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Pronozin AY, Paulish AA, Zavarzin EA, Prikhodko AY, Prokhoshin NM, Kruchinina YV, Goncharov NP, Komyshev EG, Genaev MA. Automatic morphology phenotyping of tetra- and hexaploid wheat spike using computer vision methods. Vavilovskii Zhurnal Genet Selektsii 2021; 25:71-81. [PMID: 34901705 PMCID: PMC8629366 DOI: 10.18699/vj21.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/31/2020] [Accepted: 01/02/2021] [Indexed: 11/19/2022] Open
Abstract
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.
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Affiliation(s)
- A Yu Pronozin
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Paulish
- Novosibirsk State University, Novosibirsk, Russia
| | - E A Zavarzin
- Novosibirsk State University, Novosibirsk, Russia
| | | | | | - Yu V Kruchinina
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomics Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N P Goncharov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State Agrarian University, Novosibirsk, Russia
| | - E G Komyshev
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia Kurchatov Genomics Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - M A Genaev
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia Kurchatov Genomics Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Kwiatek MT, Kurasiak-Popowska D, Mikołajczyk S, Niemann J, Tomkowiak A, Weigt D, Nawracała J. Cytological markers used for identification and transfer of Aegilops spp. chromatin carrying valuable genes into cultivated forms of Triticum. COMPARATIVE CYTOGENETICS 2019; 13:41-59. [PMID: 30854169 PMCID: PMC6403195 DOI: 10.3897/compcytogen.v13i1.30673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/30/2019] [Indexed: 05/26/2023]
Abstract
There are many reports describing chromosome structure, organization and evolution within goatgrasses (Aegilops spp.). Chromosome banding and fluorescence in situ hybridization techniques are main methods used to identify Aegilops Linnaeus, 1753 chromosomes. These data have essential value considering the close genetic and genomic relationship of goatgrasses with wheat (Triticumaestivum Linnaeus, 1753) and triticale (× Triticosecale Wittmack, 1899). A key question is whether those protocols are useful and effective for tracking Aegilops chromosomes or chromosome segments in genetic background of cultivated cereals. This article is a review of scientific reports describing chromosome identification methods, which were applied for development of prebreeding plant material and for transfer of desirable traits into Triticum Linnaeus, 1753 cultivated species. Moreover, this paper is a resume of the most efficient cytomolecular markers, which can be used to follow the introgression of Aegilops chromatin during the breeding process.
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Affiliation(s)
- Michał T. Kwiatek
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, PolandPoznań University of Life SciencesPoznańPoland
| | - Danuta Kurasiak-Popowska
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, PolandPoznań University of Life SciencesPoznańPoland
| | - Sylwia Mikołajczyk
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, PolandPoznań University of Life SciencesPoznańPoland
| | - Janetta Niemann
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, PolandPoznań University of Life SciencesPoznańPoland
| | - Agnieszka Tomkowiak
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, PolandPoznań University of Life SciencesPoznańPoland
| | - Dorota Weigt
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, PolandPoznań University of Life SciencesPoznańPoland
| | - Jerzy Nawracała
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, PolandPoznań University of Life SciencesPoznańPoland
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Edet OU, Gorafi YSA, Nasuda S, Tsujimoto H. DArTseq-based analysis of genomic relationships among species of tribe Triticeae. Sci Rep 2018; 8:16397. [PMID: 30401925 PMCID: PMC6219600 DOI: 10.1038/s41598-018-34811-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/26/2018] [Indexed: 11/10/2022] Open
Abstract
Precise utilization of wild genetic resources to improve the resistance of their cultivated relatives to environmental growth limiting factors, such as salinity stress and diseases, requires a clear understanding of their genomic relationships. Although seriously criticized, analyzing these relationships in tribe Triticeae has largely been based on meiotic chromosome pairing in hybrids of wide crosses, a specialized and labourious strategy. In this study, DArTseq, an efficient genotyping-by-sequencing platform, was applied to analyze the genomes of 34 Triticeae species. We reconstructed the phylogenetic relationships among diploid and polyploid Aegilops and Triticum species, including hexaploid wheat. Tentatively, we have identified the diploid genomes that are likely to have been involved in the evolution of five polyploid species of Aegilops, which have remained unresolved for decades. Explanations which cast light on the progenitor of the A genomes and the complex genomic status of the B/G genomes of polyploid Triticum species in the Emmer and Timopheevi lineages of wheat have also been provided. This study has, therefore, demonstrated that DArTseq genotyping can be effectively applied to analyze the genomes of plants, especially where their genome sequence information are not available.
