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217 results for “inbreds”
Data from: Unexpected positive and negative effects of continuing inbreeding in one of the world’s most inbred wild animals
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Sorghum leaf blight phenotypes for two recombinant inbred line populations
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Data from: Intergenerational effects of inbreeding in Nicrophorus vespilloides: offspring suffer fitness costs when either they or their parents are inbred
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Data from: Re-imagining maize inbred potential: identifying breeding crosses using genetic variance of simulated progeny
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Data from: Close kin mating, but not inbred parents, reduces hatching rates and offspring quality in a threatened tortoise
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The 49,890 SNPgenotype derived from genotyping-by-sequencing strategy for the NIP/9311 backcross inbred lines population
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Images of flowers and tubers produced by potato recombinant inbred lines
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Data from: Differential changes in bone strength of two inbred mouse strains following administration of a sclerostin-neutralizing antibody during growth
Administration of sclerostin-neutralizing antibody (Scl-Ab) treatment has been shown to elicit an anabolic bone response in growing and adult mice. Prior work characterized the response of individual mouse strains but did not establish whether the impact of Scl-Ab on whole bone strength would vary across different inbred mouse strains. Herein, we tested the hypothesis that two inbred mouse strains (A/J and C57BL/6J (B6)) will show different whole bone strength outcomes following sclerostin-neutralizing antibody (Scl-Ab) treatment during growth (4.5 – 8.5 weeks of age). Treated B6 femurs showed a significantly greater stiffness (S) (68.8% vs. 46.0%) and maximum load (ML) (84.7% vs. 44.8%) compared to A/J. Although treated A/J and B6 femurs showed greater cortical area (Ct.Ar) similarly relative to their controls (37.7% in A/J and 41.1% in B6), the location of new bone deposition responsible for the greater mass differed between strains and may explain the greater whole bone strength observed in treated B6 mice. A/J femurs showed periosteal expansion and endocortical infilling, while B6 femurs showed periosteal expansion. Post-yield displacement (PYD) was smaller in treated A/J femurs (-61.2%, p < 0.001) resulting in greater brittleness compared to controls; an effect not present in B6 mice. Inter-strain differences in S, ML, and PYD led to divergent changes in work-to-fracture (Work). Work was 27.2% (p = 0.366) lower in treated A/J mice and 66.2% (p < 0.001) greater in treated B6 mice relative to controls. Our data confirmed the anabolic response to Scl-Ab shown by others, and provided evidence suggesting the mechanical benefits of Scl-Ab administration may be modulated by genetic background, with intrinsic growth patterns of these mice guiding the location of new bone deposition. Whether these differential outcomes will persist in adult and elderly mice remains to be determined.
Data from: Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity
Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Wild potato species serve as a resource for the introgression of important agronomic traits into cultivated potato. One key species is Solanum chacoense and the diploid, inbred clone M6, which is self-compatible and has desirable tuber market quality and disease resistance traits. Sequencing and assembly of the genome of the M6 clone of S. chacoense generated an assembly of 825,767,562 bp in 8,260 scaffolds with an N50 scaffold size of 713,602 bp. Pseudomolecule construction anchored 508 Mb of the genome assembly into 12 chromosomes. Genome annotation yielded 49,124 high confidence gene models representing 37,740 genes. Comparative analyses of the M6 genome with six other Solanaceae species revealed a core set of 158,367 Solanaceae genes and 1,897 genes unique to three potato species. Analysis of single nucleotide polymorphisms across the M6 genome revealed enhanced residual heterozygosity on chromosomes 4, 8 and 9 relative to the other chromosomes. Access to the M6 genome provides a resource for identification of key genes for important agronomic traits and aids in genome-enabled development of inbred diploid potatoes with the potential to accelerate potato breeding.
