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BACop, an algorithm that anchors optical contigs onto the iMap. BACop (Materials and Methods) employs four distinct steps for anchoring optical contigs; we illustrate the first three steps here: (A) Restriction fragments of an optical contig map are matched against BAC sequences comprising multiple sub-contigs. (B) Matching BAC sequence contigs are located along the optical contig map. (C) Dynamic programming places BACs onto optical map contigs. Seq. = sequence, frag = restriction fragment, and BAC = bacterial artificial chromosome.
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About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence b...
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Citations
... High-throughput genotyping methods effectively determine and delineate the genetic relationships among inbred populations. Diagnostic molecular markers provide a high level of accuracy in identifying the genetic constitution of individuals to guide hybrid breeding [13,16,40]. The SNP markers are widely used to assess genetic diversity and relationships [28,41], select breeding parents [42,43], and identify novel genes linked to economically important traits [44,45]. ...
Analyses of the genetic distance and composition of inbred lines are a prerequisite for parental selection and to exploit heterosis in plant breeding programs. The study aimed to assess genetic diversity and population structure of a maize germplasm panel comprising 182 founder lines and 866 derived inbred lines using Single Nucleotide Polymorphism (SNP) markers to identify genetically unique lines for hybrid breeding. The founder lines were genotyped with 1201 SNPs, and the derived lines with 1484 SNPs. Moderate genetic variation, with genetic diversity ranging from 0.004 to 0.44 with a mean of 0.25, was recorded for the founder lines, while corresponding values of 0.004 to 0.34 with a mean of 0.13 were recorded for the derived lines. Heterozygosity values ranging from 0.00 to 0.24 and a mean of 0.08 were recorded for both lines. Of the SNP markers used, 82% of the 1201 markers and 84% of the 1484 markers exhibited polymorphism information content ranging from 0.25 to 0.50. Analysis of molecular variance revealed significant genetic differences (P ≤ 0.001) among and within populations in the founder and derived lines. Most detected variations, i.e., 97% and 88.38%, were attributed to within populations in the founder and derived lines, respectively. Population structure analysis identified three distinct subpopulations among founder lines and two among derived lines. Cluster analysis supported the population structure The following genetically distant founder and derived inbred lines were selected: G15NL337 and G15NL312 (Cluster 1), 15ARG152 and RGS-PL44 (Cluster 2), RGS-PL44 and 15ARG149 (Cluster 2), and RGS-PL33 and RGS-PL44 (Cluster 2), respectively. The selected lines are genetically distinct and recommended for marker-assisted hybrid maize breeding to exploit the frequency of beneficial alleles. This study provides valuable insights for maize breeding programs, enabling the exploitation of beneficial alleles and contributing to improved crop yields and food security through hybrid breeding.
... Maize is one of the most important cereal crops in the world. A lot of repeat and rearranged sequences make its genome much more complex than those of Arabidopsis and rice (Schnable et al. 2009;Zhou et al. 2009). This might lead to evolutional and functional diversification among the members of the ZmBES1/BZR1 gene family. ...
... Such changes may also arise from natural and artificial introgression of genome fragments from another species [44,45]. Additionally, mobile genetic elements, both in quantity and type, significantly contribute to these modifications of the genome [46]. DNA modifications, such as methylation, can modify recognition sequences for restriction enzymes. ...
In recent years, high-throughput sequencing methods have become increasingly popular in molecular biology laboratories, mainly due to the relatively low cost of small, benchtop platforms, the simplicity of library preparation, and the low price per unit of information. Sequencing huge and complex genomes, such as cereal genomes, remains challenging and may not always be necessary. Therefore, several techniques have been developed to sequence a reduced representation of the genome. The most flexible and widely used of these is ddRAD-Seq, which uses a pair of restriction enzymes to generate a pool of DNA fragments. The aim of this study was to validate in vitro the efficacy of different combinations of restriction enzymes for ddRAD-Seq library construction in barley and maize. Eleven pairs of restriction enzymes were selected and tested to determine the concentrations of fragments with the expected length range and to select suitable pairs for sampling the genomes of these two cereals using ddRAD-Seq. For the selected pairs, i.e., PstI—MspI and HindIII—FspBI for barley and maize, respectively, libraries were prepared for NGS sequencing on Illumina MiSeq. Sequencing confirmed the suitability of the selected enzymes to perform ddRAD-Seq in different genotypes. The results presented can be used for extensive research on these important cereal species.
