Search

Naturally occurring autopolyploid species, such as the autotetraploid potato Solanum tuberosum, face a variety of challenges during meiosis. These include proper pairing, recombination and correct segregation of multiple homologous chromosomes, which can form complex multivalent configurations at metaphase I, and in turn alter allelic segregation ratios through double reduction. Here, we present a reference map of meiotic stages in diploid and tetraploid S. tuberosum using fluorescence in situ hybridisation (FISH) to differentiate individual meiotic chromosomes 1 and 2. A diploid-like behaviour at metaphase I involving bivalent configurations was predominant in all three tetraploid varieties. The crossover frequency per bivalent was significantly reduced in the tetraploids compared with a diploid variety, which likely indicates meiotic adaptation to the autotetraploid state. Nevertheless, bivalents were accompanied by a substantial frequency of multivalents, which varied by variety and by chromosome (7–48%). We identified possible sites of synaptic partner switching, leading to multivalent formation, and found potential defects in the polymerisation and/or maintenance of the synaptonemal complex in tetraploids. These findings demonstrate the rise of S. tuberosum as a model for autotetraploid meiotic recombination research and highlight constraints on meiotic chromosome configurations and chiasma frequencies as an important feature of an evolved autotetraploid meiosis.

With a rapidly increasing population, diminishing resource availability, and variation in environment, there is a need to change agricultural production to deliver long-term food security. To deliver such change, we need crops that are productive and tolerant to different stress factors. The traditional methods of obtaining data for phenotyping under field conditions, e.g., for morphological traits such as canopy structure or physiological traits such as plant stress-related traits, are laborious and time-consuming. A variety of imaging tools in the visible, spectral, and thermal infrared ranges allow data collection for quantitative studies of complex traits and crop monitoring. These tools can be used on crop phenotyping and monitoring platforms for high-throughput assessment of traits in order to better understand plant stress responses and the physiological pathways underlying yield. The applications and brief review of these imaging techniques are described and discussed in this chapter.

Canopy temperature, detected by thermal imaging, is a good predictor of rice yield performance under drought and shows genetic variation in an association mapping panel., Drought-stressed plants display reduced stomatal conductance, which results in increased leaf temperature by limiting transpiration. In this study, thermal imaging was used to quantify the differences in canopy temperature under drought in a rice diversity panel consisting of 293 indica accessions. The population was grown under paddy field conditions and drought stress was imposed for 2 weeks at flowering. The canopy temperature of the accessions during stress negatively correlated with grain yield (r= –0.48) and positively with plant height (r=0.56). Temperature values were used to perform a genome-wide association (GWA) analysis using a 45K single nucleotide polynmorphism (SNP) map. A quantitative trait locus (QTL) for canopy temperature under drought was detected on chromosome 3 and fine-mapped using a high-density imputed SNP map. The candidate genes underlying the QTL point towards differences in the regulation of guard cell solute intake for stomatal opening as the possible source of temperature variation. Genetic variation for the significant markers of the QTL was present only within the tall, low-yielding landraces adapted to drought-prone environments. The absence of variation in the shorter genotypes, which showed lower leaf temperature and higher grain yield, suggests that breeding for high grain yield in rice under paddy conditions has reduced genetic variation for stomatal response under drought.

Generation of a dense SNP-based linkage map of a diploid potato population and identification of major QTLs for tuber shape and eye depth on chromosomes 2 and 10. This paper reports the construction of a genetic map of a highly heterozygous full-sib diploid potato population (06H1) based on the use of a set of 8,303 single nucleotide polymorphism (SNP) markers. The map contains 1,355 distinct loci and 2,157 SNPs, 802 of which co-segregate with other markers. We find high levels of collinearity between the 12 chromosomal maps with a recently improved version of the potato genome assembly, with the expected genetic clustering in centromeric regions. The linkage maps are used in combination with highly detailed phenotypic assessments conducted over two growing seasons to perform quantitative trait loci analysis of two important potato traits, tuber shape and eye depth. The major loci segregating for tuber shape in 06H1 map to loci on chromosomes 2 and 10, with smaller effects mapping to three other chromosomes. A major locus for tuber eye depth co-locates with the tuber shape locus on chromosome 10. To assess when tuber shape is established in the developing tuber, we have performed staged observations of tuber formation. Our observations suggest that tuber shape is determined very early in tuber development.

