Introgressed DNA within a Zea mays near isogenic line displays lower levels of 24nt sRNA expression than the homologous region from the recurrent parent

Near isogenic lines (NILs) are a classical genetic tool used to dissect the actions of an allele when placed in a uniform genetic background. Although the goal of NIL creation is to examine the effects of a single allele in isolation, DNA linked to the allele is invariably retained and can confound any allele specific effects. In addition to genetic variation, highly polymorphic species like <i>Zea mays</i> will contain introgressed polymorphisms encompassing transposable elements (TEs) and the cis acting small RNA (sRNA) that represses them. Through transcriptomics, we described the sRNA and TE transcriptional expression differences between a W22-derived introgression and its homologous B73 region. As anticipated, many sRNA expression differences were found. Unexpectedly, however, 24nt sRNA expression over the introgressed region was low overall compared to both the homologous B73 region and the rest of the genome. Across the introgression, low sRNA expression was accompanied by increased TE transcription. Possible explanations for the observed trends in sRNA and TE expression across the introgression are discussed. These findings support the notion that any introgressed allele is in an epigenetic environment distinct from that found at the allele from the recurrent parent. Additionally, these results suggest that further study of sRNA expression levels during the introgression process is warranted.

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Excision Patterns of Activator (Ac) and Dissociation (Ds) Elements in Zea mays L.: Implications for the Regulation of Transposition

Genetics ◽

10.1093/genetics/144.4.1851 ◽

1996 ◽

Vol 144 (4) ◽

pp. 1851-1869 ◽

Cited By ~ 1

Author(s):

Manfred Heinlein

Keyword(s):

Zea Mays ◽

Zea Mays L ◽

Waxy Gene ◽

Transposition Frequency ◽

Cis Acting ◽

Dosage Effects ◽

In Trans ◽

Ds Excision ◽

Maize Kernels ◽

Strong Contrast

The pattern of aleurone variegation of maize kernels carrying Ac and bz-m2(DI) as reporter allele for Ac activity depends on the dosage of both Ac and Ds. Alterations of Ac dosage can abolish Ds excision at certain times and allow it to occur at other times. wx-m7 and wx-m9 are different Ac insertions in the Waxy gene which have different dosage effects on Ds excision. Kernels, heterozygous for the two Ac alleles and being either wx-m7/wx-m7/wx-m9 or wx-m9/wx-m9/wx-m7 exhibit characteristic patterns of predominantly late excisions; this is in strong contrast to the pattern of early excisions present on wx-m7/wx-m7/wx-m7 homozygotes. This observation supports the hypothesis that the Ac alleles express different amounts of transposase (TPase) during development and that above a certain level of TPase transposition is inhibited. Furthermore, experimental results suggest that the frequency of Ac-induced events is influenced by the dosage and composition of the transactivated Ds or Ac allele. Thus, transposition frequency seems not to be exclusively determined in trans by the amount of active TPase, but also by specific cis-acting properties of the TPase substrate.

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Detection of Epidemic USA300 Community-Associated Methicillin-Resistant Staphylococcus aureus Strains by Use of a Single Allele-Specific PCR Assay Targeting a Novel Polymorphism of Staphylococcus aureus pbp3

Journal of Clinical Microbiology ◽

10.1128/jcm.00417-13 ◽

2013 ◽

Vol 51 (8) ◽

pp. 2541-2550 ◽

Cited By ~ 14

Author(s):

S. G. Chadwick ◽

A. Prasad ◽

W. L. Smith ◽

E. Mordechai ◽

M. E. Adelson ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Methicillin Resistant Staphylococcus Aureus ◽

Pcr Assay ◽

Methicillin Resistant ◽

Specific Pcr ◽

Allele Specific ◽

Single Allele ◽

Specific Pcr Assay ◽

Allele Specific Pcr

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Prediction of smoking by multiplex bisulfite PCR with long amplicons considering allele-specific effects on DNA methylation

Clinical Epigenetics ◽

10.1186/s13148-018-0565-1 ◽

2018 ◽

Vol 10 (1) ◽

Cited By ~ 7

Author(s):

Nikolay Kondratyev ◽

Arkady Golov ◽

Margarita Alfimova ◽

Tatiana Lezheiko ◽

Vera Golimbet

Keyword(s):

Dna Methylation ◽

Specific Effects ◽

Allele Specific

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Identification of a non‐coding SNP associated with risk for non‐syndromic orofacial clefting with allele‐specific effects on IRF6 expression in vitro

The FASEB Journal ◽

10.1096/fasebj.2021.35.s1.04015 ◽

2021 ◽

Vol 35 (S1) ◽

Author(s):

Priyanka Kumari ◽

Ryan Friedman ◽

Lira Pi ◽

Annika Helverson ◽

Sarah Curtis ◽

...

Keyword(s):

Orofacial Clefting ◽

Specific Effects ◽

Allele Specific ◽

Coding Snp

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Identification of an evolutionarily conserved 110 base-pair cis-acting regulatory sequence that governs Wnt-1 expression in the murine neural plate

Development ◽

10.1242/dev.125.14.2735 ◽

1998 ◽

Vol 125 (14) ◽

pp. 2735-2746 ◽

Cited By ~ 3

Author(s):

D.H. Rowitch ◽

Y. Echelard ◽

P.S. Danielian ◽

K. Gellner ◽

S. Brenner ◽

...