Data from: A single migrant enhances the genetic diversity of an inbred puma population
Migration is essential for maintaining genetic diversity among populations, and pumas (Puma concolor) provide an excellent model for studying the genetic impacts of migrants on populations isolated by increasing human development. In densely populated southern California, USA, puma populations on the east and west side of interstate highway 15 (I-15) have become fragmented into a small inbred population on the west side (Santa Ana Mountains) and a relatively larger, more diverse population on the east side (Eastern Peninsular Range). From 146 sampled pumas, genetic analyses indicate seven pumas crossed I-15 over the last 15 years, including four males from west to east, and three males from east to west. However, only a single migrant (named M86) was detected to have produced offspring and contribute to gene flow across the I-15 barrier. Prior to the M86 migration, the Santa Ana population exhibited inbreeding and had significantly lower genetic diversity than the Eastern Peninsular Range population. After M86 emigrated, he sired 11 offspring with Santa Ana females, decreasing inbreeding measures and raising heterozygosity to levels similar to pumas in the Eastern Peninsular Range. The emigration of M86 also introduced new alleles into the Santa Ana population, although allelic richness still remained significantly lower than the Eastern Peninsular population. Our results clearly show the benefit of a single migrant to the genetics of a small, isolated population. However, ongoing development and habitat loss on both sides of I-15 will increasingly strengthen the barrier to successful migration. Further monitoring, and potential human intervention, including minimizing development effects on connectivity, adding or improving freeway crossing structures, or animal translocation, may be needed to ensure adequate gene flow and long-term persistence of the Santa Ana puma population.
Data from: Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants
Maize is well known for its exceptional structural diversity, including copy number variants (CNVs) and presence/absence variants (PAVs), and there is growing evidence for the role of structural variation in maize adaptation. While PAVs have been described in this important crop species, the extent of presence/absence variation and the relative position of inbred-specific regions remain to be elucidated. De novo genome sequencing of the F2 maize inbred line which played a key role in European breeding programs over the past 50 years revealed thousands of novel genomic regions, making up 88Mb of DNA, that are present in the F2 but not in B73. Comparison of B73 and F2 PAV localization revealed contrasted chromosomal distributions between the two inbreds and specific evolutionary dynamics of PAVs as compared to SNPs. Detailed sequence and functional annotation of F2 PAV sequences revealed hundreds of new genes with transcriptional support, but also a large fraction of repetitive sequences. Detailed analysis of sequence breakpoint highlights the role of double strand break repair, but also transposon insertion in PAV generation. Typing of the B73 and F2 PAVs in maize temperate inbreds revealed that some PAVs are found only in European Flint material, thus pinpointing structural features that may be at the origin of adaptive traits involved in the success of this material. Linkage disequilibrium (LD) analysis revealed that LD is strong within PAVs, as expected by the absence of recombination in crosses where PAV is missing in one of the parents.
Data from: Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize
Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison of these two assemblies revealed over 2,500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7,128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.
Data from: Intraspecific competition and inbreeding depression: increased competitive effort by inbred males is costly to outbred opponents
A recent theoretical model suggests that intraspecific competition is an important determinant of the severity of inbreeding depression. The reason for this is that intraspecific competition is density dependent, leading to a stronger negative effect on inbred individuals if they are weaker competitors than outbred ones. In support of this prediction, previous empirical work shows that inbred individuals are weaker competitors than outbred ones and that intraspecific competition often exacerbates inbreeding depression. Here, we report an experiment on the burying beetle Nicrophorus vespilloides, in which we recorded the outcome of competition over a small vertebrate carcass between an inbred or outbred male resident caring for a brood and a size-matched inbred or outbred male intruder. We found that inbred males were more successful as intruders in taking over a carcass from a male resident and were injured more frequently as either residents or intruders. Furthermore, inbred males gained less mass during the breeding attempt and had a shorter adult life span than outbred males. Finally, successful resident males reared a substantially smaller brood comprised of lighter larvae when the intruder was inbred than when it was outbred. Our results shows that inbred males increased their competitive effort, thus contradicting previous work suggesting that inbred males are weaker competitors. Furthermore, our results shows that inbred intruders impose a greater cost to resident males, suggesting that outbred individuals can suffer fitness costs as a result of competition with inbred ones.
