Automatic morphology phenotyping of tetra- and hexaploid wheat spike using computer vision methods

Intraspecific classification of cultivated plants is necessary for the conservation of biological diversity, study of their origin and their phylogeny. The modern cultivated wheat species originated from three wild diploid ancestors as a result of several rounds of genome doubling and are represented by di-, tetra- and hexaploid species. The identification of wheat ploidy level is one of the main stages of their taxonomy. Such classification is possible based on visual analysis of the wheat spike traits. The aim of this study is to investigate the morphological characteristics of spikes for hexa- and tetraploid wheat species based on the method of high-performance phenotyping. Phenotyping of the quantitative characteristics of the spike of 17 wheat species (595 plants, 3348 images), including eight tetraploids (Triticum aethiopicum, T. dicoccoides, T. dicoccum, T. durum, T. militinae, T. polonicum, T. timopheevii, and T. turgidum) and nine hexaploids (T. compactum, T. aestivum, i:ANK-23 (near-isogenic line of T. aestivum cv. Novosibirskaya 67), T. antiquorum, T. spelta (including cv. Rother Sommer Kolben), T. petropavlovskyi, T. yunnanense, T. macha, T. sphaerococcum, and T. vavilovii), was performed. Wheat spike morphology was described on the basis of nine quantitative traits including shape, size and awns area of the spike. The traits were obtained as a result of image analysis using the WERecognizer program. A cluster analysis of plants according to the characteristics of the spike shape and comparison of their distributions in tetraploid and hexaploid species showed a higher variability of traits in hexaploid species compared to tetraploid ones. At the same time, the species themselves form two clusters in the visual characteristics of the spike. One type is predominantly hexaploid species (with the exception of one tetraploid, T. dicoccoides). The other group includes tetraploid ones (with the exception of three hexaploid ones, T. compactum, T. antiquorum, T. sphaerococcum, and i:ANK-23). Thus, it has been shown that the morphological characteristics of spikes for hexaploid and tetraploid wheat species, obtained on the basis of computer analysis of images, include differences, which are further used to develop methods for plant classifications by ploidy level and their species in an automatic mode

Crop pangenomes

Progress in genome sequencing, assembly and analysis allows for a deeper study of agricultural plants’ chromosome structures, gene identif ication and annotation. The published genomes of agricultural plants proved to be a valuable tool for studing gene functions and for marker-assisted and genomic selection. However, large structural genome changes, including gene copy number variations (CNVs) and gene presence/absence variations (PAVs), prevail in crops. These genomic variations play an important role in the functional set of genes and the gene composition in individuals of the same species and provide the genetic determination of the agronomically important crops properties. A high degree of genomic variation observed indicates that single reference genomes do not represent the diversity within a species, leading to the pangenome concept. The pangenome represents information about all genes in a taxon: those that are common to all taxon members and those that are variable and are partially or completely specif ic for particular individuals. Pangenome sequencing and analysis technologies provide a large-scale study of genomic variation and resources for an evolutionary research, functional genomics and crop breeding. This review provides an analysis of agricultural plants’ pangenome studies. Pangenome structural features, methods and programs for bioinformatic analysis of pangenomic data are described