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Development and application of oligonucleotide-based chromosome painting for chromosome 4D of Triticum aestivum L.
Chromosome Res. 2020 06; 28(2):171-182.CR

Abstract

Chromosome painting is a useful technique for distinguishing specific chromosomes (fragments), elucidating the genetic relationships of different genomes or chromosomes, and identifying chromosomal rearrangements. The development of chromosome- or genome-specific probes is fundamental for chromosome painting. The possibility for developing such probes specifically painting homoeologous chromosomes in allopolyploid species has been questioned since that chromosomes belonging to the same homoeologous group share highly conserved sequences. In the present study, we attempted to construct a wheat chromosome 4D-specific oligo probe library by selecting 4D-specific sequences in reference genome of common wheat cv. Chinese Spring (CS, 2n = 6x = 42, AABBDD). The synthesized library contains 27,392 oligos. Oligo painting using the probe library confirmed its specificity, shown by that only chromosome 4D could be painted in three wheat genotypes and CS nulli-tetrasomic line N4AT4D. Oligo painting was successfully used to define the 4D breakpoints in CS deletion lines involving 4D and two wheat-Haynaldia villosa 4D-4V translocation lines. Thirteen wheat relatives and a Triticum durum-H. villosa amphiploid were used for oligo painting. Except the 4D in two Aegilops tauschii accessions, the 4M in Ae. comosa and 4U in Ae. umbellulata could be painted. In tetraploid Ae. ventricosa, both 4D and 4M could be painted; however, the signal intensity of 4M was less compared with 4D. No painted chromosome was observed for the other alien species. This indicated that the relationship among D/M/U was closer than that among D/A/B as well as D with genomes H/R/Ss/Sc/Y/P/N/J. Our successful development of 4D-specific oligo probe library may serve as a model for developing oligo probes specific for other homoeologous chromosomes.

Authors+Show Affiliations

State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China.Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China.Co-Innovation Center for Sustainable Forestry in Southern China/Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China. hywang@njau.edu.cn.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China. xiuew@njau.edu.cn.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32002727

Citation

Song, Xinying, et al. "Development and Application of Oligonucleotide-based Chromosome Painting for Chromosome 4D of Triticum Aestivum L." Chromosome Research : an International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology, vol. 28, no. 2, 2020, pp. 171-182.
Song X, Song R, Zhou J, et al. Development and application of oligonucleotide-based chromosome painting for chromosome 4D of Triticum aestivum L. Chromosome Res. 2020;28(2):171-182.
Song, X., Song, R., Zhou, J., Yan, W., Zhang, T., Sun, H., Xiao, J., Wu, Y., Xi, M., Lou, Q., Wang, H., & Wang, X. (2020). Development and application of oligonucleotide-based chromosome painting for chromosome 4D of Triticum aestivum L. Chromosome Research : an International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology, 28(2), 171-182. https://doi.org/10.1007/s10577-020-09627-0
Song X, et al. Development and Application of Oligonucleotide-based Chromosome Painting for Chromosome 4D of Triticum Aestivum L. Chromosome Res. 2020;28(2):171-182. PubMed PMID: 32002727.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Development and application of oligonucleotide-based chromosome painting for chromosome 4D of Triticum aestivum L. AU - Song,Xinying, AU - Song,Rongrong, AU - Zhou,Jiawen, AU - Yan,Wenkai, AU - Zhang,Tao, AU - Sun,Haojie, AU - Xiao,Jin, AU - Wu,Yufeng, AU - Xi,Mengli, AU - Lou,Qunfeng, AU - Wang,Haiyan, AU - Wang,Xiue, Y1 - 2020/01/30/ PY - 2019/11/14/received PY - 2020/01/24/accepted PY - 2020/01/23/revised PY - 2020/2/1/pubmed PY - 2021/6/9/medline PY - 2020/2/1/entrez KW - Chromosome painting KW - Fluorescent in situ hybridization (FISH) KW - Oligo probe library KW - Wheat SP - 171 EP - 182 JF - Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology JO - Chromosome Res VL - 28 IS - 2 N2 - Chromosome painting is a useful technique for distinguishing specific chromosomes (fragments), elucidating the genetic relationships of different genomes or chromosomes, and identifying chromosomal rearrangements. The development of chromosome- or genome-specific probes is fundamental for chromosome painting. The possibility for developing such probes specifically painting homoeologous chromosomes in allopolyploid species has been questioned since that chromosomes belonging to the same homoeologous group share highly conserved sequences. In the present study, we attempted to construct a wheat chromosome 4D-specific oligo probe library by selecting 4D-specific sequences in reference genome of common wheat cv. Chinese Spring (CS, 2n = 6x = 42, AABBDD). The synthesized library contains 27,392 oligos. Oligo painting using the probe library confirmed its specificity, shown by that only chromosome 4D could be painted in three wheat genotypes and CS nulli-tetrasomic line N4AT4D. Oligo painting was successfully used to define the 4D breakpoints in CS deletion lines involving 4D and two wheat-Haynaldia villosa 4D-4V translocation lines. Thirteen wheat relatives and a Triticum durum-H. villosa amphiploid were used for oligo painting. Except the 4D in two Aegilops tauschii accessions, the 4M in Ae. comosa and 4U in Ae. umbellulata could be painted. In tetraploid Ae. ventricosa, both 4D and 4M could be painted; however, the signal intensity of 4M was less compared with 4D. No painted chromosome was observed for the other alien species. This indicated that the relationship among D/M/U was closer than that among D/A/B as well as D with genomes H/R/Ss/Sc/Y/P/N/J. Our successful development of 4D-specific oligo probe library may serve as a model for developing oligo probes specific for other homoeologous chromosomes. SN - 1573-6849 UR - https://www.unboundmedicine.com/medline/citation/32002727/Development_and_application_of_oligonucleotide_based_chromosome_painting_for_chromosome_4D_of_Triticum_aestivum_L_ L2 - https://doi.org/10.1007/s10577-020-09627-0 DB - PRIME DP - Unbound Medicine ER -