Identification of QTLs for eight agronomically important traits using an ultra-high-density map based on SNPs generated from high-throughput sequencing in sorghum under contrasting photoperiods

Knowledge on population diversity and structure is of fundamental importance for conifer breeding programs. In this study, we concentrated on the development and application of high-density single nucleotide polymorphism (SNP) markers through a high-throughput sequencing technique termed as specific-locus amplified fragment sequencing (SLAF-seq) for the economically important conifer tree species, Chinese fir (Cunninghamia lanceolata). Based on the SLAF-seq, we successfully established a high-density SNP panel consisting of 108,753 genomic SNPs from Chinese fir. This SNP panel facilitated us in gaining insight into the genetic base of the Chinese fir advance breeding population with 221 genotypes for its genetic variation, relationship and diversity, and population structure status. Overall, the present population appears to have considerable genetic variability. Most (94.15%) of the variability was attributed to the genetic differentiation of genotypes, very limited (5.85%) variation occurred on the population (sub-origin set) level. Correspondingly, low FST (0.0285–0.0990) values were seen for the sub-origin sets. When viewing the genetic structure of the population regardless of its sub-origin set feature, the present SNP data opened a new population picture where the advanced Chinese fir breeding population could be divided into four genetic sets, as evidenced by phylogenetic tree and population structure analysis results, albeit some difference in membership of the corresponding set (cluster vs. group). It also suggested that all the genetic sets were admixed clades revealing a complex relationship of the genotypes of this population. With a step wise pruning procedure, we captured a core collection (core 0.650) harboring 143 genotypes that maintains all the allele, diversity, and specific genetic structure of the whole population. This generalist core is valuable for the Chinese fir advanced breeding program and further genetic/genomic studies.

Download Full-text

Construction and Analysis of High-Density Linkage Map Using High-Throughput Sequencing Data

PLoS ONE ◽

10.1371/journal.pone.0098855 ◽

2014 ◽

Vol 9 (6) ◽

pp. e98855 ◽

Cited By ~ 144

Author(s):

Dongyuan Liu ◽

Chouxian Ma ◽

Weiguo Hong ◽

Long Huang ◽

Min Liu ◽

...

Keyword(s):

Linkage Map ◽

High Throughput ◽

High Throughput Sequencing ◽

High Density ◽

Sequencing Data ◽

High Throughput Sequencing Data ◽

High Density Linkage Map

Download Full-text

Identification of QTLs for 14 Agronomically Important Traits in Setaria italica Based on SNPs Generated from High-Throughput Sequencing

G3 Genes|Genome|Genetics ◽

10.1534/g3.117.041517 ◽

2017 ◽

Vol 7 (5) ◽

pp. 1587-1594 ◽

Cited By ~ 14

Author(s):

Kai Zhang ◽

Guangyu Fan ◽

Xinxin Zhang ◽

Fang Zhao ◽

Wei Wei ◽

...

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Setaria Italica ◽

Agronomically Important Traits

Download Full-text

A new mouse SNP genotyping assay for speed congenics: combining flexibility, affordability, and power

BMC Genomics ◽

10.1186/s12864-021-07698-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Kimberly R. Andrews ◽

Samuel S. Hunter ◽

Brandi K. Torrevillas ◽

Nora Céspedes ◽

Sarah M. Garrison ◽

...

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Cost Effective ◽

High Density ◽

Snp Genotyping ◽

Mouse Strains ◽

Bioinformatic Pipeline ◽

Genotyping Assay ◽

Sequencing Technologies ◽

Diagnostic Snps

Abstract Background Speed congenics is an important tool for creating congenic mice to investigate gene functions, but current SNP genotyping methods for speed congenics are expensive. These methods usually rely on chip or array technologies, and a different assay must be developed for each backcross strain combination. “Next generation” high throughput DNA sequencing technologies have the potential to decrease cost and increase flexibility and power of speed congenics, but thus far have not been utilized for this purpose. Results We took advantage of the power of high throughput sequencing technologies to develop a cost-effective, high-density SNP genotyping assay that can be used across many combinations of backcross strains. The assay surveys 1640 genome-wide SNPs known to be polymorphic across > 100 mouse strains, with an expected average of 549 ± 136 SD diagnostic SNPs between each pair of strains. We demonstrated that the assay has a high density of diagnostic SNPs for backcrossing the BALB/c strain into the C57BL/6J strain (807–819 SNPs), and a sufficient density of diagnostic SNPs for backcrossing the closely related substrains C57BL/6N and C57BL/6J (123–139 SNPs). Furthermore, the assay can easily be modified to include additional diagnostic SNPs for backcrossing other closely related substrains. We also developed a bioinformatic pipeline for SNP genotyping and calculating the percentage of alleles that match the backcross recipient strain for each sample; this information can be used to guide the selection of individuals for the next backcross, and to assess whether individuals have become congenic. We demonstrated the effectiveness of the assay and bioinformatic pipeline with a backcross experiment of BALB/c-IL4/IL13 into C57BL/6J; after six generations of backcrosses, offspring were up to 99.8% congenic. Conclusions The SNP genotyping assay and bioinformatic pipeline developed here present a valuable tool for increasing the power and decreasing the cost of many studies that depend on speed congenics. The assay is highly flexible and can be used for combinations of strains that are commonly used for speed congenics. The assay could also be used for other techniques including QTL mapping, standard F2 crosses, ancestry analysis, and forensics.

Download Full-text

Bulk Segregant Analysis Followed by High-Throughput Sequencing Reveals the Neurospora Cell Cycle Gene,ndc-1, To Be Allelic with the Gene for Ornithine Decarboxylase,spe-1

Eukaryotic Cell ◽

10.1128/ec.00016-11 ◽

2011 ◽

Vol 10 (6) ◽

pp. 724-733 ◽

Cited By ~ 54

Author(s):

Kyle R. Pomraning ◽

Kristina M. Smith ◽

Michael Freitag

Keyword(s):

Cell Cycle ◽

Ornithine Decarboxylase ◽

High Throughput ◽

Bulk Segregant Analysis ◽

High Throughput Sequencing ◽

Nuclear Division ◽

High Density ◽

Cell Cycle Gene ◽

Wild Type ◽

Content Type

ABSTRACTWith the advent of high-throughput DNA sequencing, it is now straightforward and inexpensive to generate high-density small nucleotide polymorphism (SNP) maps. Here we combined high-throughput sequencing with bulk segregant analysis to expedite mutation mapping. The general map location of a mutation can be identified by a single backcross to a strain enriched in SNPs compared to a standard wild-type strain. Bulk segregant analysis simultaneously increases the likelihood of determining the precise nature of the mutation. We present here a high-density SNP map betweenNeurospora crassaMauriceville-1-c (FGSC2225) and OR74A (FGSC2489), the strains most typically used byNeurosporaresearchers to carry out mapping crosses. We further have demonstrated the utility of the Mauriceville sequence and our approach by mapping the mutation responsible for the only existing temperature-sensitive (ts) cell cycle mutation inNeurospora,nuclear division cycle-1(ndc-1). The single T-to-C point mutation maps to the gene encoding ornithine decarboxylase (ODC),spe-1(NCU01271), and changes a Phe to a Ser residue within a highly conserved motif next to the catalytic site of the enzyme. By growth on spermidine and complementation with a wild-typespe-1gene, we showed that the defect inspe-1is responsible for the tsndc-1mutation. Based on our results, we propose changingndc-1tospe-1ndc, which reflects that this mutation results in an ODC with a specific nuclear division defect.

Download Full-text