scholarly journals High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS)

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Subodh Verma ◽  
Shefali Gupta ◽  
Nitesh Bandhiwal ◽  
Tapan Kumar ◽  
Chellapilla Bharadwaj ◽  
...  
Keyword(s):  
Linkage Map ◽  
Cicer Arietinum ◽  
Genotyping By Sequencing ◽  
High Density ◽  
Cicer Arietinum L ◽  
Map Construction ◽  
Seed Trait ◽  
High Density Linkage Map

RAD-seq-Based High-Density Linkage Map Construction and QTL Mapping of Biomass-Related Traits in Sorghum using the Japanese Landrace Takakibi NOG

2020 ◽  
Vol 61 (7) ◽  
pp. 1262-1272
Author(s):  
Hiromi Kajiya-Kanegae ◽  
Hideki Takanashi ◽  
Masaru Fujimoto ◽  
Motoyuki Ishimori ◽  
Norikazu Ohnishi ◽  
...  
Keyword(s):  
Linkage Map ◽  
High Density ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genetic Traits ◽  
Map Construction ◽  
Days To Heading ◽  
High Density Linkage Map ◽  
Sorghum Bicolor L

Abstract Sorghum [Sorghum bicolor (L.) Moench] grown locally by Japanese farmers is generically termed Takakibi, although its genetic diversity compared with geographically distant varieties or even within Takakibi lines remains unclear. To explore the genomic diversity and genetic traits controlling biomass and other physiological traits in Takakibi, we focused on a landrace, NOG, in this study. Admixture analysis of 460 sorghum accessions revealed that NOG belonged to the subgroup that represented Asian sorghums, and it was only distantly related to American/African accessions including BTx623. In an attempt to dissect major traits related to biomass, we generated a recombinant inbred line (RIL) from a cross between BTx623 and NOG, and we constructed a high-density linkage map based on 3,710 single-nucleotide polymorphisms obtained by restriction-site-associated DNA sequencing of 213 RIL individuals. Consequently, 13 fine quantitative trait loci (QTLs) were detected on chromosomes 2, 3, 6, 7, 8 and 9, which included five QTLs for days to heading, three for plant height (PH) and total shoot fresh weight and two for Brix. Furthermore, we identified two dominant loci for PH as being identical to the previously reported dw1 and dw3. Together, these results corroborate the diversified genome of Japanese Takakibi, while the RIL population and high-density linkage map generated in this study will be useful for dissecting other important traits in sorghum.

scholarly journals Effect of marker segregation distortion on high density linkage map construction and QTL mapping in Soybean (Glycine max L.)

Heredity ◽  
2019 ◽  
Vol 123 (5) ◽  
pp. 579-592 ◽  
Author(s):  
Jian-Fang Zuo ◽  
Yuan Niu ◽  
Peng Cheng ◽  
Jian-Ying Feng ◽  
Shi-Feng Han ◽  
...  
Keyword(s):  
Glycine Max ◽  
Qtl Mapping ◽  
Linkage Map ◽  
Segregation Distortion ◽  
High Density ◽  
Map Construction ◽  
Glycine Max L ◽  
Marker Segregation Distortion ◽  
High Density Linkage Map

scholarly journals SimpleMap: A Pipeline to Streamline High‐Density Linkage Map Construction

2015 ◽  
Vol 8 (2) ◽  
Author(s):  
Abdulqader Jighly ◽  
Reem Joukhadar ◽  
Manickavelu Alagu
Keyword(s):  
Linkage Map ◽  
High Density ◽  
Map Construction ◽  
High Density Linkage Map

scholarly journals Restriction site-associated DNA sequencing for SNP discovery and high-density genetic map construction in southern catfish ( Silurus meridionalis )

2018 ◽  
Vol 5 (5) ◽  
pp. 172054 ◽  
Author(s):  
Mimi Xie ◽  
Yao Ming ◽  
Feng Shao ◽  
Jianbo Jian ◽  
Yaoguang Zhang ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Restriction Site ◽  
Genome Structure ◽  
High Density ◽  
Genetic Maps ◽  
High Quality ◽  
Silurus Meridionalis ◽  
Map Construction ◽  
High Density Linkage Map

Single-nucleotide polymorphism (SNP) markers and high-density genetic maps are important resources for marker-assisted selection, mapping of quantitative trait loci (QTLs) and genome structure analysis. Although linkage maps in certain catfish species have been obtained, high-density maps remain unavailable in the economically important southern catfish ( Silurus meridionalis ). Recently developed restriction site-associated DNA (RAD) markers have proved to be a promising tool for SNP detection and genetic map construction. The objective of the present study was to construct a high-density linkage map using SNPs generated by next-generation RAD sequencing in S. meridionalis for future genetic and genomic studies. An F1 population of 100 individuals was obtained by intraspecific crossing of two wild heterozygous individuals. In total, 77 634 putative high-quality bi-allelic SNPs between the parents were discovered by mapping the parents' paired-end RAD reads onto the reference contigs from both parents, of which 54.7% were transitions and 45.3% were transversions (transition/transversion ratio of 1.2). Finally, 26 714 high-quality RAD markers were grouped into 29 linkage groups by using de novo clustering methods (Stacks). Among these markers, 4514 were linked to the female genetic map, 23 718 to the male map and 6715 effective loci were linked to the integrated map spanning 5918.31 centimorgans (cM), with an average marker interval of 0.89 cM. High-resolution genetic maps are a useful tool for both marker-assisted breeding and various genome investigations in catfish, such as sequence assembly, gene localization, QTL detection and genome structure comparison. Hence, such a high-density linkage map will serve as a valuable resource for comparative genomics and fine-scale QTL mapping in catfish species.

scholarly journals Development of a High‐Density Linkage Map and Tagging Leaf Spot Resistance in Pearl Millet Using Genotyping‐by‐Sequencing Markers

2016 ◽  
Vol 9 (2) ◽  
Author(s):  
Somashekhar M. Punnuri ◽  
Jason G. Wallace ◽  
Joseph E. Knoll ◽  
Katie E. Hyma ◽  
Sharon E. Mitchell ◽  
...  
Keyword(s):  
Linkage Map ◽  
Pearl Millet ◽  
Leaf Spot ◽  
Genotyping By Sequencing ◽  
High Density ◽  
High Density Linkage Map
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