Meiotic crossovers characterized by haplotype-specific chromosome painting in maize

Martins, Lívia do Vale; Fan, Yu; Zhao, Hainan; Dennison, Tesia; Lauter, Nick; Wang, Haiyan; Deng, Zuhu; Thompson, Addie; Semrau, Kassandra; Rouillard, Jean-Marie; Birchler, James A.; Jiang, Jiming

doi:10.1038/s41467-019-12646-z

Cited by 47 publications

(24 citation statements)

References 54 publications

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“…The presence of hot spots of genetic recombination is also indicated by the presence of red (high LD) and blue (low LD) bands or stripes along each chromosome we observed (Fig. 2 c) and similar observations were also reported by Thirunavukkaraasu et al 34 through linkage disequilibrium heatmap and by Martins et al 32 through FISH chromosome painting.…”

Section: Discussionsupporting

confidence: 91%

“…1 ) and Martins et al 32 . The underlying genomic mechanism determining the observed SNP loci distribution pattern is unclear and it has been known that the distal regions of a chromosome turn to have relatively high level of genetic recombination and are less methylated than the pericentromeric regions (the region near centromere) 32 , 33 . LD decay very rapidly on all 10 chromosomes and reached r 2 = 0.11 at about 20 Kb on average (Fig.…”

Section: Discussionmentioning

confidence: 97%

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Genetic variation and population structure in China summer maize germplasm

Shu

Cao

et al. 2021

Sci Rep

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Maize (Zea mays L.) germplasm in China Summer maize ecological region (CSM) or central corn-belt of China is diverse but has not been systematically characterized at molecular level. In this study, genetic variation, genome diversity, linkage disequilibrium patterns, population structure, and characteristics of different heterotic groups were studied using 525,141 SNPs obtained by Genotyping-By-Sequencing (GBS) for 490 inbred lines collected from researchers at CSM region. The SNP density is lower near centromere, but higher near telomere region of maize chromosome, the degree of linkage disequilibrium (r2) vary at different chromosome regions. Majority of the inbred lines (66.05%) show pairwise relative kinship near zero, indicating a large genetic diversity in the CSM breeding germplasm. Using 4849 tagSNPs derived from 3618 haplotype blocks, the 490 inbred lines were delineated into 3 supergroups, 6 groups, and 10 subgroups using ADMIXTURE software. A procedure of assigning inbred lines into heterotic groups using genomic data and tag-SNPs was developed and validated. Genome differentiation among different subgroups measured by Fst, and the genetic diversity within each subgroup measured by GD are both large. The share of heterotic groups that have significant North American germplasm contribution: P, SS, IDT, and X, accounts about 54% of the CSM breeding germplasm collection and has increased significantly in the last two decades. Two predominant types of heterotic pattern in CSM region are: M-Reid group × TSPT group, and X subgroup × Local subgroups.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 97%

Genetic variation and population structure in China summer maize germplasm

Shu

Cao

et al. 2021

Sci Rep

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“…The availability of reference sequence genomes for many plants has allowed the design of synthetic oligonucleotide (oligo) probes for FISH applications a paradigm shift from the traditional FISH probes using cloned DNA sequences (Beliveau et al ., 2012; Jiang, 2019). Oligo probes producing a unique barcode for each basic chromosome, as well as chromosome‐specific oligo probes, have started to be used, in particular to establish karyotypes and to identify chromosome rearrangements (Braz et al ., 2018; Albert et al ., 2019; Song et al ., 2020; Xi et al ., 2020), and to study chromosome pairing at meiosis (Han et al ., 2015; He et al ., 2018; do Vale Martins et al ., 2019).…”

Section: Introductionmentioning

confidence: 99%

Sugarcane genome architecture decrypted with chromosome‐specific oligo probes

Piperidis

D’Hont

2020

The Plant Journal

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SUMMARY Sugarcane (Saccharum spp.) is probably the crop with the most complex genome. Modern cultivars (2n = 100–120) are highly polyploids and aneuploids derived from interspecific hybridization between Saccharum officinarum (2n = 80) and Saccharum spontaneum (2n = 40–128). Chromosome‐specific oligonucleotide probes were used in combination with genomic in situ hybridization to analyze the genome architecture of modern cultivars and representatives of their parental species. The results validated a basic chromosome number of x = 10 for S. officinarum. In S. spontaneum, rearrangements occurred from a basic chromosome of x = 10, probably in the Northern part of India, in two steps leading to x = 9 and then x = 8. Each step involved three chromosomes that were rearranged into two. Further polyploidization led to the wide geographical extension of clones with x = 8. We showed that the S. spontaneum contribution to modern cultivars originated from cytotypes with x = 8 and varied in proportion between cultivars (13–20%). Modern cultivars had mainly 12 copies for each of the first four basic chromosomes, and a more variable number for those basic chromosomes whose structure differs between the two parental species. One−four of these copies corresponded to entire S. spontaneum chromosomes or interspecific recombinant chromosomes. In addition, a few inter‐chromosome translocations were revealed. The new information and cytogenetic tools described in this study substantially improve our understanding of the extreme level of complexity of modern sugarcane cultivar genomes.

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“…Oligonucleotide-based FISH technology has been applied for various research areas, including traditional cytogenetic studies and burgeoning 3D genome researches [7,8,18,19,22,64,72,73,80]. With the help of advanced technology, the mysteries of genomes are gradually being brought to light.…”

Section: Resultsmentioning

confidence: 99%

“…In addition, with the development of DNA sequencing and synthesis technologies, a new generation of FISH techniques, called oligonucleotide fluorescence in situ hybridization (oligo-FISH), which utilizes single-copy oligonucleotides (oligos) as FISH probes, has been established. In recent years, increasing numbers of researchers have embedded this method in their studies [6][7][8].…”

Section: Introductionmentioning

confidence: 99%

Single Copy Oligonucleotide Fluorescence In Situ Hybridization Probe Design Platforms: Development, Application and Evaluation

Liu

Zhang

2021

IJMS

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Oligonucleotides fluorescence in situ hybridization (Oligo-FISH) is an emerging technology and is an important tool in research areas such as detection of chromosome variation, identification of allopolyploid, and deciphering of three-dimensional (3D) genome structures. Based on the demand for highly efficient oligo probes for oligo-FISH experiments, increasing numbers of tools have been developed for probe design in recent years. Obsolete oligonucleotide design tools have been adapted for oligo-FISH probe design because of their similar considerations. With the development of DNA sequencing and large-scale synthesis, novel tools have been designed to increase the specificity of designed oligo probes and enable genome-scale oligo probe design, which has greatly improved the application of single copy oligo-FISH. Despite this, few studies have introduced the development of the oligo-FISH probe design tools and their application in FISH experiments systematically. Besides, a comprehensive comparison and evaluation is lacking for the available tools. In this review, we provide an overview of the oligo-FISH probe design process, summarize the development and application of the available tools, evaluate several state-of-art tools, and eventually provide guidance for single copy oligo-FISH probe design.

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Meiotic crossovers characterized by haplotype-specific chromosome painting in maize

Cited by 47 publications

References 54 publications

Genetic variation and population structure in China summer maize germplasm

Genetic variation and population structure in China summer maize germplasm

Sugarcane genome architecture decrypted with chromosome‐specific oligo probes

Single Copy Oligonucleotide Fluorescence In Situ Hybridization Probe Design Platforms: Development, Application and Evaluation

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