Identification and Characterization of Segregation Distortion Loci on Cotton Chromosome 18

Dai, Baosheng; Guo, Huiling; Huang, Cong; Ahmed, Muhammad Mahmood; Lin, Zhenhua

doi:10.3389/fpls.2016.02037

Cited by 26 publications

(36 citation statements)

References 58 publications

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“…Segregation distortion (SD) is a general phenomenon in plants, but the percentage, degree and genetic effects may vary significantly across species (Dai et al 2016;Zhou et al 2015;Taylor and Ingvarsson 2003). In maize, it has been reported that 18 chromosome regions on 10 chromosomes were associated with SD (Lu, Romero-Severson, and Bernardo 2002) while 14 SD regions were reported for barley (Li et al 2010).…”

Section: Discussionmentioning

confidence: 99%

The first genetic linkage map forFraxinus pennsylvanicaand syntenic relationships with four related species

Koch

Coggeshall

et al. 2018

Preprint

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Green ash (Fraxinus pennsylvanica) is an outcrossing, diploid (2n=46) hardwood tree species, native to North America. Native ash species in North America are being threatened by the rapid invasion of emerald ash borer (EAB, Agrilus planipennis) from Asia. Green ash, the most widely distributed ash species, is severely affected by EAB infestation, yet few resources for genetic studies and improvement of green ash are available. In this study, a total of 5,712 high quality single nucleotide polymorphisms (SNPs) were discovered using a minimum allele frequency of 1% across the entire genome through genotyping-by-sequencing. We also screened hundreds of genomic-and EST-based microsatellite markers (SSRs) from previous de novo assemblies (Staton et al. 2015;Lane et al. 2016). A first genetic linkage map of green ash was constructed from 91 individuals in a full-sib family, combining 2,719 SNP and 84 SSR segregating markers among the parental maps. The consensus SNP and SSR map contains a total of 1,201 markers in 23 linkage groups spanning 2008.87cM, at an average inter-marker distance of 1.67 cM with a minimum logarithm of odds (LOD) of 6 and maximum recombination fraction of 0.40. Comparisons of the organization the green ash map with the genomes of asterid species coffee and tomato, and genomes of the rosid species poplar and peach, showed areas of conserved gene order, with overall synteny strongest with coffee. KeywordsGreen ash, linkage map, single nucleotide polymorphism (SNP), simple sequence repeats (SSRs), Genotyping-by-Sequencing (GBS), syntenyThe genetic and molecular mechanisms underlying diverse biological traits in green ash are unknown. Genetic linkage maps are powerful tools for genomics and genetics research. With a large number of DNA markers, fine mapping of quantitative trait loci (QTL) can support marker-assisted selection for breeding programs. Candidate genes can also be positioned within the quantitative trait locus (QTL) regions identified by association studies. Combined with transcriptome studies, differentially expressed genes can be mapped and localized so that genes related to specific traits of interest can be characterized. In addition, linkage maps can also be used to conduct comparative analyses with other species to detect genomic synteny and to improve and correct chromosome-scale genome assemblies. Linkage maps have been reported in many non-model species (Tian et al. 2015;Moumouni et al. 2015;Raman et al. 2014), but the resolution of genetic maps depends on the number of markers segregating in the mapping population.Recently, the innovation of NGS methods for genetic marker discovery combined with reduced costs has facilitated the genotyping of thousands of SNPs across hundreds of samples. New methods, such as reduced-representation libraries (RRLs) (Van Tassell et al. 2008), restriction-site associated sequencing (RAD-seq) (Davey and Blaxter 2010) and genotyping-bysequencing (GBS) (Elshire et al. 2011), utilize restriction enzyme digestion of target genomes to reduce the complex...

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Section: Discussionmentioning

confidence: 99%

The first genetic linkage map forFraxinus pennsylvanicaand syntenic relationships with four related species

Koch

Coggeshall

et al. 2018

Preprint

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“…Markers showing distortion have been recorded in a number of crops 90,91 . Markers displaying SD can be useful in QTL mapping 92 as they are often linked to candidate genes for specific traits.…”

Section: Crossover Frequency and Recombination Varied Between Maps Dmentioning

confidence: 99%

“…For instance, it was found that regions of SD in sweet cherry, where 8% of markers showed distortion, are linked with hotspots containing fruit and bloom time traits, as well as a self-incompatibility modifier locus 93 . In cotton, several important agronomic traits have been recorded on chromosome 18 where 34% of markers showed distortion 90 .…”