Keyword(s):

Base Pair ◽

Regulatory Element ◽

Regulatory Region ◽

Neural Plate ◽

Homologous Region ◽

Regulatory Sequence ◽

Embryonic Mouse ◽

Cis Acting ◽

Evolutionarily Conserved

The generation of anterior-posterior polarity in the vertebrate brain requires the establishment of regional domains of gene expression at early somite stages. Wnt-1 encodes a signal that is expressed in the developing midbrain and is essential for midbrain and anterior hindbrain development. Previous work identified a 5.5 kilobase region located downstream of the Wnt-1 coding sequence which is necessary and sufficient for Wnt-1 expression in vivo. Using a transgenic mouse reporter assay, we have now identified a 110 base pair regulatory sequence within the 5.5 kilobase enhancer, which is sufficient for expression of a lacZ reporter in the approximate Wnt-1 pattern at neural plate stages. Multimers of this element driving Wnt-1 expression can partially rescue the midbrain-hindbrain phenotype of Wnt-1(−/−) embryos. The possibility that this region represents an evolutionarily conserved regulatory module is suggested by the identification of a highly homologous region located downstream of the wnt-1 gene in the pufferfish (Fugu rubripes). These sequences are capable of appropriate temporal and spatial activation of a reporter gene in the embryonic mouse midbrain; although, later aspects of the Wnt-1 expression pattern are absent. Genetic evidence has implicated Pax transcription factors in the regulation of Wnt-1. Although Pax-2 binds to the 110 base pair murine regulatory element in vitro, the location of the binding sites could not be precisely established and mutation of two putative low affinity sites did not abolish activation of a Wnt-1 reporter transgene in vivo. Thus, it is unlikely that Pax proteins regulate Wnt-1 by direct interactions with this cis-acting regulatory region. Our analysis of the 110 base pair minimal regulatory element suggests that Wnt-1 regulation is complex, involving different regulatory interactions for activation and the later maintenance of transgene expression in the dorsal midbrain and ventral diencephalon, and at the midbrain-hindbrain junction.

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Differential Activity of Ras1 during Patterning of the Drosophila Dorsoventral Axis

Genetics ◽

10.1093/genetics/144.4.1545 ◽

1996 ◽

Vol 144 (4) ◽

pp. 1545-1557 ◽

Cited By ~ 1

Author(s):

Jon D Schnorr ◽

Celeste A Berg

Keyword(s):

Tyrosine Kinases ◽

P Element ◽

Embryonic Patterning ◽

Loss Of Function ◽

Wing Vein ◽

Border Cell ◽

Specific Effects ◽

Vein Formation ◽

Allele Specific ◽

Development Analysis

In Drosophila, the Ras1 gene is required downstream of receptor tyrosine kinases for correct eye development, embryonic patterning, wing vein formation, and border cell migration. Here we characterize a P-element allele of Ras1, Ras15703, that affects viability, eye morphogenesis, and early and late stages of oogenesis. Flies transheterozgyous for Ras15703 and existing EMS-induced Ras1 alleles are viable and exhibit a range of eye and eggshell defects. Differences in the severity of these phenotypes in different tissues suggest that there are allele-specific effects of Ras1 in development. Analysis of rescue constructs demonstrates that these differential phenotypes are due to loss of function in Ras1 alone and not due to effects on neighboring genes. Females mutant at the Ras1 locus lay eggs with reduced or missing dorsal eggshell structures. We observe dominant interactions between Ras1 mutants and other dorsoventral pathway mutants, including and Egfrtop and gurken. Ras1 is also epistatic to K10. Unlike Egfrtop and gurken mutants, however, Ras1 females are moderately fertile, laying eggs with ventralized eggshells that can hatch normal larvae. These results suggest that Ras1 may have a different requirement in the patterning of the eggshell axis than in the patterning of the embryonic axis during oogenesis.

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Two SNP Mutations Turned off Seed Shattering in Rice

Plants ◽

10.3390/plants8110475 ◽

2019 ◽

Vol 8 (11) ◽

pp. 475

Author(s):

Yu Zhang ◽

Jiawu Zhou ◽

Ying Yang ◽

Walid Hassan Elgamal ◽

Peng Xu ◽

...

Keyword(s):

Ssr Marker ◽

Wild Relatives ◽

Ancestral Haplotype ◽

Recurrent Parent ◽

Isogenic Line ◽

Chromosome 4 ◽

Cultivated Rice ◽

Japonica Variety ◽

Seed Shattering ◽

Shed Light

Seed shattering is an important agronomic trait in rice domestication. In this study, using a near-isogenic line (NIL-hs1) from Oryza barthii, we found a hybrid seed shattering phenomenon between the NIL-hs1 and its recurrent parent, a japonica variety Yundao 1. The heterozygotes at hybrid shattering 1 (HS1) exhibited the shattering phenotype, whereas the homozygotes from both parents conferred the non-shattering. The causal HS1 gene for hybrid shattering was located in the region between SSR marker RM17604 and RM8220 on chromosome 4. Sequence verification indicated that HS1 was identical to SH4, and HS1 controlled the hybrid shattering due to harboring the ancestral haplotype, the G allele at G237T site and C allele at C760T site from each parent. Comparative analysis at SH4 showed that all the accessions containing ancestral haplotype, including 78 wild relatives of rice and 8 African cultivated rice, had the shattering phenotype, whereas all the accessions with either of the homozygous domestic haplotypes at one of the two sites, including 17 wild relatives of rice, 111 African cultivated rice and 65 Asian cultivated rice, showed the non-shattering phenotype. Dominant complementation of the G allele at G237T site and the C allele at C760T site in HS1 led to a hybrid shattering phenotype. These results help to shed light on the nature of seed shattering in rice during domestication and improve the moderate shattering varieties adapted to mechanized harvest.

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