Identification of favorable SNP alleles and candidate genes for traits related to early maturity via GWAS in upland cotton

Su, Junji; Pang, Chaoyou; Wei, Hengling; Li, Libei; Liang, Bing; Wang, Caixiang; Song, Meizhen; Wang, Hantao; Zhao, Shuqi; Jia, Xiaoyun; Mao, Guangzhi; Huang, Long; Geng, Dandan; Wang, Chengshe; Fan, Shuli; Yu, Shuang

doi:10.1186/s12864-016-2875-z

Cited by 89 publications

(92 citation statements)

References 53 publications

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“…The SLAF-seq approach was used to genotype the natural population as described in a previous study30, and 691,978 SNPs were identified with call success. A total of 81,675 SNPs were selected for further analyses after excluding the SNPs with more than 10% missing data, a minor allele frequency (MAF) <5%, and an average marker density of 1 SNP per 24.85 kb30.…”

Section: Resultsmentioning

confidence: 99%

“…A total of 81,675 SNPs were selected for further analyses after excluding the SNPs with more than 10% missing data, a minor allele frequency (MAF) <5%, and an average marker density of 1 SNP per 24.85 kb30. To estimate the genetic diversity of natural populations, these SNPs were divided into 26 groups according to chromosome, and the genetic diversity values were calculated for each group.…”

Section: Resultsmentioning

confidence: 99%

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Two genomic regions associated with fiber quality traits in Chinese upland cotton under apparent breeding selection

Pang

et al. 2016

Sci Rep

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Fiber quality is one of the most important agronomic traits of cotton, and understanding the genetic basis of its target traits will accelerate improvements to cotton fiber quality. In this study, a panel comprising 355 upland cotton accessions was used to perform genome-wide association studies (GWASs) of five fiber quality traits in four environments. A total of 16, 10 and 7 SNPs were associated with fiber length (FL), fiber strength (FS) and fiber uniformity (FU), respectively, based on the mixed linear model (MLM). Most importantly, two major genomic regions (MGR1 and MGR2) on chromosome Dt7 and four potential candidate genes for FL were identified. Analyzing the geographical distribution of favorable haplotypes (FHs) among these lines revealed that two favorable haplotype frequencies (FHFs) were higher in accessions from low-latitude regions than in accessions from high-latitude regions. However, the genetic diversity of lines from the low-latitude regions was lower than the diversity of lines from the high-latitude regions in China. Furthermore, the FHFs differed among cultivars developed during different breeding periods. These results indicate that FHs have undergone artificial selection during upland cotton breeding in recent decades in China and provide a foundation for the further improvement of fiber quality traits.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Two genomic regions associated with fiber quality traits in Chinese upland cotton under apparent breeding selection

Pang

et al. 2016

Sci Rep

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“…The co‐located region related to early maturity could easily be used for cotton breeding by recombination and exchange (Figure c). Furthermore, we observed that the candidate genes associated with yield and fibre quality, especially traits that were amenable to selection, such as BW, FP, LP, FL and FS (Figure S11, Table S11), were also located in high‐recombination regions based on previous studies (Su et al ., ; Fang et al ., ; Huang et al ., ; Sun et al ., ; Wang et al ., ; Ma et al ., ). Recombination hot spot regions carrying favourable mutations can be further utilized in important genetic regions (Hartl and Clark, ).…”

Section: Discussionmentioning

confidence: 99%

Population genomics reveals a fine‐scale recombination landscape for genetic improvement of cotton

et al. 2019

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Summary Recombination breaks up ancestral linkage disequilibrium, creates combinations of alleles, affects the efficiency of natural selection, and plays a major role in crop domestication and improvement. However, there is little knowledge regarding the variation in the population‐scaled recombination rate in cotton. We constructed recombination maps and characterized the difference in the genomic landscape of the population‐scaled recombination rate between Gossypium hirsutum and G. arboreum and sub‐genomes based on the 381 sequenced G. hirsutum and 215 G. arboreum accessions. Comparative genomics identified large structural variations and syntenic genes in the recombination regions, suggesting that recombination was related to structural variation and occurred preferentially in the distal chromosomal regions. Correlation analysis indicated that recombination was only slightly affected by geographical distribution and breeding period. A genome‐wide association study (GWAS) was performed with 15 agronomic traits using 267 cotton accessions and identified 163 quantitative trait loci (QTL) and an important candidate gene (Ghir_COL2) for early maturity traits. Comparative analysis of recombination and a GWAS revealed that the QTL of fibre quality traits tended to be more common in high‐recombination regions than were those of yield and early maturity traits. These results provide insights into the population‐scaled recombination landscape, suggesting that recombination contributed to the domestication and improvement of cotton, which provides a useful reference for studying recombination in other species.

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“…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

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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.

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Identification of favorable SNP alleles and candidate genes for traits related to early maturity via GWAS in upland cotton

Cited by 89 publications

References 53 publications

Two genomic regions associated with fiber quality traits in Chinese upland cotton under apparent breeding selection

Two genomic regions associated with fiber quality traits in Chinese upland cotton under apparent breeding selection

Population genomics reveals a fine‐scale recombination landscape for genetic improvement of cotton

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

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