Oligo painting FISH was established to identify all chromosomes in banana (Musa spp.) and to anchor pseudomolecules of reference genome sequence of Musa acuminata spp. malaccensis “DH Pahang” to individual chromosomes in situ. A total of 19 chromosome/chromosome-arm specific oligo painting probes were developed and were shown to be suitable for molecular cytogenetic studies in genus Musa. For the first time, molecular karyotypes of diploid M. acuminata spp. malaccensis (A genome), M. balbisiana (B genome), and M. schizocarpa (S genome) from the Eumusa section of Musa, which contributed to the evolution of edible banana cultivars, were established. This was achieved after a combined use of oligo painting probes and a set of previously developed banana cytogenetic markers. The density of oligo painting probes was sufficient to study chromosomal rearrangements on mitotic as well as on meiotic pachytene chromosomes. This advance will enable comparative FISH mapping and identification of chromosomal translocations which accompanied genome evolution and speciation in the family Musaceae.
Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.
The genus Silene includes a plethora of dioecious and gynodioecious species. Two species, Silene latifolia (white campion) and Silene dioica (red campion), are dioecious plants, having heteromorphic sex chromosomes with an XX/XY sex determination system. The X and Y chromosomes differ mainly in size, DNA content and posttranslational histone modifications. Although it is generally assumed that the sex chromosomes evolved from a single pair of autosomes, it is difficult to distinguish the ancestral pair of chromosomes in related gynodioecious and hermaphroditic plants. We designed an oligo painting probe enriched for X-linked scaffolds from currently available genomic data and used this probe on metaphase chromosomes of S. latifolia (2n = 24, XY), S. dioica (2n = 24, XY), and two gynodioecious species, S. vulgaris (2n = 24) and S. maritima (2n = 24). The X chromosome-specific oligo probe produces a signal specifically on the X and Y chromosomes in S. latifolia and S. dioica, mainly in the subtelomeric regions. Surprisingly, in S. vulgaris and S. maritima, the probe hybridized to three pairs of autosomes labeling their p-arms. This distribution suggests that sex chromosome evolution was accompanied by extensive chromosomal rearrangements in studied dioecious plants.
Edible banana cultivars are diploid, triploid, or tetraploid hybrids, which originated by natural cross hybridization between subspecies of diploid Musa acuminata, or between M. acuminata and diploid Musa balbisiana. The participation of two other wild diploid species Musa schizocarpa and Musa textilis was also indicated by molecular studies. The fusion of gametes with structurally different chromosome sets may give rise to progenies with structural chromosome heterozygosity and reduced fertility due to aberrant chromosome pairing and unbalanced chromosome segregation. Only a few translocations have been classified on the genomic level so far, and a comprehensive molecular cytogenetic characterization of cultivars and species of the family Musaceae is still lacking. Fluorescence in situ hybridization (FISH) with chromosome-arm-specific oligo painting probes was used for comparative karyotype analysis in a set of wild Musa species and edible banana clones. The results revealed large differences in chromosome structure, discriminating individual accessions. These results permitted the identification of putative progenitors of cultivated clones and clarified the genomic constitution and evolution of aneuploid banana clones, which seem to be common among the polyploid banana accessions. New insights into the chromosome organization and structural chromosome changes will be a valuable asset in breeding programs, particularly in the selection of appropriate parents for cross hybridization.
33Sustainable food production in the context of climate change necessitates diversification of 34 agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria 35 exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we 36 established high-quality genomic resources to facilitate fonio improvement through molecular 37 breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 38 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population 39 structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic 40 factors. Two genes associated with seed size and shattering showed signatures of selection. Most 41 known domestication genes from other cereal models however have not experienced strong 42 selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and 43 dry environments. 44 45 agriculture 1-3 . The Food and Agriculture Organization of the United Nations (FAO) stated that arid 50 and semi-arid regions are the most vulnerable environments to increasing uncertainties in regional 51 and global food production 4 . In most countries of Africa and the Middle East, agricultural 52 productivity will decline in the near future 4 , because of climate change, land degradation, and 53 groundwater depletion 5 . Agricultural selection, from the early steps of domestication to modern-54 day crop breeding, has resulted in a marked decrease in agrobiodiversity 6,7 . Today, three cereal 55 4 crops alone, bread wheat (Triticum aestivum), maize (Zea mays), and rice (Oryza sativa) account 56 for more than half of the globally consumed calories 8 . 57Many of today's major cereal crops, including rice and maize, originated in relatively humid 58 tropical and sub-tropical regions 9,10 . Although plant breeding has adapted the major cereal crops 59 to a wide range of climates and cultivation practices, there is limited genetic diversity within these 60 few plant species for cultivation in the most extreme environments. On the other hand, crop wild 61 relatives and orphan crops are often adapted to extreme environments and their utility to unlock 62 marginal lands for agriculture has recently regained interest 2,6,[11][12][13][14] . Current technological advances 63 in genomics and genome editing provide an opportunity to rapidly domesticate wild relatives and 64 to improve orphan crops 15,16 . De novo domestication of wild species or rapid improvement of semi-65 domesticated crops can be achieved in less than a decade by targeting a few key genes 6 . 66White fonio (Digitaria exilis (Kippist) Stapf) (Fig. 1) is an indigenous African millet species with 67 a great potential for agriculture in marginal environments 17,18 . Fonio is cultivated under a large 68 range of environmental conditions, from a tropical monsoon climate in western Guinea to a hot, 69 arid desert climate (BWh) in the Sahel zone. Some extra-early matur...
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