A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq)

Xu, Xuewen; Xu, Rui-Xue; Zhu, Biyun; Yu, Ting; Qu, Wenqin; Lu, Lu; Xu, Qiang; Qi, Xiaohua; Chen, Xuehao

doi:10.3389/fpls.2014.00768

Cited by 79 publications

(69 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The SLAF library was constructed following previous studies (Trick et al, 2012; Sun et al, 2013; Xu et al, 2015b) with minor modifications. In brief, we used Triticum aestivum as reference genome for a preliminary SLAF experiment to determine conditions and appropriate restriction enzymes.…”

Section: Methodsmentioning

confidence: 99%

“…Candidate genes for targeting traits can be identified rapidly using super-BSA. This approach was successfully used in detection of QTL, fine mapping of candidate genes and development of molecular markers in high plants (Trick et al, 2012; Qin et al, 2015; Xu et al, 2015a,b). In our previous studies, several genes for TGW, including TaCKOX6a02 (Lu et al, 2015), Tackx4 (Chang et al, 2015), and TaTGW6 (Hu et al, 2016), have been identified using RIL from a cross between Jing 411 and Hongmangchun 21.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Cloning and Characterization of TaTGW-7A Gene Associated with Grain Weight in Wheat via SLAF-seq-BSA

Zhang

Liu

et al. 2016

Front. Plant Sci.

View full text Add to dashboard Cite

Thousand-grain weight (TGW) of wheat (Triticum aestivum L.) contributes significantly to grain yield. In the present study, a candidate gene associated with TGW was identified through specific-locus amplified fragment sequencing (SLAF-seq) of DNA bulks of recombinant inbred lines (RIL) derived from the cross between Jing 411 and Hongmangchun 21. The gene was located on chromosome 7A, designated as TaTGW-7A with a complete genome sequence and an open reading frame (ORF). A single nucleotide polymorphism (SNP) was present in the first exon between two alleles at TaTGW-7A locus, resulting in a Val to Ala substitution, corresponding to a change from higher to lower TGW. Cleaved amplified polymorphic sequence (CAPS) (TGW7A) and InDel (TG9) markers were developed to discriminate the two alleles TaTGW-7Aa and TaTGW-7Ab for higher and lower TGW, respectively. A major QTL co-segregating with TaTGW-7A explained 21.7–27.1% of phenotypic variance for TGW in the RIL population across five environments. The association of TaTGW-7A with TGW was further validated in a natural population and Chinese mini-core collections. Quantitative real-time PCR revealed higher transcript levels of TaTGW-7Aa than those of TaTGW-7Ab during grain development. High frequencies of the superior allele TaTGW-7Aa for higher TGW in Chinese mini-core collections (65.0%) and 501 wheat varieties (86.0%) indicated a strong and positive selection of this allele in wheat breeding. The molecular markers TGW7A and TG9 can be used for improvement of TGW in breeding programs.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Cloning and Characterization of TaTGW-7A Gene Associated with Grain Weight in Wheat via SLAF-seq-BSA

Zhang

Liu

et al. 2016

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…SLAF-seq is more appropriate for GWAS than using SNP chips, can obtain millions of SNPs at once, and detect novel SNPs on the genome (Xu et al, 2015). SLAF-seq can be applied to species with a reference genome, as well as to species without a reference genome (Sun et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

A genome-wide association study of growth trait-related single nucleotide polymorphisms in Chinese Yancheng chickens

Cf¹,

Yj²,

Zhang³

et al. 2015

Genet. Mol. Res.

View full text Add to dashboard Cite

ABSTRACT. Chicken (Gallus gallus) growth traits are important economic traits, and many studies have been conducted on genetic selection for body weight. However, most of these studies have detected functional chromosome mutations or regions by conventional molecular markers or gene chips. In this study, we performed a new genome-wide association study using specific-locus amplified fragment sequencing (SLAFseq) technology in purebred Yancheng chickens. Single nucleotide polymorphisms (SNPs) that were significantly associated with phenotypic traits were identified by GAPIT-compressed mixed linear models. Eighteen SNP markers reached 5% Bonferroni genome-wide significance. A region spanning 72.3 to 82.1 Mb on GGA4 had a strong influence on growth traits. Four genes (FAM184B, KCNIP4, MIR15A, and GLI3) were closely associated with body weight. Some SNPs were coincident with previously reported quantitative trait locus regions. Our results would promote the researches of Chinese chickens and accelerate the utilization of Chinese chicken, specially Yancheng chicken.

show abstract

“…The SLAF-seq strategy, a novel NGS-based method, has been applied widely in de novo SNP discovery and genotyping of large populations [18], such as highdensity genetic map construction of cucumbers [32], candidate genes analysis of cotton [33], and high-quality SNP identification of rapeseed [34]. However, there have been few reports about the application of SLAFseq technology in resistance breeding of livestock, and to our best knowledge, this study is the first report of pig inguinal/scrotal hernias at genome-wide significance using SLAF-seq technology.…”

Section: Discussionmentioning

confidence: 99%

WITHDRAWN: Genome-wide association analysis of inguinal/scrotal hernia in pigs using specific length amplified fragment (SLAF) sequencing

Zou¹,

Zuo²,

Zhu³

et al. 2017

Oncotarget

View full text Add to dashboard Cite

Inguinal and scrotal hernias are the most frequent congenital disorders in pigs, and they may cause severe economic loss in the pig breeding industry. Genetic factors play a significant role in the susceptibility to hernias, but the genetic mechanisms of inguinal/scrotal hernia are poorly understood. In this study, we performed a genome-wide association study (GWAS) with specific-locus amplified fragment sequencing (SLAF-seq) on 120 (59 cases and 61 controls) full and half sib pigs to identify genetic loci underlying variations in inguinal/scrotal hernias. A total of 218,460 high-quality SNPs were generated for further statistical analysis with casecontrols and the farmCPU model. Based on these two methods, a total of 59 SNPs were significantly (P < 0.01) associated with inguinal/scrotal hernia. Finally, 14 novel candidate genes implicated in the defect were identified, and 5 genes (CPNE5, DEGS1, PLCG2, PRKCE and NUAK1) were related to cell apoptosis, which is one of the pivotal pathogenesis factors of inguinal/scrotal hernia. In addition, 4 of them were shown strong associations with the hernia were confirmed in 270 samples (P < 0.05). This finding provides new evidence that genes related to cell apoptosis may be associated with inguinal/scrotal hernias.

show abstract

A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq)

Cited by 79 publications

References 39 publications

Cloning and Characterization of TaTGW-7A Gene Associated with Grain Weight in Wheat via SLAF-seq-BSA

Cloning and Characterization of TaTGW-7A Gene Associated with Grain Weight in Wheat via SLAF-seq-BSA

A genome-wide association study of growth trait-related single nucleotide polymorphisms in Chinese Yancheng chickens

WITHDRAWN: Genome-wide association analysis of inguinal/scrotal hernia in pigs using specific length amplified fragment (SLAF) sequencing

Contact Info

Product

Resources

About