Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR

Motivation: The investigation of quantitative trait loci (QTL) is an essential component in our understanding of how organisms vary phenotypically. However, many important crop species are polyploid (carrying more than two copies of each chromosome), requiring specialised tools for such analyses. Moreover, deciphering meiotic processes at higher ploidy levels is not straightforward, but is necessary to understand the reproductive dynamics of these species, or uncover potential barriers to their genetic improvement. Results: Here we present polyqtlR, a novel software tool to facilitate such analyses in (auto)polyploid crops. It performs QTL interval mapping in F1 populations of outcrossing polyploids of any ploidy level using identity-by-descent (IBD) probabilities. The allelic composition of discovered QTL can be explored, enabling favourable alleles to be identified and tracked in the population. Visualisation tools within the package facilitate this process, and options to include genetic co-factors and experimental factors are included. Detailed information on polyploid meiosis including prediction of multivalent pairing structures, detection of preferential chromosomal pairing and location of double reduction events can be performed. Availability and implementation: polyqtlR is freely available from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polyqtlR.

Ciliary control of meiotic chromosomal pairing mechanics and germ cell morphogenesis

Meiosis is a cellular program essential for the production of haploid gametes. A hallmark of meiosis is chromosomal pairing via synaptonemal complexes, and a major focus traditionally has been to understand synaptonemal complex formation. However, chromosomal pairing also depends on cytoplasmic counterparts that tether and rotate telomeres on the nuclear envelope, shuffling chromosomes and mechanically driving their homology searches1–8. Rotating telomeres slide on perinuclear microtubules and are ultimately pulled towards the centrosome7,9,10, forming the “zygotene chromosomal bouquet configuration”11. The bouquet is universally conserved and is essential for pairing and fertility1–8,12. However, despite its discovery in 190011, how the cytoplasmic counterparts of bouquet formation are mechanically regulated has remained enigmatic. Here, by studying zebrafish oogenesis, we report and comprehensively characterize the “zygotene cilium” - a previously unrecognized cilium in oocytes. We show that the zygotene cilium specifically connects to the bouquet centrosome and constitutes a cable system of the cytoplasmic bouquet machinery. Farther, zygotene cilia extend throughout the germline cyst, a conserved cellular organization of germ cells. By analyzing multiple ciliary mutants, we demonstrate that the zygotene cilium is essential for chromosomal pairing, germ cell morphogenesis, ovarian development and fertility. We further show that the zygotene cilium is conserved in both male meiosis in zebrafish, as well as in mammalian oogenesis. Our work uncovers the novel concept of a cilium as a critical player in meiosis and sheds new light on reproduction phenotypes in ciliopathies. Furthermore, most cells in metazoans are ciliated and exhibit specific nuclear dynamics. We propose a cellular paradigm that cilia can control chromosomal dynamics.

Intra- and intergenomic chromosomal pairing in artificially polyploidized elephant grass and pearl millet hybrids

The objective of this work was to evaluate, by genomic in situ hybridization (GISH), pairing configurations as potential indicators of recombination between chromosomes of different parental genomes, in two interspecific hybrids (elephant grass x pearl millet) artificially polyploidized. Anthers from young flower buds were used in the chromosomal preparations. The genomic probe was prepared with pearl millet DNA and labeled with biotin-16-dUTP by the nick translation reaction. Blocking DNA was prepared with genomic elephant grass DNA. The homoeologous intergenomic pairing, observed in the two hybrids, indicates the possibility of recombination between chromosomes of the parental genomes.

Transcriptional Adaptor ADA3 of Drosophila melanogaster Is Required for Histone Modification, Position Effect Variegation, and Transcription

ABSTRACT The Drosophila melanogaster gene diskette (also known as dik or dAda3) encodes a protein 29% identical to human ADA3, a subunit of GCN5-containing histone acetyltransferase (HAT) complexes. The fly dADA3 is a major contributor to oogenesis, and it is also required for somatic cell viability. dADA3 localizes to chromosomes, and it is significantly reduced in dGcn5 and dAda2a, but not in dAda2b, mutant backgrounds. In dAda3 mutants, acetylation at histone H3 K9 and K14, but not K18, and at histone H4 K12, but not K5, K8, and K16, is significantly reduced. Also, phosphorylation at H3 S10 is reduced in dAda3 and dGcn5 mutants. Variegation for white (w m4 ) and scute (Hw v ) genes, caused by rearrangements of X chromosome heterochromatin, is modified in a dAda3 + gene-dosage-dependent manner. The effect is not observed with rearrangements involving Y heterochromatin (bw D ), euchromatin (Scutoid), or transvection effects on chromosomal pairing (white and zeste interaction). Activity of scute gene enhancers, targets for Iroquoi transcription factors, is abolished in dAda3 mutants. Also, Iroquoi-associated phenotypes are sensitive to dAda3 + gene dosage. We conclude that dADA3 plays a role in HAT complexes which acetylate H3 and H4 at specific residues. In turn, this acetylation results in chromatin structure effects of certain rearrangements and transcription of specific genes.