Identification of Ear Morphology Genes in Maize (Zea mays L.) Using Selective Sweeps and Association Mapping

The performance of maize hybrids largely depend on two parental inbred lines. Improving inbred lines using artificial selection is a key task in breeding programs. However, it is important to elucidate the effects of this selection on inbred lines. Altogether, 208 inbred lines from two maize heterosis groups, named Shaan A and Shaan B, were sequenced by the genotype-by-sequencing to detect genomic changes under selection pressures. In addition, we completed genome-wide association analysis in 121 inbred lines to identify candidate genes for ear morphology related traits. In a genome-wide selection scan, the inbred lines from Shaan A and Shaan B groups showed obvious population divergences and different selective signals distributed in 337 regions harboring 772 genes. Meanwhile, functional enrichment analysis showed those selected genes are mainly involved in regulating cell development. Interestingly, some ear morphology related traits showed significant differentiation between the inbred lines from the two heterosis groups. The genome-wide association analysis of ear morphology related traits showed that four associated genes were co-localized in the selected regions with high linkage disequilibrium. Our spatiotemporal pattern and gene interaction network results for the four genes further contribute to our understanding of the mechanisms behind ear and fruit length development. This study provides a novel insight into digging a candidate gene for complex traits using breeding materials. Our findings in relation to ear morphology will help accelerate future maize improvement.

Participation of Green Organs to Grain Filling in Triticum turgidum var durum Grown under Mediterranean Conditions

In wheat, flag leaf, stem, chaff and awns contribute to grain filling through photosynthesis and/or re-mobilization. Environmental and genetic effects on the relative contribution of each organ were examined by analyzing the consequences of sink-source manipulations (shading and excision) and by comparing carbon isotope discrimination (Δ) values in dry matter (at maturity) and sap (two weeks after anthesis) in six durum wheat genotypes grown in two contrasting seasons. The contribution of flag leaf, stem, chaff and awns to grain filling, estimated by sink-source manipulations, highly varied with the season. The contribution of ear photosynthesis and re-mobilization from the stem increased with post-anthesis water stress. They showed a large genetic variation that was, however, not clearly associated to morphological characteristics of ear and stem. Isotopic imprints of chaff on grain Δ were identified as a possible surrogate of the destructive and cumbersome sink-source manipulations to evaluate the contribution of carbon assimilated in ears or re-mobilized from stem. This might facilitate screening of genetic resources and allow the combining of favourable drought tolerance mechanisms in wheat.

Does the morphology of the ear of the Chinese bamboo rat (Rhizomys sinensis) show "Subterranean" characteristics?

In spite of the growing interest in rodents with subterranean activity in general and the spalacids (Spalacidae) in particular, little is known about the biology of most members of this clade, such as the Chinese bamboo rat (Rhizomys sinensis). Here, we analyzed the ear morphology of R. sinensis with respect to hearing specialization for subterranean or aboveground modes of communication. It is well-known that ecology and style of life of a particular species can be reflected in morphology of its ear, its hearing and vocalization, so we expect that such information could provide us insight into its style of life and its sensory environment. The ratio between the eardrum and stapedial footplate areas, which influences the efficiency of middle ear sound transmission, suggests low hearing sensitivity, as is typical for subterranean species. The cochlea had 3.25 coils and resembled species with good low frequency hearing typical for subterranean mammals. The length of the basilar membrane was 18.9 ± 0.8 mm and its width slowly increased towards the cochlear apex from 60 to 85 μm. The mean density of outer hair cells was 344 ± 22 and of inner hair cells 114 ± 7.3 per 1 mm length of the organ of Corti, and increased apically. These values (except for relatively low hair cell density) usually characterize ears specialized for low frequency hearing. There was no evidence for an acoustic fovea. Apart of low hair cell density which is common in aboveground animals, this species has also relatively large auricles, suggesting the importance of sound localization during surface activity. The ear of the Chinese bamboo rat thus contains features typical for both aboveground and subterranean mammals and suggests that this spalacid has fossorial habits combined with regular aboveground activity.

Phenotypic sub-grouping in microtia using a statistical and a clinical approach

The clinical presentation of microtia varies widely from minimal morphological abnormalities to complete absence of the ear. In this study we sought to identify and characterize sub-groups of microtia using a statistical and a clinical approach. Photographs of 86 ears were classified in relation to all the external ear components. We used cluster analysis and rater's clinical opinion to identify groups with similar phenotypes in two separate analyses. We used Cramer's Phi coefficient of association to assess the similarity among the clinician's groupings as well as among the statistical sub-phenotypic groups and each of the clinician's groupings. The cluster analysis initially divided the 86 ears into a more and a less severe group. The less severe group included two sub-groups that included ears classified as normal and a group that had very few anomalous components. The group of 48 more affected ears all had abnormalities of the helix crus; antihelix-stem, -superior crus and -inferior crus; and antitragus. These were further divided into 4 sub-phenotypes. There was a moderate degree of association among the raters' groupings (Cramer's Phi: 0.64 to 0.73). The statistical and clinical groupings had a lower degree of association (Cramer's Phi: 0.49 to 0.58). Using standardized characterization of structural abnormalities of the ear we identified six distinct phenotypic groups; correlations with clinicians' groupings were moderate. These clusters may represent groups of ear malformations associated with the same etiology, similar time of insult or target cell population during embryonic development. The results will help inform investigations on etiology.