Frequent numerical and structural chromosome changes in early generations of synthetic hexaploid wheat

Modern hexaploid wheat (Triticum aestivum L.; AABBDD) evolved from a hybrid of tetraploid wheat (closely related to Triticum turgidum L. ssp. durum (Desf.) Husn., AABB) and goatgrass (Aegilops tauschii Coss., DD). Variations in chromosome structure and ploidy played important roles in wheat evolution. How these variations occurred and their role in expanding the genetic diversity in modern wheat is mostly unknown. Synthetic hexaploid wheat (SHW) can be used to investigate chromosome variation that occurs during the early generations of existence. SHW lines derived by crossing durum wheat ‘Langdon’ with twelve Ae. tauschii accessions were analyzed using oligonucelotide probe multiplex fluorescence in situ hybridization (FISH) to metaphase chromosomes and SNP markers. Cluster analysis based on SNP markers categorized them into three groups. Among 702 plants from the S8 and S9 generations, 415 (59.12%) carried chromosome variations involving all 21 chromosomes but with different frequencies for each chromosome and sub-genome. Total chromosome variation frequencies varied between lines, but there was no significant difference among the three groups. The non-random chromosome variations in SHW lines detected in this research may be an indication that similar variations occurred in the early stages of wheat polyploidization and played important roles in wheat evolution.

Further insights on chromosomal evolution of the genus Enyalius with karyotype description of Enyalius boulengeri Etheridge, 1969 (Squamata, Leiosauridae)

The genus Enyalius is composed of 10 described species inhabiting forest areas in Amozônia, Cerrado and Atlantic forest biomes. Currently, eight species with high levels of chromosome variation have been karyotyped. The study aims to characterize the karyotype of Enyalius boulengeri, with classical and molecular techniques, and improve knowledge about the karyotype evolution of the lizard genus Enyalius. The species has 2n = 36 chromosomes (8m + 4sm + 24mc), FN = 24; NORs and 18S rDNA were subtelomeric and located on chromosome pair 2. Repetitive DNA probes (CAT)10 accumulated on centromeric and terminal regions of some macrochromosomes. (GA)15 probe showed conspicuous accumulation on the pericentromeric region of chromosome pairs 1 and 6. Repetitive FISH patterns obtained with (GC)15 probe marked the pericentromeric region of the first chromosome pair. All probes showed accumulation in the microchromosomes. The chromosomal formula found on E. boulengeri has been considered the ancestral karyotype for pleurodont Iguania. The genus Enyalius is characterized by two distinctive chromosomal groups; one with highly conserved karyotypes, whereas the other is karyotypically diverse. Our molecular cytogenetics data are promising and will increase knowledge about the genus Enyalius chromosome evolution.

Diversity of reptile sex chromosome evolution revealed by cytogenetic and linked-read sequencing

Reptile sex determination is attracting much attention because the great diversity of sex-determination and dosage compensation mechanisms permits us to approach fundamental questions about sex chromosome turnover and evolution. However, reptile sex chromosome variation remains largely uncharacterized and no reptile master sex determination genes have yet been identified. Here we describe a powerful and cost-effective chromosomics approach, combining probes generated from the microdissected sex chromosomes with transcriptome sequencing to explore this diversity in non-model Australian reptiles with heteromorphic or cryptic sex chromosomes. We tested the pipeline on a turtle, a gecko, and a worm-lizard, and we also identified sequences located on sex chromosomes in a monitor lizard using linked-read sequencing. Genes identified on sex chromosomes were compared to the chicken genome to identify homologous regions among the four species. We identified candidate sex determining genes within these regions, including conserved vertebrate sex-determining genes pdgfa, pdgfra amh and wt1, and demonstrated their testis or ovary-specific expression. All four species showed gene-by-gene rather than chromosome-wide dosage compensation. Our results imply that reptile sex chromosomes originated by the independent acquisition of sex-determining genes on different autosomes, as well as translocations between different ancestral macro- and micro-chromosomes. We discuss the evolutionary drivers of the slow differentiation, but rapid turnover, of reptile sex chromosomes.

Chromosome Stability of Synthetic-Natural Wheat Hybrids

Primary allopolyploids are not only ideal materials to study species evolution, but also important bridges in incorporating genetic diversity of wild species into crops. Primary allopolyploids typically exhibit chromosome instability that a disadvantage trait in crop breeding. Newly synthesized hexaploid wheat has been widely used in wheat genetics and breeding studies. To better understand the cytological and genetic basis of chromosome instability, this study investigated the chromosomes of a large number of seeds derived from the synthetic wheat SHW-L1 and its hybrids with natural wheat. SHW-L1 exhibited persistent chromosome instability since we observed a high frequent chromosome variation de novo generated from euploid SHW-L1 plants at the 14th generation of selfing (F14). High frequent chromosome variations were also observed in the F2 hybrids and most of the analyzed recombinant inbred lines (RILs) at F14, derived from the cross of SHW-L1 with common wheat variety Chuanmai 32. Chromosome instability was associated with frequent univalency during meiotic metaphase I. The experiment on reciprocal crosses between SHW-L1 and Chuanmai 32 indicated that cytoplasm has not obvious effects on chromosome instability. An analysis on 48 F14 RILs revealed chromosome variation frequency was not associated with the Ph1 alleles from either SHW-L1 or Chuanmai 32, rejecting the hypothesis that chromosome instability was due to the Ph1 role of synthetic wheat. In the analyzed RILs, chromosome instability influences the phenotype uniformity, showing as obvious trait differences among plants within a RIL. However, the analyzed commercial varieties only containing ∼12.5% genomic components of synthetic wheat were chromosomally stable, indicating that chromosome instability caused by synthetic wheat can be effectively overcome by increasing the genetic background of common wheat.

Normal Chromosomal Variation

Knowing what is normal and what is not is becoming a particular challenge in this era of molecular karyotyping. This chapter reviews the normal chromosome variation from classical times, now very well understood. This is followed by a discussion of the complexity and uncertainty that the molecular approach has, in this century, challenged researchers with. In particular, the chapter discusses the concept of the copy number variant (CNV) and how the harmlessness, or not, of a CNV may be assessed. Mention is made of CNVs potentially acting as “second hits,” such that, while nonpathogenic in one setting, they may contribute to an abnormal phenotype in the context of another, independent chromosome abnormality or CNV. The “sliding scale” of interpretation from “known pathogenic” through “known benign” Is noted. The chapter refers to useful databases to which the counselor may have access.