... Арабидопсис (119,1 Mb) и рис (373,8 Mb) обладают одними из самых маленьких геномов среди соответственно двудольных и однодольных растений, и их геномы считаются эталонными в своих классах (https://www.ncbi.nlm.nih.gov/), для кукурузы характерен один из самых длинных геномов среди однодольных (2,3 Gb) (70). ...
... Арабидопсис (119,1 Mb) и рис (373,8 Mb) обладают одними из самых маленьких геномов среди соответственно двудольных и однодольных растений, и их геномы считаются эталонными в своих классах (https://www.ncbi.nlm.nih.gov/), для кукурузы характерен один из самых длинных геномов среди однодольных (2,3 Gb) (70). ...
... The Optical Mapping System [42,43] creates restriction maps from individual genomic DNA molecules that are assembled, de novo, into physical maps spanning entire genomes. Such maps have been successfully applied to many large-scale sequencing projects [44][45][46][47][48] and to the discernment of human structural variation [49]. Recent work has centered on approaches that integrate map and sequence data at an early stage of the assembly process [50]. ...
Background: The process of generating raw genome sequence data continues to become cheaper, faster, and
more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging.
Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability,
hardware requirements, acceptance of newer read technologies) and in their final output (composition of
assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled
genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in
genome assembly.
Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species
(a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated
these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From
over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies.
Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of
their genes and overall genome structure. However, the high degree of variability between the entries suggests that
there is still much room for improvement in the field of genome assembly and that approaches which work well in
assembling the genome of one species may not necessarily work well for another.
... Арабидопсис (119,1 Mb) и рис (373,8 Mb) обладают одними из самых маленьких геномов среди соответственно двудольных и однодольных растений, и их геномы считаются эталонными в своих классах (https://www.ncbi.nlm.nih.gov/), для кукурузы характерен один из самых длинных геномов среди однодольных (2,3 Gb) (70). ...
... Optical mapping for plant genome analyses has been performed to identify BAC contigs and correct genome assembly errors over the past decade. Optical mapping techniques had been applied in rice [80], medicago [81], maize [82] and tomato [83]. Concerning the identification of the large SVs at chromosomal scale, modern systems based on optical mapping technology such as the Bionano Genomics Saphyr system have remarkable sensitivity towards detection of genome-wide SVs. ...
Background
The use of image analysis to understand the structure of chromosome and chromatin is critical to the study of genetic evolution and diversification. Furthermore, a detailed chromosome map and the structure of chromatin in the nucleus may contribute to the plant breeding and the study of fundamental biology and genetics in organisms.
Results
In plants with a fully annotated genome project, such as the Leguminosae species, the integration of genetic information, including DNA sequence data, a linkage map, and the cytological quantitative chromosome map could further improve their genetic value. The numerical parameters of chromocenters in 3D can provide useful genetic information for phylogenetic studies of plant diversity and heterochromatic markers whose epigenetic changes may explain the developmental and environmental changes in the plant genome. Extended DNA fibers combined with fluorescence in situ hybridization revealed the highest spatial resolution of the obtained genome structure. Moreover, image analysis at the nano‐scale level using a helium ion microscope revealed the surface structure of chromatin, which consists of chromatin fibers compacted into plant chromosomes.
Conclusions
The studies described in this review sought to measure and evaluate chromosome and chromatin using the image analysis method, which may reduce measurement time and improve resolution. Further, we discussed the development of an effective image analysis to evaluate the structure of chromosome and chromatin. An effective application study of cell biology and the genetics of plants using image analysis methods is expected to be a major propeller in the development of new applications.