Potato is produced on all continents except Antarctica and is the world’s third most important food crop. Potato production has increased dramatically in developing countries in the past two decades, and has now overtaken that in the developed world, underlining the growing importance of potato as a staple food crop to meet the demands of increasing human populations. Potato is also an important source of starch. It has been adapted for cultivation in a wide range of environments and, with the availability of significant germplasm resources, the potential to further exploit its natural biodiversity is considerable. Potato yields vary considerably across the world, with the lowest being in Sub-Saharan Africa

Magnetic resonance imaging (MRI) is a powerful tool for generating 3-dimensional structural and functional image data. MRI has already proven valuable in creating atlases of mouse and quail development. Here, we have exploited high resolution MRI to determine the parameters necessary to acquire images of the chick embryo eye. Using a 9.4 Tesla (400 MHz) high field ultra-shielded and refrigerated magnet (Bruker), MRI was carried out on paraformaldehyde-fixed chick embryos or heads at E4, E6, E8, and E10. Image data were processed using established and custom packages (MRICro, ImageJ, ParaVision, Bruker and mri3dX). Voxel dimensions ranged from 62.5 microm to 117.2 microm. We subsequently used the images obtained from the MRI data in order to make precise measurements of chick embryo eye surface area, volume and axial length from E4 to E10. MRI was validated for accurate sizing of ocular tissue features by direct comparison with previously published literature. Furthermore, we demonstrate the utility of high resolution MRI for making accurate measurements of morphological changes due to experimental manipulation of chick eye development, thereby facilitating a better understanding of the effects on chick embryo eye development and growth of such manipulations. Chondroitin sulphate or heparin were microinjected into the vitreous cavity of the right eyes of each of 3 embryos at E5. At E10, embryos were fixed and various eye parameters (volume, surface area, axial length and equatorial diameter) were determined using MRI and normalised with respect to the un-injected left eyes. Statistically significant alterations in eye volume (p0.05; increases with chondroitin sulphate and decreases with heparin) and changes in vitreous homogeneity were observed in embryos following microinjection of glycosaminoglycans. Furthermore, in the heparin-injected eyes, significant disturbances at the vitreo-retinal boundary were observed as well as retinal folding and detachment confirming histological observations. These data reveal the utility and superiority of MRI for producing images enabling quantification of experimentally induced changes in eye volume and structure. The results indicate that MRI is an important tool that could become a routine approach for rapid and sensitive phenotypic analysis of normal chick ocular development and morphology as well as potentially the effects of surgical or genetic manipulations of chick embryo eyes in live embryos in ovo.

Canopy temperature, a surrogate for stomatal conductance, is shown to be a good indicator of plant water status and a potential tool for phenotyping and irrigation scheduling. Measurement of stomatal conductance and leaf temperature has traditionally been done by using porometers or gas exchange analyzers and fine-wire thermocouples attached to the leaves, which are labor intensive and point measurements. The advent of remote or proximal thermal sensing technologies has provided the potential for scaling up to leaves, plants, and canopies. Thermal cameras with a temperature resolution of0.1 K now allow one to study the temperature variation within and between plants. This chapter discusses some applications of infrared thermography for assessing drought and other abiotic and biotic stress and outlines some of the main factors that need to be considered when applying this to the study of leaf or canopy temperature whether in controlled environments or in the field.

Canopy temperature, a surrogate for stomatal conductance, is shown to be a good indicator of plant water status and a potential tool for phenotyping and irrigation scheduling. Measurement of stomatal conductance and leaf temperature has traditionally been done by using porometers or gas exchange analyzers and fine-wire thermocouples attached to the leaves, which are labor intensive and point measurements. The advent of remote or proximal thermal sensing technologies has provided the potential for scaling up to leaves, plants, and canopies. Thermal cameras with a temperature resolution of

Potato (Solanum tuberosum L.) is often considered as a drought sensitive crop and its sustainable production is threatened due to frequent drought episodes. There has been much research aiming to understand the physiological, biochemical, and genetic basis of drought tolerance in potato as a basis for improving production under drought conditions. The complex phenotypic response of potato plants to drought is conditioned by the interactive effects of the plant's genotypic potential, developmental stage, and environment. Effective crop improvement for drought tolerance will require the pyramiding of many disparate characters, with different combinations being appropriate for different growing environments. An understanding of the interaction between below ground water uptake by the roots and above ground water loss from the shoot system is essential. The development of high throughput precision phenotyping platforms is providing an exciting new tool for precision screening, which, with the incorporation of innovative screening strategies, can aid the selection and pyramiding of drought-related genes appropriate for specific environments. Outcomes from genomics, proteomics, metabolomics, and bioengineering advances will undoubtedly compliment conventional breeding strategies and presents an alternative route toward development of drought tolerant potatoes. This review presents an overview of past research activity, highlighting recent advances with examples from other crops and suggesting future research directions.

