Empirical threshold values for quantitative trait mapping.

Over the past two decades, research in forest tree genomics has lagged behind that of model and agricultural systems. However, genomic research in forest trees is poised to enter into an important and productive phase owing to the advent of next-generation sequencing technologies, the enormous genetic diversity in forest trees and the need to mitigate the effects of climate change. Research on long-lived woody perennials is extending our molecular knowledge of complex life histories and adaptations to the environment - enriching a field that has traditionally drawn biological inference from a few short-lived herbaceous species.

Forest tree genomics: growing resources and applications.

During the last two decades, 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 systems. Therefore, alternative approaches have been suggested, and one of these approaches makes use of linkage disequilibrium (LD)-based association analysis. Although this approach of association analysis has already been used for studies on genetics of complex traits (including different diseases) in humans, its use in plants has just started. In the present review, we first define and distinguish between LD and association mapping, and then briefly describe various measures of LD and the two methods of its depiction. We then give a list of different factors that affect LD without discussing them, and also discuss the current issues of LD research in plants. Later, we also describe the various uses of LD in plant genomics research and summarize the present status of LD research in different plant genomes. In the end, we discuss briefly the future prospects of LD research in plants, and give a list of softwares that are useful in LD research, which is available as electronic supplementary material (ESM).

/pdf/linkage-disequilibrium-and-association-studies-in-higher-16ui1uj3xs.pdf

Linkage disequilibrium and association studies in higher plants: present status and future prospects.

Several new initiatives have been launched recently to sequence conifer genomes including pines, spruces and Douglas-fir. Owing to the very large genome sizes ranging from 18 to 35 gigabases, sequencing even a single conifer genome had been considered unattainable until the recent throughput increases and cost reductions afforded by next generation sequencers. The purpose of this review is to describe the context for these new initiatives. A knowledge foundation has been acquired in several conifers of commercial and ecological interest through large-scale cDNA analyses, construction of genetic maps and gene mapping studies aiming to link phenotype and genotype. Exploratory sequencing in pines and spruces have pointed out some of the unique properties of these giga-genomes and suggested strategies that may be needed to extract value from their sequencing. The hope is that recent and pending developments in sequencing technology will contribute to rapidly filling the knowledge vacuum surrounding their structure, contents and evolution. Researchers are also making plans to use comparative analyses that will help to turn the data into a valuable resource for enhancing and protecting the world’s conifer forests.

/pdf/towards-decoding-the-conifer-giga-genome-3hlqb46v4s.pdf

Towards decoding the conifer giga-genome.

We present here the first study of linkage disequilibrium (LD) in cultivated grapevine, Vitis vinifera L. subsp. vinifera (sativa), an outcrossing highly heterozygous perennial species. Our goal was to characterize the amount and pattern of LD at the scale of a few centiMorgans (cM) between 38 microsatellite loci located on five linkage groups, in order to assess its origin and potential applications. We used a core collection of 141 cultivars representing the diversity of the cultivated compartment. LD was evaluated with both independence tests and multilocus r2, both on raw genotypic and reconstructed haplotypic data. Significant genotypic LD was found only within linkage groups, extending up to 16.8 cM. It appeared not to be influenced by the weak structure of the sample and seemed to be mainly of haplotypic origin. Significant haplotypic LD was found over 30 cM. Both genotypic and haplotypic r2 values declined to around 0.1 within 5-10 cM, suggesting a rather narrow genetic base of the cultivated compartment and limited recombination since domestication events. These first results open up a few application opportunities for association mapping of QTLs and marker assisted selection.

Linkage disequilibrium in cultivated grapevine, Vitis vinifera L.

The objective of this study was to determine the genetic location and effects of genomic regions controlling wood density at three stages, i.e., rings corresponding to ages 1–5 (WD1_5), rings corresponding to ages 6–10 (WD6_10), and outer wood density (WD14) in a full-sib pedigree (850.055×850.096) of Pinus radiata. The number of offspring measured at these three stages were 80, 93 and 93, respectively. Only a single linkage group of the parent 850.55 was considered for mapping quantitative trait loci (QTLs). A multiple-marker least-squares approach was employed for mapping QTLs for each of the three traits, using a single-QTL model. Logistic regression was used for multiple-trait QTL mapping. Critical values for test-statistic were calculated empirically by ’shuffling’ the data. A putative QTL with large effect on WD1_5 appears to be segregating at the 73 cM position (experimentwise P<0.01). The width of the 95% bootstrap confidence interval for this putative QTL was 40 cM (i.e. 56–96 cM). The effect of this QTL on the expression of wood density at later stages was diminished. From multiple-trait analysis, two marker locations (at 66 cM and 91 cM) were found to be significantly associated (experimentwise P <0.05) with the expression of wood density at different ages. These results are encouraging for the application of marker information to early selection in order to increase juvenile wood density, although the putative QTLs detected in this study need to be verified in an independent population.

https://link.springer.com/content/pdf/10.1007/s001220051372.pdf

Multiple-marker mapping of wood density loci in an outbred pedigree of radiata pine

Linkage analysis is commonly used to find marker-trait associations within the full-sib families of forest tree and other species. Study of marker-trait associations at the population level is termed linkage-disequilibrium (LD) mapping. A female-tester design comprising 200 full-sib families generated by crossing 40 pollen parents with five female parents was used to assess the relationship between the marker-allele frequency classes obtained from parental genotypes at SSR marker loci and the full-sib family performance (average predicted breeding value of two parents) in radiata pine ( Pinus radiata D. Don). For alleles (at a marker locus) that showed significant association, the copy number of that allele in the parents was significantly correlated, either positively or negatively, with the full-sib family performance for various economic traits. Regression of parental breeding value on its genotype at marker loci revealed that most of the markers that showed significant association with full-sib family performance were not significantly associated with the parental breeding values. This suggests that over-representation of the female parents in our sample of 200 full-sib families could have biased the process of detecting marker-trait associations. The evidence for the existence of marker-trait LD in the population studied is rather weak and would require further testing. The exact test for genotypic disequilibrium between pairs of linked or unlinked marker loci revealed non-significant LD. Observed genotypic frequencies at several marker loci were significantly different from the expected Hardy-Weinberg equilibrium. The possibilities of utilising marker-trait associations for early selection, among-family selection and selecting parents for the next generation of breeding are also discussed.

/pdf/testing-for-linkage-disequilibrium-in-the-new-zealand-jbu31nnkz6.pdf

Testing for linkage disequilibrium in the New Zealand radiata pine breeding population

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Multiple-marker mapping of wood density loci in an outbred pedigree of radiata pine

Testing for linkage disequilibrium in the New Zealand radiata pine breeding population