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Affiliation(s)
- Offiong U Edet
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.,United Graduate School of Agricultural Sciences, Tottori University, Tottori, 680-8553, Japan
| | - Yasir S A Gorafi
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.,Agricultural Research Corporation (ARC), P. O. Box 126, Wad Madani, Sudan
| | - Shuhei Nasuda
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
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Botticella E, Pucci A, Sestili F. Molecular characterisation of two novel starch granule proteins 1 in wild and cultivated diploid A genome wheat species. JOURNAL OF PLANT RESEARCH 2018; 131:487-496. [PMID: 29260339 DOI: 10.1007/s10265-017-1005-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/04/2017] [Indexed: 06/07/2023]
Abstract
Starch synthase IIa, also known as starch granule protein 1 (SGP-1), plays a key role in amylopectin biosynthesis. The absence of SGP-1 in cereal grains is correlated to dramatic changes in the grains' starch content, structure, and composition. An extensive investigation of starch granule proteins in this study revealed a polymorphism in the electrophoretic mobility of SGP-1 between two species of wheat, Triticum urartu and T. monococcum; this protein was, however, conserved among all other Triticum species that share the A genome inherited from their progenitor T. urartu. Two different electrophoretic profiles were identified: SGP-A1 proteins of T. urartu accessions had a SDS-PAGE mobility similar to those of tetraploid and hexaploid wheat species; conversely, SGP-A1 proteins of T. monococcum ssp. monococcum and ssp. boeoticum accessions showed a different electrophoretic mobility. The entire coding region of the two genes was isolated and sequenced in an attempt to explain the polymorphism identified. Several single nucleotide polymorphisms (SNPs) responsible for amino acid changes were identified, but no indel polymorphism was observed to explain the difference in electrophoretic mobility. Amylose content did not differ significantly among T. urartu, T. monococcum ssp. boeoticum and T. monococcum ssp. monococcum, except in one accession of the ssp. boeoticum. Conversely, several interspecific differences were observed in viscosity properties (investigated as viscosity profiles using a rapid visco analyzer-RVA profiles) of these cereal grains. T. monococcum ssp. boeoticum accessions had the lowest RVA profiles, T. urartu accessions had an intermediate RVA profile, whereas T. monococcum ssp. monococcum showed the highest RVA profile. These differences could be associated with the numerous amino acid and structural changes evident among the SGP-1 proteins.
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Affiliation(s)
- Ermelinda Botticella
- Department of Agriculture and Forestry Sciences, University of Tuscia, Via S. Camillo de Lellis SNC, Viterbo, Italy
| | - Anna Pucci
- Department of Agriculture and Forestry Sciences, University of Tuscia, Via S. Camillo de Lellis SNC, Viterbo, Italy
| | - Francesco Sestili
- Department of Agriculture and Forestry Sciences, University of Tuscia, Via S. Camillo de Lellis SNC, Viterbo, Italy.
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Adonina IG, Goncharov NP, Badaeva ED, Sergeeva EM, Petrash NV, Salina EA. (GAA)n microsatellite as an indicator of the A genome reorganization during wheat evolution and domestication. COMPARATIVE CYTOGENETICS 2015; 9:533-47. [PMID: 26753073 PMCID: PMC4698569 DOI: 10.3897/compcytogen.v9i4.5120] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/15/2014] [Indexed: 05/02/2023]
Abstract
Although the wheat A genomes have been intensively studied over past decades, many questions concerning the mechanisms of their divergence and evolution still remain unsolved. In the present study we performed comparative analysis of the A genome chromosomes in diploid (Triticum urartu Tumanian ex Gandilyan, 1972, Triticum boeoticum Boissier, 1874 and Triticum monococcum Linnaeus, 1753) and polyploid wheat species representing two evolutionary lineages, Timopheevi (Triticum timopheevii (Zhukovsky) Zhukovsky, 1934 and Triticum zhukovskyi Menabde & Ericzjan, 1960) and Emmer (Triticum dicoccoides (Körnicke ex Ascherson & Graebner) Schweinfurth, 1908, Triticum durum Desfontaines, 1798, and Triticum aestivum Linnaeus, 1753) using a new cytogenetic marker - the pTm30 probe cloned from Triticum monococcum genome and containing (GAA)56 microsatellite sequence. Up to four pTm30 sites located on 1AS, 5AS, 2AS, and 4AL chromosomes have been revealed in the wild diploid species, although most accessions contained one-two (GAA)n sites. The domesticated diploid species Triticum monococcum differs from the wild diploid species by almost complete lack of polymorphism in the distribution of (GAA)n site. Only one (GAA)n site in the 4AL chromosome has been found in Triticum monococcum. Among three wild emmer (Triticum dicoccoides) accessions we detected 4 conserved and 9 polymorphic (GAA)n sites in the A genome. The (GAA)n loci on chromosomes 2AS, 4AL, and 5AL found in of Triticum dicoccoides were retained in Triticum durum and Triticum aestivum. In species of the Timopheevi lineage, the only one, large (GAA)n site has been detected in the short arm of 6A(t) chromosome. (GAA)n site observed in Triticum monococcum are undetectable in the A(b) genome of Triticum zhukovskyi, this site could be eliminated over the course of amphiploidization, while the species was established. We also demonstrated that changes in the distribution of (GAA)n sequence on the A-genome chromosomes of diploid and polyploid wheats are associated with chromosomal rearrangements/ modifications, involving mainly the NOR (nucleolus organizer region)-bearing chromosomes, that took place during the evolution of wild and domesticated species.
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Affiliation(s)
- Irina G. Adonina
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, pr. Lavrentieva 10, Novosibirsk, 630090 Russia
| | - Nikolay P. Goncharov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, pr. Lavrentieva 10, Novosibirsk, 630090 Russia
| | - Ekaterina D. Badaeva
- N.I.Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina street 3, Moscow 119991, Russia
| | - Ekaterina M. Sergeeva
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, pr. Lavrentieva 10, Novosibirsk, 630090 Russia
| | - Nadezhda V. Petrash
- Siberian Research Institute of Plant Growing and Selection – Branch of ICG SB RAS, Krasnoobsk, Novosibirsk Region, Russia
| | - Elena A. Salina
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, pr. Lavrentieva 10, Novosibirsk, 630090 Russia
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Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats. Mol Genet Genomics 2010; 283:551-63. [DOI: 10.1007/s00438-010-0539-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 03/29/2010] [Indexed: 01/02/2023]
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