Quantification of Pupil Parameters in Diseased and Normal Eyes With Near Infrared Iris Transillumination Imaging

Purpose: To investigate near infrared iris transillumination (NIRit) imaging as a new method to quantify pupil shape, size, and position because the imaging modality can uniquely provide simultaneous information regarding iris structural details that influence pupil characteristics and because exploration of related techniques could promote discovery helpful to clinical research and care. Methods: Digital NIRit images of normal and diseased eyes were used along with computer-assisted techniques to quantify four primary pupil parameters, including pupil roundness (PR), pupil ovalness (PO), pupil size (PS), and pupil eccentricity (PE). A combined measure of PR and PO was also developed, i.e., the pupil circularity index (PCI). Repeatability of the measures was studied and example analyses were performed. Results: Pupil measures could be calculated for right eyes of 307 subjects (164 normal, 143 other), with <0.5% exclusions due to image quality. Repeatability study did not show significant bias (P<0.05) for any of the four primary measures. Example analyses could show age associated differences in pupil shape (>50 year-olds had less regular pupils than <50-year-olds: median PCI=0.009 vs 0.006; P<0.01), and that a group of pigment dispersion syndrome subjects (N=27) had less regular pupils than a group of matched controls (PO=0.9966 vs. 0.9990; P<0.05). Conclusions: Digital NIRit imaging can provide novel, reliable, and informative methods to quantify pupil characteristics while providing simultaneous information about iris structure that may influence these parameters

Genetic dissection of QTLs and differentiation analysis of alleles for heading date genes in rice

<div><p>Heading date is an important agronomic trait in rice (<i>Oryza sativa</i> L.); it determines the geographical and seasonal adaptability of the crop. Single segment substitution lines (SSSLs) have become the preferred experimental materials in mapping functional genetic variations as the particular chromosome segments from donor genotypes can be evaluated for their impact on the phenotype in a recurrent recipient background. The phenotypic differences can be attributed to the control of quantitative trait loci (QTLs). Here, we evaluated a library consisting of 1,123 SSSLs in the same genetic background of an elite rice variety, Huajingxian74 (HJX74), and revealed four SSSLs, W05-1-11-2-7-6 (W05), W08-16-3-2 (W08), W12-28-58-03-19-1 (W12), and W22-9-5-2-4-9-3 (W22), which had a significantly different heading date compared to HJX74. To further genetically dissect the QTLs controlling heading date on chromosomes 3, 6, and 10, four SSSLs were used to develop 15 secondary SSSLs with the smaller substituted segments. The <i>qHD-3</i> heading date QTL detected in W05 and W08 was delimited to an interval of 4.15 cM, whereas <i>qHD-6-1</i> and <i>qHD-6-2</i> heading date QTLs dissected from the substituted segments in W12 were mapped to the intervals of 2.25-cM and 2.55-cM, respectively. The <i>qHD-10</i> QTL detected on the substituted segment in W22 was mapped to an interval of 6.85-cM. The nucleotide and amino acid sequence changes for those genes in the secondary SSSLs were also revealed. The allele variations of those genes might contribute to the heading date QTLs on chromosome 3 (<i>DTH3</i>, <i>OsDof12</i>, and <i>EHD4</i>), chromosome 6 (<i>Hd3a</i>, <i>Hd17</i>, and <i>RFT1</i>), and chromosome 10 (<i>Ehd1</i> and <i>Ehd2</i>). These sequence variations in heading date genes would be useful resources for further studying the function of genes, and would be important for rice breeding. Overall, our results indicate that secondary SSSLs were powerful tools for genetic dissection of QTLs and identification of differentiation in the genes.</p></div

Alignment of Hd17 amino acid sequences from HJX74 and W12-S4.

<p>The green triangles indicate the prematurely terminated coding site in W12-S4, whereas red triangles indicate amino acid substitutions between HJX74 and W12-S4.</p

Putative candidate genes of each QTL.

<p>Putative candidate genes of each QTL.</p

The substituted segments in the four SSSLs and their days to heading in 2014 and 2015.

<p>The substituted segments in the four SSSLs and their days to heading in 2014 and 2015.</p

Genetic dissection and fine mapping of QTLs for heading date on rice chromosome 6.

<p>Genetic dissection and fine mapping of QTLs for heading date on rice chromosome 6.</p

Mapping intervals and allelic effects of QTLs for heading date in the SSSLs.

<p>Mapping intervals and allelic effects of QTLs for heading date in the SSSLs.</p

Alignment of <i>DTH3</i> coding sequences from HJX74, W05-S2 and W08-S3.

<p>The green triangles indicate the locus of CDS sequence from W08-S3, whereas red triangles indicate the locus of CDS sequence from W05-S2.</p

Alignment of <i>Ehd2</i> coding sequences from HJX74 and W22-S2.

<p>The green triangles indicate the start of deletion/insertion variation between HJX74 and W22-S2, whereas red triangles indicate nucleotide substitutions between HJX74 and W22-S2.</p

Alignment of <i>Hd17</i> coding sequences from HJX74 and W12-S4.

<p>The green triangles indicate the start of deletion/insertion variations between HJX74 and W12-S4, whereas red triangles indicate nucleotide substitutions between HJX74 and W12-S4.</p