The rapid development of genomic technology has made high throughput genotyping widely accessible but the associated high throughput phenotyping is now the major limiting factor in genetic analysis of traits. This paper evaluates the use of thermal imaging for the high throughput field phenotyping of Solanum tuberosum for differences in stomatal behaviour. A large multi-replicated trial of a potato mapping population was used to investigate the consistency in genotypic rankings across different trials and across measurements made at different times of day and on different days. The results confirmed a high degree of consistency between the genotypic rankings based on relative canopy temperature on different occasions. Genotype discrimination was enhanced both through normalising data by expressing genotype temperatures as differences from image means and through the enhanced replication obtained by using overlapping images. A Monte Carlo simulation approach was used to confirm the magnitude of genotypic differences that it is possible to discriminate. The results showed a clear negative association between canopy temperature and final tuber yield for this population, when grown under ample moisture supply. We have therefore established infrared thermography as an easy, rapid and non-destructive screening method for evaluating large population trials for genetic analysis. We also envisage this approach as having great potential for evaluating plant response to stress under field conditions.

Purpose. To investigate the extent to which shared genetic variants control (1) multiple ocular component dimensions and (2) both normal eye length and susceptibility to visually induced myopic eye growth. \ud \ud Methods. Two laboratory-reared populations of chicks were examined. The first was a three-generation pedigree of White Leghorn (WL) birds used in a selective breeding experiment testing susceptibility to monocular deprivation of sharp vision (DSV). The chicks were assessed before (age, 4 days) and after 4 days of treatment with diffusers. The second was the 10th generation of an advanced intercross line (AIL) derived from a broiler-layer cross (age, 3 weeks). Variance components analysis was used to estimate heritability and to assess the evidence for shared genetic determination. \ud \ud Results. All measured ocular components were moderately or highly heritable (range, 0.36–0.61; all P < 0.001) in both chick populations, and there were strong genetic correlations across the traits, corneal curvature, vitreous chamber depth, and axial length. The genetic correlations between eye size and myopia susceptibility traits were not significantly different from 0. \ud \ud Conclusions. The genetic variants controlling ocular component dimensions in chicks are shared across some ocular traits (corneal curvature, vitreous chamber depth, and axial length) but distinct for others (lens thickness and corneal thickness). The genetic variants controlling susceptibility to visually induced myopia in chicks are different from those controlling normal eye size

Purpose. There is considerable variation in the degree of form-deprivation myopia (FDM) induced in chickens by a uniform treatment regimen. Sex and pretreatment eye size have been found to be predictive of the rate of FD-induced eye growth. Therefore, this study was undertaken to test whether the greater rate of myopic eye growth in males is a consequence of their larger eyes or of some other aspect of their sex.\ud \ud Methods. Monocular FDM was induced in 4-day-old White Leghorn chicks for 4 days. Changes in ocular component dimensions and refractive error were assessed by A-scan ultrasonography and retinoscopy, respectively. Sex identification of chicks was performed by DNA test. Relationships between traits were assessed by multiple regression.\ud \ud Results. FD produced (mean ± SD) 13.47 ± 3.12 D of myopia and 0.47 ± 0.14 mm of vitreous chamber elongation. The level of induced myopia was not significantly different between the sexes, but the males had larger eyes initially and showed greater myopic eye growth than did the females. In multiple linear regression analysis, the partial correlation between sex and the degree of induced eye growth remained significant (P = 0.008) after adjustment for eye size, whereas the partial correlation between initial eye size and the degree of induced eye growth was no longer significant after adjustment for sex (P = 0.11). After adjustment for other factors, the chicks' sex accounted for 6.4% of the variation in FD-induced vitreous chamber elongation.\ud \ud Conclusions. The sex of the chick influences the rate of experimentally induced myopic eye growth, independent of its effects on eye size.

