High-resolution genetic map construction and QTL analysis of important fiber traits in kenaf using RAD-seq

Abstract Quantitative trait locus (QTL) mapping is a useful method for revealing the mechanism of complex genetic traits and identifying new genomic information to accelerate crop improvement. In the present study, 154 F2:3 strains and their parents were used for restriction site-associated DNA sequencing, single-nucleotide polymorphism (SNP) identification, and genetic map construction. After filtering based on stringent filtering standards, 297.5 Gb of clean data were obtained. Further, 5,191 polymorphic SNP markers were identified from each sample, of which 1,997 polymorphic SNP markers were successfully mapped onto 18 different linkage groups. Six QTLs (QPH, QFBW, QDBW, QFW, QFT, and QFC) were identified based on the genetic map using the multiple QTL mapping (MQM) method, which were then assigned to three linkage groups, LG16, LG8, and LG3. QPH, QFBW, QDBW, and QFW were related to fiber yield, while QFT and QFC were related to fiber quality. This is the first study of its kind to map QTL of fiber yield and fiber quality, which will facilitate further understanding of the molecular genetic basis of these traits. However, there are limitations regarding the utilization of this map because several large gaps remain in some linkage groups. Therefore, additional markers need to be developed to further narrow these regions.

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Genetic Map Construction and Fiber Quality QTL Mapping Using the CottonSNP80K Array in Upland Cotton

Frontiers in Plant Science ◽

10.3389/fpls.2018.00225 ◽

2018 ◽

Vol 9 ◽

Cited By ~ 20

Author(s):

Zhaoyun Tan ◽

Zhiqin Zhang ◽

Xujing Sun ◽

Qianqian Li ◽

Ying Sun ◽

...

Keyword(s):

Qtl Mapping ◽

Genetic Map ◽

Upland Cotton ◽

Fiber Quality ◽

Map Construction

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EVOLUTION OF DNA SEQUENCING METHODS AND PROSPECTS FOR THEIR USE IN FORENSIC DNA EXAMINATION

Young Scientist ◽

10.32839/2304-5809/2020-11-87-27 ◽

2020 ◽

Vol 11 (87) ◽

Author(s):

Zhanna Bazyliuk ◽

Keyword(s):

Dna Sequencing ◽

Molecular Genetic ◽

Genetic Research ◽

Snp Markers ◽

Degraded Dna ◽

Phenotypic Traits ◽

Nucleotide Polymorphisms ◽

Biological Origin ◽

Genetic Traits ◽

Str Loci

The study of the human genome makes it possible to use genetic information to identify individual traits, diagnosis of diseases and forecasting and prevention of their development, promotes a personal approach when choosing treatment methods; population research, ethnogenesis and evolutionary processes. Introduction of DNA sequencing methods in domestic genetic fingerprinting will contribute to a more informative establishment of human genetic traits. The main purpose of molecular genetic research is to establish the genetic features of missing people, their relatives, to conduct paternity, to identify traces of biological origin and their identification. This article talks about the gradual development of DNA sequencing technology, which is conventionally divided into three types. The first type includes sequencing using capillary electrophoresis and pyrosequencing. The second type is high-throughput pyrosequencing, semiconductor, cyclic ligase, and the use of fluorescently labeled precursors, based on the sequencing of millions of DNA fragments simultaneously. The third stage includes methods that do not require prior sample preparation. These are methods of nanoporous sequencing, sequencing of one molecule, one-molecular sequencing. Today, each of the sequencing methods is aimed at performing different tasks. A number of methods are promising in the field of molecular-genetic examination. In world jurisprudence, sequencing is implemented mainly with the help of devices - Illumina’s, MiSeq FGx, Ion Torrent PGM from ThermoFisher and Ion S5. Research in forensic expertise of single nucleotide polymorphisms (SNP), sequencing of STR-loci and mitochondrial DNA, STR-loci and SNP-markers of the Y chromosome, will provide a high level of information, determination of human phenotypic traits, the possibility of establishing genetic traits from significantly degraded DNA. This article deals with modern problems of identification of human genetic traits and the prospect of introduction of the newest methods of sequencing for their qualitative and complete establishment.

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High-Density Genetic Map Construction and QTL Mapping of Leaf and Needling Traits in Ziziphus jujuba Mill

Frontiers in Plant Science ◽

10.3389/fpls.2019.01424 ◽

2019 ◽

Vol 10 ◽

Cited By ~ 2

Author(s):

Zhongtang Wang ◽

Zhong Zhang ◽

Haixia Tang ◽

Qiong Zhang ◽

Guangfang Zhou ◽

...

