Gene expression analysis and SNP/InDel discovery to investigate yield heterosis of two rubber tree F1 hybrids.
As an important industrial material, natural rubber is mainly harvested from the rubber tree. Rubber tree breeding is inefficient, expensive and time-consuming, whereas marker-assisted selection is a feasible method for early selection of high-yield hybrids. We thus sequenced and analyzed the transcriptomes of two parent rubber trees (RRIM 600 and PR 107) and their most productive hybrids (RY 7-33-97 and RY 7-20-59) to understand their gene expression patterns and genetic variations including single nucleotide polymorphisms (SNPs) and small insertions/deletions (InDels). We discovered >31,000 genetic variations in 112,702 assembled unigenes. Our results showed that the higher yield in F1 hybrids was positively associated with their higher genome heterozygosity, which was further confirmed by genotyping 10 SNPs in 20 other varieties. We also showed that RY 7-33-97 and RY 7-20-59 were genetically closer to RRIM 600 and PR 107, respectively, in agreement with both their phenotypic similarities and gene expression profiles. After identifying ethylene- and jasmonic acid-responsive genes at the transcription level, we compared and analyzed the genetic variations underlying rubber biosynthesis and the jasmonic acid and ethylene pathways in detail. Our results suggest that genome-wide genetic variations play a substantive role in maintaining rubber tree heterosis.
Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China.
Dejun
D
Li
Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China.
Rizhong
R
Zeng
State Key Laboratory of Plant Genomics and National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 5 Datun Road, Chaoyang District, 100101 Beijing, China.
Yan
Y
Li
Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China.|College of Horticulture &Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China.
Manman
M
Zhao
Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China.
Jinquan
J
Chao
Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China.
Yu
Y
Li
State Key Laboratory of Plant Genomics and National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 5 Datun Road, Chaoyang District, 100101 Beijing, China.
Kai
K
Wang
State Key Laboratory of Plant Genomics and National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 5 Datun Road, Chaoyang District, 100101 Beijing, China.
Lihuang
L
Zhu
Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China.
Wei-Min
WM
Tian
State Key Laboratory of Plant Genomics and National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 5 Datun Road, Chaoyang District, 100101 Beijing, China.
Chengzhi
C
Liang
D003517:Cyclopentanes / Q000494:pharmacology; D005030:Ethylenes / Q000494:pharmacology; D015870:Gene Expression; D017343:Genes, Plant; D018745:Genome, Plant; D005838:Genotype; D028482:Hevea / Q000235:genetics* / Q000378:metabolism; D006823:Hybrid Vigor; D054643:INDEL Mutation; D007840:Latex / Q000096:biosynthesis; D054883:Oxylipins / Q000494:pharmacology; D020641:Polymorphism, Single Nucleotide; D059467:Transcriptome / Q000235:genetics*
D003517:Cyclopentanes; D005030:Ethylenes; D007840:Latex; D054883:Oxylipins; C011006:jasmonic acid; C036216:ethylene