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Development of DNA Markers From Physically Mapped Loci in Aegilops comosa and Aegilops umbellulata Using Single-Gene FISH and Chromosome Sequences.
Front Plant Sci. 2021; 12:689031.FP

Abstract

Breeding of agricultural crops adapted to climate change and resistant to diseases and pests is hindered by a limited gene pool because of domestication and thousands of years of human selection. One way to increase genetic variation is chromosome-mediated gene transfer from wild relatives by cross hybridization. In the case of wheat (Triticum aestivum), the species of genus Aegilops are a particularly attractive source of new genes and alleles. However, during the evolution of the Aegilops and Triticum genera, diversification of the D-genome lineage resulted in the formation of diploid C, M, and U genomes of Aegilops. The extent of structural genome alterations, which accompanied their evolution and speciation, and the shortage of molecular tools to detect Aegilops chromatin hamper gene transfer into wheat. To investigate the chromosome structure and help develop molecular markers with a known physical position that could improve the efficiency of the selection of desired introgressions, we developed single-gene fluorescence in situ hybridization (FISH) maps for M- and U-genome progenitors, Aegilops comosa and Aegilops umbellulata, respectively. Forty-three ortholog genes were located on 47 loci in Ae. comosa and on 52 loci in Ae. umbellulata using wheat cDNA probes. The results obtained showed that M-genome chromosomes preserved collinearity with those of wheat, excluding 2 and 6M containing an intrachromosomal rearrangement and paracentric inversion of 6ML, respectively. While Ae. umbellulata chromosomes 1, 3, and 5U maintained collinearity with wheat, structural reorganizations in 2, 4, 6, and 7U suggested a similarity with the C genome of Aegilops markgrafii. To develop molecular markers with exact physical positions on chromosomes of Aegilops, the single-gene FISH data were validated in silico using DNA sequence assemblies from flow-sorted M- and U-genome chromosomes. The sequence similarity search of cDNA sequences confirmed 44 out of the 47 single-gene loci in Ae. comosa and 40 of the 52 map positions in Ae. umbellulata. Polymorphic regions, thus, identified enabled the development of molecular markers, which were PCR validated using wheat-Aegilops disomic chromosome addition lines. The single-gene FISH-based approach allowed the development of PCR markers specific for cytogenetically mapped positions on Aegilops chromosomes, substituting as yet unavailable segregating map. The new knowledge and resources will support the efforts for the introgression of Aegilops genes into wheat and their cloning.

Authors+Show Affiliations

Institute of Experimental Botany of the Czech Academy of Sciences, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia. Agricultural Research Centre, Field Crops Research Institute, Cairo, Egypt.Institute of Experimental Botany of the Czech Academy of Sciences, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia.ELKH Centre for Agricultural Research, Agricultural Institute, Martonvásár, Hungary.ELKH Centre for Agricultural Research, Agricultural Institute, Martonvásár, Hungary.ELKH Centre for Agricultural Research, Agricultural Institute, Martonvásár, Hungary.Institute of Experimental Botany of the Czech Academy of Sciences, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia.Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.NBIS (National Bioinformatics Infrastructure Sweden, Science for Life Laboratory), Division of Cell Biology, Department of Clinical and Experimental Medicine, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden.ELKH Centre for Agricultural Research, Agricultural Institute, Martonvásár, Hungary.Institute of Experimental Botany of the Czech Academy of Sciences, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia.Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, United States.Institute of Experimental Botany of the Czech Academy of Sciences, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia.Institute of Experimental Botany of the Czech Academy of Sciences, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia. ELKH Centre for Agricultural Research, Agricultural Institute, Martonvásár, Hungary.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

