scholarly journals Construction of a High-density Genetic Linkage Map and QTL Analysis of Resistance to Cucumber Mosaic Virus in Luffa cylindrica (L.) Roem. Based on Specific Length Amplified Fragment Sequencing

2019 ◽  
Author(s):  
Lina Lou ◽  
Zhe Liu ◽  
Xiaohong Liu ◽  
Xiaojun Su
Keyword(s):  
Linkage Map ◽  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Average Distance ◽  
High Density ◽  
Chromosome 1 ◽  
Pcr Analysis ◽  
Nucleotide Polymorphisms ◽  
Luffa Cylindrica ◽  
Cmv Resistance

Abstract Background: Luffa cylindrica L. is an economically important vegetable crop that is consumed globally. Cucumber mosaic virus (CMV) is an important virus affecting Luffa spp. No specific high-density maps have been constructed owing to a lack of efficient markers. Furthermore, no genes or quantitative trait loci (QTLs) are reportedly responsible for CMV resistance in Luffa spp. The development of next-generation sequencing has enabled discovery of single nucleotide polymorphisms and high-throughput genotyping of large populations. Results: A total of 271.01 Mb pair-end reads were generated. The average sequencing depth was 86.19× in both maternal and parental lines, and 14.57× in each F 2 individual. When filtering low-depth specific locus amplified fragment (SLAF) tags, 100,077 high-quality SLAFs were detected, and 7,405 of them were polymorphic. Finally, 3,701 of the polymorphic markers were selected for genetic map construction, and 13 linkage groups were generated. The map spanned 1,518.56 cM with an average distance of 0.41 cM between adjacent markers. Our results also revealed that CMV resistance was regulated by QTLs. Based on the newly constructed high-density map, two loci located on chromosome 1 (100.072 ~ 100.457 cM) and 4 (42.475 ~ 44.398 cM) were identified to regulate CMV resistance in L. cylindrica . A gag-polypeptide of LTR copia-type retrotransposon was predicted as the candidate gene responsible for CMV resistance in L. cylindrica . Conclusions: A high-density linkage map of L. cylindrica was constructed using SLAF. QTL mapping based on CMV disease phenotypes of F 2 led to the identification of two QTL on chromosome 1 and 4, respectively. Kompetitive allele-specific PCR analysis of 60 F 2 individuals, which gave rise to F 2:3 individuals, was carried out. We found that the QTL on chromosome 1 was associated with CMV resistance. Mapping of CMV QTL combined with the transcriptomic sequence alignment identified a gag-polypeptide of LTR copia-type retrotransposon as the most likely causal gene.

scholarly journals Construction of a High-density Genetic Linkage Map and QTL Analysis of Resistance to Cucumber Mosaic Virus in Luffa cylindrica (L.) Roem. Based on Specific Length Amplified Fragment Sequencing

2019 ◽  
Author(s):  
Lina Lou ◽  
Zhe Liu ◽  
Xiaohong Liu ◽  
Xiaojun Su
Keyword(s):  
Linkage Map ◽  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Average Distance ◽  
High Density ◽  
Chromosome 1 ◽  
Pcr Analysis ◽  
Nucleotide Polymorphisms ◽  
Luffa Cylindrica ◽  
Cmv Resistance

Abstract Background: Luffa cylindrica L. is an economically important vegetable crop that is consumed globally. Cucumber mosaic virus (CMV) is an important virus affecting Luffa spp. No specific high-density maps have been constructed owing to a lack of efficient markers. Furthermore, no genes or quantitative trait loci (QTLs) are reportedly responsible for CMV resistance in Luffa spp. The development of next-generation sequencing has enabled discovery of single nucleotide polymorphisms and high-throughput genotyping of large populations. Results: A total of 271.01 Mb pair-end reads were generated. The average sequencing depth was 86.19× in both maternal and parental lines, and 14.57× in each F 2 individual. When filtering low-depth specific locus amplified fragment (SLAF) tags, 100,077 high-quality SLAFs were detected, and 7,405 of them were polymorphic. Finally, 3,701 of the polymorphic markers were selected for genetic map construction, and 13 linkage groups were generated. The map spanned 1,518.56 cM with an average distance of 0.41 cM between adjacent markers. Our results also revealed that CMV resistance was regulated by QTLs. Based on the newly constructed high-density map, two loci located on chromosome 1 (100.072 ~ 100.457 cM) and 4 (42.475 ~ 44.398 cM) were identified to regulate CMV resistance in L. cylindrica . A gag-polypeptide of LTR copia-type retrotransposon was predicted as the candidate gene responsible for CMV resistance in L. cylindrica . Conclusions: A high-density linkage map of L. cylindrica was constructed using SLAF. QTL mapping based on CMV disease phenotypes of F 2 led to the identification of two QTL on chromosome 1 and 4, respectively. Kompetitive allele-specific PCR analysis of 60 F 2 individuals, which gave rise to F 2:3 individuals, was carried out. We found that the QTL on chromosome 1 was associated with CMV resistance. Mapping of CMV QTL combined with the transcriptomic sequence alignment identified a gag-polypeptide of LTR copia-type retrotransposon as the most likely causal gene.

