Characterization of a large sex determination region in Salix purpurea L. (Salicaceae)

Zhou, Ran; Macaya‐Sanz, David; Rodgers-Melnick, Eli; Carlson, Craig H.; Gouker, Fred E.; Evans, Luke M.; Schmutz, Jeremy; Jenkins, Jerry; Yan, Juying; Tuskan, Gerald A.; Smart, Lawrence B.; DiFazio, Stephen P.

doi:10.1007/s00438-018-1473-y

Cited by 63 publications

(88 citation statements)

References 92 publications

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“…These can be readily differentiated by examining the relative depth of coverage when aligning male versus female short read sequences against these references. After identifying the location of the SDR based on the presence of sex-biased markers [18], the initial Chromosome 15 assembly appeared to consist of a mix of Z and W scaffolds in the SDR (Additional File 2: Figure S1a). We therefore sought to create a new assembly with Z and W haplotypes assembled to separate chromosomes.…”

Section: Resultsmentioning

confidence: 99%

“…Sex determination is similarly diverse within the Salicaceae family. SDRs have been consistently found on chromosome 15 with female heterogamety in multiple Salix species [18–20]. This is quite different from the closely-related genus Populus where sex determining regions consistently occur on chromosome 19, with most species showing male heterogamety [21, 22].…”

Section: Introductionmentioning

confidence: 99%

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A Willow Sex Chromosome Reveals Convergent Evolution of Complex Palindromic Repeats

Zhou

Macaya‐Sanz

Carlson

et al. 2019

Preprint

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1 Background 2 Sex chromosomes in a wide variety of species share common characteristics, including the 3 presence of suppressed recombination surrounding sex determination loci. They have arisen 4 independently in numerous lineages, providing a conclusive example of convergent evolution. 5Mammalian sex chromosomes contain multiple palindromic repeats across the non-recombining 6 region that facilitate sequence conservation through gene conversion, and contain genes that are 7 crucial for sexual reproduction. Plant sex chromosomes are less well understood, and in 8 particular it is not clear how coding sequence conservation is maintained in the absence of 9 homologous recombination. 10 Results 11 Here we present the first evidence of large palindromic structures in a plant sex chromosome, 12 based on a highly contiguous assembly of the W chromosome of the dioecious shrub Salix 13 purpurea. Two consecutive palindromes span over a region of 200 kb, with conspicuous 20 kb 14 stretches of highly conserved sequences among the four arms. The closely-related species S. 15 suchowensis also has two copies of a portion of the palindrome arm and provides strong 16 evidence for gene conversion. Four genes in the palindrome are homologous to genes in the SDR 17 of the closely-related genus Populus, which is located on a different chromosome. These genes 18 show distinct, floral-biased expression patterns compared to paralogous copies on autosomes.19 Conclusion 20The presence of palindromic structures in sex chromosomes of mammals and plants highlights 21 the intrinsic importance of these features in adaptive evolution in the absence of recombination. 22Convergent evolution is driving both the independent establishment of sex chromosomes as well 23 as their fine-scale sequence structure. 24 26 103 297 kb in length lacked mapped markers and could not be placed unambiguously. 104Location of the SDR 105 We repeated sex association analysis with our new assembly with Chr15Z removed. 106Among 54,959 tested SNPs, all 105 significantly sex-associated SNPs were present only on 107 Chr15W (Fig. 1a; Additional File 2: Figure S2a-c), and markers from PARs and other scaffolds 108 in the main genome did not show any sex association (Additional File 2: Figure S2a). The eight 109 top-ranking sex-associated markers were distributed from 7.66 Mb to 8.66 Mb. Sex-associated 110 markers were primarily heterozygous in females and homozygous in males, confirming our 111 previously-reported observation of ZW sex determination in S. purpurea [18].

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Willow Sex Chromosome Reveals Convergent Evolution of Complex Palindromic Repeats

Zhou

Macaya‐Sanz

Carlson

et al. 2019

Preprint

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“…Genetics and genomics, combined with extensive phenotyping, have substantially improved the genetic basis of biomass‐related traits in willow and are now being developed in targeted breeding via MAS. This underpinning work has been conducted on large specifically developed biparental Salix mapping populations (Hanley & Karp, ; Zhou et al, ), as well as GWAS panels (Hallingbäck et al, ).…”

Section: Willowmentioning

confidence: 99%

“…This underpinning work has been conducted on large specifically developed biparental Salix mapping populations CLIFTON-BROWN ET AL. | 135 (Hanley & Karp, 2014;Zhou et al, 2018), as well as GWAS panels (Hallingbäck et al, 2016).…”

Section: Willowmentioning

confidence: 99%

Breeding progress and preparedness for mass‐scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar

et al. 2018

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Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output–input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed‐based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass‐scale deployment of PBCs.

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“…The study of plant sex extends the field of genes-to-ecosystems research beyond the influence of general genetic variation within individuals (Schweitzer et al 2004 to the influence of male and female individuals within species (Hultine et al 2016). The influences of dioecy on ecosystem function need further exploration, especially since the expression of sex in dioecious plants is not straightforward (Rowland et al 2002, Zhou et al 2018. Additionally, understanding the influence of sex on ecosystem processes is crucial as climate and landscapes change since plant sexes may be differentially challenged by shifting climatic regimes (Hultine et al 2016).…”

Section: Discussionmentioning

confidence: 99%

Plant sex influences aquatic–terrestrial interactions

et al. 2020

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A growing body of research shows that plant genetic factors can influence ecosystem processes and structure communities, but one aspect that has received little study is sex differentiation in dioecious plants. Since headwater streams are reliant on riparian leaf litterfall, plant sex differences in leaf traits may influence in-stream processes. Sitka willow (Salix sitchensis) at Mount St. Helens is dioecious and heavily infested with the stem-boring weevil (Cryptorhynchus lapathi), which causes branch dieback and summer litterfall. We found that female willow shrubs tend to grow closer to the stream bank, are more likely to be infected by the weevil, and have 42% higher litter C:N than male willows. These factors may lead to increased litter inputs and slower litter mass loss for female willows. The combination of colonization location, herbivore attack, altered litter quality, and slower mass loss results in female shrubs providing more sustained carbon and nutrient resources to microbes and invertebrates in the early successional streams at Mount St. Helens. In addition, since dioecy is a relatively common trait in riparian habitats, it is possible that plant sex plays a far more interesting role in structuring linked terrestrial-aquatic communities and ecosystem processes than previously understood.

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Characterization of a large sex determination region in Salix purpurea L. (Salicaceae)

Cited by 63 publications

References 92 publications

A Willow Sex Chromosome Reveals Convergent Evolution of Complex Palindromic Repeats

A Willow Sex Chromosome Reveals Convergent Evolution of Complex Palindromic Repeats

Breeding progress and preparedness for mass‐scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar

Plant sex influences aquatic–terrestrial interactions

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