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. 2008 Mar;18(3):422-30.
doi: 10.1101/gr.7076308. Epub 2008 Feb 6.

Genome structure and emerging evidence of an incipient sex chromosome in Populus

Tongming Yin  1 , Stephen P Difazio, Lee E Gunter, Xinye Zhang, Michell M Sewell, Scott A Woolbright, Gery J Allan, Collin T Kelleher, Carl J Douglas, Mingxiu Wang, Gerald A Tuskan
Affiliations

Genome structure and emerging evidence of an incipient sex chromosome in Populus

Tongming Yin et al. Genome Res. 2008 Mar.

Abstract

The genus Populus consists of dioecious woody species with largely unknown genetic mechanisms for gender determination. We have discovered genetic and genomic features in the peritelomeric region of chromosome XIX that suggest this region of the Populus genome is in the process of developing characteristics of a sex chromosome. We have identified a gender-associated locus that consistently maps to this region. Furthermore, comparison of genetic maps across multiple Populus families reveals consistently distorted segregation within this region. We have intensively characterized this region using an F(1) interspecific cross involving the female genotype that was used for genome sequencing. This region shows suppressed recombination and high divergence between the alternate haplotypes, as revealed by dense map-based genome assembly using microsatellite markers. The suppressed recombination, distorted segregation, and haplotype divergence were observed only for the maternal parent in this cross. Furthermore, the progeny of this cross showed a strongly male-biased sex ratio, in agreement with Haldane's rule that postulates that the heterogametic sex is more likely to be absent, rare, or sterile in interspecific crosses. Together, these results support the role of chromosome XIX in sex determination and suggest that sex determination in Populus occurs through a ZW system in which the female is the heterogametic gender.

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Figures

Figure 1.
Figure 1.
The consensus genetic map for Populus. (Black) AFLP markers; (red) the framework SSR markers in Family 13 and Family 331; (green) the alternative SSR markers genotyped in Family 13; (blue) the alternative SSR markers genotyped in Family 331; (SEX) the gender determination locus. The markers in bins have the same consensus position. The consensus map was established from genotypes of different pedigrees, and thus, the genetic distance does not reflect the recombination rate between markers but rather only marker orders on the consensus map. Note SSR primers were developed from different sequence data (for marker nomenclature, see text).
Figure 2.
Figure 2.
Forty-seven NBS-LRR genes localize to a 2.45-Mb region at the peritelomeric end of chromosome XIX. The physical length is estimated by the assembled sequence scaffold lengths plus the averaged gap length among scaffolds. The green portion of the vertical bar indicates the distorted region; the blue portion indicates the nondistorted region; the white portion indicates sequence gaps; the horizontal black bars show the physical positions of NBS-LRR genes; and the red letters are the serial number of NBS-LRR genes based on their physical orders along the chromosome. The ruler to the left of the chromosomal bar indicates the physical length in base pairs. Only one NBS-LRR gene would be expected in the corresponding 2.45-Mb region based on a uniform average genome-wide distribution assumption.
Figure 3.
Figure 3.
Relationship between the physical (middle) and gender-specific genetic maps (left and right) of scaffold 117 in Family 545. This scaffold was positioned in the peritelomeric region of chromosome XIX. We detected recombination suppression in the upper 706-kb region of this scaffold containing an overabundant number of NBS-LRR genes. In contrast, the lower 257-kb region is rich with recombination hotspots in both the maternal and paternal parents. Moreover, genotyping revealed more heterozygous loci in the maternal genotype than in the paternal genotype on this scaffold. Values in parentheses are χ2 statistics for tests of segregation distortion. Alleles from the maternal parent showed strong and consistent segregation distortion, whereas alleles from the paternal parent generally conformed to Mendelian expectations (χ2 critical value = 3.84 for α ≤ 0.05).
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