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Journal of Integrative Agriculture  2021, Vol. 20 Issue (9): 2333-2342    DOI: 10.1016/S2095-3119(20)63289-0
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Integrating the physical and genetic map of bread wheat facilitates the detection of chromosomal rearrangements
ZHAO Lai-bin1*, XIE Die1*, HUANG Lei1, ZHANG Shu-jie1, LUO Jiang-tao2, JIANG Bo3, NING Shun-zong3, ZHANG Lian-quan1, YUAN Zhong-wei3, WANG Ji-rui3, ZHENG You-liang3, LIU Deng-cai1, HAO Ming3 
1 Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China
2 Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, P.R.China
3 State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R.China
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Abstract  
The bread wheat genome harbors a high content of repetitive DNA, which is amenable to detection and characterization using fluorescence in situ hybridization (FISH) karyotyping.  An integrated genetic map was derived from a recombinant inbred population bred from a cross between a synthetic hexaploid wheat and a commercial Chinese bread wheat cultivar, based on 28 variable FISH sites and >150 000 single nucleotide polymorphism (SNP) loci.  The majority (20/28) of the variable FISH sites were physically located within a chromosomal region consistent with the genetic location inferred from that of their co-segregating SNP loci.  The eight exceptions reflected the presence of either a translocation (1R/1B, 1A/7A) or a presumptive intra-chromosomal inversion (4A).  For eight out of the nine FISH sites detected on the Chinese Spring (CS) karyotype, there was a good match with the reference genome sequence, indicating that the most recent assembly has dealt well with the problem of placing tandem repeats.  The integrated genetic map produced for wheat is informative as to the location of blocks of tandemly repeated DNA and can aid in improving the quality of the genome sequence assembly in regions surrounding these blocks.
 
Keywords:  Triticeae        Triticum turgidum        repetitive DNA sequences        fluorescence in situ hybridization (FISH)        wheat genome        synthetic hexaploid wheat  
Received: 02 March 2020   Accepted: 20 July 2021
Fund: This research was financially supported by the National Key Research and Development Program of China (2016YFD0102000).
Corresponding Authors:  Correspondence LIU Deng-cai, Tel: +86-28-86290004, E-mail: dcliu7@yahoo.com; HAO Ming, Tel: +86-28-82650313, E-mail: haomingluo@foxmail.com    
About author:  ZHAO Lai-bin, Tel: +86-28-84504260, E-mail: laibinzhao@126.com; XIE Die, Tel: +86-28-82650313, E-mail: 852286660@qq.com; * These authors contributed equally to this study.

Cite this article: 

ZHAO Lai-bin, XIE Die, HUANG Lei, ZHANG Shu-jie, LUO Jiang-tao, JIANG Bo, NING Shun-zong, ZHANG Lian-quan, YUAN Zhong-wei, WANG Ji-rui, ZHENG You-liang, LIU Deng-cai, HAO Ming. 2021. Integrating the physical and genetic map of bread wheat facilitates the detection of chromosomal rearrangements. Journal of Integrative Agriculture, 20(9): 2333-2342.

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