Mutation rate analysis via parent–progeny sequencing of the perennial peach. II. No evidence for recombination-associated mutation

Wang, Long; Zhang, Yanchun; Qin, Chao; Tian, Dacheng; Yang, Sihai; Hurst, Laurence D.

doi:10.1098/rspb.2016.1785

Cited by 5 publications

(4 citation statements)

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“…Homologous alleles of the SD1 gene and other height‐related genes have been reported in previous studies, e.g. Rht gene (‘green revolution’ gene in wheat) (Peng et al ., ), Sdw1 gene (‘green revolution’ gene in barley) (Xu et al ., ), GA5 gene (in Arabidopsis) (Barboza et al ., ), BR2 gene (in maize) (Multani, ), DW3 (in sorghum) (Multani, ), and PpeGID1c (in peach) (Hu et al ., ; Wang et al ., ). All of these genes carry several natural alleles and affect correspondingly obvious phenotypes.…”

Section: Discussionmentioning

confidence: 97%

High‐resolution insight into recombination events at the SD1 locus in rice

Jia

Zhang

et al. 2018

The Plant Journal

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These authors contributed equally to this work. SUMMARYRecombination during meiosis plays an important role in genome evolution by reshuffling existing genetic variations into fresh combinations with the possibility of recovery of lost ancestral genotypes. While crossover (CO) events have been well studied, gene conversion events (GCs), which represent non-reciprocal information transfer between chromosomes, are poorly documented and difficult to detect due to their relatively small converted tract size. Here, we document these GC events and their phenotypic effects at an important locus in rice containing the SD1 gene, where multiple defective alleles contributed to the semidwarf phenotype of rice in the 'Green Revolution' of the 1960s. Here, physical separation of two defects allows recombination to generate the wild-type SD1 gene, for which plant height can then be used as a reporter. By screening 18 000 F 2 progeny from a cross between two semi-dwarf cultivars that carry these different defective alleles, we detected 24 GC events, indicating a conversion rate of~3.3 3 10 À4 per marker per generation in a single meiotic cycle in rice. Furthermore, our data show that indels and single-nucleotide polymorphisms (SNPs) do not differ significantly in GC rates, at least at the SD1 locus. Our results provide strong evidence that GC by itself can regain an ancestral phenotype that was lost through mutation. This GC detection approach is likely to be broadly applicable to natural or artificial alleles of other phenotyperelated functional genes, which are abundant in other plant genomes.

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Section: Discussionmentioning

confidence: 97%

High‐resolution insight into recombination events at the SD1 locus in rice

Jia

Zhang

et al. 2018

The Plant Journal

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“…However, similar studies in plant hybrids still remain in infancy. Besides few recent studies involving analysis of mutation accumulation rates in Arabidopsis and peach hybrids, there is no information on this theme from other plant species [13,14,15,16]. Interestingly, the available studies insinuate that hybridization does affect mutations in offspring.…”

Section: Introductionmentioning

confidence: 99%

Effect of Hybridization on Somatic Mutations and Genomic Rearrangements in Plants

Bashir

Mishra

Hasan

et al. 2018

IJMS

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Hybridization has been routinely practiced in agriculture to enhance the crop yield. Principally, it can cause hybrid vigor where hybrid plants display increased size, biomass, fertility, and resistance to diseases, when compared to their parents. During hybridization, hybrid offspring receive a genomic shock due to mixing of distant parental genomes, which triggers a myriad of genomic rearrangements, e.g., transpositions, genome size changes, chromosomal rearrangements, and other effects on the chromatin. Recently, it has been reported that, besides genomic rearrangements, hybridization can also alter the somatic mutation rates in plants. In this review, we provide in-depth insights about hybridization triggered genomic rearrangements and somatic mutations in plants.

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“…Noticing the extreme scarcity of unambiguous cases of genetic mosaics in wild plants, despite biased research efforts toward species expected to be more prone to mosaics (long-lived, clonal, highly branched), Herrera hypothesizes that they are far less frequent among wild plants than among cultivated plants (Herrera 2009). Domesticated peach, compared to wild peach, did not show any increase in recombination rate and mutation rate near recombination events in a sequencing study (Wang et al 2016). However, no general conclusion can be derived from this unique study with its sample size of one.…”

Section: The Genetically Heterogeneous Individual Plantmentioning

confidence: 62%

An Herbiary of Plant Individuality

Gerber¹

2018

Philosophy, Theory, and Practice in Biology

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Questioning the nature of individuality has a long and a rich history, both in philosophy and in biology. Because they differ in several features from the pervasive vertebrate-human model, plants have been considered as complicating the question. Here, the various plant species on which authors-whether biologists or philosophers-rely to build the picture of plant individuality are examined and tracked for their peculiarities, thus constituting an "herbiary" of plant individuality. The herbiary of plant individuality has as its members species exhibiting a diverse collection of traits and illustrating different questions related to plant individuality. This essay assesses the peculiarity of the features of these plants and the reality of their differences from animals. Because some plant features are supposed to pose a threat to individual genetic homogeneity, higher heterogeneity has been assumed for plants compared to animals. Moreover, individual plants are sometimes identified with communities. How does this supposed heterogeneity appear in particular species? Cultivated plants exhibit distinctive diversity, and their overrepresentation in the study of plant diversity might bias the way plant individuality is understood. Just as there is a vertebrate bias, there may also be a cultivated plant bias. Recent results bring plants much closer to animals in terms of cellular functioning, so plants might not be so different from animals with respect to their diversity, and consequently their individuality.

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Mutation rate analysis via parent–progeny sequencing of the perennial peach. II. No evidence for recombination-associated mutation

Cited by 5 publications

References 57 publications

High‐resolution insight into recombination events at the SD1 locus in rice

High‐resolution insight into recombination events at the SD1 locus in rice

Effect of Hybridization on Somatic Mutations and Genomic Rearrangements in Plants

An Herbiary of Plant Individuality

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