PMID- 34740239
OWN - NLM
STAT- MEDLINE
DCOM- 20220222
LR  - 20220826
IS  - 1943-2631 (Electronic)
IS  - 0016-6731 (Print)
IS  - 0016-6731 (Linking)
VI  - 219
IP  - 3
DP  - 2021 Nov 5
TI  - LD-CNV: rapid and simple discovery of chromosomal translocations using linkage 
      disequilibrium between copy number variable loci.
LID - 10.1093/genetics/iyab137 [doi]
LID - iyab137
AB  - Large-scale structural variations, such as chromosomal translocations, can have 
      profound effects on fitness and phenotype, but are difficult to identify and 
      characterize. Here, we describe a simple and effective method aimed at 
      identifying translocations using only the dosage of sequence reads mapped on the 
      reference genome. We binned reads on genomic segments sized according to 
      sequencing coverage and identified instances when copy number segregated in 
      populations. For each dosage-polymorphic 1 Mb bin, we tested independence, 
      effectively an apparent linkage disequilibrium (LD), with other variable bins. In 
      nine potato (Solanum tuberosum) dihaploid families translocations affecting 
      pericentromeric regions were common and in two cases were due to genomic 
      misassembly. In two populations, we found evidence for translocation affecting 
      euchromatic arms. In cv. PI 310467, a nonreciprocal translocation between 
      chromosomes (chr.) 7 and 8 resulted in a 5-3 copy number change affecting several 
      Mb at the respective chromosome tips. In cv. "Alca Tarma," the terminal arm of 
      chr. 4 translocated to the tip of chr. 1. Using oligonucleotide-based fluorescent 
      in situ hybridization painting probes (oligo-FISH), we tested and confirmed the 
      predicted arrangement in PI 310467. In 192 natural accessions of Arabidopsis 
      thaliana, dosage haplotypes tended to vary continuously and resulted in higher 
      noise, while apparent LD between pericentromeric regions suggested the effect of 
      repeats. This method, LD-CNV, should be useful in species where translocations 
      are suspected because it tests linkage without the need for genotyping.
CI  - (c) The Author(s) 2021. Published by Oxford University Press on behalf of Genetics 
      Society of America. All rights reserved. For permissions, please email: 
      journals.permissions@oup.com.
FAU - Comai, Luca
AU  - Comai L
AUID- ORCID: 0000-0003-2642-6619
AD  - Department of Plant Biology and Genome Center, University of California, Davis, 
      Davis, CA 95616, USA.
FAU - Amundson, Kirk R
AU  - Amundson KR
AD  - Department of Plant Biology and Genome Center, University of California, Davis, 
      Davis, CA 95616, USA.
FAU - Ordonez, Benny
AU  - Ordonez B
AUID- ORCID: 0000-0003-4554-4354
AD  - Department of Plant Biology and Genome Center, University of California, Davis, 
      Davis, CA 95616, USA.
FAU - Zhao, Xin
AU  - Zhao X
AD  - Department of Plant Biology and Genome Center, University of California, Davis, 
      Davis, CA 95616, USA.
FAU - Braz, Guilherme Tomaz
AU  - Braz GT
AUID- ORCID: 0000-0002-0803-7778
AD  - Department of Plant Biology, Michigan State University, East Lansing, MI 48824, 
      USA.
FAU - Jiang, Jiming
AU  - Jiang J
AUID- ORCID: 0000-0002-6435-6140
AD  - Department of Plant Biology, Michigan State University, East Lansing, MI 48824, 
      USA.
AD  - Department of Horticulture, Michigan State University, East Lansing, MI 48824, 
      USA.
FAU - Henry, Isabelle M
AU  - Henry IM
AUID- ORCID: 0000-0002-6796-1119
AD  - Department of Plant Biology and Genome Center, University of California, Davis, 
      Davis, CA 95616, USA.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
PL  - United States
TA  - Genetics
JT  - Genetics
JID - 0374636
SB  - IM
MH  - Arabidopsis/genetics
MH  - Chromosome Mapping/*methods
MH  - Chromosomes, Plant/*genetics
MH  - DNA Copy Number Variations
MH  - Feasibility Studies
MH  - Haplotypes
MH  - In Situ Hybridization, Fluorescence
MH  - *Linkage Disequilibrium
MH  - Quantitative Trait Loci
MH  - Solanum tuberosum/genetics
MH  - *Translocation, Genetic
PMC - PMC8570776
OTO - NOTNLM
OT  - DNA sequence
OT  - chromosome
OT  - copy number variation
OT  - linkage disequilibrium
OT  - structural variation
OT  - translocation
EDAT- 2021/11/06 06:00
MHDA- 2022/02/23 06:00
PMCR- 2022/08/24
CRDT- 2021/11/05 20:22
PHST- 2021/06/19 00:00 [received]
PHST- 2021/08/13 00:00 [accepted]
PHST- 2021/11/05 20:22 [entrez]
PHST- 2021/11/06 06:00 [pubmed]
PHST- 2022/02/23 06:00 [medline]
PHST- 2022/08/24 00:00 [pmc-release]
AID - 6357040 [pii]
AID - iyab137 [pii]
AID - 10.1093/genetics/iyab137 [doi]
PST - ppublish
SO  - Genetics. 2021 Nov 5;219(3):iyab137. doi: 10.1093/genetics/iyab137.