Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps.
The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker-based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal "pseudomolecules".
Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom.
Sanjeev Kumar
SK
Sharma
Daniel
D
Bolser
Jan
J
de Boer
Mads
M
Sønderkær
Walter
W
Amoros
Martin Federico
MF
Carboni
Juan Martín
JM
D'Ambrosio
German
G
de la Cruz
Alex
A
Di Genova
David S
DS
Douches
Maria
M
Eguiluz
Xiao
X
Guo
Frank
F
Guzman
Christine A
CA
Hackett
John P
JP
Hamilton
Guangcun
G
Li
Ying
Y
Li
Roberto
R
Lozano
Alejandro
A
Maass
David
D
Marshall
Diana
D
Martinez
Karen
K
McLean
Nilo
N
Mejía
Linda
L
Milne
Susan
S
Munive
Istvan
I
Nagy
Olga
O
Ponce
Manuel
M
Ramirez
Reinhard
R
Simon
Susan J
SJ
Thomson
Yerisf
Y
Torres
Robbie
R
Waugh
Zhonghua
Z
Zhang
Sanwen
S
Huang
Richard G F
RG
Visser
Christian W B
CW
Bachem
Boris
B
Sagredo
Sergio E
SE
Feingold
Gisella
G
Orjeda
Richard E
RE
Veilleux
Merideth
M
Bonierbale
Jeanne M E
JM
Jacobs
Dan
D
Milbourne
David Michael Alan
DM
Martin
Glenn J
GJ
Bryan
D015415:Biomarkers / Q000378:metabolism; D002874:Chromosome Mapping / Q000592:standards*; D032461:Chromosomes, Plant / Q000235:genetics* / Q000378:metabolism; D018745:Genome, Plant; D020407:Internet; D011198:Solanum tuberosum / Q000235:genetics*; D014584:User-Computer Interface
D015415:Biomarkers
Solanaceae; genetic map; genome anchoring; physical map; potato; pseudomolecules; scaffold orientation; sequence-tagged sites