this disease. Resistance often breaks down due to emergence of new races; hence identification of novel resistance donors is indispensable. In this study, a panel of 80 released varieties from National Rice Research Institute, Cuttack was genotyped with 36 molecular markers that were linked to 36 different blast resistance genes, to investigate the varietal genetic diversity and molecular marker-trait association with blast resistance. The polymorphism information content of 36 loci varied from 0.11 to 0.37 with an average of 0.34. The cluster analysis and population structure categorized the 80 National Rice Research Institute released varieties (NRVs) into three major genetic groups. The principal co-ordinate analysis displays the distribution of resistant and moderately resistant NRVs into different groups. Analysis of molecular variance result demonstrated maximum (97%) diversity within populations and minimum (3%) diversity between populations. Among tested markers, two markers (RM7364 and pi21_79-3) corresponding tothe blast resistance genes (Pi56(t) and pi21) were significantly associated and explained a phenotypic variance of 4.9 to 5.1% with the blast resistance. These associated genes could be introgressed through marker-assisted to develop durable blast resistant rice varieties. The selected resistant NRVs could be good donors for the blast resistance in rice crop improvement research.

Genetic dissection of grain iron and zinc concentrations in lentil (Lens culinaris Medik.)

Iron (Fe) and zinc (Zn) deficiencies are wide spread in South Asia and Africa. Biofortification of food crops is a viable means of addressing micronutrient deficiencies. Lentil is an important pulse crop that provides affordable source of proteins, minerals, fibre and carbohydrates for micronutrient deficient countries. An association mapping (AM) panel of 96 diverse lentil genotypes fromIndia and Mediterranean region was evaluated for three seasons and genotyped using 80 polymorphic simple-sequence repeat (SSR) markers for identification of the markers associated with grain Fe and Zn concentrations. A Bayesian model based clustering identified five subpopulations, adequately explaining the genetic structure of the AM panel. The linkage disequilibrium (LD) analysis usingmixed linear model (MLM) identified two SSR markers, GLLC106 and GLLC108, associated with grain Fe concentration explaining 17% and 6% phenotypic variation, respectively and three SSR markers (PBALC 364, PBALC 92 and GLLC592) associated with grain Zn concentration, explaining 6%, 8% and 13% phenotypic variation, respectively. The identified SSRs exhibited consistentperformance across three seasons and have potential for utilization in lentil molecular breeding programme.

Molecular markers in management of ex situ PGR – A case study.

Worldwide germplasm collections contain about 7.4 million accessions of plant genetic resources for food and agriculture. One of the 10 largest ex situ genebanks of our globe is located at the Leibniz Institute of Plant Genetics and Crop Plant Research in Gatersleben, Germany. Molecular tools have been used for various gene bank management practices including characterization and utilization of the germplasm. The results on genetic integrity of longterm- stored gene bank accessions of wheat (self-pollinating) and rye (open-pollinating) cereal crops revealed a high degree of identity for wheat. In contrast, the out-pollinating accessions of rye exhibited shifts in allele frequencies. The genetic diversity of wheat and barley germplasm collected at intervals of 40 to 50 years in comparable geographical regions showed qualitative rather than a quantitative change in diversity. The inter- and intraspecific variation of seed longevity was analysed and differences were detected. Genetic studies in barley, wheat and oilseed rape revealed numerous QTL, indicating the complex and quantitative nature of seed longevity. Some of the loci identified were in genomic regions that co-localize with genes determining agronomic traits such as spike architecture or biotic and abiotic stress response. Finally, a genome-wide association mapping analysis of a core collection of wheat for flowering time was performed using diversity array technology (DArT) markers. Maker trait associations were detected in genomic regions where major genes or QTL have been described earlier. In addition, new loci were also detected, providing opportunities to monitor genetic variation for crop improvement.

The genetic dissection of quantitative traits in crops

Most traits of interest in plant breeding show quantitative inheritance, which complicate the breeding process since phenotypic performances only partially reflects the genetic values of individuals. The genetic variation of a quantitative trait is assumed to be controlled by the collective effects of quantitative trait loci (QTLs), epistasis (interaction between QTLs), the environment, and interaction between QTL and environment. Exploiting molecular markers in breeding involve finding a subset of markers associated with one or more QTLs that regulate the expression of complex traits. Many QTL mapping studies conducted in the last two decades identified QTLs that generally explained a significant proportion of the phenotypic variance, and therefore, gave rise to an optimistic assessment of the prospects of markers assisted selection. Linkage analysis and association mapping are the two most commonly used methods for QTL mapping. This review provides an overview of the two QTL mapping methods, including mapping population type and size, phenotypic evaluation of the population, molecular profiling of either the entire or a subset of the population, marker-trait association analysis using different statistical methods and software as well as the future prospects of using markers in crop improvement.

Linkage disequilibrium, genetic association mapping and gene localization in crop plants

DNA-based molecular markers have been extensively utilized for a variety of studies in both plant and animal systems. One of the major uses of these markers is the construction of genome-wide molecular maps and the genetic analysis of simple and complex traits. However, these studies are generally based on linkage analysis in mapping populations, thus placing serious limitations in using molecular markers for genetic analysis in a variety of plant populations. Therefore, alternative approach has been suggested, linkage disequilibrium-based association analysis which detects and locates quantitative trait loci (QTL) by the strength of the correlation between a trait and a marker. Although association analysis has already been used for studies on genetics of complex traits in humans, its use in plants has newly started. In the present review, we describe what is known about variation in linkage disequilibrium (LD) and summarize published results on association studies in crop plant species. We give a list of different factors affecting LD, and discuss the current issues of LD research in plants. Later, we also describe the various uses of LD in crop plants research and summarize the present status of LD researches in different plant genomes. Finally, future key issues about the application of these studies on the localization of genes in these crop plants have been also discussed.

Integrating genomics into Eucalyptus breeding

The advent of high throughput genomic technologies has opened new perspectives in the speed, scale and detail with which one can investigate genes, genomes and complex traits in Eucalyptus species. A genomic approach to a more detailed understanding of important metabolic and physiological processes, which affect tree growth and stress resistance, and the identification of genes and their allelic variants, which determine the major chemical and physical features of wood properties, should eventually lead to new opportunities for directed genetic modifications of far-reaching economic impact in forest industry. It should be kept in mind, however, that basic breeding strategies, coupled with sophisticated quantitative methods, breeder's experience and breeder's intuition, will continue to generate significant genetic gains and have a clear measurable impact on production forestry. Even with a much more global view of genetic processes, genomics will only succeed in contributing to the development of improved industrial forests if it is strongly interconnected with intensive fieldwork and creative breeding. Integrated genomic projects involving multi-species expressed sequence tag sequencing and quantitative trait locus detection, single nucleotide polymorphism discovery for association mapping, and the development of a gene-rich physical map for the Eucalyptus genome will quickly move toward linking phenotypes to genes that control the wood formation processes that define industrial-level traits. Exploiting the full power of the superior natural phenotypic variation in wood properties found in Eucalyptus genetic resources will undoubtedly be a key factor to reach this goal.