Genes underlying quantitative variation in ecologically important traits: PIF4 (PHYTOCHROME INTERACTING FACTOR 4) is associated with variation in internode length, flowering time, and fruit set in Arabidopsis thaliana
Genes underlying quantitative variation in ecologically important traits: PIF4 (PHYTOCHROME INTERACTING FACTOR 4) is associated with variation in internode length, flowering time, and fruit set in Arabidopsis thaliana
复制标题
DOI：
10.1111/j.1365-294x.2010.04538.x
复制
发表时间：
2010-03-01
影响因子：
4.9
通讯作者：
Weinig, Cynthia
中科院分区：
文献类型：
--
作者：
Brock, Marcus T.;Maloof, Julin N.;Weinig, Cynthia
关联研究利用跨越无数世代的重组作用来确定构成数量性状的基因座。我们采用候选基因关联分析、分离分析和局部连锁不平衡(LD)分析来评估PIF4(植物激素相互作用因子4)的分子变异对拟南芥重要生态性状的潜在因果效应。对14个自然基因的序列多样性进行了初步分析，发现PIF4存在一个中频替换多态。对161份天然种质进行了PIF4基因分型，并在高密度和低密度环境下对早期节间长度、花序长度、开花天数和开花间隔(抽蕾到开花之间的天数)的平均长度进行了筛选，以检验基因型与表型的相关性。在161份材料中，PIF4与早期节间长度相关，而PIF4x处理互作与开花间隔相关。此外，在一组分离PIF4多态的重组自交系中，PIF4处的核苷酸替换与早期节间长度、开花天数和座果时间共分离，这表明关联图谱小组中神秘的群体结构和伴随的具有物理距离的座位的Ld不能解释所观察到的关联。最后，在20个重新测序的基因型的一组假染色体中，Ld似乎在PIF4附近迅速衰退，这表明侧翼基因座对观察到的关联作用很小。综上所述，这些结果表明，PIF4可能通过影响生殖时机而影响初级花序上的早期节间长度，而这些性状反过来又影响适合度。
Association studies utilize the action of recombination over numerous generations to identify loci that underlie quantitative traits. We use a candidate-gene association approach, segregation analyses and analyses of local linkage disequilibrium (LD) to evaluate the potentially causal effects of molecular variation at PIF4 (PHYTOCROME INTERACTING FACTOR 4) on ecologically important traits in Arabidopsis thaliana. A preliminary analysis of sequence diversity in 14 natural genotypes revealed one intermediate-frequency replacement polymorphism at PIF4. A sample of 161 natural accessions was genotyped at PIF4 and screened for average length of early internodes, inflorescence length, days to flowering and flowering interval (days between bolting and flowering) under high- and low-density environments to test for genotype-phenotype associations. PIF4 was associated with early internode lengths, while the PIF4x treatment interaction was associated with flowering interval in the panel of 161 accessions. Further, in a set of recombinant inbred lines that segregate for the PIF4 polymorphism, nucleotide substitutions at PIF4 co-segregated with early internode lengths, days to flowering and fruit set, suggesting that cryptic population structure in the association-mapping panel and attendant LD with a physically distant locus do not account for the observed association. Finally, in a panel of pseudochromosomes from 20 re-sequenced genotypes, LD appeared to decay rapidly in the immediate vicinity of PIF4, suggesting that flanking loci contribute little to the observed association. In sum, the results suggest that PIF4 causally affects early internode lengths on the primary inflorescence, potentially via effects on reproductive timing and that these traits in turn affect fitness.