scholarly journals Cucumber mosaic virus resistance and reproductive biology of brazilian melon accessions

2019 ◽  
Vol 41 (5) ◽  
Author(s):  
Nadia Carolina Sanabria-Verón ◽  
Cláusio Antônio Ferreira de Melo ◽  
Jadergudson Pereira ◽  
Glauber Henrique de Sousa Nunes ◽  
Ohana Luiza Santos de Oliveira ◽  
...  
Keyword(s):  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Reproductive Biology ◽  
Pollen Viability ◽  
Breeding Population ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Reproductive Characteristics ◽  
Quantitative Expression ◽  
Cmv Resistance

Abstract In melon (Cucumis melo) the resistance to Cucumber Mosaic Virus (CMV) and the knowledge about reproductive characteristics are important for selection of genitors for breeding population. So, the objective was to investigate if different accessions of melon from a Brazilian germplasm bank have variability in resistance to CMV (FNY strain) and polymorphism in resistance loci markers, as well as whether there is genetic diversity on resistance and floral morphology descriptors and reproductive biology, aiming at genetic improvement. The symptoms induced by CMV were evaluated in 52 melon genotypes which were genotyped with three markers of single nucleotide polymorphisms related to CMV resistance. A sample of 24 genotypes was characterized for floral and reproductive descriptors. The significant variation in resistance levels allows classifying the accessions in five groups. The polymorphisms detected by the markers were independently distributed in these groups, consistent with the oligogenic quantitative expression of the melon’s resistance. There were significant differences between accessions in floral and reproductive descriptors. Through the Ward-MLM multivariate strategy, these accesses were distributed into seven groups with distinct reproductive characteristics, including variability in pollen viability. Therefore, there are Brazilian accessions of melon that have resistance to CMV, as well as variability in reproductive characteristics.

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 Breeding Snap Beans for Cucumber Mosaic Virus (CMV) Resistance

HortScience ◽  
2004 ◽  
Vol 39 (4) ◽  
pp. 869C-869 ◽  
Author(s):  
Phillip Griffiths*
Keyword(s):  
Common Bean ◽  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Core Collection ◽  
Interspecific Crosses ◽  
Dry Bean ◽  
Snap Bean ◽  
The Core ◽  
Foliar Symptoms ◽  
Cmv Resistance

Cucumber mosaic virus (CMV) is an aphid-transmitted virus that infects snap bean growing regions in New York State and Wisconsin. The core collection of common bean accessions (Phaseolus vulgaris), the complete collection of scarlet runner bean accessions (Phaseolus coccineus) and snap/dry bean cultivars were screened for resistance to CMV. Although variation in foliar symptom expression was observed, no resistance was observed in 93 snap bean and16 dry bean cultivars tested, and only one of the 406 accessions from the core collection (PI 309881) was symptomless. PI 309881 did not have common bean characteristics, and was later identified as a tepary bean (Phaseolus acutifolius) accession based on morphology and PCR-RFLP of chloroplast DNA. Screening of 260 P. coccineus accessions was inaccurate when a visual rating of foliar symptoms was used. It was necessary to determine infection using ELISA and test plant screening with grey zuccini. Using this approach it was determined that 80 P. coccineus accessions were susceptible to CMV; however, the remaining accessions provided possible sources for transfer of CMV resistance to snap bean. Crosses of P. coccineus accessions were made to breeding line 5-593 and backcrossed to 5-593 and snap bean cultivar `Hystyle'. PI 309881 was crossed with ICA Pijao in order to develop interspecific hybrids. Populations were developed from the interspecific crosses/backcrosses and evaluated for CMV resistance using ELISA and visual ratings of foliar symptoms.

scholarly journals Construction of a high-density linkage map and detection of sex-specific markers in Penaeus japonicus

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12390
Author(s):  
Yaqun Zhang ◽  
Chuantao Zhang ◽  
Na Yao ◽  
Jingxian Huang ◽  
Xiangshan Sun ◽  
...  
Keyword(s):  
Sex Determination ◽  
Linkage Map ◽  
Genetic Linkage ◽  
Molecular Mechanisms ◽  
Genetic Linkage Map ◽  
Genotyping By Sequencing ◽  
High Density ◽  
Nucleotide Polymorphisms ◽  
Penaeus Japonicus ◽  
Genetic Mechanisms