Section: Crossover Frequency and Recombination Varied Between Maps Dmentioning

confidence: 99%

Maximising recombination across macadamia populations to generate linkage maps for genome anchoring

Langdon

King

Baten

et al. 2020

Sci Rep

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the proteaceae genus Macadamia has a recent history of domestication as a commercial nut crop. We aimed to establish the first sequence-based haploid-correlated reference genetic linkage maps for this primarily outcrossing perennial tree crop, with marker density suitable for genome anchoring. Four first generation populations were used to maximise the segregation patterns available within full-sib, biparental and self-pollinated progeny. This allowed us to combine segregation data from overlapping subsets of >4,000 informative sequence-tagged markers to increase the effective coverage of the karyotype represented by the recombinant crossover events detected. All maps had 14 linkage groups, corresponding to the Macadamia haploid chromosome number, and enabled the anchoring and orientation of sequence scaffolds to construct a pseudo-chromosomal genome assembly for macadamia. Comparison of individual maps indicated a high level of congruence, with minor discrepancies satisfactorily resolved within the integrated maps. The combined set of maps significantly improved marker density and the proportion (70%) of the genome sequence assembly anchored. Overall, increasing our understanding of the genetic landscape and genome for this nut crop represents a substantial advance in macadamia genetics and genomics. The set of maps, large number of sequence-based markers and the reconstructed genome provide a toolkit to underpin future breeding that should help to extend the macadamia industry as well as provide resources for the long term conservation of natural populations in eastern Australia of this unique genus.

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“…In an F2 population originating from a biparental cross, the expected ratio of genotypes AA:AB:BB (progeny homozygous for the allele from the first parent, heterozygotes and progeny homozygous for the allele from the second parent) in absence of segregation distortion is 1:2:1. Segregation distortion is observed across a wide range of taxa, including animals such as Drosophila [1,2] and mice [3], as well as crop species, including cotton [4], maize [5,6], potato [7], chickpea [8], barley [9] and wheat [10][11][12]. The primary explanation of the cause of segregation distortion is a selection pressure operating against one of the parental alleles at some stage of the development cycle, whether at meiosis through meiotic drive [1], through male gamete competition [4], or at the level of the zygote.…”

Section: Introductionmentioning

confidence: 99%

“…The diversity of criteria used in the literature reflect the difficulty of answering this question. Some authors settle for a simple chi-square test with the minimum significance threshold of p < 0.05 [5,10,[14][15][16], others report multiple significance thresholds [7,[17][18][19][20], whilst others use corrections for multiple testing, including false discovery rate (FDR) [11,12,21] and the even stricter Bonferroni correction [4,22]. This inconsistency has the further implication that many of the studies on segregation distortion are not comparable, which is problematic for the general advancement of our knowledge of segregation distortion.…”

Section: Introductionmentioning

confidence: 99%

Segregation distortion: Utilizing simulated genotyping data to evaluate statistical methods

et al. 2020

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Segregation distortion is the phenomenon in which genotypes deviate from expected Mendelian ratios in the progeny of a cross between two varieties or species. There is not currently a widely used consensus for the appropriate statistical test, or more specifically the multiple testing correction procedure, used to detect segregation distortion for high-density single-nucleotide polymorphism (SNP) data. Here we examine the efficacy of various multiple testing procedures, including chi-square test with no correction for multiple testing, falsediscovery rate correction and Bonferroni correction using an in-silico simulation of a biparental mapping population. We find that the false discovery rate correction best approximates the traditional p-value threshold of 0.05 for high-density marker data. We also utilize this simulation to test the effect of segregation distortion on the genetic mapping process, specifically on the formation of linkage groups during marker clustering. Only extreme segregation distortion was found to effect genetic mapping. In addition, we utilize replicate empirical mapping populations of wheat varieties Avalon and Cadenza to assess how often segregation distortion conforms to the same pattern between closely related wheat varieties.

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Identification and Characterization of Segregation Distortion Loci on Cotton Chromosome 18

Cited by 26 publications

References 58 publications

The first genetic linkage map forFraxinus pennsylvanicaand syntenic relationships with four related species

The first genetic linkage map forFraxinus pennsylvanicaand syntenic relationships with four related species

Maximising recombination across macadamia populations to generate linkage maps for genome anchoring

Segregation distortion: Utilizing simulated genotyping data to evaluate statistical methods

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