Characterization of genomic sequence showing strong association with polyembryony among diverse Citrus species and cultivars, and its synteny with Vitis and Populus

Nakano, Michiharu; Shimada, Takehiko; Endo, Tetsuro; Fujii, Hiroshi; Nesumi, Hirohisa; Kita, Masakazu; Ebina, Masumi; Shimizu, Tokurou; Omura, Mitsuo

doi:10.1016/j.plantsci.2011.08.002

Cited by 49 publications

(34 citation statements)

References 33 publications

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“…The cosegregation of the MITE insertion in the promoter region of CitRWP with the polyembryonic phenotype lends more support to the single dominant mutation model for the emergence of apomixis in mandarin. Our genomic analysis localized the candidate region to an 80-kb interval containing 11 genes, which was embedded in a 380-kb region reported by a previous study 12 . In this interval, we identified a promising candidate gene for the single dominant allele responsible for polyembryony in citrus.…”

Section: Discussionmentioning

confidence: 73%

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Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction

et al. 2017

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The emergence of apomixis-the transition from sexual to asexual reproduction-is a prominent feature of modern citrus. Here we de novo sequenced and comprehensively studied the genomes of four representative citrus species. Additionally, we sequenced 100 accessions of primitive, wild and cultivated citrus. Comparative population analysis suggested that genomic regions harboring energy- and reproduction-associated genes are probably under selection in cultivated citrus. We also narrowed the genetic locus responsible for citrus polyembryony, a form of apomixis, to an 80-kb region containing 11 candidate genes. One of these, CitRWP, is expressed at higher levels in ovules of polyembryonic cultivars. We found a miniature inverted-repeat transposable element insertion in the promoter region of CitRWP that cosegregated with polyembryony. This study provides new insights into citrus apomixis and constitutes a promising resource for the mining of agriculturally important genes.

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Section: Discussionmentioning

confidence: 73%

“…Molecular markers linked to a polyembryony locus have been reported 7,11 . This locus was later mapped to a genomic region that spans approximately 380 kb 12 . Genes differentially expressed during polyembryogenesis have also been identified [13][14][15] .…”

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confidence: 99%

Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction

et al. 2017

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“…For example, kunenbo is self-incompatible [124], but Kishu and Satsuma are not. Both kunenbo and Satsuma are polyembryonic but Kishu is monoembryonic [70]. Nakano et al isolated candidate genes involved in the polyembryony of Satsuma [131].…”

Section: Discussionmentioning

confidence: 99%

“…Citrus genome sequence resources in public databases, including BAC end sequences of Clementine [69] and Satsuma [70,71], and whole genome shotgun sequences of sweet orange ‘Ridge Pineapple’ in the trace file repository of Sanger reads (ftp://ftp.ncbi.nlm.nih.gov/pub/TraceDB/citrus_sinensis/), were also used for DNA marker design. Preliminary evaluation of the quality and length of each of these data sets was carried out using pregap4 [72], then a consensus sequence set was obtained for each set with Mira assembler [73] to reduce redundancy.…”

Section: Methodsmentioning

confidence: 99%

Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

et al. 2016

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Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins. Structure analysis with DNA markers that are in Hardy–Weinberg equilibrium deduce three basic taxa coinciding with the current understanding of citrus ancestors. Genotyping analysis of 101 indigenous citrus varieties with 123 selected DNA markers infers the parentages of 22 indigenous citrus varieties including Satsuma, Temple, and iyo, and single parents of 45 indigenous citrus varieties, including kunenbo, C. ichangensis, and Ichang lemon by allele-sharing and parentage tests. Genotyping analysis of chloroplast and mitochondrial genomes using 11 DNA markers classifies their cytoplasmic genotypes into 18 categories and deduces the combination of seed and pollen parents. Likelihood ratio analysis verifies the inferred parentages with significant scores. The reconstructed genealogy identifies 12 types of varieties consisting of Kishu, kunenbo, yuzu, koji, sour orange, dancy, kobeni mikan, sweet orange, tachibana, Cleopatra, willowleaf mandarin, and pummelo, which have played pivotal roles in the occurrence of these indigenous varieties. The inferred parentage of the indigenous varieties confirms their hybrid origins, as found by recent studies.

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“…As sporophytic apomixis only involves a single component (autonomous development of embryos) compared to multiple components of gametophytic apomixis, it may be simplest genetically to introduce sporophytic apomixis into crops. Although no genes responsible for sporophytic apomixis have yet been identified, a single genomic locus has been identified in Citrus which is currently being explored by map-based cloning (Nakano et al 2012). …”

Section: Why Study Apomixis?mentioning

confidence: 99%

Seeds of doubt: Mendel’s choice of Hieracium to study inheritance, a case of right plant, wrong trait

et al. 2016

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Key message In this review, we explore Gregor Mendel’s hybridization experiments with Hieracium , update current knowledge on apomictic reproduction and describe approaches now being used to develop true-breeding hybrid crops. AbstractFrom our perspective, it is easy to conclude that Gregor Mendel’s work on pea was insightful, but his peers clearly did not regard it as being either very convincing or of much importance. One apparent criticism was that his findings only applied to pea. We know from a letter he wrote to Carl von Nägeli, a leading botanist, that he believed he needed to “verify, with other plants, the results obtained with Pisum”. For this purpose, Mendel adopted Hieracium subgenus Pilosella, a phenotypically diverse taxon under botanical study at the time. What Mendel could not have known, however, is that the majority of these plants are not sexual plants like pea, but instead are facultatively apomictic. In these forms, the majority of seed arises asexually, and such progeny are, therefore, clones of the maternal parent. Mendel obtained very few hybrids in his Hieracium crosses, yet we calculate that he probably emasculated in excess of 5000 Hieracium florets to even obtain the numbers he did. Despite that effort, he was perplexed by the results, and they ultimately led him to conclude that “the hybrids of Hieracium show a behaviour exactly opposite to those of Pisum”. Apomixis is now a topic of intense research interest, and in an ironic twist of history, Hieracium subgenus Pilosella has been developed as a molecular model to study this trait. In this paper, we explore further Mendel’s hybridization experiments with Hieracium, update current knowledge on apomictic reproduction and describe approaches now being used to develop true-breeding hybrid crops.

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Characterization of genomic sequence showing strong association with polyembryony among diverse Citrus species and cultivars, and its synteny with Vitis and Populus

Cited by 49 publications

References 33 publications

Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction

Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction

Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

Seeds of doubt: Mendel’s choice of Hieracium to study inheritance, a case of right plant, wrong trait

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