... Maize (Zea mays L.) with wheat and rice provides food for more than 4.5 billion people in hundreds of developing countries. Maize production is an important position in the world economy; it is affected by abiotic and biotic stresses, soil fertility, quality seed and fertilizers, levels of mechanization, and post-harvest management [1,2]. It ranks third in the world in terms of distribution (143 million ha), in front of which are wheat (215 million ha) and rice (151 million ha), while in Serbia it ranks first [3][4][5]. ...
Maize ranks first among worldwide production and an important source of human and
animal feed. Its production can be affected by management practices and climatic conditions. The objective of this study was to estimate stability of yield and hundred grains weight of six maize genotypes during two growing seasons at two locations, subjected to four different treatments: T1 treatment—without herbicide, Control; T2
treatment—active substance Nicosulfuron and Motivell commercial preparation; T3
treatment—active substance Rimsulfuron and Tarot; and, T4 treatment—active substance Forasulfuron and Equip. Additive main effects and multiplicative interaction—AMMI model and genotype × environment interaction—GGE biplot were used to estimate GEI—genotype by environment interaction. The results showed that the influence of genotype (G), year (Y), locality (L), treatment (T) and all interaction on hundred grains weight were significant. The share of genotypes in the total phenotypic variance was 64.70%, while the share in total interaction was 26.88%. The share of IPCA1 in terms of G × T interaction was 50.6%, while share of IPCA2 was 44.74%, which comprised together 94.80% of interaction. The first IPCA1 axis showed high share in the total interaction, which indicates out significance of genotype in total variation and interaction, while high level of IPCA2 indicates a significant treatment effect. Genotype L-6 had the same mass of 100 grains (37.96 g) during both years of testing, while genotype L-1, with 4.46 g, had the largest difference between years. This clearly indicates the influence of genotype but also stress under the influence of sulfonylureas and environmental factors. The maize genotype with the highest values of hundred grains weight, L-5 and L-6, expressed the highest values of grain yield (4665 kg ha−1 and 4445 kg ha−1).
... Thus, optical mapping has assisted in the assembly of a variety of species -including various prokaryotic species [9][10][11], rice [12], maize [13], mouse [14], goat [15], parrot [4], and amborella trichopoda [5]. Bionano Genomics has enabled the automated generation of the data, enabling the data to become more wide-spread. ...
... Figure 2 demonstrates how the skip-segment tolerates a deleted cut-site. For example, given k = 3 , D = 25 , and R = [7,18,13 [5, 13, 2] . We are now going to define the prefix and suffix bi-labels. ...
Genome wide optical maps are high resolution restriction maps that give a unique numeric representation to a genome. They are produced by assembling hundreds of thousands of single molecule optical maps, which are called Rmaps. Unfortunately, there are very few choices for assembling Rmap data. There exists only one publicly-available non-proprietary method for assembly and one proprietary software that is available via an executable. Furthermore, the publicly-available method, by Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006), follows the overlap-layout-consensus (OLC) paradigm, and therefore, is unable to scale for relatively large genomes. The algorithm behind the proprietary method, Bionano Genomics’ Solve, is largely unknown. In this paper, we extend the definition of bi-labels in the paired de Bruijn graph to the context of optical mapping data, and present the first de Bruijn graph based method for Rmap assembly. We implement our approach, which we refer to as rmapper , and compare its performance against the assembler of Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006) and Solve by Bionano Genomics on data from three genomes: E. coli , human, and climbing perch fish ( Anabas Testudineus ). Our method was able to successfully run on all three genomes. The method of Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006) only successfully ran on E. coli . Moreover, on the human genome rmapper was at least 130 times faster than Bionano Solve, used five times less memory and produced the highest genome fraction with zero mis-assemblies. Our software, rmapper is written in C++ and is publicly available under GNU General Public License at https://github.com/kingufl/Rmapper .