Data from: Interplay between age-based competitive asymmetries within the brood and direct competition between inbred and outbred offspring in a burying beetle
Theory suggests that intraspecific competition associated with direct competition between inbred and outbred individuals should be an important determinant of the severity of inbreeding depression. The reason is that, if outbred individuals are stronger competitors than inbred ones, direct competition should have a disproportionate effect on the fitness of inbred individuals. However, an individual's competitive ability is not only determined by its inbreeding status but also by competitive asymmetries that are independent of an individual's inbreeding status. When this is the case, such competitive asymmetries may shape the outcome of direct competition between inbred and outbred individuals. Here we investigate the interface between age-based competitive asymmetries within broods and direct competition between inbred and outbred offspring in the burying beetle Nicrophorus vespilloides. We found that inbred offspring had lower survival than outbred ones confirming that there was inbreeding depression. Furthermore, seniors (older larvae) grew to a larger size and had higher survival than juniors (younger larvae), confirming that there were age-based competitive asymmetries. Nevertheless, there was no evidence that direct competition between inbred and outbred larvae exacerbated inbreeding depression, no evidence that inbreeding depression was more severe in juniors, and no evidence that inbred juniors suffered disproportionately due to competition from outbred seniors. Our results suggest that direct competition between inbred and outbred individuals does not necessarily exacerbate inbreeding depression and that inbred individuals are not always more sensitive to poor and stressful conditions than outbred ones.
Data from: Inbred and furious: negative association between aggression and genetic diversity in highly inbred fish
Aggressive behaviour plays an important role in securing resources, defending against predators and shaping social interactions. Although aggression can have positive effects on growth and reproductive success, it is also energetically costly and may increase injury and compromise survival. Individual genetic diversity has been positively associated with aggression, but the cause for such an association is not clear, and it might be related to the ability to recognize kin. To disentangle the relationships between genetic diversity, kinship and aggression, we quantified aggressive behaviour in a wild, self-fertilizing fish (Kryptolebias marmoratus) with naturally variable degrees of genetic diversity, relatedness and familiarity. We found that in contrast to captive fish, levels of aggression among wild K. marmoratus are positively associated with individual homozygosity, but not with relatedness or familiarity. We suggest that the higher aggression shown by homozygous fish could be related to better kin discrimination and may be facilitated by hermaphrodite competition for scarce males, given the fitness advantages provided by outcrossing in terms of parasite resistance. It seems likely that the relationship between aggression and genetic diversity is largely influenced by both the environment and population history.
Data from: Severe inbreeding depression and no evidence of purging in an extremely inbred wild species - the Chatham Island black robin
Although evidence of inbreeding depression in wild populations is well established, the impact of genetic purging in the wild remains controversial. The contrasting effects of inbreeding depression, fixation of deleterious alleles by genetic drift and the purging of deleterious alleles via natural selection mean that predicting fitness outcomes in populations subjected to prolonged bottlenecks is not straightforward. We report results from a long-term pedigree study of arguably the world's most inbred wild species of bird: the Chatham Island black robin Petroica traversi, in which conditions were ideal for purging to occur. Contrary to expectations, black robins showed a strong, negative relationship between inbreeding and juvenile survival, yielding lethal equivalents (2B) of 6.85. We also determined that the negative relationship between inbreeding and survival did not appear to be mediated by levels of ancestral inbreeding and may be attributed in part to un-purged lethal recessives. Although the black robin demographic history provided ideal conditions for genetic purging, our results show no clear evidence of purging in the major life-history trait of juvenile survival. Our results also show no evidence of fixation of deleterious alleles in juvenile survival, but do confirm that continued high levels of contemporary inbreeding in a historically inbred population could lead to additional severe inbreeding depression.
Variation in leaf transcriptome responses to elevated ozone corresponds with physiological sensitivity to ozone across maize inbred lines
<p>All FASTA files used for BLAST analyses and all BLAST results for <a href="https://doi.org/10.1093/genetics/iyac080">https://doi.org/10.1093/genetics/iyac080</a> are included. Descriptions of each file can be found in README_maize_genetics_2022_zenodo.csv and further information about the content of the files can be found on <a href="https://github.com/McIntyre-Lab/papers/tree/master/nanni_maize_2022">github</a>.</p>
Genotype by sequencing data from CHPRRU2, a panel of 282 maize inbred lines.
<p>Genotype by sequencing data from CHPRRU2, a panel of 282 maize inbred lines.</p>
Exploration of the yield potential of mesoamerican wild common beans from contrasting eco-geographic regions by nested recombinant inbred populations
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Data from: Severe inbreeding depression and no evidence of purging in an extremely inbred wild species - the Chatham Island black robin
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
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