mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat.
Nascent allohexaploid wheat may represent the initial genetic state of common wheat (Triticum aestivum), which arose as a hybrid between Triticum turgidum (AABB) and Aegilops tauschii (DD) and by chromosome doubling and outcompeted its parents in growth vigor and adaptability. To better understand the molecular basis for this success, we performed mRNA and small RNA transcriptome analyses in nascent allohexaploid wheat and its following generations, their progenitors, and the natural allohexaploid cultivar Chinese Spring, with the assistance of recently published A and D genome sequences. We found that nonadditively expressed protein-coding genes were rare but relevant to growth vigor. Moreover, a high proportion of protein-coding genes exhibited parental expression level dominance, with genes for which the total homoeolog expression level in the progeny was similar to that in T. turgidum potentially participating in development and those with similar expression to that in Ae. tauschii involved in adaptation. In addition, a high proportion of microRNAs showed nonadditive expression upon polyploidization, potentially leading to differential expression of important target genes. Furthermore, increased small interfering RNA density was observed for transposable element-associated D homoeologs in the allohexaploid progeny, which may account for biased repression of D homoeologs. Together, our data provide insights into small RNA-mediated dynamic homoeolog regulation mechanisms that may contribute to heterosis in nascent hexaploid wheat.
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Aili
http://orcid.org/0000-0001-9004-192X
A
Li
Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
Dengcai
http://orcid.org/0000-0001-5508-1125
D
Liu
Novogene Bioinformatics Institute, Beijing 100083, China.
Jun
http://orcid.org/0000-0001-9488-7682
J
Wu
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Xubo
X
Zhao
Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
Ming
M
Hao
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Shuaifeng
S
Geng
Novogene Bioinformatics Institute, Beijing 100083, China.
Jun
J
Yan
Novogene Bioinformatics Institute, Beijing 100083, China.
Xiaoxue
X
Jiang
Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
Lianquan
L
Zhang
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Junyan
J
Wu
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Lingjie
L
Yin
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Rongzhi
R
Zhang
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Liang
L
Wu
Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
Youliang
Y
Zheng
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China maolong@caas.cn.
Long
http://orcid.org/0000-0002-3377-4040
L
Mao