Purpose A reduction in the power of the crystalline lens during childhood is thought to be important in the emmetropization of the maturing eye. However, in humans and model organisms, little is known about the factors that determine the dimensions of the crystalline lens and in particular whether these different parameters (axial thickness, surface curvatures, equatorial diameter, and volume) are under a common source of control or regulated independently of other aspects of eye size and shape. Methods Using chickens from a broiler-layer experimental cross as a model system, three-dimensional magnetic resonance imaging (MRI) scans were obtained at 115-µm isotropic resolution for one eye of 501 individuals aged 3-weeks old. After fixation with paraformaldehyde, the excised eyes were scanned overnight (16 h) in groups of 16 arranged in a 2×2×4 array. Lens dimensions were calculated from each image by fitting a three-dimensional mesh model to the lens, using the semi-automated analysis program mri3dX. The lens dimensions were compared to measures of eye and body size obtained in vivo using techniques that included keratometry and A-scan ultrasonography. Results A striking finding was that axial lens thickness measured using ex vivo MRI was only weakly correlated with lens thickness measured in vivo by ultrasonography (r=0.19, p

Myopia development is characterised by an increased axial eye length. Therefore, identifying factors that influence eye size may provide new insights into the aetiology of myopia. In humans, axial length is positively correlated to height and weight, and in mice, eye weight is positively correlated with body weight. The purpose of this study was to examine the relationship between eye size and body size in chickens from a genetic cross in which alleles with major effects on eye and body size were segregating. Chickens from a cross between a layer line (small body size and eye size) and a broiler line (large body and eye size) were interbred for 10 generations so that alleles for eye and body size would have the chance to segregate independently. At 3 weeks of age, 510 chicks were assessed using in vivo high resolution A-scan ultrasonography and keratometry. Equatorial eye diameter and eye weight were measured after enucleation. The variations in eye size parameters that could be explained by body weight (BW), body length (BL), head width (HW) and sex were examined using multiple linear regression. It was found that BW, BL and HW and sex together predicted 51–56% of the variation in eye weight, axial length, corneal radius, and equatorial eye diameter. By contrast, the same variables predicted only 22% of the variation in lens thickness. After adjusting for sex, the three body size parameters predicted 45–49% of the variation in eye weight, axial length, corneal radius, and eye diameter, but only 0.4% of the variation in lens thickness. In conclusion, about half of the variation in eye size in the chickens of this broiler-layer advanced intercross line is likely to be determined by pleiotropic genes that also influence body size. Thus, mapping the quantitative trait loci (QTL) that determine body size may be useful in understanding the genetic determination of eye size (a logical inference of this result is that the 20 or more genetic variants that have recently been shown to influence human height may also be found to influence axial eye length). Furthermore, adjusting for body size will be essential in mapping pure eye size QTL in this chicken population, and may also have value in mapping eye size QTL in humans.

Purpose: Mandel et al recently reported that season of birth and daylight hours (photoperiod) at birth were associated with moderate and high levels of myopia in Israeli conscripts. We sought to investigate whether these associations were evident in subjects from the United Kingdom (UK). Design: Retrospective cross-sectional study. Participants: The study population comprised 74,459 subjects aged 18 to 100 years attending UK optometry practices for an eye examination. Methods: Data comprising non-cycloplegic spectacle prescription, sex, date of birth, and date of eye examination were collected from UK optometry practices. The average refractive error in fellow eyes was used to classify the degree of myopia in diopters (D) for each subject as follows: absent (??0.75 D), low (?0.75 to ?2.99 D), moderate (?3.00 to ?5.99 D), or high (??6.00 D). The average monthly hours of daylight for London, UK, were classified into 1 of 4 “photoperiod categories,” following Mandel et al. The odds ratio (OR) for each level of severity of myopia was calculated using multivariate logistic regression with age, sex, and either season of birth or photoperiod category as risk factors. Main Outcome Measures: The OR for season of birth and photoperiod category as potential risk factors for myopia. Results: Season of birth was significantly associated with the presence of high myopia: Subjects born in summer or autumn were more likely to be highly myopic compared with those born in winter (summer OR ? 1.17; 95% confidence interval [CI], 1.05–1.30; P ? 0.006; autumn OR ? 1.16; 95% CI, 1.04–1.30; P ? 0.007). However, season of birth was not a significant risk factor for low or moderate myopia. Photoperiod category was weakly associated with low myopia (OR ? 0.94; 95% CI, 0.89–0.99; P ? 0.019), but with a direction of effect opposite to that observed by Mandel et al. Conclusions: As in Israel, a disproportionate number of UK high myopes were born in summer or autumn rather than in winter. However, unlike the situation in Israel, this association does not seem to be related to daylight hours during the postnatal period, implicating alternative physiologic influences that vary with season, such as birth weight.