Penaeus japonicus is one of the most important farmed shrimp species in many countries. Sexual dimorphism is observed in P. japonicus, in which females grow faster and larger than males; therefore, a unisexual female culture of P. japonicus could improve the efficiency of productivity. However, the genetic mechanisms underlying sex determination in P. japonicus are unclear. In this study, we constructed a high-density genetic linkage map of P. japonicus using genotyping-by-sequencing (GBS) technology in a full-sib family. The final map was 3,481.98 cM in length and contained 29,757 single nucleotide polymorphisms (SNPs). These SNPs were distributed on 41 sex-averaged linkage groups, with an average inter-marker distance of 0.123 cM. One haplotype, harboring five sex-specific SNPs, was detected in linkage group 1 (LG1), and its corresponding confidence interval ranged from 211.840 to 212.592 cM. Therefore, this high-density genetic linkage map will be informative for genome assembly and marker-assisted breeding, and the sex-linked SNPs will be helpful for further studies on molecular mechanisms of sex determination and unisexual culture of P. japonicus in the future.

scholarly journals Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F1 population of Catalpa bungei × Catalpa duclouxii Dode

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Nan Lu ◽  
Miaomiao Zhang ◽  
Yao Xiao ◽  
Donghua Han ◽  
Ying Liu ◽  
...  
Keyword(s):  
Plant Growth ◽  
Genetic Map ◽  
Average Distance ◽  
Leaf Traits ◽  
Interval Mapping ◽  
High Density ◽  
Nucleotide Polymorphisms ◽  
Significant Qtls ◽  
Leaf Trait ◽  
Catalpa Bungei

Abstract Background Catalpa bungei is an important tree species used for timber in China and widely cultivated for economic and ornamental purposes. A high-density linkage map of C. bungei would be an efficient tool not only for identifying key quantitative trait loci (QTLs) that affect important traits, such as plant growth and leaf traits, but also for other genetic studies. Results Restriction site-associated DNA sequencing (RAD-seq) was used to identify molecular markers and construct a genetic map. Approximately 280.77 Gb of clean data were obtained after sequencing, and in total, 25,614,295 single nucleotide polymorphisms (SNPs) and 2,871,647 insertions-deletions (InDels) were initially identified in the genomes of 200 individuals of a C. bungei (7080) × Catalpa duclouxii (16-PJ-3) F1 population and their parents. Finally, 9072 SNP and 521 InDel markers that satisfied the requirements for constructing a genetic map were obtained. The integrated genetic map contained 9593 pleomorphic markers in 20 linkage groups and spanned 3151.63 cM, with an average distance between adjacent markers of 0.32 cM. Twenty QTLs for seven leaf traits and 13 QTLs for plant height at five successive time points were identified using our genetic map by inclusive composite interval mapping (ICIM). Q16–60 was identified as a QTL for five leaf traits, and three significant QTLs (Q9–1, Q18–66 and Q18–73) associated with plant growth were detected at least twice. Genome annotation suggested that a cyclin gene participates in leaf trait development, while the growth of C. bungei may be influenced by CDC48C and genes associated with phytohormone synthesis. Conclusions This is the first genetic map constructed in C. bungei and will be a useful tool for further genetic study, molecular marker-assisted breeding and genome assembly.

scholarly journals An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Lidia de los Ríos-Pérez ◽  
Julien A. Nguinkal ◽  
Marieke Verleih ◽  
Alexander Rebl ◽  
Ronald M. Brunner ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genome Assembly ◽  
Large Scale ◽  
High Density ◽  
Whole Genome Sequencing Data ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Sander Lucioperca ◽  
Economic Significance ◽  
Marker Distance

AbstractPikeperch (Sander lucioperca) is a fish species with growing economic significance in the aquaculture industry. However, successful positioning of pikeperch in large-scale aquaculture requires advances in our understanding of its genome organization. In this study, an ultra-high density linkage map for pikeperch comprising 24 linkage groups and 1,023,625 single nucleotide polymorphisms markers was constructed after genotyping whole-genome sequencing data from 11 broodstock and 363 progeny, belonging to 6 full-sib families. The sex-specific linkage maps spanned a total of 2985.16 cM in females and 2540.47 cM in males with an average inter-marker distance of 0.0030 and 0.0026 cM, respectively. The sex-averaged map spanned a total of 2725.53 cM with an average inter-marker distance of 0.0028 cM. Furthermore, the sex-averaged map was used for improving the contiguity and accuracy of the current pikeperch genome assembly. Based on 723,360 markers, 706 contigs were anchored and oriented into 24 pseudomolecules, covering a total of 896.48 Mb and accounting for 99.47% of the assembled genome size. The overall contiguity of the assembly improved with a scaffold N50 length of 41.06 Mb. Finally, an updated annotation of protein-coding genes and repetitive elements of the enhanced genome assembly is provided at NCBI.

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