2018
DOI: 10.3389/fpls.2017.02199
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Dissection of Insertion–Deletion Variants within Differentially Expressed Genes Involved in Wood Formation in Populus

Abstract: Short insertions and deletions (InDels) are one of the major genetic variants and are distributed widely across the genome; however, few investigations of InDels have been conducted in long-lived perennial plants. Here, we employed a combination of RNA-seq and population resequencing to identify InDels within differentially expressed (DE) genes underlying wood formation in a natural population of Populus tomentosa (435 individuals) and utilized InDel-based association mapping to detect the causal variants unde… Show more

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Cited by 20 publications
(13 citation statements)
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“…This is because simultaneous deletion of both genes would negate synthesis of feruloyl CoA and its downstream product coniferyl alcohol a precursor for the guaiacyl subunit of lignin. Such negative epistasis between the two genes has indeed been found previously in P. tomentosa using association mapping (Gong et al , 2018). Four other synthetic lethal pairs were also identified between enzymes belonging to BCAA metabolism and pantothenate and CoA biosynthesis.…”
Section: Resultssupporting
confidence: 81%
“…This is because simultaneous deletion of both genes would negate synthesis of feruloyl CoA and its downstream product coniferyl alcohol a precursor for the guaiacyl subunit of lignin. Such negative epistasis between the two genes has indeed been found previously in P. tomentosa using association mapping (Gong et al , 2018). Four other synthetic lethal pairs were also identified between enzymes belonging to BCAA metabolism and pantothenate and CoA biosynthesis.…”
Section: Resultssupporting
confidence: 81%
“…Therefore, the influence of each of these factors on heritability strongly depends on the population sampled and inclusion of sophisticated genotyping tools in the case of epigenetics. The incorporation of a combination of advanced statistical models such as regional heritability mapping (RHM) and the detection of structural variants, insertion/deletions (InDels) and copy number variants in GWAS studies from several tree species has resulted in higher heritabilities being detected (Resende et al ., ; Gong et al ., )…”
Section: Resultsmentioning
confidence: 99%
“…Therefore, the influence of each of these factors on heritability strongly depends on the population sampled and inclusion of sophisticated genotyping tools in the case of epigenetics. The incorporation of a combination of advanced statistical models such as regional heritability mapping (RHM) and the detection of structural variants, insertion/deletions (InDels) and copy number variants in GWAS studies from several tree species has resulted in higher heritabilities being detected (Resende et al, 2017a;Gong et al, 2018) Trait trajectories and functional mapping EBVs were plotted as phenotype data versus 14 consecutive cambial ages ( Figure 1). All phenotypes under investigation are represented with thin light blue (Black average) curves, to visualize the nature of variation and growth trajectories of the phenotype (Figure 1 and Supporting Information Figure S1).…”
Section: Resultsmentioning
confidence: 99%
“…SV在基因组内分布广泛, 可显著影响表型变 异和基因组进化 [74] , 是林木GWAS研究下一步需要重 点关注的标记类型. 例如, Gong等人 [18] 在毛白杨生长 和木材品质性状的关联分析中发现, InDel平均可解释 表型变异的14.7%, 远大于SNP对表型变异的解析度 (约为5%). 由于林木基因组高度杂合, SV的检测较为 困难, 对其的研究鲜见报道 [16] .…”
Section: Gwas策略在林木复杂性状研究中的应 用热点unclassified