Most astigmats have a similar level of astigmatism in each eye. However, there is controversy over whether the astigmatic axes in fellow eyes typically show direct or mirror symmetry. We carried out a statistical analysis designed to address this issue.The median absolute difference in the astigmatic axes of fellow eyes was calculated for a sample of 50 995 astigmats (subjects with at least 0.25 D of astigmatism in each eye). This was done, firstly, for a 'direct symmetry model' in which the difference in axis was calculated as |AxisR - AxisL| and secondly, for a 'mirror symmetry model' in which the difference in axis was calculated as |AxisR - (180 - AxisL)|.Under the direct symmetry model, the median absolute difference in the axis of astigmatism between fellow eyes was 20 degrees. Under the mirror symmetry model, the median absolute difference in the axis of astigmatism between fellow eyes was significantly lower, at 10 degrees (p10e-100). Comparable results were found when the analysis was restricted to subjects with: lower levels of astigmatism (or =1.00 D), higher levels of astigmatism (1.00 D), against-the-rule astigmatism, with-the-rule astigmatism or oblique astigmatism (all p10e-100).Our results show that mirror, rather than direct, symmetry is the norm.

Intraocular pressure (IOP), an important risk factor for glaucoma, is a continuous trait determined by a complex set of genetic and environmental factors that are largely unknown. Genetic studies in laboratory animals may facilitate the identification of genes that affect IOP. We examined the use of the rebound tonometer for measuring IOP in non-anaesthetised birds, along with the device’s robustness to alignment errors. Calibration curves were obtained by measuring the IOP of cannulated chicken eyes with the rebound tonometer over a range of pressures. To simulate different types of alignment errors that might be expected with measurement of IOP in alert chickens, for some calibrations the tonometer was positioned (1) at various distances from the cornea, (2) laterally displaced from the visual axis, or (3) angled away from the visual axis. In vivo measurements were taken on three-week-old alert chickens from a layer line, a broiler line, and a layer-broiler ‘‘advanced intercross line’’ (AIL) designed to facilitate QTL mapping. The rebound tonometer showed excellent linearity (R2 ¼ 0.95e0.99) during calibration, as well as robustness to variation in the probe-to-cornea distance over the range 3e5 mm and to lateral displacement over the range 0e2 mm. However, the tonometer appeared less robust to off-axis misalignment over the range 0e20? (P < 0.05). Also, the slope of calibration curves sometimes differed between eyes (P < 0.001), presumably reflecting differences in ocular structure. The IOP measured in non-anaesthetised three-week-old AIL chickens was 17.51 ? 0.13 mmHg (mean ? S.E.; N ¼ 105 birds). IOP was significantly associated with corneal thickness (P < 0.05) and body weight (P < 0.001) in a regression model. Replicate measurements were necessary in order to gauge IOP accurately in individual birds; a series of seven tonometry sessions over a 12-h period during the light phase of the light/dark cycle permitted IOP to be measured with a 95% CI of ?0.7 mmHg. IOP did not differ significantly between the broiler and layer chicken lines which served as the progenitor lines for the AIL. In conclusion, the rebound tonometer permits rapid estimation of IOP in chickens and is well tolerated. The small alignment errors that are expected when taking measurements in non-anaesthetised animals are unlikely to affect accuracy. Since high IOP is a major risk factor for glaucoma, identifying QTL controlling IOP may offer future health benefits. However, our preliminary findings highlight several obstacles to mapping such QTL using the chicken advanced intercross line evaluated here.

Purpose. To test whether the interanimal variability in susceptibility to visually induced myopia is genetically determined. \ud \ud Methods. Monocular deprivation of sharp vision (DSV) was induced in outbred White Leghorn chicks aged 4 days. After 4 days' DSV, myopia susceptibility was quantified by the relative changes in axial length and refraction. Chicks in the extreme tails of the distribution of susceptibility to DSV were kept and paired for breeding (high- and low-susceptibility lines). A second round of selection was then performed. The third generation of chicks, derived from the selected parents, was assessed after either monocular DSV (4 or 10 days) or lens wear. \ud \ud Results. After two rounds of selective breeding, the chicks from the high-susceptibility line developed approximately twice as much myopia in response to 4 days' DSV as did those from the low-susceptibility line (P < 0.001). All ocular component dimensions differed significantly (P < 0.001) between the two selected lines, both before treatment and in the responses of the treated eye. When DSV was conducted for 10 days, the relative changes in axial length and refractive error were still significantly different between the high and low lines (P < 0.001). The chicks bred for high or low susceptibility to DSV also showed significantly different responses to minus lens wear, but not to plus lens wear. Additive genetic effects explained ∼50% of the interanimal variability in response to DSV. \ud \ud Conclusions. Genes and environment interact to shape refractive development in chicks.