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Title:Characterization of the sex chromosomes in spinach
Author(s):Wadlington, William H
Director of Research:Ming, Ray
Doctoral Committee Chair(s):Ming, Ray
Doctoral Committee Member(s):Heath, Katy; Downie, Stephen; Tranel, Pat; Hanzawa, Yoshie
Department / Program:Plant Biology
Discipline:Plant Biology
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):spinach, sex chromosomes, dioecy
Abstract:Plant sex chromosomes have evolved from the autosomes of hermaphroditic species to maintain dioecy. The major barriers to sex chromosome characterization have been the inherent difficulties of working with a non-recombining sex determining region that make sequencing and mapping the Male-Specific region of the Y chromosome (MSY) painstaking. Here we use YY spinach (Spinacia oleracea L.) to characterize the MSY and the X-specific region of the X chromosome. A screen of 395 accessions in the USDA germplasm collection found a single accession that segregates YY progeny. The YY genotype was verified by a genetic cross and a novel X-specific marker. Potential novel X-specific sequences were found by depth of coverage analysis comparing alignments of male and female sequences to an XX reference. Of the 19 candidates found by depth of coverage, only one was verified as X-specific. The marker SpoX amplifies products from XX and XY but not YY templates. Pooled genomic DNA of 16 YY individuals selected by SpoX was sequenced at 63X using PacBio. Sequence data was assembled into an 823 Mbp assembly using CANU so the YY assembly could be compared to a 911 Mbp XX assembly. Seven genes that were non-repetitive sequences were found on a 1.14 X-specific contig from the XX assembly, and were queried by BLAST to the YY assembly to find their MSY homologs, which totaled 427 kb of novel Y chromosome sequence. On the Y contigs, the percentage uncovered by female k-mers decreased from 9.5% to 0.6% between positions 65.8 Mbp and 66.7 Mbp on the X chromosome, indicating that it is the location of one of the boundaries of the non-recombining region. The discovery of an accession which reliably segregates YY plants makes for unprecedented opportunity to study X and Y chromosomes in spinach. By comparing YY and XX genomes, the genomic basis of X and Y chromosome differentiation and evolution that gave rise to dioecy can be elucidated.
Issue Date:2017-06-19
Type:Thesis
URI:http://hdl.handle.net/2142/98172
Rights Information:Copyright 2017 William Wadlington
Date Available in IDEALS:2017-09-29
Date Deposited:2017-08


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