Keyword(s):

Qtl Mapping ◽

Genetic Map ◽

High Density ◽

Map Construction ◽

Ziziphus Jujuba

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Genetic mapping of male sterility and pollen fertility QTLs in triticale with sterilizing Triticum timopheevii cytoplasm

Journal of Applied Genetics ◽

10.1007/s13353-020-00595-z ◽

2020 ◽

Author(s):

Marzena Wasiak ◽

Agnieszka Niedziela ◽

Henryk Woś ◽

Mirosław Pojmaj ◽

Piotr Tomasz Bednarek

Keyword(s):

Male Sterility ◽

Genetic Map ◽

Pollen Sterility ◽

Snp Markers ◽

Hybrid Seed Production ◽

Triticum Timopheevii ◽

Crop Species ◽

Sugar Beets ◽

Map Construction ◽

Explained Variance

AbstractCytoplasmic male sterility (CMS) phenomenon is widely exploited in commercial hybrid seed production in economically important crop species, including rye, wheat, maize, rice, sorghum, cotton, sugar beets, and many vegetables. Although some commercial successes, little is known about QTLs responsible for the trait in case of triticale with sterilizing Triticum timopheevii (Tt) cytoplasm. Recombinant inbred line (RIL) F6 mapping population encompassing 182 individuals derived from the cross of individual plants representing the HT352 line and cv Borwo was employed for genetic map construction using SNP markers and identification of QTLs conferring pollen sterility in triticale with CMS Tt. The phenotypes of the F1 lines resulting from crossing of the HT352 (Tt) with HT352 (maintainer) × Borwo were determined by assessing the number of the F2 seeds per spike. A genetic map with 21 linkage groups encompasses 29,737 markers and spanned over the distance of 2549 cM. Composite (CIM) and multiple (MIM) interval mappings delivered comparable results. Single QTLs mapped to the 1A, 1B, 2A, 2R, 3B, 3R, 4B, and 5B chromosomes, whereas the 5R and 6B chromosomes shared 3 and 2 QTLs, respectively. The QTLs with the highest LOD score mapped to the 5R, 3R, 1B, and 4B chromosomes; however, the QRft-5R.3 has the highest explained variance of the trait.

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Molecular Genetic Map Construction and QTL Analysis for Fruit Maturation Period in Litchi

Biotechnology & Biotechnological Equipment ◽

10.5504/bbeq.2011.0046 ◽

2011 ◽

Vol 25 (2) ◽

pp. 2315-2320 ◽

Cited By ~ 2

Author(s):

Y.H. Zhao ◽

Y.S. Guo ◽

J.X. Fu ◽

S.S. Huang ◽

B.B. Lu ◽

...

Keyword(s):

Genetic Map ◽

Qtl Analysis ◽

Molecular Genetic ◽

Fruit Maturation ◽

Maturation Period ◽

Map Construction ◽

Molecular Genetic Map

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A Molecular Genetic Map and Electrophoretic Karyotype of the Plant Pathogenic Fungus Cochliobolus sativus

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2002.15.5.481 ◽

2002 ◽

Vol 15 (5) ◽

pp. 481-492 ◽

Cited By ~ 48

Author(s):

Shaobin Zhong ◽

Brian J. Steffenson ◽

J. Patrick Martinez ◽

Lynda M. Ciuffetti

Keyword(s):

Genetic Map ◽

Length Polymorphism ◽

Fragment Length Polymorphism ◽

Molecular Genetic ◽

Aflp Markers ◽

Cochliobolus Sativus ◽

Electrophoretic Karyotype ◽

Linkage Groups ◽

Molecular Genetic Map ◽

Map Distance

A molecular genetic map was constructed and an electrophoretic karyotype was resolved for Cochliobolus sativus, the causal agent of spot blotch of barley and wheat. The genetic map consists of 27 linkage groups with 97 amplified fragment length polymorphism (AFLP) markers, 31 restriction fragment length polymorphism (RFLP) markers, two polymerase chain reaction amplified markers, the mating type locus (CsMAT), and a gene (VHv1) conditioning high virulence on barley cv. Bowman. These linkage groups covered a map distance of 849 cM. The virulence gene VHv1 cosegregated with six AFLP markers and was mapped on one of the major linkage groups. Fifteen chromosome-sized DNAs were resolved in C. sativus isolates ND93-1 and ND90Pr with contour-clamped homogeneous electric field (CHEF) electrophoresis combined with telo-mere probe analysis of comigrating chromosome-sized DNAs. The chromosome sizes ranged from 1.25 to 3.80 Mbp, and the genome size of the fungus was estimated to be approximately 33 Mbp. By hybridizing genetically mapped RFLP and AFLP markers to CHEF blots, 25 of the 27 linkage groups were assigned to specific chromosomes. The barley-specific virulence locus VHv1 was localized on a chromosome of 2.80 Mbp from isolate ND90Pr in the CHEF gel. The total map length of the fungus was estimated to be at least 1,329 cM based on the map distance covered by the linked markers and the estimated gaps. Therefore, the physical to genetic distance ratio is approximately 25 kb/cM. Construction of a high-resolution map around target loci will facilitate the cloning of the genes conferring virulence and other characters in C. sativus by a map-based cloning strategy.

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