34211490

Citation

Said, Mahmoud, et al. "Development of DNA Markers From Physically Mapped Loci in Aegilops Comosa and Aegilops Umbellulata Using Single-Gene FISH and Chromosome Sequences." Frontiers in Plant Science, vol. 12, 2021, p. 689031.
Said M, Holušová K, Farkas A, et al. Development of DNA Markers From Physically Mapped Loci in Aegilops comosa and Aegilops umbellulata Using Single-Gene FISH and Chromosome Sequences. Front Plant Sci. 2021;12:689031.
Said, M., Holušová, K., Farkas, A., Ivanizs, L., Gaál, E., Cápal, P., Abrouk, M., Martis-Thiele, M. M., Kalapos, B., Bartoš, J., Friebe, B., Doležel, J., & Molnár, I. (2021). Development of DNA Markers From Physically Mapped Loci in Aegilops comosa and Aegilops umbellulata Using Single-Gene FISH and Chromosome Sequences. Frontiers in Plant Science, 12, 689031. https://doi.org/10.3389/fpls.2021.689031
Said M, et al. Development of DNA Markers From Physically Mapped Loci in Aegilops Comosa and Aegilops Umbellulata Using Single-Gene FISH and Chromosome Sequences. Front Plant Sci. 2021;12:689031. PubMed PMID: 34211490.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Development of DNA Markers From Physically Mapped Loci in Aegilops comosa and Aegilops umbellulata Using Single-Gene FISH and Chromosome Sequences. AU - Said,Mahmoud, AU - Holušová,Katerina, AU - Farkas,András, AU - Ivanizs,László, AU - Gaál,Eszter, AU - Cápal,Petr, AU - Abrouk,Michael, AU - Martis-Thiele,Mihaela M, AU - Kalapos,Balázs, AU - Bartoš,Jan, AU - Friebe,Bernd, AU - Doležel,Jaroslav, AU - Molnár,István, Y1 - 2021/06/15/ PY - 2021/03/31/received PY - 2021/05/19/accepted PY - 2021/7/2/entrez PY - 2021/7/3/pubmed PY - 2021/7/3/medline KW - Aegilops comosa KW - Aegilops umbellulata KW - chromosome flow sorting and sequencing KW - chromosome rearrangements KW - goat grasses KW - homoeologous relationships KW - molecular markers KW - single-gene FISH SP - 689031 EP - 689031 JF - Frontiers in plant science JO - Front Plant Sci VL - 12 N2 - Breeding of agricultural crops adapted to climate change and resistant to diseases and pests is hindered by a limited gene pool because of domestication and thousands of years of human selection. One way to increase genetic variation is chromosome-mediated gene transfer from wild relatives by cross hybridization. In the case of wheat (Triticum aestivum), the species of genus Aegilops are a particularly attractive source of new genes and alleles. However, during the evolution of the Aegilops and Triticum genera, diversification of the D-genome lineage resulted in the formation of diploid C, M, and U genomes of Aegilops. The extent of structural genome alterations, which accompanied their evolution and speciation, and the shortage of molecular tools to detect Aegilops chromatin hamper gene transfer into wheat. To investigate the chromosome structure and help develop molecular markers with a known physical position that could improve the efficiency of the selection of desired introgressions, we developed single-gene fluorescence in situ hybridization (FISH) maps for M- and U-genome progenitors, Aegilops comosa and Aegilops umbellulata, respectively. Forty-three ortholog genes were located on 47 loci in Ae. comosa and on 52 loci in Ae. umbellulata using wheat cDNA probes. The results obtained showed that M-genome chromosomes preserved collinearity with those of wheat, excluding 2 and 6M containing an intrachromosomal rearrangement and paracentric inversion of 6ML, respectively. While Ae. umbellulata chromosomes 1, 3, and 5U maintained collinearity with wheat, structural reorganizations in 2, 4, 6, and 7U suggested a similarity with the C genome of Aegilops markgrafii. To develop molecular markers with exact physical positions on chromosomes of Aegilops, the single-gene FISH data were validated in silico using DNA sequence assemblies from flow-sorted M- and U-genome chromosomes. The sequence similarity search of cDNA sequences confirmed 44 out of the 47 single-gene loci in Ae. comosa and 40 of the 52 map positions in Ae. umbellulata. Polymorphic regions, thus, identified enabled the development of molecular markers, which were PCR validated using wheat-Aegilops disomic chromosome addition lines. The single-gene FISH-based approach allowed the development of PCR markers specific for cytogenetically mapped positions on Aegilops chromosomes, substituting as yet unavailable segregating map. The new knowledge and resources will support the efforts for the introgression of Aegilops genes into wheat and their cloning. SN - 1664-462X UR - https://www.unboundmedicine.com/medline/citation/34211490/Development_of_DNA_Markers_From_Physically_Mapped_Loci_in_Aegilops_comosa_and_Aegilops_umbellulata_Using_Single_Gene_FISH_and_Chromosome_Sequences_ DB - PRIME DP - Unbound Medicine ER -
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