A simple method to separate base population and segregation effects in genomic relationship matrices

Background

Genomic selection and estimation of genomic breeding values (GBV) are widely used in cattle and plant breeding. Several studies have attempted to detect population subdivision by investigating the structure of the genomic relationship matrix G. However, the question of how these effects influence GBV estimation using genomic best linear unbiased prediction (GBLUP) has received little attention.

Methods

We propose a simple method to decompose G into two independent covariance matrices, one describing the covariance that results from systematic differences in allele frequencies between groups at the pedigree base (G_A^*) and the other describing genomic relationships (G_S) corrected for these differences. Using this decomposition and F_st statistics, we examined whether observed genetic distances between genotyped subgroups within populations resulted from the heterogeneous genetic structure present at the base of the pedigree and/or from breed divergence. Using this decomposition, we tested three models in a forward prediction validation scenario on six traits using Brown Swiss and dual-purpose Fleckvieh cattle data. Model 0 (M0) used both components and is equivalent to the model using the standard G-matrix. Model 1 (M1) used G_S only and model 2 (M2), an extension of M1, included a fixed genetic group effect. Moreover, we analyzed the matrix of contributions of each base group (Q) and estimated the effects and prediction errors of each base group using M0 and M1.

Results

The proposed decomposition of G helped to examine the relative importance of the effects of base groups and segregation in a given population. We found significant differences between the effects of base groups for each breed. In forward prediction, differences between models in terms of validation reliability of estimated direct genomic values were small but predictive power was consistently lowest for M1. The relative advantage of M0 or M2 in prediction depended on breed, trait and genetic composition of the validation group. Our approach presents a general analogy with the use of genetic groups in conventional animal models and provides proof that standard GBLUP using G yields solutions equivalent to M0, where base groups are considered as correlated random effects within the additive genetic variance assigned to the genetic base.     

Mechanism of assembly of G protein betagamma subunits by protein kinase CK2-phosphorylated phosducin-like protein and the cytosolic chaperonin complex

Phosducin-like protein (PhLP) is a widely expressed binding partner of the G protein betagamma subunit complex (Gbetagamma) that has been recently shown to catalyze the formation of the Gbetagamma dimer from its nascent polypeptides. Phosphorylation of PhLP at one or more of three consecutive serines (Ser-18, Ser-19, and Ser-20) is necessary for Gbetagamma dimer formation and is believed to be mediated by the protein kinase CK2. Moreover, several lines of evidence suggest that the cytosolic chaperonin complex (CCT) may work in concert with PhLP in the Gbetagamma-assembly process. The results reported here delineate a mechanism for Gbetagamma assembly in which a stable ternary complex is formed between PhLP, the nascent Gbeta subunit, and CCT that does not include Ggamma. PhLP phosphorylation permits the release of a PhLP x Gbeta intermediate from CCT, allowing Ggamma to associate with Gbeta in this intermediate complex. Subsequent interaction of Gbetagamma with membranes releases PhLP for another round of assembly.     

100% complete assignment of non-labile 1H, 13C, and 15N signals for calcium-loaded calbindin D9k P43G

Here we present the 100% complete assignment chemical shift of non-labile ¹H, ¹⁵N and ¹³C nuclei of Calbindin D_9k P43G. The assignment includes all non-exchangeable side chain nuclei, including ones that are rarely reported, such as LysNζ as well as the termini. NMR experiments required to achieve truly complete assignments are discussed. To the best of our knowledge our assignments for Calbindin D_9k extend beyond previous studies reaching near-completeness (Vis et al. in Biochem 33:14858–14870, 1994; Yamazaki et al. in J Am Chem Soc 116:6464–6465, 1994; Yamazaki et al. in Biochem 32:5656–5669, 1993b).     

Notes on Withania (Solanaceae) in Somalia

The identity of Withania reichenbachii is established, the name is neotypified, and the species is described and illustrated. The new combination W. grisea (Hepper & Boulos) Thulin is made. The typification of W. somnifera is discussed, and it is concluded that the present typification can stand. A key to and a synopsis of the four species of Withania now recognised in Somalia are given.     

A new species of Momordica (Cucurbitaceae) from tropical Africa

Momordica littorea , sp. nov., a dioecious climber with succulent 3-foliolate leaves and conspicuously bracteate flowers from coastal regions of southern Somalia and Kenya, is described and illustrated.     

Exacum (Gentianaceae) on the Arabian peninsula and Socotra

Three species of Exacum are recognized on the Arabian peninsula and Socotra, E. arabicum sp. nov. in Yemen and Oman, E. affine on Socotra and in Oman, and E. caeruleum on Socotra. E. gracilipes and E. socotranum are reduced to synonyms of E. affine.     

Indigofera platyspira (Leguminosae), a new species from Kenya with Medicago-like fruits

The new species Indigofera platyspira , from silty or sandy soils in the Wajir and Isiolo Districts in Kenya, is described and illustrated. I. platyspira is probably a member of I. sect. Alternifoliolae , but differs from all previously known species in this section in its flat and spirally coiled pods that much resemble the fruits of certain species of Medicago.     

Structural changes associated with parotid “Degeneration secretion” after post-ganglionic sympathectomy in rats

Parotid glands of rat have been examined 12, 24 and 48 hours after avulsion of the cervical sympathetic ganglion and compared with normally innervated left glands. Formaldehyde-induced fluorescence showed a relatively normal complement of adrenergic nerves at 12 hours but most of the nerves had lost their noradrenaline content by 24 hours and no fluorescent nerves were detected at 48 hours. Ultrastructural degenerative changes in axons were rare at 12 hours, common at 24 hours, and the degenerating axons appeared to have disappeared by 48 hours. The glands looked whitish and pale and similar to the controls at 12 and 48 hours but were pinkish and oedematous on the sympathectomised side at 24 hours. Correspondingly the acini were loaded with secretory granules at 12 and 48 hours but were extensively depleted of granules at 24 hours. This loss of granules is considered to be due to sympathetic "degeneration secretion" caused by the release of noradrenaline from the degenerating adrenergic nerves between 12 and 24 hours after ganglionectomy. This is thought to be the first example of morphological change resulting from "degeneration activation" to be recorded microscopically.