Integrating the physical and genetic map of bread wheat facilitates the detection of chromosomal rearrangements

doi:10.1016/S2095-3119(20)63289-0

Journal of Integrative Agriculture ›› 2021, Vol. 20 ›› Issue (9): 2333-2342.DOI: 10.1016/S2095-3119(20)63289-0

收稿日期:2020-03-02 出版日期:2021-09-01 发布日期:2021-07-20

Integrating the physical and genetic map of bread wheat facilitates the detection of chromosomal rearrangements

ZHAO Lai-bin^1*, XIE Die^1*, 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

¹Triticeae 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

Received:2020-03-02 Online:2021-09-01 Published:2021-07-20
Contact: 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.
Supported by:
This research was financially supported by the National Key Research and Development Program of China (2016YFD0102000).

摘要/Abstract

摘要：

本研究利用一个人工合成小麦与普通小麦品种构建的重组自交系，构建了一张包含28个FISH多态性标记和超过150000个单核苷酸多态性（single nucleotide polymorphism，SNP）标记的整合图谱。锚定在整合图谱的28个FISH标记中，20个FISH标记的共分离SNP标记推断的物理位置与原位杂交的物理位置一致。另外8个位置不一致的FISH标记是由亲本含有的易位染色体（1R/1B和1A/7A）或臂内倒位染色体（4A）所导致。9个在于中国春染色体上也具有杂交信号的FISH标记中，8个FISH标记的杂交信号位置与通过参考基因组序列锚定的物理位置一致，表明当前中国春参考基因组对重复序列的组装效果较好。因此，整合图谱对定位重复序列以及提高对基因组重复序列的组装精度方面具有一定利用价值。

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.

Key words: Triticeae , Triticum turgidum , repetitive DNA sequences , fluorescence in situ hybridization (FISH) , wheat genome , synthetic hexaploid wheat

. [J]. Journal of Integrative Agriculture, 2021, 20(9): 2333-2342.

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. Integrating the physical and genetic map of bread wheat facilitates the detection of chromosomal rearrangements[J]. Journal of Integrative Agriculture, 2021, 20(9): 2333-2342.

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Integrating the physical and genetic map of bread wheat facilitates the detection of chromosomal rearrangements

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