Premium
Genetic variants in micro RNA biogenesis genes as novel indicators for secondary growth in Populus
Author(s) -
Chen Beibei,
Chen Jinhui,
Du Qingzhang,
Zhou Daling,
Wang Longxin,
Xie Jianbo,
Li Ying,
Zhang Deqiang
Publication year - 2018
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/nph.15262
Subject(s) - biology , genetics , microrna , gene , single nucleotide polymorphism , quantitative trait locus , epistasis , phenotype , genetic variation , function (biology) , computational biology , genotype
Summary Micro RNA s (mi RNA s) function as key regulators of complex traits, but how genetic alterations in mi RNA biogenesis genes (mi RBG s) affect quantitative variation has not been elucidated. We conducted transcript analyses and association genetics to investigate how mi RBG s, mi RNA genes ( MIRNA s ) and their respective targets contribute to secondary growth in a natural population of 435 Populus tomentosa individuals. This analysis identified 29 843 common single‐nucleotide polymorphisms ( SNP s; frequency > 0.10) within 682 genes (80 mi RBG s, 152 MIRNA s , and 457 mi RNA targets). Single‐ SNP association analysis found SNP s in 234 candidate genes exhibited significant additive/dominant effects on phenotypes. Among these, specific candidates that associated with the same traits produced 791 mi RBG – MIRNA –target combinations, suggesting possible genetic mi RBG – MIRNA and MIRNA –target interactions, providing an important clue for the regulatory mechanisms of mi RBG s. Multi‐ SNP association found 4672 epistatic pairs involving 578 genes that showed significant associations with traits and identified 106 mi RBG – MIRNA –target combinations. Two multi‐hierarchical networks were constructed based on correlations of mi RBG –mi RNA and mi RNA –target expression to further probe the mechanisms of trait diversity underlying changes in mi RBG s. Our study opens avenues for the investigation of mi RNA function in perennial plants and underscored mi RBG s as potentially modulating quantitative variation in traits.