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.

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 Identification of fruit size associated quantitative trait loci featuring SLAF based high-density linkage map of goji berry (Lycium spp.)

2020 ◽  
Author(s):  
Fazal Rehman ◽  
Haiguang Gong ◽  
Zhong Li ◽  
Shaohua Zeng ◽  
Tianshun Yang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Linkage Map ◽  
Genetic Map ◽  
De Novo ◽  
Fruit Size ◽  
Leaf Size ◽  
High Density ◽  
Potential Candidate ◽  
Goji Berry ◽  
High Density Linkage Map

Abstract Background: Goji (Lycium spp., 2n = 24) is a perennial woody plant bearing functional properties. Fruit size associated attributes are important for evaluating small-fruited goji berry and plant architecture. The domestication traits are regulated quantitatively in crop plants but fewer studies have attempted on genomic regions corresponding to the fruit traits.Results: In this study, we established high-resolution map using SLAF-seq for de novo SNPs detection, based on 305 F1 offspring derived from L. chinense and L. barbarum. This genetic map contained 3,495 SNP markers on 12 LGs, spanning 1,649.03 cM with 0.47 cM average interval. Female and male parents had sequencing depth of 72.43-fold and 60.43-fold, respectively, while 15.23-fold detected for individuals. Phenotype data were obtained for 2 years and included 3rd year data as an average. QTL mapping analysis resulted in 117 QTLs corresponding to all traits, of which 23 QTLs in 2 years and 6 QTLs in 3rd years were detected. 6 promising QTLs, qFW10-3.1, qFL10-2.1, qLL10-2.1, qLD10-2.1, qLD12-4.1 and qLA10-2.1 were discovered influencing fruit weight, fruit length and leaf size related attributes covering an interval ranged 13.74-76.61 cM on LG10 with peak LOD up to 14.21 and PVE 19.3%. Additionally, 3 QTLs, qFS-1, qFS-2 and qFF-1, targeting fruit sweetness and fruit firmness were also identified in this study. Strikingly, among stable QTLs, qFL10-2.1, was co-localized to qLL10-2.1, qLD10-2.1, qLA10-2.1 and harbored significantly similar markers distribution, while qLL10-2.1 was the major and stable QTL with LOD ranged from 8.71-14.21 and PVE 12.3-19.3%. As LG10 harbored most of the fruit and leaf size related QTLs, we might speculate that it could be a hotspot region regulating fruit size and plant architectures.Conclusions: This report highlighted that the high-density linkage map construction using SLAF-seq is an important means for profound QTL mapping approach. Substantially, we utilized highly saturated genetic map to find out genetic locus targeting fruit and leaf size related attributes under QTL mapping. Our results will shed light on domestication traits and further strengthen molecular and genetic underpinnings of goji berry. Moreover, these findings would facilitate to assemble reference genome, determining potential candidate genes and marker-assisted breeding.

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 A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits

2018 ◽  
Author(s):  
L. Hibrand Saint-Oyant ◽  
T. Ruttink ◽  
L. Hamama ◽  
I. Kirov ◽  
D. Lakwani ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Structure ◽  
High Density ◽  
Genetic Maps ◽  
Reference Sequence ◽  
Cut Flowers ◽  
High Quality ◽  
Ploidy Levels ◽  
Potted Plants ◽  
Ornamental Traits

ABSTRACTRose is the world’s most important ornamental plant with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Rose has a complex genome with high heterozygosity and various ploidy levels. Our objectives were (i) to develop the first high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short read sequencing, and anchoring to a high-density genetic map and (ii) to study the genome structure and the genetic basis of major ornamental traits.We produced a haploid rose line from R. chinensis ‘Old Blush’ and generated the first rose genome sequence at the pseudo-molecule scale (512 Mbp with N50 of 3.4 Mb and L75 of 97). The sequence was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features including the pericentromeric regions through annotation of TE families and positioned centromeric repeats using FISH. Genetic diversity was analysed by resequencing eight Rosa species. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and number of flower petals. A rose APETALA2 homologue is proposed to be the major regulator of petals number in rose. This reference sequence is an important resource for studying polyploidisation, meiosis and developmental processes as we demonstrated for flower and prickle development. This reference sequence will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

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 Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12504
Author(s):  
Guan Li ◽  
Yichen Cheng ◽  
Man Yin ◽  
Jinyu Yang ◽  
Jiezheng Ying ◽  
...  
Keyword(s):  
Grain Yield ◽  
Linkage Map ◽  
Genetic Map ◽  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Recombinant Inbred Line Population ◽  
Recombinant Inbred ◽  
High Density ◽  
Rice Grain ◽  
High Density Linkage Map

Background The panicle is the most important organ in rice, and all the panicle-related traits are correlated with rice grain yield. Understanding the underlying genetic mechanisms controlling panicle development is very important for improving rice production. Methods Nine panicle-related traits including heading date, panicle length, number of primary branches, number of secondary branches, number of grains per panicle, number of panicles per plant, number of filled grains per plant, seed-setting rate, and grain yield per plant were investigated. To map the quantitative trait loci (QTLs) for the nine panicle-related traits, a PCR-based genetic map with 208 markers (including 121 simple sequence repeats and 87 InDels) and a high-density linkage map with 18,194 single nucleotide polymorphism (SNP) markers were both used. Results Using a recombinant inbred line population derived from an indica variety Huanghuazhan and a japonica line Jizi 1560, a total of 110 and 112 QTLs were detected for panicle-related traits by PCR-based genetic map and by high-density linkage map, respectively. Most of the QTLs were clustered on chromosomes 1, 2, 3, 6, and 7 while no QTLs were detected on chromosome 10. Almost all the QTLs with LOD values of more than 5.0 were repeatedly detected, indicating the accuracy of the two methods and the stability of the QTL effects. No genes for panicle-related traits have been previously reported in most of these regions. QTLs found in JD1006–JD1007 and RM1148–RM5556 with high LOD and additive values deserved further research. The results of this study are beneficial for marker-assisted breeding and provide research foundation for further fine-mapping and cloning of these QTLs for panicle-related traits.

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