Jiantao Guan1,2, Yaoguang Xu1,2, Yang Yu1,2, Jun Fu1,2, Fei Ren3, Jiying Guo3, Jianbo Zhao3, Quan Jiang4, Jianhua Wei5,6, Hua Xie7,8. 1. Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China. 2. Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, People's Republic of China. 3. Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China. 4. Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China. quanj@vip.sina.com. 5. Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China. weijianhua@baafs.net.cn. 6. Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, People's Republic of China. weijianhua@baafs.net.cn. 7. Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China. xiehua@baafs.net.cn. 8. Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, People's Republic of China. xiehua@baafs.net.cn.
Abstract
BACKGROUND: Structural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic variation, yet the impacts of SVs remain largely unexplored in crops. RESULTS: Here, we generate a high-quality de novo genome assembly for a flat-fruit peach cultivar and produce a comprehensive SV map for peach, as a high proportion of genomic sequence is occupied by heterozygous SVs in the peach genome. We conduct population-level analyses that indicate SVs have undergone strong purifying selection during peach domestication, and find evidence of positive selection, with a significant preference for upstream and intronic regions during later peach improvement. We perform a SV-based GWAS that identifies a large 1.67-Mb heterozygous inversion that segregates perfectly with flat-fruit shape. Mechanistically, this derived allele alters the expression of the PpOFP2 gene positioned near the proximal breakpoint of the inversion, and we confirm in transgenic tomatoes that PpOFP2 is causal for flat-fruit shape. CONCLUSIONS: Thus, beyond introducing new genomics resources for peach research, our study illustrates how focusing on SV data can drive basic functional discoveries in plant science.
BACKGROUND: Structural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic variation, yet the impacts of SVs remain largely unexplored in crops. RESULTS: Here, we generate a high-quality de novo genome assembly for a flat-fruit peach cultivar and produce a comprehensive SV map for peach, as a high proportion of genomic sequence is occupied by heterozygous SVs in the peach genome. We conduct population-level analyses that indicate SVs have undergone strong purifying selection during peach domestication, and find evidence of positive selection, with a significant preference for upstream and intronic regions during later peach improvement. We perform a SV-based GWAS that identifies a large 1.67-Mb heterozygous inversion that segregates perfectly with flat-fruit shape. Mechanistically, this derived allele alters the expression of the PpOFP2 gene positioned near the proximal breakpoint of the inversion, and we confirm in transgenic tomatoes that PpOFP2 is causal for flat-fruit shape. CONCLUSIONS: Thus, beyond introducing new genomics resources for peach research, our study illustrates how focusing on SV data can drive basic functional discoveries in plant science.
Entities:
Keywords:
Fruit shape; Genome-wide association study; Large heterozygous inversion; Peach genome assembly; Population dynamics; PpOFP2; Structure variation
Authors: Katerina Kraft; Andreas Magg; Verena Heinrich; Christina Riemenschneider; Robert Schöpflin; Julia Markowski; Daniel M Ibrahim; Rocío Acuna-Hidalgo; Alexandra Despang; Guillaume Andrey; Lars Wittler; Bernd Timmermann; Martin Vingron; Stefan Mundlos Journal: Nat Cell Biol Date: 2019-02-11 Impact factor: 28.824
Authors: Christopher Arlt; Po-Ya Wu; Marius Weisweiler; Delphine Van Inghelandt; Thomas Hartwig; Benjamin Stich Journal: Theor Appl Genet Date: 2022-08-27 Impact factor: 5.574