High-density SNP genetic linkage map construction and quantitative trait locus mapping for resistance to cucumber mosaic virus in tobacco (Nicotiana tabacum L.)

Cheng, Lei; Chen, Jiayao; Jiang, Caihong; Ma, Bing; Ren, Min; Cheng, Yazeng; Liú, Dan; Geng, Ruimei; Yang, Aiguo

doi:10.1016/j.cj.2018.11.010

Cited by 25 publications

(14 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Currently, single nucleotide polymorphism (SNP) markers have become an attractive alternative to SSR markers given the progress in genomic research and high-throughput sequencing [ 36 , 37 ]. Although the diversity level of single locus is lower than that of SSR marker, and more loci are required to equal SSR detection effect, as dimorphic markers, SNPs can provide objective and readily distinguishable results that are well suited for DUS testing.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and fingerprinting of 33 standard flue-cured tobacco varieties for use in distinctness, uniformity, and stability testing

Geng

Cheng

et al. 2020

BMC Plant Biol

Self Cite

View full text Add to dashboard Cite

Background: At present, the distinctness, uniformity, and stability (DUS) testing of flue-cured tobacco (Nicotiana tabacum L.) depends on field morphological identification, which is problematic in that it is labor intensive, timeconsuming, and susceptible to environmental impacts. In order to improve the efficiency and accuracy of tobacco DUS testing, the development of a molecular marker-based method for genetic diversity identification is urgently needed. Results: In total, 91 simple sequence repeats (SSR) markers with clear and polymorphic amplification bands were obtained with polymorphism information content, Nei index, and Shannon information index values of 0.3603, 0.4040, and 0.7228, respectively. Clustering analysis showed that the 33 study varieties, which are standard varieties for flue-cured tobacco DUS testing, could all be distinguished from one another. Further analysis showed that a minimum of 25 markers were required to identify the genetic diversity of these varieties. Following the principle of two markers per linkage group, 48 pairs of SSR markers were selected. Correlation analysis showed that the genetic relationships revealed by the 48 SSR markers were consistent with those found using the 91 SSR markers. Conclusions: The genetic fingerprints of the 33 standard varieties of flue-cured tobacco were constructed using 48 SSR markers, and an SSR marker-based identification technique for new tobacco varieties was developed. This study provides a reliable technological approach for determining the novelty of new tobacco varieties and offers a solid technical basis for the accreditation and protection of new tobacco varieties.

show abstract

Section: Discussionmentioning

confidence: 99%

Genetic diversity and fingerprinting of 33 standard flue-cured tobacco varieties for use in distinctness, uniformity, and stability testing

Geng

Cheng

et al. 2020

BMC Plant Biol

Self Cite

View full text Add to dashboard Cite

show abstract

“…In this framework, SNPs are highly informative markers and this peculiarity is calculated as Minor Allele Frequency (MAF). SNPs are considered interesting for many goals when MAF values are >0.05 (Biswas et al , 2015; Cheng et al , 2019) but their main usefulness is due to the transferability across genotypes (>0.1; Lijavetzky et al , 2007). In the current study, MAF was calculated for each biallelic mutation.…”

Section: Resultsmentioning

confidence: 99%

Mining downy mildew susceptibility genes: a diversity study in grapevine

Pirrello

Zeilmaker²,

Bianco

et al. 2020

Preprint

View full text Add to dashboard Cite

AcknowledgmentsCP acknowledges funding from a FEM PhD fellowship at University of Udine, including a support from SciENZA Biotechnologies bv. Conflict of Interest StatementThe authors declare no conflict of interest. AbstractSeveral pathogens continuously threaten viticulture worldwide. Until now, the investigation on resistance loci has been the main trend to understand the interaction between grapevine and mildew causal agents. Dominantly inherited gene-based resistance has shown to be race-specific in some cases, to confer partial immunity and to be potentially overcome within a few years since its introgression. Recently, on the footprint of research conducted on Arabidopsis, the putative hortologues of genes associated with downy mildew susceptibility in this species, have been discovered also in the grapevine genome. In this work, we deep-resequenced four putative susceptibility genes in 190 highly genetically diverse grapevine genotypes to discover new sources of broad-spectrum recessively inherited resistance. The scouted genes are VvDMR6-1, VvDMR6-2, VvDLO1, VvDLO2 and predicted to be involved in susceptibility to downy mildew. From all identified mutations, 56% were Single Nucleotide Polymorphisms (SNPs) in heterozygosity, while the remaining 44% were homozygous. Regarding the identified mutations with putative impact on gene function, we observed ~4% genotypes mutated in VvDMR6-1 and ~8% mutated in VvDMR6-2, only a handful of genotypes that were mutated in both genes. ~2% and ~7% genotypes showed mutations in VvDLO1 and VvDLO2 respectively, and again a few genotypes resulted mutated in both genes. In particular, 80% of impacting mutations were heterozygous while 20% were homozygous.The current results will inform grapevine genetics and corroborate genomic-assisted breeding programs for resistance to biotic stresses.A survey on the genetic diversity of downy mildew susceptibility genes in grapevine varieties and wild species reveals a potential valuable for genomic-assisted breeding as well as tailored gene editing to induce disease resistance.

show abstract

“…Currently, single nucleotide polymorphism (SNP) markers have become an attractive alternative to SSR markers given the progress in genomic research and high-throughput sequencing [36] [37]. As dimorphic markers, SNPs can provide objective and readily distinguishable results that are well suited for DUS testing.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and fingerprinting of 33 standard flue-cured tobacco varieties for use in distinctness, uniformity, and stability testing

Geng

Cheng

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Background: At present, the distinctness, uniformity, and stability (DUS) testing of flue-cured tobacco ( Nicotiana tabacum L.) depends on field morphological identification, which is problematic in that it is intensive, time-consuming, and susceptible to environmental impacts. In order to improve the efficiency and accuracy of tobacco DUS testing, the development of a molecular marker-based method for genetic diversity identification is urgently needed. Results: In total, 91 simple sequence repeats (SSR) markers with clear and polymorphic amplification bands were obtained with polymorphism information content, Nei index, and Shannon information index values of 0.3603, 0.4040, and 0.7228, respectively. Clustering analysis showed that the 33 study varieties, which are standard varieties for flue-cured tobacco DUS testing, could all be distinguished from one another. Further analysis showed that a minimum of 25 markers were required to identify the genetic diversity of these varieties. Following the principle of two markers per linkage group, 48 pairs of SSR markers were selected. Correlation analysis showed that the genetic relationships revealed by the 48 SSR markers were consistent with those found using the 91 SSR markers. Conclusions: The genetic fingerprints of the 33 standard varieties of flue-cured tobacco were constructed using 48 SSR markers, and an SSR marker-based identification technique for new tobacco varieties was developed. This study provides a reliable technological approach for determining the novelty of new tobacco varieties and offers a solid technical basis for the accreditation and protection of new tobacco varieties.

show abstract

High-density SNP genetic linkage map construction and quantitative trait locus mapping for resistance to cucumber mosaic virus in tobacco (Nicotiana tabacum L.)

Cited by 25 publications

References 57 publications

Genetic diversity and fingerprinting of 33 standard flue-cured tobacco varieties for use in distinctness, uniformity, and stability testing

Genetic diversity and fingerprinting of 33 standard flue-cured tobacco varieties for use in distinctness, uniformity, and stability testing

Mining downy mildew susceptibility genes: a diversity study in grapevine

Genetic diversity and fingerprinting of 33 standard flue-cured tobacco varieties for use in distinctness, uniformity, and stability testing

Contact Info

Product

Resources

About